Structure, catalytic mechanism, and membrane interaction of the mTOR activator Rheb
by
Mohammad Taghi Mazhab Jafari
A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Medical Biophysics University of Toronto
© Copyright by Mohammad Taghi Mazhab Jafari 2014
Structure, catalytic mechanism, and membrane interaction of the mTOR activator Rheb
Mohammad Taghi Mazhab Jafari
Doctor of Philosophy
Department of Medical Biophysics University of Toronto
2014 Abstract
The activator of mammalian target of rapamycin complex 1 (mTORC1), Ras homolog enriched in brain
(Rheb), is a membrane-associated protein belonging to the Ras subfamily of small GTPases. Rheb’s slow GTPase activity is stimulated by the GTPase activating protein (GAP) domain of tuberous sclerosis
complex 1 and 2 (TSC1/2). Rheb hyperactivation, through its overexpression or loss of TSC1/2 GAP
function, results in hyperactivated mTORC1 signaling culminating in tumourigenesis. The molecular
details of Rheb GTP hydrolysis and the effect of membrane association on Rheb structure, dynamics and
its GTPase function are currently not fully understood. The studies presented in this thesis focus on two
key determinants of Rheb function i) the mechanism of Rheb GTP hydrolysis and ii) the structural and
functional consequence of Rheb-bilayer membrane interaction. Through studies of fluorescent
nucleotides, we revealed that the conserved G2-box residue Tyr35 auto-inhibits GTP hydrolysis in
Rheb. We demonstrated that a non-canonical catalytic residue, Asp65, in the switch II region of Rheb,
contributed more to the GTP hydrolysis rate than Gln64, which corresponds to the canonical Ras Gln61.
This non-canonical auto-inhibited mechanism of GTP hydrolysis was required for optimal mTORC1
regulation. These structural insights were then used to guide the design of novel gain- and loss-of
function mutants by substitutions of the ultra-conserved G3-box Gly63 of Rheb. Finally, using solution
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NMR spectroscopy, we monitored the Rheb GTPase cycle and characterized its nucleotide-dependent membrane orientations on nanodisc-based phospholipid bilayers. Rheb was shown to sample two orientations in which its C-terminal helix was semi-perpendicular or semi-parallel with respect to the
bilayer plane. The semi-parallel orientation, where switch II residues critical for mTORC1
communication are accessible, was favored in the GTP bound conformation, suggesting that membrane-
tethering modulates Rheb function. These structural insights into the catalytic machinery of Rheb and its
membrane interface suggest new approaches to modulate these key determinants of Rheb function
through small molecules towards development of therapeutic avenues for Rheb-mediated pathogenesis
such as tuberous sclerosis or cancer.
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Acknowledgments
First and foremost, I would like to thank my supervisor Dr. Mitsu Ikura for his guidance, support, and understanding. I could have not accomplished any portion of this research without his supervision. His passion for science was a continuous source of inspiration for me over the years. I learned key aspects of successful research from him, including critical thinking.
I am grateful to my supervisory committee members; Dr. Lewis Kay and Dr. Vuk Stambolic. Their expert inputs were critical to the success of this thesis. Thank you for your advise, supervision and encouragement, which kept me on the right path.
I am also thankful to my collaborators, Vanessa De Palma and Jason Ho from Dr. Stambolic lab for the cell biology experiments.
I had the honor of working with and learning from many excellent current and former members of Ikura’s lab including; Dr. Christopher Marshall, Dr. Peter Stathopulos, Dr. Genevieve Seabrook, Dr. Noboru Ishiyama, Le Zheng, Dr. Feng Wang, Carol Liu, and Dr. Fernando Amador. I would like to specially thank Chris, who was involved in all aspects of my projects and gave valuable inputs and suggestions.
Finally, I would like to thank my family; my parents Mohammad Mazhab-Jafari and Ziba Fadavi and my brother Hamed Mazhab-Jafari for all their sacrifice that provided me with the opportunity to carry out this research. Words cannot express my grateful feelings for you.
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Table of Contents
Acknowledgements……………………………………………………………………………………….iv
Table of Contents ………………………………………………………………………………………...v
List of Tables …………………………………………………………………………………………….x
List of Figures …………………………………………………………………………………………...xi
List of Appendices ……………………………………………………………………………………...xiv
List of Abbreviations …………………………………………………………………………………...xv
Chapter 1: Introduction and Thesis Overview ………………………………………………………...1
1.1 General introduction to small GTPase proteins……………………………………………………….2
1.2 Introduction to Rheb………………………………………………………………...... 3
1.3 Biophysical and biochemical properties of Rheb…………………………………...... 6
1.4 Pathogenesis of Rheb………………………………………………………………………………….9
1.5 Thesis Overview and Rationale……………………………………………………………………...11
1.6 Attributions…………………………………………………………………………………………..12
1.7 References……………………………………………………………………………………………12
Chapter 2: Fluorescent-tagged Nucleotides Alter the Native GTPase Cycle …………………….…17
2.1 Abstract………………………………………………………………………………………………18
2.2 Introduction………………………………………………………………………...... 19
2.3 Results………………………………………………………………………………………………..20
2.3.1 The effect of mant on the intrinsic rate of nucleotide hydrolysis………………………….20
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2.3.2 The effect of mant on the rate of GAP-catalyzed nucleotide hydrolysis…………………..23
2.3.3 The effect of mant on the GEF-mediated nucleotide exchange…………………………....25
2.4 Discussion……………………………………………………………………………………………28
2.4.1 Intrinsic hydrolysis of GTP and mantGTP………………………………………………...28
2.4.2 GAP-catalyzed GTP hydrolysis by HRas and Rheb…………………………………….…30
2.4.3 GEF-accelerated nucleotide exchange of HRas and RhoA………………………………..31
2.5 Experimental Procedures…………………………………………………………………………….32
2.5.1 Protein preparation…………………………………………………………………………32
2.5.2 NMR-based GTPase, GAP and GEF assays……………………………………………….33
2.5.3 Fluorescence-based GTPase assay…………………………………………………………34
2.6 References……………………………………………………………………………………………34
Chapter 3: Mechanism of GTP hydrolysis by Rheb ……………………………………………..…...36
3.1 Abstract…………………………………………………………………………………………..…..37
3.2 Introduction………………………………………………………………………………………..…38
3.3 Results………………………………………………………………………………………………..39
3.3.1 Rheb Tyr35 inhibits intrinsic GTPase activity……………………………………………..39
3.3.2 Structural basis for the Tyr35 auto-inhibitory function……………………………………40
3.3.3 Identification of a catalytic residue for GTP hydrolysis…………………………………...42
3.3.4 Involvement of Rheb’s Asp65 and Tyr35 in TSC2GAP-mediated GTP hydrolysis…...... 47
3.3.5 Thermodynamic basis for the Tyr35 auto-inhibitory function…………………………….49
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3.3.6 Regulation of mTORC1 by growth factors involves the non-canonical catalytic and autoinhibitory mechanisms…………………………………………………………….………...54
3.4 Discussion……………………………………………………………………………………….…...57
3.5 Experimental Procedures……………………………………………………………………….……60
3.5.1 Protein preparation………………………………………………………………….……...60
3.5.2 Crystallization and data collection………………………………………………….……...61
3.5.3 Structure determination and refinement…………………………………………….……...61
3.5.4 NMR-based GTPase assays…………………………………………………………….…62
3.5.5 Thermodynamic measurements……………………………………………………….…..63
3.5.6 Cell-based phosphorylation assay……………………………………………………..…...63
3.5.7 Nucleotide binding in vivo…………………………………………………………………64
3.6 References……………………………………………………………………………………………65
Chapter 4: Structure-guided design of novel active and inactive Rheb mutants using single site modifications ……………………………………………………………………………………………68
4.1 Abstract……………………………………………………………………………………………....69
4.2 Introduction…………………………………………………………………………………………..70
4.3 Results and Discussion……………………………………………………………………………....72
4.4 Experimental Procedures…………………………………………………………………………….78
4.4.1 Protein Preparation…………………………………………………………………………78
4.4.2 NMR-based Real-time GTPase assay……………………………………………………...78
4.4.3 Crystallization and Data Collection………………………………………………………..79
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4.4.4 Structure Determination and Refinement………………………………………………….79
4.4.5 Cell-based Phosphorylation Assays………………………………………………………..80
4.5 References……………………………………………………………………………………………82
Chapter 5: Structural and Functional consequence of Rheb-membrane interaction ……………...84
5.1 Abstract………………………………………………………………………………………………85
5.2 Introduction…………………………………………………………………………………………..86
5.3 Results and Discussion………………………………………………………………………………88
5.4 Experimental Procedures……………………………………………………………………….……99
5.4.1 Protein preparations………………………………………………………………….…….99
5.4.2 Preparation of Rheb-nanodisc complex…………………………………………………..100
5.4.3 NMR- measurements……………………………………………………………………..101
5.4.4 Real-time NMR-based GTPase assay………………………………………………….…103
5.4.5 Molecular docking simulation……………………………………………………………103
5.5 References……………………………………………………………………………………….….106
Chapter 6: Conclusions and Future directions ……………...………………………………………108
6.1 Conclusions…………………………………………………………………………………………109
6.2 Future Directions…………………………………………………………………………………...110
6.2.1 Engineering GTPase probes by structure-guided mutations of G3-box glycine………....110
6.2.2 Drugging Rheb……………………………………………………………………………111
6.2.3 Probing membrane-dependent regulation of KRas-effector interaction………………….111
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6.3 Closing Remarks……………………………………………………………………………………112
6.4 References…………………………………………………………………………………………..114
Appendix A……………………………………………………………………………………………..116
Appendix B……………………………………………………………………………………………..118
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List of Tables
Table 2.1 The rates of intrinsic and GAP mediated nucleotide hydrolysis for three small GTPase proteins…………………………………………………………………………………………………..23
Table 2.2: The rates of GEF mediated nucleotide exchange for HRas and RhoA proteins……………..27
Table 3.1 Summary of thermodynamic activation parameters…………………………………………..54
Table 3.2 Data collection and refinement statistics……………………………………………………...62
Table 4.1 Data collection and refinement statistics……………………………………………………...81
Table 5.1 Resonance assignment of Rheb HVR………………………………………………….…....101
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List of Figures
Figure 1.1 Sequence alignment of Rheb with other small GTPase proteins investigated in this thesis...... 3
Figure 1.2 Schematic illustration of Rheb in the mTORC1 signaling pathway…………………………..5
Figure 1.3 Overall structure of active Rheb and comparison with that of HRas……………………….....8
Figure 2.1 Effect of mant-substituted GTP on the intrinsic nucleotide hydrolysis of Ras, Rheb and RhoA……………………………………………………………………………………………………..19
Figure 2.2 Comparison of the real-time NMR and fluorescence-substituted nucleotide-based GTPase assays…………………………………………………………………………………………………….21
Figure 2.3 Perturbation of the native structure of GTPase proteins by mant-tagged nucleotides……….22
Figure 2.4 Effects of mant-substituted GTP on GAP-mediated nucleotide hydrolysis by HRas and Rheb……………………………………………………………………………………………………...24
Figure 2.5 Effects of mant-substituted nucleotides on GEF-mediated nucleotide exchange for HRas and RhoA……………………………………………………………………………………………………..26
Figure 2.6 Complementary assays of the effects of mant-substituted nucleotides on GEF-mediated nucleotide exchange for HRas and RhoA………………………………………………………………..27
Figure 2.7 mantGTP-induced chemical shift perturbations in Ras, Rheb and RhoA……………………29
Figure 2.8 Rheb Gln64 is not involved in the rapid hydrolysis of mantGTP……………………………30
Figure 3.1 Rapid hydrolysis of mantGTP by Rheb is related to autoinhibitory role of Tyr35…………..40
Figure 3.2 Structure and dynamics of Rheb Y35A……………………………………………………....41
Figure 3.3 Mutagenic analysis of potential catalytic residues in Rheb Y35A…………………………...43
Figure 3.4 Role of Asp65 in intrinsic and GAP-mediated GTP hydrolysis by Rheb……………………45
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Figure 3.5 Effect on Rheb GTPase activity of mutations of acidic and electronegative residues in switch II………………………………………………………………………………………………………….46
Figure 3.6. Structure-function analysis of the position of putative catalytic residues and the conserved switch I Tyrosine in small GTPases……………………………………………………………………...48
Figure 3.7 Perturbation of Rheb HSQC spectrum by Tyr35 mutation…………………………………..50
Figure 3.8 Minimal chemical shift perturbation associated with mutation of Rheb Asp65…………….51
Figure 3.9 Tyr35 hydroxyl is required for TSC2GAP-assisted GTP hydrolysis………………………...52
Figure 3.10 Effect of Tyr35 and Asp65 mutations on the thermodynamic activation parameters for GTP hydrolysis by Rheb………………………………………………………………………………………53
Figure 3.11 Mutations of Rheb catalytic and autoinhibitory residues impact Rheb’s activation level and mTORC1 phosphorylation of p70 S6K…………………………………………………………………55
Figure 3.12 Effects of Y35A and D65A mutations in Rheb on mTORC1 activity……………………...56
Figure 3.13 Schematic model of intrinsic and TSC2GAP-stimulated GTP hydrolysis by Rheb………..59
Figure 4.1) Manipulation of the GTPase cycle of Rheb and mTOR signaling through substitutions of Gly63…………………………………………………………………………………………………….71
Figure 4.2 Conservation of the G3-box glycine and structural basis for the functional properties of Rheb Gly63Ala/Val mutants…………………………………………………………………………………..73
Figure 4.3 Electron densities of the catalytic sites of wild-type Rheb and its Gly63 mutations………..74
Figure 4.4 Intrinsic nucleotide hydrolysis and exchange of Rap1A GTPase and its Gly60 mutations…77
Figure 5.1 Tethering Rheb to a bilayer membrane inhibits nucleotide exchange and activation……….87
Figure 5.2 Preparation of Rheb-nanodisc complex……………………………………………………...89
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Figure 5.3 Backbone 15N relaxation data for Rheb-GDP 1-181 in free (black) and nanodisc-bound (red) states……………………………………………………………………………………………………...91
Figure 5.4 Backbone 15N relaxation data for Rheb-GMPPNP 1-181 in free (black) and nanodisc-bound (red) states………………………………………………………………………………………………..92
Figure 5.5 Identification of the Rheb-membrane interface and its modulation by the bound nucleotide.93
Figure 5.6 Residues affected by PRE localized on the HADDOCK models…………………………….94
Figure 5.7 Cluster analysis of final HADDOCK solutions………………………………………………95
Figure 5.8 Subtle changes in surface electrostatics upon nucleotide exchange………………………….97
Figure 5.9 Formation of a Rheb-PDE δ complex is compatible with Rheb-nanodisc model 2, but not model 1…………………………………………………………………………………………………..98
Figure 6.1 Backbone and side chain assignments of free KRas4B in complex with GMPPNP…….…113
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List of Appendices
Appendix A……………………………………………………………………………………………..116
Appendix B…………………………………………………………………………………………….118
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List of Abbreviations
4E-BP (eIF)4E-binding proteins
Arf ADP ribosylation factor
BMRB Biological Magnetic Resonance Bank
CNS Crystallography & NMR System
Coot Crystallographic Object-Oriented Toolkit
DH-PH Dbl homology-Pleckstrin-homology
DOPC 1,2-dioleoyl-sn -glycero-3-phosphocholine
DOPS 1,2-dioleoyl-sn-glycero-3-phospho-L-serine
DTT Dithiothreitol
ER Endoplasmic reticulum
EDTA Ethylenediaminetetraacetic acid
FKBP FK506-binding protein
FRET Fluorescence resonance energy transfer
FTI Farnesyltransferase Inhibitors
GAP GTPase activating protein
GDI Guanine Dissociation Inhibitor
GEF Guanine Exchange Factor
GMPPNP 5'-Guanylyl imidodiphosphate
cat H2O Catalytic water
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HADDOCK High Ambiguity Driven biomolecular DOCKing
HVR Hyper Variable Region
IPTG Isopropyl β-D-1-thiogalactopyranoside
LC3 Light Chain 3
Mant 2'(3')-O-(N-Methylanthraniloyl)
MCF-7 Michigan Cancer Foundation-7
MD Molecular Dynamics
MSP Membrane Scaffold Protein
mTORC1 mammalina Target of Rapamycin Complex 1
NBS Nucleotide Binding Site
NMR Nuclear Magnetic Resonance
NOE Nuclear Overhauser effect
PAM Associated with Myc
PDE phosphodiesterase
PE-DTPA(Ga 3+ ) 1,2-distearoyl-sn -glycero-3-phosphoethanolamine-N- diethylenetriaminepentaacetic acid (gadolinium salt)
PE-MCC 1,2-dioleoyl-sn -glycero-3-phosphoethanolamine-N-[4-(p- maleimidomethyl)cyclohexane-carboxamide]
PI3K Phosphatidylinositol 3-kinases
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POPC 1-palmitoyl-2-oleoyl-sn -glycero-3-phosphocholine
PRAK p38-regulated/activated kinase
PRE Paramagnetic Relaxation Enhancement
Ran Ras-related nuclear
Ras Rat sarcoma
RBD Ras Binding Domain
Rheb Ras homolog enriched in brain
RhebL1 Ras homolog enriched in brain-like 1
Rho Ras homolog
RMSD Root Mean Square Deviation
S6K S6 Kinase
PAGE polyacrylamide gel electrophoresis
SDS sodium dodecyl sulfate
SOS Son of Sevenless
SRP signal recognition particle
TCEP tris(2-carboxyethyl)phosphine
TRIS tris(hydroxymethyl)aminomethane
UV Ultraviolet
WT Wild Type
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CHAPTER 1
Introduction and Thesis Overview
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1.1 General introduction to small GTPase proteins: The Rat sarcoma (Ras) superfamily of small GTPases are ~21 kDa globular protein-nucleotide complexes that control diverse signaling networks affecting cell growth, proliferation and differentiation, intracellular trafficking, cellular morphology, mobility, chemotaxis and apoptosis (Wittinghofer and Vetter 2011; Cherfils and Zeghouf 2013). Deregulation of GTPase signaling has immense implications on human health and can result in life-threatening diseases such as cancer. The superfamily was originally divided into five subfamilies, based on cellular function and sequence similarities (Wennerberg et al. 2005). These include Ras, Ras homolog (Rho), Ras related in brain (Rab), ADP ribosylation factor (Arf), and Ras-related nuclear (Ran) subfamilies. A more recent phylogenetic analysis has identified additional small GTPases that are yet to be classified into a specific subfamily (Rojas et al. 2012). The superfamily members contain five conserved sequence motifs, identified as the G1 to G5 boxes, which are required for interactions with nucleotides, effectors, and regulators (Figure 1.1). The G1, G2 and G3 boxes reside within functionally important and dynamic regions of GTPase proteins. The G1 box forms a loop/helix structural motif termed the P-loop, which is responsible for phosphate binding, whereas G2 and G3 are found within switch I and II, respectively, which are responsible for interaction with effectors and regulators of GTPases (Wittinghofer and Vetter 2011). Additionally, most members of the superfamily are targeted to intracellular membrane compartments through post-translational modifications whereby hydrophobic moieties are covalently attached to either the N- or C-terminus (Ahearn et al. 2012). A universal feature of the small GTPases is their ability to bind guanine nucleotides, specifically, guanosine di-(GDP) and tri-(GTP) phosphates, and cycle between GDP- and GTP-bound states. When bound to GTP they adopt a conformation that allows recognition and activation of downstream effector proteins. Hydrolysis of the γ-phosphate of GTP converts the GTPases to a GDP-bound inactive state, where they can no longer functionally interact with their effectors. The GTPase can then be reactivated by exchange of GDP for a new molecule of GTP, driven in part by the higher concentrations of GTP in eukaryotic cells (Traut 1994). The rate of this cycle depends in part on intrinsic properties of each GTPase, including their relative affinities for GDP and GTP and the efficiency of their nucleotide hydrolyzing machinery (Li and Zhang 2004). However the rate of the GTPase cycle is tightly linked to internal and external stimuli of the cell that are transmitted to the small GTPase by the action of upstream regulators, such as guanine exchange factors (GEF), which accelerate the intrinsic nucleotide exchange, and GTPase activating proteins (GAP), which accelerate the intrinsic GTP hydrolysis.
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Figure 1.1 Sequence alignment of Rheb with other small GTPase proteins investigated in this thesis. Alignment of Rheb is shown with its close homologues K- and H-Ras isoforms and Rap1A, as well as the more distant homologue RhoA, from the Rho subfamily. Conserved amino acids are highlighted in green, those conserved in more than half of the alignment are shown in yellow, and semi- conserved amino acids in cyan. G1 to G5 boxes are indicated with solid bars and the P-loop, switch I and switch II regions are indicated in red. The hyper variable region (HVR) is indicated with a green bar, and the CaaX (C is Cys, a is aliphatic aa, X is any aa) box is highlighted with a rectangle.
The Ras superfamily is an excellent example of achieving functional diversity within a similar structural framework. Therefore, detailed understanding of the structural and dynamic properties of these switch proteins is critical to the understanding of their function in cells and can aid in therapeutic intervention for patients suffering from diseases associated with aberrant GTPase function.
1.2 Introduction to Rheb:
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The main focus of this thesis is an important disease-related member of the Ras subfamily called Ras homolog enriched in brain (Rheb). Rheb was originally discovered in a screen for genes induced in hippocampal granule cells of Rat by seizures and by N-methyl-aspartate (NMDA)-dependent synaptic activity (Yamagata et al. 1994). Sequence analysis identified Rheb as a member of the Ras superfamily of small GTP binding proteins with the highest similarity to Rap1A and H-Ras GTPases. Subsequently, the gene encoding human Rheb was identified on chromosome 7 (Gromov et al. 1995; Mizuki et al. 1996), and a second Rheb-like 1 (RhebL1) gene was later identified on chromosome 12 (Patel et al. 2003). Rheb is expressed ubiquitously with higher expression levels in skeletal and cardiac muscle whereas RhebL1 is primarily expressed in the brain. Rheb homologs have been found in yeast, slime mold, fungi, fruit fly and zebra fish (Reuther and Der 2000). Rheb was shown to bind to and hydrolyze GTP with a rate slower than that of H-Ras (Marshall et al. 2009). Like its close homolog H-Ras, Rheb was shown to be farnesylated in cells (Clark et al. 1997) suggesting membrane association. Rheb was originally described to interact with Raf-1 kinase and antagonize Ras signaling and transformation (Clark et al. 1997; Yee and Worley 1997). Later it was shown that Rheb affinity for Raf-1 is 1000-fold lower than that of Ras (Karassek et al.), thus Raf might not be a physiological effector. Loss of the Rheb ortholog Rhb1 in fission yeast mimics the nitrogen-starvation induced phenotype and growth arrest (Mach et al. 2000), and Drosophila Rheb is required for cell growth and cell cycle progression (Patel et al. 2003). In 2003, several independent groups showed that Rheb is involved in the target of rapamycin complex 1 (TORC1) signaling pathway (Figure 1.2) in Drosophila melanogaster and mammalian cells (Garami et al. 2003; Saucedo et al. 2003; Stocker et al. 2003). Rheb was found to promote cellular growth in a mTOR- (mammalian TOR) dependent manner in response to insulin and nutrient availability. This activity required phosphorylation and activation of the TOR substrate p70 S6 Kinase, driving protein translation and cell growth (Ruvinsky and Meyuhas 2006). Another major Rheb- regulated target of mTORC1 was identified as eukaryotic initiation factor (eIF)4E-binding proteins (4E- BPs), involved in cap-dependent translation (Beretta et al. 1996; Bommareddy et al. 2009). The molecular mechanism by which Rheb activates mTORC1 is not yet fully understood and is still a matter of debate (Bai et al. 2007; Sun et al. 2008; Wang et al. 2008; Sato et al. 2009). It is however clear that Rheb activates mTORC1 kinase activity in a GTP-dependent manner (Sancak et al. 2007), but paradoxically both GDP- and GTP-bound states of Rheb were reported to interact with mTORC1 (Long et al. 2005). Biochemical and genetic studies placed Rheb downstream of the tumor suppressors tuberous sclerosis complex 1 and 2 (TSC 1/2) in both Drosophila and mammalian cells (Garami et al.
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2003; Inoki et al. 2003; Tee et al. 2003; Zhang et al. 2003). Rheb was shown to be a direct target of TSC2 GTPase activating domain (GAP) activity both in vitro and in vivo (Inoki et al. 2003). The isolated TSC2 GAP domain was later shown to accelerate the slow intrinsic GTP hydrolysis rate of
Figure 1.2 Schematic illustration of Rheb in the mTORC1 signaling pathway. Rheb-GTP stimulates the kinase activity of mammalian target of rapamycin complex 1 (mTORC1) that phosphorylates its substrates including 4E-BP1 and p70S6K1 promoting protein biosynthesis and cell cycle progression. Rheb intrinsic GTP hydrolysis rate is accelerated via the GAP activity of TSC1/2, which is regulated in response to the availability of growth factors, and energy stress.
Rheb in vitro (Scrima et al. 2008; Marshall et al. 2009). The GAP function of TSC 1/2 is tightly regulated by upstream signaling via phosphorylation events in response to internal and external
6 nutritional and energy status of the cell (Huang and Manning 2008). Hence, Rheb acts as a switch to regulate cellular growth and cell cycle progression in response to nutrient availability, energy status and hypoxia, via bridging TSC 1/2 to mTORC1 activity. Interestingly, it was recently recognized that under certain stress conditions such as UV irradiation and cellular intoxication, Rheb can switch from a pro- growth signaling molecule to a pro-apoptotic one using both canonical (mTORC1-dependent) and non- canonical (mTORC1-independent) signaling networks (Ehrkamp et al. 2013). Some of the interesting non-canonical and membrane-dependent interactions reported for Rheb include; interaction with mitochondrial autophagic receptor Nix and the autophagosomal protein LC3-II in promoting mitophagy (Melser et al. 2013); regulation of FKBP38 interaction with anti-apoptotic proteins Bcl-2 and Bcl-XL (Ma et al. 2010); an inhibitory interaction between Rheb and Bnip3 in hypoxia-mediated inhibition of mTORC1 signaling (Li et al. 2007); and sequestration of farnesylated Rheb by cAMP hydrolyzing enzyme phosphodiesterase 4D (PDE4D) (Kim et al. 2010), and the proposed solubilizing factor for farnesylated Ras-subfamily proteins, PDE δ (Ismail et al. 2011).
Currently, there is no consensus on the identity of the protein, if any, that plays the role of a Rheb GEF. There is debate whether the translationally controlled tumor protein (TCTP) is the physiological GEF for this small GTPase (Hsu et al. 2007; Rehmann et al. 2008; Wang et al. 2008; Dong et al. 2009). Interestingly, recent studies have proposed other potential GEFs for Rheb including; the E3 ubiquitin ligase Protein Associated with Myc (PAM) (Maeurer et al. 2009) and deacetylated soluble αβ -tubulin (Lee et al. 2013). In both cases, it remains to be determined whether the newly identified candidates possess direct GEF-function toward Rheb in vitro using purified recombinant proteins.
1.3 Biophysical and biochemical properties of Rheb: Rheb is a 184-amino acid GTPase, containing 6 conserved sequence elements that are hallmarks of the Ras subfamily. These include G1 to G5 boxes, as descried above plus a C-terminal CaaX box (where C is cysteine, a is aliphatic amino acid, and X is any amino acid). Rheb is post-translationally modified via farnesylation, cleavage of the aaX tripeptide and carboxymethylation of the C-terminal cysteine by the concerted actions of farnesyltransferase, Ras converting enzyme 1 (Rce1) and isoprenylcysteine carboxyl methyltransferase (Icmt ) enzymes, respectively (Seabra 1998). These modifications target Rheb to intracellular membrane compartments such as the ER, Golgi apparatus, and lysosome
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(Takahashi et al. 2005; Buerger et al. 2006). Inhibition of Rheb farnesylation, via mutation of the CaaX box Cys residue or treatment with farnesyltransferase inhibitors (FTIs), drastically reduces Rheb’s ability to stimulate mTORC1 activity in cells (Buerger et al. 2006; Finlay et al. 2007). Although Rheb shares 34% sequence identity with H-Ras and harbors many conserved sequence elements through G1- G5 boxes, two key sequence variations were observed upon its discovery. In Ras, codons 12 and 13 encode two conserved Glycine residues, mutations of which result in oncogenic Ras molecules that are constitutively GTP bound (Figure 1.3) (Prior et al. 2012). The structural basis for the Gly12 and Gly13 mutation-mediated oncogenic transformation in Ras is well characterized (Krengel et al. 1990). For example, H-Ras G12V, a high frequency mutation in various tumor types, sterically blocks the canonical catalytic residue, Gln61 (H-Ras numbering), from the nucleotide binding site, impairing GTP hydrolysis. Gln61 is positioned at the N-terminus of switch II and it is shown to stimulate the GTP hydrolysis reaction by interacting with a water molecule positioned in-line with the γ-phosphate of GTP cat (aka , the catalytic water, H2O ). In Rheb the corresponding codons (15 and 16) encode Arginine and Serine residues, respectively. However, the slow GTP hydrolysis by Rheb is not due to the presence of these residues at codons 15 and 16. In cells over-expressing Rheb, R15G and S16G mutations did not affect its activation state (Im et al. 2002), suggesting that Arg15 and Ser16 did not affect the Rheb-GTP levels, where the function of TSC2GAP is limiting.
Compared to Ras, Rheb exists in a high activation state in cells (Im et al. 2002). Initial characterization of Rheb’s intrinsic GTP hydrolysis rate suggested Rheb possesses a slower GTP hydrolysis rate than Ras (Aspuria and Tamanoi 2004). This was confirmed by the use of the novel real-time NMR-based GTPase assay that accurately measured the nucleotide hydrolysis rate of Rheb to be 10 times slower than that of H-Ras (Marshall et al. 2009). A potential structural explanation for this low GTPase activity was found eleven years after Rheb was first discovered. Crystal structures of Rheb were solved in both an inactive GDP-bound state (PDB: 1XTQ) and active states bound to GTP (PDB: 1XTS) and GMPPNP-bound, a non-hydrolyzable analog of GTP (PDB: 1XTR) (Yu et al. 2005). The overall fold is typical of Ras subfamily members, namely a six-stranded β-sheet and five α-helices forming a globular 20 kDa protein (Figure 1.3). However, two important structural differences were observed in the switch I and II regions of the GMPPNP-bound state compared to that observed in H-Ras. In Rheb, switch I forms a lid that covers the phosphate groups of the nucleotide and simultaneously creates a pore to the
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cat bulk solvent, which is occupied by the H 2O . This lid is formed by the H-bonding interaction between the hydroxyl group of the conserved Tyr35 in switch I of Rheb and the γ-phosphate (Figure 1.3).
Figure 1.3 Overall structure of active Rheb and comparison with that of H-Ras. Crystal structure of Rheb bound to GMPPNP (PDB: 1XTR) is shown in green. The nucleotide is shown with stick. The inset
9 shows the positions of key residues within the nucleotide binding site of Rheb and H-Ras (cyan) (PDB: cat 5P21). The H 2O is presented with spheres. The backbones of Tyr35, Gln61 and Gln64 are not shown.
In H-Ras, the equivalent tyrosine (Tyr32) is in an open conformation that does not interact with the γ- phosphate, thus exposing the nucleotide phosphate groups to the solvent (Figure 1.3). This conformational divergence could aid in differential recognition of interactors by Ras versus Rheb. For example, the open conformation of Ras Tyr32 allows p120 RasGAP to insert an Arginine ( aka the Arginine finger) into the nucleotide binding site to stimulate GTP hydrolysis (Scheffzek et al. 1997). The second difference involves the conformation of switch II. Whereas the H-Ras switch II harbors a 10-residue curved alpha helix and is relatively detached from the globular G-domain, in Rheb switch II is mainly unstructured and forms tight contacts with the G-domain (Figure 1.3). The structural consequence of this conformation is a net removal of the switch II residues from the nucleotide binding site of Rheb compared to that of H-Ras. The point of divergence begin after the conserved DxxG motif 2+ cat at the N-terminus of switch II, a conserved curved loop structure responsible for Mg and H 2O coordination. This unique switch II configuration flips the Gln64 (corresponding to H-Ras Gln61) side chain away from the nucleotide binding pocket and traps it within a hydrophobic pocket underneath switch II formed by Leu12, Phe70, Pro71, Tyr74, and Ile99. A salt bridge between Glu66 in switch II and Lys91 of the α3 helix stabilizes switch II away from the nucleotide binding site. Further stabilization is achieved by polar interaction between the Lys102 of α3 helix and the backbone carbonyl of Glu66. This switch II conformation of Rheb provides additional space that accommodates the Arg15 side chain that is not available in the H-Ras structure. Hence, the structural analysis indicated that although Rheb possesses a glutamine residue corresponding to H-Ras Gln61, this residue does not participate in GTP hydrolysis. This was later confirmed via NMR-based GTPase assay, demonstrating that the Q64L mutation in Rheb has minor effects on both intrinsic and TSC2GAP-mediated GTP hydrolysis (Marshall et al. 2009).
1.4 Pathogenesis of Rheb: Rheb is involved in the pathogenesis of the tuberous sclerosis disease, which is an autosomal dominant genetic disorder with a prevalence of ~1 in 8,000 (Napolioni and Curatolo 2008). Mutations in tsc 1 and tsc 2 genes that disrupt TSC1/2 GAP function in tuberous sclerosis and lymphangioleiomyomatosis (LAM) diseases result in high levels of Rheb-GTP that constitutively activate mTORC1. Tuberous sclerosis disease is characterized by multiple benign tumor formation in multiple organ systems. The
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symptoms include autism, developmental delay, hematuria (blood in urine), cardiac arrhythmia and skin disfigurement.
Additionally, numerous studies have suggested Rheb to be directly involved in tumorgenesis. Constitutively activated Rheb mutants have been shown to induce oncogenic transformation in cell culture (Jiang and Vogt 2008) and it has been well established that transcriptional- and translational- mediated elevation of Rheb expression contributes to its hyperactivation (Norsted Gregory et al. 2010; Cao et al. 2013). Elevated levels of Rheb result in high activation levels due to limiting GAP function of TSC1/2. The highly GTP-loaded Rheb constitutively signals to mTORC1 to promote cellular growth and cell cycle progression. The elevated expression of Rheb has been found in fibroadenoma (Eom et al. 2008), shown to be critical and sufficient for skin epithelial carcinogenesis (Lu et al. 2010), and to cause prostate cancer (Nardella et al. 2008; Kobayashi et al. 2010) and lymphomagenesis (Mavrakis et al. 2008). An increase in Rheb activation state has also been demonstrated to drive 17-beta estradiol (E(2))- dependent proliferation of the MCF-7 breast cell line (Yu and Henske 2006).
Where mutations of Gly12, Gly13 and Gln61 result in oncogenic transformation of Ras, Rheb has not been associated with any particular oncogenic mutation. However, recent high-thoughput cancer genome sequencing analyses of tumor samples from patients with various tumour types including lung, breast, urinary tract, endometrium, colon, kidney and stomach has revealed multiple missense mutations throughout the Rheb gene (COSMIC database). The mutations map to the important structural regions in Rheb including the P-loop, switch I and II. Residues with the highest frequency mutations are Tyr35 (to Asn) (Lawrence et al. 2014) and Glu139 (to Lys, Glu, and Asp). Tyr35 is in the middle of switch I (G2 box) and, as noted above, covers the nucleotide-binding pocket from the bulk solvent. Glu139 is at the C-terminus of α5 near a site of post-translational modification (Ser130 at the N-terminus of α5). Rheb nucleotide loading is inhibited by phosphorylation of Ser130 by p38-regulated/activated kinase (PRAK) (Zheng et al. 2011). The functional properties of these Rheb mutants are yet to be characterized to determine weather they drive tumorgenesis.
To target deregulated mTORC1 signaling, several therapeutic strategies are being investigated. First is the direct inhibition of mTORC1 via small molecules. Rapamycin and its synthetic analogs (Rapalogs), also known as the first-generation mTOR inhibitors, inhibit phosphorylation of a subset of mTORC1
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substrates (Kang et al. 2013). Rapmycin directly blocks substrate recruitment by forming a complex with FK506-binding protein 12 (FKBP12) and binding to the FKBP12–rapamycin-binding (FRB) domain of mTORC1, close to the kinase catalytic site (Choi et al. 1996; Yang et al. 2013). Clinical trials have shown that rapalogs are cytostatic and tend to be stabilizers of diseases rather than causing disease regression (Wander et al. 2011). In addition, rapalog-mediated inhibition of mTORC1 fails to suppress a negative feedback loop that results in phosphorylation-mediated activation of AKT (Wan et al. 2007). More recently, ATP-binding site inhibitors, also known as second-generation mTOR inhibitors, were developed, which directly compete with ATP binding and inhibit the kinase activity of both mTORC1 and mTORC2 for all substrates (Zaytseva et al. 2012). However, they display cytotoxic effects and are only partially effective in K-Ras driven tumors (Zaytseva et al. 2012). An alternate strategy involves prevention of Rheb association with bilayer membranes through the use of FTIs, which block farnesylation of Rheb and its ability to signal to mTORC1 in the cells, but suffer from non-specificity (Mavrakis et al. 2008). Interestingly, a cytotoxic biphenyl compound, 4,4 ′-biphenol was shown to interact with Rheb switch II region, block mTORC1 signaling and induce cell death (Schopel et al. 2013). However the affinity of the compound was low (Kd in millimolar range), indicating the requirement for structure-guided optimization of the compound.
1.5 Thesis Overview and Rationale: From the above discussion it is clear that two key physiological properties of Rheb are directly linked to human diseases: (a) its GTP hydrolysis rate and (b) its membrane association. The studies presented in this thesis are basic research aimed at gaining an atomic-resolution understanding of Rheb’s catalytic mechanism and its interaction with phospholipid bilayers. The information gained, could aid in the i) mechanistic understanding of disease-associated mutations in Rheb, ii) development of small molecules that specifically target the disease-associated Rheb mutant states, iii) development of novel probes to study the biology of the mTORC1 pathway, and iv) characterization of the Rheb-membrane interface and its implication for Rheb signaling.
The catalytic mechanism of Rheb GTP hydrolysis is described in Chapters 2, 3 and 4, representing three published manuscripts. When I commenced my Ph. D. studies, Dr. Marshall published a novel method for quantitatively measuring the rate of the GTPase cycle using native nucleotides via real-time NMR- based GTPase assay (Marshall et al. 2009). Hence, in my first study (chapter 2), I examined the effect of
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widely used fluorescent nucleotide analogs, 2'(3')-O-(N-Methylanthraniloyl)-(mant)-GDP and mant- GTP in modulating the kinetics of the GTPase cycle. Chapter 3 describes a structure-function study of the non-canonical GTP catalytic mechanism of Rheb that was initially revealed by studies of Rheb hydrolysis of the mant-nucleotide. Chapter 4 describes the structure-guided development of novel gain- of-function and loss-of-function mutants of Rheb using the knowledge gained from its nucleotide catalytic mechanism.
The Rheb-membrane interaction is described in Chapter 5, representing our published work on a novel NMR-based method for studying GTPase-membrane interaction at atomic resolution using nanodisc- based lipid bilayers. These methods demonstrated effects of membrane binding on Rheb’s GTPase cycle, as well as determining the orientation of Rheb with respect to the lipid bilayer in both GDP- and GTP- bound states.
Chapter 6 includes concluding remarks and future directions, including (i) potential applications of the gain- and loss-of-function Rheb mutants generated via structure-guided design, and (ii) the feasibility of applying nanodisc-GTPase methodology to other disease-related GTPases, such as K-Ras, and its complexes with different Ras Binding Domains (RBDs).
1.6 Attributions: The cell-based assays of nucleotide binding (Chapter 3) and mTORC1 phosphorylation (Chapter 3 and 4) were performed by our collaborators, Vanessa Di Palma and Jason Ho, from Dr. Vuk Stambolic’s Lab (Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, University of Toronto).
1.7 References:
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Melser S, Chatelain EH, Lavie J, Mahfouf W, Jose C, Obre E, Goorden S, Priault M, Elgersma Y, Rezvani HR et al. 2013. Rheb regulates mitophagy induced by mitochondrial energetic status. Cell Metab 17 : 719-730. Mizuki N, Kimura M, Ohno S, Miyata S, Sato M, Ando H, Ishihara M, Goto K, Watanabe S, Yamazaki M et al. 1996. Isolation of cDNA and genomic clones of a human Ras-related GTP-binding protein gene and its chromosomal localization to the long arm of chromosome 7, 7q36. Genomics 34 : 114-118. Napolioni V, Curatolo P. 2008. Genetics and molecular biology of tuberous sclerosis complex. Curr Genomics 9: 475-487. Nardella C, Chen Z, Salmena L, Carracedo A, Alimonti A, Egia A, Carver B, Gerald W, Cordon-Cardo C, Pandolfi PP. 2008. Aberrant Rheb-mediated mTORC1 activation and Pten haploinsufficiency are cooperative oncogenic events. Genes Dev 22 : 2172-2177. Norsted Gregory E, Codeluppi S, Gregory JA, Steinauer J, Svensson CI. 2010. Mammalian target of rapamycin in spinal cord neurons mediates hypersensitivity induced by peripheral inflammation. Neuroscience 169 : 1392-1402. Patel PH, Thapar N, Guo L, Martinez M, Maris J, Gau CL, Lengyel JA, Tamanoi F. 2003. Drosophila Rheb GTPase is required for cell cycle progression and cell growth. J Cell Sci 116 : 3601-3610. Prior IA, Lewis PD, Mattos C. 2012. A comprehensive survey of Ras mutations in cancer. Cancer Res 72 : 2457-2467. Rehmann H, Bruning M, Berghaus C, Schwarten M, Kohler K, Stocker H, Stoll R, Zwartkruis FJ, Wittinghofer A. 2008. Biochemical characterisation of TCTP questions its function as a guanine nucleotide exchange factor for Rheb. FEBS Lett 582 : 3005-3010. Reuther GW, Der CJ. 2000. The Ras branch of small GTPases: Ras family members don't fall far from the tree. Curr Opin Cell Biol 12 : 157-165. Rojas AM, Fuentes G, Rausell A, Valencia A. 2012. The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol 196 : 189-201. Ruvinsky I, Meyuhas O. 2006. Ribosomal protein S6 phosphorylation: from protein synthesis to cell size. Trends Biochem Sci 31 : 342-348. Sancak Y, Thoreen CC, Peterson TR, Lindquist RA, Kang SA, Spooner E, Carr SA, Sabatini DM. 2007. PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase. Mol Cell 25 : 903-915. Sato T, Nakashima A, Guo L, Tamanoi F. 2009. Specific activation of mTORC1 by Rheb G-protein in vitro involves enhanced recruitment of its substrate protein. J Biol Chem 284 : 12783-12791. Saucedo LJ, Gao X, Chiarelli DA, Li L, Pan D, Edgar BA. 2003. Rheb promotes cell growth as a component of the insulin/TOR signalling network. Nat Cell Biol 5: 566-571. Scheffzek K, Ahmadian MR, Kabsch W, Wiesmuller L, Lautwein A, Schmitz F, Wittinghofer A. 1997. The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277 : 333-338. Schopel M, Jockers KF, Duppe PM, Autzen J, Potheraveedu VN, Ince S, Yip KT, Heumann R, Herrmann C, Scherkenbeck J et al. 2013. Bisphenol A Binds to Ras Proteins and Competes with Guanine Nucleotide Exchange: Implications for GTPase-Selective Antagonists. J Med Chem 56 : 9664-9672. Scrima A, Thomas C, Deaconescu D, Wittinghofer A. 2008. The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues. Embo J 27 : 1145-1153. Seabra MC. 1998. Membrane association and targeting of prenylated Ras-like GTPases. Cell Signal 10 : 167-172.
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Stocker H, Radimerski T, Schindelholz B, Wittwer F, Belawat P, Daram P, Breuer S, Thomas G, Hafen E. 2003. Rheb is an essential regulator of S6K in controlling cell growth in Drosophila. Nat Cell Biol 5: 559-565. Sun Y, Fang Y, Yoon MS, Zhang C, Roccio M, Zwartkruis FJ, Armstrong M, Brown HA, Chen J. 2008. Phospholipase D1 is an effector of Rheb in the mTOR pathway. Proc Natl Acad Sci U S A 105 : 8286-8291. Takahashi K, Nakagawa M, Young SG, Yamanaka S. 2005. Differential membrane localization of ERas and Rheb, two Ras-related proteins involved in the phosphatidylinositol 3-kinase/mTOR pathway. J Biol Chem 280 : 32768-32774. Tee AR, Manning BD, Roux PP, Cantley LC, Blenis J. 2003. Tuberous sclerosis complex gene products, Tuberin and Hamartin, control mTOR signaling by acting as a GTPase-activating protein complex toward Rheb. Curr Biol 13 : 1259-1268. Traut TW. 1994. Physiological concentrations of purines and pyrimidines. Mol Cell Biochem 140 : 1-22. Wan X, Harkavy B, Shen N, Grohar P, Helman LJ. 2007. Rapamycin induces feedback activation of Akt signaling through an IGF-1R-dependent mechanism. Oncogene 26 : 1932-1940. Wander SA, Hennessy BT, Slingerland JM. 2011. Next-generation mTOR inhibitors in clinical oncology: how pathway complexity informs therapeutic strategy. J Clin Invest 121 : 1231-1241. Wang X, Fonseca BD, Tang H, Liu R, Elia A, Clemens MJ, Bommer UA, Proud CG. 2008. Re- evaluating the roles of proposed modulators of mammalian target of rapamycin complex 1 (mTORC1) signaling. J Biol Chem 283 : 30482-30492. Wennerberg K, Rossman KL, Der CJ. 2005. The Ras superfamily at a glance. J Cell Sci 118 : 843-846. Wittinghofer A, Vetter IR. 2011. Structure-function relationships of the G domain, a canonical switch motif. Annu Rev Biochem 80 : 943-971. Yamagata K, Sanders LK, Kaufmann WE, Yee W, Barnes CA, Nathans D, Worley PF. 1994. rheb, a growth factor- and synaptic activity-regulated gene, encodes a novel Ras-related protein. J Biol Chem 269 : 16333-16339. Yang H, Rudge DG, Koos JD, Vaidialingam B, Yang HJ, Pavletich NP. 2013. mTOR kinase structure, mechanism and regulation. Nature 497 : 217-223. Yee WM, Worley PF. 1997. Rheb interacts with Raf-1 kinase and may function to integrate growth factor- and protein kinase A-dependent signals. Mol Cell Biol 17 : 921-933. Yu J, Henske EP. 2006. Estrogen-induced activation of mammalian target of rapamycin is mediated via tuberin and the small GTPase Ras homologue enriched in brain. Cancer Res 66 : 9461-9466. Yu Y, Li S, Xu X, Li Y, Guan K, Arnold E, Ding J. 2005. Structural basis for the unique biological function of small GTPase RHEB. J Biol Chem 280 : 17093-17100. Zaytseva YY, Valentino JD, Gulhati P, Evers BM. 2012. mTOR inhibitors in cancer therapy. Cancer Lett 319 : 1-7. Zhang Y, Gao X, Saucedo LJ, Ru B, Edgar BA, Pan D. 2003. Rheb is a direct target of the tuberous sclerosis tumour suppressor proteins. Nat Cell Biol 5: 578-581. Zheng M, Wang YH, Wu XN, Wu SQ, Lu BJ, Dong MQ, Zhang H, Sun P, Lin SC, Guan KL et al. 2011. Inactivation of Rheb by PRAK-mediated phosphorylation is essential for energy- depletion-induced suppression of mTORC1. Nat Cell Biol 13 : 263-272.
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CHAPTER 2
Real-time NMR assays on Rheb, Ras, and RhoA GTPase cycles
This chapter has been reformatted from the original publication: Mazhab-Jafari MT, Marshall CB, Smith M, Gasmi-Seabrook GM, Stambolic V, Rottapel R, Neel BG, Ikura M. Real-time NMR study of three small GTPases reveals that fluorescent 2'(3')-O-(N-methylanthraniloyl)-tagged nucleotides alter hydrolysis and exchange kinetics. J Biol Chem. 2010 Feb 19;285(8):5132-6.
A link to the published paper can be found at: http://www.jbc.org/content/285/8/5132.long
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2.1 Abstract The Ras family of small GTPases control diverse signaling pathways through a conserved ‘switch’ mechanism, which is turned on by binding of GTP and turned off by GTP hydrolysis to GDP. Full understanding of GTPase ‘switch’ functions requires reliable, quantitative assays for nucleotide binding and hydrolysis. Fluorescently labeled guanine nucleotides, such as 2'(3')-O-(N-Methylanthraniloyl)- (mant)-substituted GTP and GDP analogs, have been widely used to investigate the molecular properties of small GTPases, including Ras and Rho. Using a recently-developed NMR method, we show that the kinetics of nucleotide hydrolysis and exchange by three small GTPases, alone and in the presence of their cognate GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs), are affected by the presence of the fluorescent mant moiety. Intrinsic hydrolysis of mantGTP by Rheb is ~10-times faster than that of GTP, whereas it is 3.4-times slower with RhoA. On the other hand, the mant tag inhibits TSC2GAP-catalyzed GTP hydrolysis by Rheb but promotes p120 RasGAP-catalyzed GTP hydrolysis by HRas. GEF catalyzed nucleotide exchange for both HRas and RhoA were inhibited by mant-substituted nucleotides, and the degree of inhibition depends highly on the GTPase and whether the assay measures association of mantGTP with, or dissociation of mantGDP from the GTPase. These results indicate that the mant moiety has significant and unpredictable effects on GTPase reaction kinetics and underscore the importance of validating its use in each assay.
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2.2 Introduction: The Ras superfamily of small GTPases plays vital roles in the integrated network of cellular signaling. They are “turned on” by binding to GTP and adopting a conformation that allows modulation of their downstream effectors. The proteins are then “turned off” by hydrolysis of the γ-phosphate of GTP and conversion to GDP (Figure 2.1a). The relative amounts of activated GTP-bound and inactive GDP- bound forms of GTPases are tightly regulated by GAPs, which catalyze nucleotide hydrolysis, and GEFs, which promote nucleotide exchange. Mutation or unregulated expression of the small GTPase proteins or their respective GAPs and GEFs can deregulate the GTPase cycle and lead to diseases such as cancer, neurodegeneration and mental disabilities (Ahmadian et al. 1996). A B
C
Figure 2.1 Effect of mant-substituted GTP on the intrinsic nucleotide hydrolysis of Ras, Rheb and RhoA. a) Nucleotide dependent conformational changes in GTPases. Nucleotide hydrolysis and exchange are correlated with conformational changes that are readily probed in two dimensional 1H-15 N HSQC spectra (PDB: 1XTS green, 1XTQ cyan). b) The chemical structure of mantGTP (ChemSketch (Spessard 1998)) is shown with the mant moiety at the 3’ position of the ribose ring. In solution, this moiety exhibits slow chemical exchange between the 2’ and 3’ positions of the ribose ring, producing an equilibrium ratio of 4:6 (Neal et al. 1990). c) The time course of intrinsic GTP (black) and mantGTP (green) hydrolysis by HRas, Rheb and RhoA probed via real time solution NMR spectroscopy. All the proteins were fully loaded with GTP or mantGTP before the start of the assay, as assessed by 1H-15 N HSQC. The rates are displayed with a histogram for each curve in inserted panel c. See appendix A for description of equations.
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Although several methods for monitoring GTP hydrolysis and nucleotide exchange of small GTPase proteins have been developed (Ahmadian et al. 1996; Zhang and Zheng 1998; Albert and Gallwitz 2000; Futai et al. 2004), the assay most widely used to monitor kinetics employs the fluorescently labeled guanosine nucleotide analogs 2'(3')-O-(N-Methylanthraniloyl) - GTP/GDP (mantGTP / mantGDP), which are sensitive to the hydrophobic environment of proteins (Figure 2.1b). Because of high sensitivity and selectivity, mantGTP and mantGDP have been widely used in the field (Sondermann et al. 2004; Mou et al. 2005; Gureasko et al. 2008), however, the use of these nucleotide analogs is justified only if they report reaction kinetics and thermodynamics that are consistent with the natural ligands GTP and GDP. Previously, some inconsistencies between native GTP and mantGTP were observed in nucleotide hydrolysis assays of Ras and RhoA with their cognate GAPs (Moore et al. 1993; Eberth et al. 2005). However, these fluorescent probes have never been fully assessed due to the lack of appropriate methodology.
Recently we developed an NMR-based real-time assay to monitor the rate of GTP hydrolysis of Ras homolog enriched in brain (Rheb), enabling us to monitor GTPase reactions using native GTP and GDP (Figure 2.2b) (Marshall et al. 2009). We have demonstrated that the real-time NMR methodology can be successfully used to assay nucleotide exchange in RhoA (Gasmi-Seabrook et al. 2010). This methodology requires no chemical modification of the protein or the nucleotide, which can perturb the native structure of the protein (Figure 2.3), and has the ability to sense subtle changes in the rate of catalysis in real-time fashion. In this study we employed the NMR methodology to examine how the fluorescent adduct on mantGTP and mantGDP affects the kinetics of nucleotide hydrolysis and exchange of three small GTPases (HRas, Rheb and RhoA) alone and in the presence of their GAPs or GEFs.
2.3 Results: 2.3.1 The effect of mant on the intrinsic rate of nucleotide hydrolysis :Mant-substituted nucleotides have been used extensively to investigate many aspects of G-protein signaling, including the kinetics and mechanisms of RasGAP-mediated GTP hydrolysis (Moore et al. 1993; Ahmadian et al. 1997; Ahmadian et al. 2002; Phillips et al. 2003) and Cdc25 SOS -mediated nucleotide exchange (Sondermann et al. 2004; Gureasko et al. 2008). We first used NMR methodology to examine whether the addition of the mant
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moiety alters the intrinsic hydrolysis rate of the GTPase domain of HRas (1-171) (Figure 2.1c) and found that it had little effect (Table 2.1), consistent with previous reports (Remmers et al. 1994). A
B
Figure 2.2 Comparison of the real-time NMR and fluorescence-substituted nucleotide-based GTPase assays. a) Fluorescence assay. Left panel: The emission spectra of Rheb-mantGTP (black) and Rheb-mantGDP (red) illustrating the decline in the fluorescence intensity accompanied by a red shift upon nucleotide hydrolysis. Right panel: The time-dependent intrinsic hydrolysis of mantGTP by Rheb monitored by fluorescence and fitted to a one-phase exponential decay. b) GTP hydrolysis by Rheb observed using NMR. Snapshots of 1H-15 N HSQC spectra collected over the time course of hydrolysis. The green box indicates the resonance specific to Gly13 of Rheb-GTP and the red box corresponds to that of Rheb-GDP.
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Figure 2.3 Perturbation of the native structure of GTPase proteins by mant-tagged nucleotides. Selected regions of 1H-15 N HSQC spectra from HRas, Rheb, and RhoA bound to GTP (green) or mantGTP (red) are shown. Dashed boxes indicate resonances that exhibit chemical shift changes between GTP and mantGTP.
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Table 2.1 The rates of intrinsic and GAP mediated nucleotide hydrolysis for three small GTPase proteins. All rates are reported in min -1.
1 2 1
1: A molar ratio of 1/2,500 HRasGAP to HRas was used. 2: A molar ratio of 1/2.2 TSC2GAP to Rheb was used.
Next, we analyzed GTP hydrolysis by Ras homolog enriched in brain (Rheb), which shares ~33% sequence identity with HRas. Surprisingly, the hydrolysis rate of mantGTP by Rheb (3.2×10 -3 min -1) was >10 times faster than that of native GTP when both reactions were monitored by NMR (Figure 2.1c). The rate constant obtained with mantGTP by NMR was identical to the value obtained using fluorescence spectroscopy (Figure 2.1c and 2.2a), demonstrating that the results are independent of the detection method. Using mantGTP to compare the activity of different GTPases, the intrinsic GTPase activity of Rheb would appear ~2 times lower than that of HRas, whereas it is actually ~32 times lower with native GTP, demonstrating that reliance on mantGTP would overlook this biologically important difference.
As a third case, the effect of the mant substitution on the GTPase activity of RhoA, which shares ~31% sequence identity with HRas and Rheb, was investigated and found to be opposite to that observed with Rheb (Figure 2.1c). The half-life of mantGTP bound to RhoA was ~155 min, 3.5 fold longer than that of native GTP (~45 min) (Table 2.1). Taken together, the results show that mant-substituted nucleotides can substantially alter the kinetics of nucleotide hydrolysis by small GTPases in a manner that could not have been predicted a priori .
2.3.2 The effect of mant on the rate of GAP-catalyzed nucleotide hydrolysis :Having established that mant can have a substantial effect on intrinsic GTPase reaction rates, we investigated the effect of
24
mantGTP on GAP-accelerated GTPase reactions. First, we used the GAP domain of the human p120- RasGAP. GTP was hydrolyzed with a rate of 2.6×10 -2 min -1 by HRas in the presence of a 1/2,500 molar ratio of RasGAP, whereas mantGTP was turned over ~5 times faster (Figure 2.4a and Table 2.1). Indeed, Moore et al. (Moore et al. 1993) previously noted that in the presence of RasGAP, p21 N-Ras hydrolyzes mantGTP more rapidly than native GTP, although the cleavage of the two nucleotides were not monitored by the same method. A
B
Figure 2.4 Effects of mant-substituted GTP on GAP-mediated nucleotide hydrolysis by HRas and Rheb. a) Time course of RasGAP-mediated nucleotide hydrolysis of HRas with GTP (black) and mantGTP (green). A molar ratio of 1:2,500 RasGAP to HRas was used. b) Time course of TSC2GAP- mediated hydrolysis of GTP (black) and mantGTP (green) bound to Rheb. A molar ratio of 1:2.2 TSC2GAP to Rheb was used for both assays. Rates extracted from each curve are displayed with an inserted histogram. Each experiment was performed in duplicate, and each curve represents a single representative experiment.
We then examined how mantGTP might affect GAP-mediated GTP hydrolysis of a second, unrelated GAP with a distinct mechanism of action, by studying Rheb and its well-characterized GAP, TSC2GAP
25
(Marshall et al. 2009). At a TSC2GAP to Rheb ratio of 1/2.2, GTP was hydrolyzed at a rate of 1.9×10 -2 min -1 whereas mantGTP was hydrolyzed ~2.5 fold more slowly (Figure 2.4b and Table 2.1). Comparing Rheb’s intrinsic rate of mantGTP hydrolysis to the GAP-catalyzed rate, TSC2GAP only produced a two- fold enhancement (Table 2.1). This contrasts sharply with the ~50 fold stimulation of Rheb GTPase activity by TSC2GAP when native GTP is used in the assay. Hence, exclusive use of mantGTP would lead to a gross underestimation of the GAP activity of TSC2 towards Rheb, underscoring the utility of the NMR-based methodology.
2.3.3 The effect of mant on the GEF-mediated nucleotide exchange :We examined how mant-substituted nucleotides affect the DH-PH PRG -mediated nucleotide exchange of RhoA (Figure 2.5a) using a procedure described elsewhere (Gasmi-Seabrook et al. 2010). In the NMR GEF assay with hydrolysable nucleotides, the readout (i.e, GDP- and GTP-specific protein cross-peaks) is determined by both exchange and intrinsic nucleotide hydrolysis. This is evident in the case of Ras and RhoA (Figure 2.5) which do not become 100% saturated with GTP or mantGTP. Hence the observed data was fit to an equation that considers exchange and hydrolysis (see appendix A), to derive the true exchange rate. We have shown that this derived rate agrees well with the rate determined for the non-hydrolysable GTP γS (Gasmi-Seabrook et al. 2010). In an assay of nucleotide association with RhoA, mantGTP exhibits a 30% lower exchange rate (4.9×10 -2 min -1) compared to native GTP (7.0×10 -2 min -1) (Table 2.2). In the literature, both the incorporation (Hutchinson and Eccleston 2000; Derewenda et al. 2004; Oleksy et al. 2004) and dissociation (Tan et al. 2002; Hemsath and Ahmadian 2005) of the mant-substituted nucleotide have been employed to study the function of RhoA and its interaction with GEFs. Hence, we also performed the ‘dissociation’ assay, initially loading RhoA with GDP or mantGDP, and monitoring exchange to GTP. In this reaction the rate of DH-PHPRG mediated nucleotide dissociation was approximately six times slower for mantGDP than for GDP (Figure 2.6a and 6c).
Previous studies have used mantGDP extensively to probe the Son of Sevenless (Cdc25 SOS ) catalyzed nucleotide exchange of Ras GTPase. Generally, Ras is preloaded with mantGDP and the decay in fluorescent intensity is monitored as this fluorescent nucleotide is displaced by unlabeled GTP (Margarit et al. 2003; Sondermann et al. 2004; Ford et al. 2005; Ford et al. 2006; Freedman et al. 2006; Gureasko et al. 2008). Here, using an NMR-based protocol similar to that described for RhoA, we show (Figure 2.5b and Table 2.2) that the rate of Cdc25 SOS -catalyzed mantGDP dissociation (7.2×10 -3 min -1) is
26
approximately 30% slower compared with that of native GDP. GEF assays using association of mant- tagged nucleotide with Ras have also been reported (Sacco et al. 2006), thus we used NMR to compare the Cdc25 SOS -catalyzed association of mantGTP and GTP. We found that the rate of association of mantGTP with HRas is ~3-fold slower than that of GTP (Figure 2.6b and 6d). A
B
Figure 2.5 Effects of mant-substituted nucleotides on GEF-mediated nucleotide exchange for HRas and RhoA. a) Time course of DH-PH PRG mediated nucleotide exchange of RhoA-GDP to GTP (black) and mantGTP (green). A molar ratio of 1/30,000 RhoA to DH-PH PRG was used for both assays. b) Time course of CDC25 SOS mediated nucleotide exchange of HRas-GDP (black) and HRas-mantGDP (green) to GTP with 1/30,000 HRas to CDC25 SOS molar ratio. Observed data (continuous lines) were fitted to an equation that considers both exchange and hydrolysis to extract the true exchange rate k ex in each experiment (see appendix A). Using this rate, exponential decay curves (dashed lines) were generated to approximate nucleotide exchange in the absence of hydrolysis. The corrected rates are displayed with an inserted histogram for each curve. Each experiment was performed in duplicate, and each curve represents a single representative experiment.
27
Table 2.2 The rates of GEF mediated nucleotide exchange for HRas and RhoA proteins. These exchange rates are reported in min -1 and determined by fitting data to an equation that considers both exchange and hydrolysis.
1: A ratio of 1/30,000 GEF to GTPase was used with 10 molar excess of nucleotide relative to GTPase.
A B
C D
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Figure 2.6 Complementary assays of the effects of mant-substituted nucleotides on GEF-mediated nucleotide exchange for HRas and RhoA. a) The DH-PH PRG mediated nucleotide exchange of RhoA- GDP to GTP (black) and mantGDP to GTP (green). A molar ratio of 1/30,000 RhoA to DH-PH PRG was used for both assays. b) The CDC25 SOS -mediated nucleotide exchange of HRas-GDP to GTP (black) or mantGTP (green). A molar ratio of 1/30,000 HRas to CDC25 SOS was used for both assays. Observed data (circles and triangles) were fitted to an equation that considers both exchange and hydrolysis to extract the true exchange rate, which was used to plot exponential decay curves (gray and green lines) (see Appendix A). These rates are displayed with a histogram for each curve in panels c and d.
2.4 Discussion: Fluorescently-labeled guanosine nucleotides have been used extensively to study nucleotide hydrolysis and exchange of GTPases. However, covalent modification of the nucleotide with a bulky fluorophore raises concerns about how this reporter moiety may perturb enzymatic activity. The NMR methodology recently developed by our group (Marshall et al. 2009) does not require any chemical modification of GTP or GDP because it makes direct observation of protein resonances that depend on nucleotide- induced changes in chemical environment of protein (Figure 2.2b). In this study, we employed this NMR method to compare native versus mant-labeled nucleotides in the kinetics of intrinsic GTPase reactions, GAP-mediated nucleotide hydrolysis, and GEF-mediated nucleotide exchange reactions of three small GTPases, HRas, Rheb, and RhoA. Our results clearly demonstrate that mant-labeled nucleotides had substantial effects on the kinetics of these reactions and that these effects were remarkably different and unpredictable with each GTPase, GAP, and GEF.
2.4.1 Intrinsic hydrolysis of GTP and mantGTP :HRas exhibited a small decrease in the intrinsic hydrolysis rate of mantGTP versus native GTP, however Rheb and RhoA were affected more drastically by this fluorescent tag. Remarkably, mant had opposite effects on Rheb and RhoA; Rheb hydrolyzed mantGTP ~10 fold faster than native GTP, whereas RhoA hydrolyzed this analog 3 fold more slowly than GTP. Thus, the effects of mant are specific to the structure and catalytic mechanism of each GTPase rather than the inherent lability of the nucleotide. With all three GTPases, the mant-adduct perturbed proximal residues in the P-loop, switch I and G-5 box, but also induced long range perturbations in several regions including switch II (Figure 2.7). The catalytic Gln of RhoA is found in switch II, thus distortion of the structure of this loop could inhibit the hydrolysis of mantGTP. Interestingly, the analogous Gln in Rheb is in an orientation that does not contribute to catalysis (Yu et al. 2005; Marshall et al. 2009). To understand the rapid hydrolysis of mantGTP by Rheb, we asked
29
A
B
C
Figure 2.7 mantGTP-induced chemical shift perturbations in Ras, Rheb and RhoA. Residues exhibiting chemical shift perturbations induced by binding of mantGTP (versus GTP) are mapped onto
30
the structures of a) Ras (PDB:5P21) , b) Rheb (PDB:1XTS) and c) RhoA (PDB:1KMQ) . Magenta colored residues correspond to small chemical shift changes (i.e., peaks partially overlap) whereas residues exhibiting large chemical shift changes or severe line broadening are colored red. Unassigned residues including prolines are indicated with dark gray. The nucleotide is shown in spheres with carbon, oxygen, nitrogen, and phosphate shown in green, red, blue, and orange respectively. The magnesium ion is shown with cyan sphere. The predicted position of the mant-moiety, which exists in equilibrium between the 2’ and 3’ hydroxyl groups of the ribose ring, is indicated in each structure by a red circle. Switch I residues of all three GTPases are broadened beyond detection in both the GTP- and mantGTP-bound states, however chemical shift perturbations would be expected based on the structure of Ras in complex with mant-dGppNHp (PDB:1GNP) , in which the mant moiety faces the switch I region of Ras.
whether the mant-induced perturbation of switch II might favor a catalytically competent conformation of Gln64. However the Q64L mutation had no effect on hydrolysis of mantGTP, indicating that this reaction occurs through more complex mechanism (Figure 2.8).
Figure 2.8 Rheb Gln64 is not involved in the rapid hydrolysis of mantGTP. The time course of mantGTP hydrolysis by wild type Rheb (black) and RhebQ64L mutant (green) probed via real time solution NMR spectroscopy. The proteins were fully loaded with mantGTP before the start of the assay, as assessed by 1H-15 N HSQC.
2.4.2 GAP-catalyzed GTP hydrolysis by HRas and Rheb:p120-RasGAP-catalyzed hydrolysis of mantGTP by HRas was ~5 fold faster than that of native GTP whereas TSC2GAP-mediated hydrolysis of mantGTP by Rheb was slower by a factor of ~2.5 relative to unmodified GTP. Considering the rapid intrinsic GTPase activity of Rheb towards mantGTP, it is apparent that TSC2GAP activity is severely inhibited by mant. These results demonstrate the unpredictable effects of mant-tagged nucleotides on intrinsic and GAP-mediated GTPase activities and highlight the utility of the NMR approach.
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Previous studies using a phosphate release assay showed that the K m of p120 RasGAP-mediated hydrolysis of p21 N-Ras-mantGTP is lower than that of the p21 N-Ras-GTP complex (Moore et al. 1993). This result suggests that mant may increase the affinity of the HRas-nucleotide complex for RasGAP, thus increasing the rate of nucleotide hydrolysis. Conversely, we propose that for Rheb the mant moiety probably hinders docking of the TSC2GAP domain to Rheb. Note that TSC2 and p120 RasGAP are not homologous, have different folds and function through distinct catalytic mechanisms. Further structural insights are required to address the mechanistic basis for the ‘mant effect’ on GAP- mediated nucleotide hydrolysis for both HRas and Rheb.
2.4.3 GEF-accelerated nucleotide exchange of HRas and RhoA :Using the aforementioned NMR-based approach (Gasmi-Seabrook et al. 2010), we performed GEF assays to measure both association and dissociation of mant-tagged nucleotides, as fluorescence-based experiments have been reported both ways in the literature (Hutchinson and Eccleston 2000; Tan et al. 2002; Margarit et al. 2003; Derewenda et al. 2004; Oleksy et al. 2004; Sondermann et al. 2004; Ford et al. 2005; Hemsath and Ahmadian 2005; Ford et al. 2006; Freedman et al. 2006; Sacco et al. 2006; Gureasko et al. 2008). Comparing dissociation, Cdc25 SOS -mediated nucleotide exchange was 30% slower when starting with mantGDP- bound HRas (mantGDP to GTP) than with GDP-bound HRas (GDP to GTP). Measuring association under the same conditions, the GDP to mantGTP exchange was ~3 times slower than GDP to GTP exchange. Similarly, DH-PH PRG -mediated nucleotide exchange was 30% slower for the GDP to mantGTP than the GDP to GTP exchange in the association assay and ~6 fold slower for the mantGDP to GTP than GDP to GTP exchange in the dissociation assay. In the crystal structure of HRas-mant dGppNHp (Scheidig et al. 1995), mant is near residue Tyr32 in switch I, which would introduce steric clashes at the primary contact point between the GTPase and Cdc25 SOS and could interfere with nucleotide exchange. Assuming the mant moiety of the nucleotide is similarly positioned on the switch I region of RhoA, it would also hinder DH-PH PRG binding to RhoA (Derewenda et al. 2004). Furthermore, mant-induced structural perturbations of the GEF binding sites in the GTPase switch regions may inhibit interactions with GEFs. The exchange kinetics reported by mant are more reliable when the dissociation assay is used for the Ras-CDC25 SOS system and the association assay is used for the RhoA-DH-PH PRG system. Note that these are the conventional fluorescence methods for each protein, nevertheless the less accurate alternative approaches are still in use. Finally, the reduced sensitivity of mantGDP-bound GTPases to the action of GEFs suggests an avenue for design of GTPase inhibitors.
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In conclusion, we have demonstrated that mant-labeled nucleotides can alter the intrinsic GTPase activity of Rheb, RhoA, the GAP-catalyzed GTP hydrolysis of HRas-RasGAP and Rheb-TSC2GAP, as well as the DH-PH PRG and CDC25 SOS -mediated nucleotide exchange of RhoA and HRas, respectively. These results reveal that the fluorescent probes could yield biochemically inaccurate data and potentially lead to misleading conclusions. The significant and unpredictable effects of the mant tag clearly indicate that mant-tagged nucleotides should be used with caution and should be validated for each GTPase system studied. At the same time, these findings provide clues as to how one could inhibit or activate specific signaling pathways using small organic molecules, which may mimic the effects of the mant-tag on small GTPases. This study also extends the utility and value of the NMR-based assays for both GTPase and GEF reactions for three small GTPases, suggesting that it will be broadly applicable to the GTPase superfamily.
2.5 Experimental procedures: 2.5.1 Protein preparation : Murine Rheb (residues 1-169), human HRas (residues 1-171) and murine RhoA (residues 1-181) were prepared according to previous protocols (Scheidig et al. 1995; Derewenda et al. 2004; Marshall et al. 2009). In brief, the three proteins were expressed in Escherichia coli (BL21), 15 o grown in minimal media supplemented with NH 4Cl at 15 C with 0.25 mM IPTG. Rheb, HRas and RhoA were expressed using pGEX2T, pET15b and pET28 vectors, respectively. All purified proteins were exchanged into NMR buffer (25 mM sodium phosphate pH 7.0, 100 mM NaCl, 5 mM MgCl 2 and 1mM DTT) in a PD MidiTrap TM G-25 column (GE healthcare). Small GTPase-proteins expressed in E. coli co-purified primarily as complexes with GDP. Tuberous sclerosis 2 (TSC2) GAP domain (residues 1525-1742: hereafter termed TSC2GAP) and the DH-PH fragment of PDZ-RhoGEF (residues 713- 1081: hereafter termed DH-PH PRG ) were prepared using pGEX2T and pGEX4T1 vectors, respectively (Derewenda et al. 2004; Marshall et al. 2009). Catalytic domain constructs of the Son of Sevenless (SOS, Cdc25 residues 566-1049: hereafter referred to as Cdc25 SOS ) and the GTPase activating domain of human GTPase activating protein p120GAP (residues 715-1047: hereafter referred to as RasGAP) were prepared as His-tagged proteins from the pET15b vector. All proteins were cleaved from their tags via thrombin.
33
2.5.2 NMR-based GTPase, GAP and GEF assays : HRas and Rheb were loaded with GTP or mantGTP by incubation with a 10 fold excess of nucleotide in the presence of 10mM EDTA. RhoA was loaded with GTP or mantGTP in the presence 0.5 M urea and 10 mM EDTA. A 1H-15 N HSQC (Heteronuclear Single Quantum Coherence) spectrum was collected to confirm full nucleotide loading, and the mixture was then passed through a de-salting column (PD MidiTrap TM G-25 (GE healthcare)) equilibrated with NMR buffer, to produce a 1:1 complex of GTPase and the nucleotide.
All NMR experiments were run on a Bruker AVANCE II 800 MHz spectrometer equipped with a 5mm TCI CryoProbe. Sensitivity enhanced 1H-15 N HSQCs with 2 scans (5 min) were run in succession to monitor the intrinsic GTP hydrolysis activity of GTPases (0.1-0.3 mM) at 20 oC. The spectra were processed with NMRPipe (Delaglio et al. 1995) and the peak heights were analyzed with Sparky (Goddard and Kneller) via Gaussian line fitting. Residues from switch I&II, P-loop, β3 & β4 and the α3 helix that exhibit distinct well-resolved peaks in each nucleotide-bound state were used as reporters of the reaction rates for each of the three GTPases, as described previously for Rheb (Marshall et al. 2009).
For the intrinsic nucleotide hydrolysis, the fraction of GTPase protein in the GDP-bound state was calculated for each reporter residue using the equation 1 for Ras and Rheb relying on both GDP and GTP peaks (see appendix A). In the case of RhoA the active state exhibited broadened and split peaks that complicate peak integration, hence we monitored (equation 2; appendix A) the appearance of GDP peaks. Data fitting was done using PRISM (GraphPad software).
To assay GAP-mediated nucleotide hydrolysis, RasGAP or TSC2GAP was added to GTP-loaded HRas or Rheb at a GAP to GTPase molar ratio of 1/2,500 or 1/2.2, respectively. The hydrolysis rate was determined by fitting the data to equation 1 in appendix A.
For GEF assays, DH-PH PRG or Cdc25 SOS were added at a molar ratio of 1/30,000 GEF to RhoA or Ras, in the presence of a 10 fold molar excess of GTP or mantGTP. All the experiments were performed in duplicate with 0.1 mM GTPase. The observed rates of nucleotide exchange assays performed with hydrolysable nucleotides are affected by intrinsic hydrolysis. Thus the observed data were fitted to an equation that considers both exchange and hydrolysis (see appendix A) to extract the true exchange rate.
34
Using this rate, an exponential decay curve was generated to approximate nucleotide exchange in the absence of hydrolysis.
2.5.3 Fluorescence-based GTPase assay :Emission spectra of 5 M Rheb-mantGTP and Rheb-mantGDP (380-525 nm) were collected at 20 oC on a Shimadzu RF-5301PC spectrofluorophotometer with excitation at 370 nm. Fluorescence emission intensity at 436 nm was monitored during the hydrolysis reaction with excitation at 370 nm. Ten measurements were collected per minute and the average and standard deviation were reported.
2.6 References:
Ahmadian MR, Hoffmann U, Goody RS, Wittinghofer A. 1997. Individual rate constants for the interaction of Ras proteins with GTPase-activating proteins determined by fluorescence spectroscopy. Biochemistry 36 : 4535-4541. Ahmadian MR, Wiesmuller L, Lautwein A, Bischoff FR, Wittinghofer A. 1996. Structural differences in the minimal catalytic domains of the GTPase-activating proteins p120GAP and neurofibromin. J Biol Chem 271 : 16409-16415. Ahmadian MR, Wittinghofer A, Herrmann C. 2002. Fluorescence methods in the study of small GTP- binding proteins. Methods Mol Biol 189 : 45-63. Albert S, Gallwitz D. 2000. Msb4p, a protein involved in Cdc42p-dependent organization of the actin cytoskeleton, is a Ypt/Rab-specific GAP. Biol Chem 381 : 453-456. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. 1995. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277-293. Derewenda U, Oleksy A, Stevenson AS, Korczynska J, Dauter Z, Somlyo AP, Otlewski J, Somlyo AV, Derewenda ZS. 2004. The crystal structure of RhoA in complex with the DH/PH fragment of PDZRhoGEF, an activator of the Ca(2+) sensitization pathway in smooth muscle. Structure 12 : 1955-1965. Eberth A, Dvorsky R, Becker CF, Beste A, Goody RS, Ahmadian MR. 2005. Monitoring the real-time kinetics of the hydrolysis reaction of guanine nucleotide-binding proteins. Biol Chem 386 : 1105- 1114. Ford B, Hornak V, Kleinman H, Nassar N. 2006. Structure of a transient intermediate for GTP hydrolysis by ras. Structure 14 : 427-436. Ford B, Skowronek K, Boykevisch S, Bar-Sagi D, Nassar N. 2005. Structure of the G60A mutant of Ras: implications for the dominant negative effect. J Biol Chem 280 : 25697-25705. Freedman TS, Sondermann H, Friedland GD, Kortemme T, Bar-Sagi D, Marqusee S, Kuriyan J. 2006. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A 103 : 16692-16697. Futai E, Hamamoto S, Orci L, Schekman R. 2004. GTP/GDP exchange by Sec12p enables COPII vesicle bud formation on synthetic liposomes. Embo J 23 : 4146-4155. Gasmi-Seabrook GM, Marshall CB, Cheung M, Kim B, Wang F, Jang YJ, Mak TW, Stambolic V, Ikura M. 2010. Real-time NMR study of guanine nucleotide exchange and activation of RhoA by PDZ-RhoGEF. J Biol Chem 285 : 5137-5145.
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Goddard TD, Kneller D. SPARKY 3. in University of California, San Francisco . Gureasko J, Galush WJ, Boykevisch S, Sondermann H, Bar-Sagi D, Groves JT, Kuriyan J. 2008. Membrane-dependent signal integration by the Ras activator Son of sevenless. Nat Struct Mol Biol 15 : 452-461. Hemsath L, Ahmadian MR. 2005. Fluorescence approaches for monitoring interactions of Rho GTPases with nucleotides, regulators, and effectors. Methods 37 : 173-182. Hutchinson JP, Eccleston JF. 2000. Mechanism of nucleotide release from Rho by the GDP dissociation stimulator protein. Biochemistry 39 : 11348-11359. Margarit SM, Sondermann H, Hall BE, Nagar B, Hoelz A, Pirruccello M, Bar-Sagi D, Kuriyan J. 2003. Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS. Cell 112 : 685-695. Marshall CB, Ho J, Buerger C, Plevin MJ, Li GY, Li Z, Ikura M, Stambolic V. 2009. Characterization of the intrinsic and TSC2-GAP-regulated GTPase activity of Rheb by real-time NMR. Sci Signal 2: ra3. Moore KJ, Webb MR, Eccleston JF. 1993. Mechanism of GTP hydrolysis by p21N-ras catalyzed by GAP: studies with a fluorescent GTP analogue. Biochemistry 32 : 7451-7459. Mou TC, Gille A, Fancy DA, Seifert R, Sprang SR. 2005. Structural basis for the inhibition of mammalian membrane adenylyl cyclase by 2 '(3')-O-(N-Methylanthraniloyl)-guanosine 5 '- triphosphate. J Biol Chem 280 : 7253-7261. Neal SE, Eccleston JF, Webb MR. 1990. Hydrolysis of GTP by p21NRAS, the NRAS protooncogene product, is accompanied by a conformational change in the wild-type protein: use of a single fluorescent probe at the catalytic site. Proc Natl Acad Sci U S A 87 : 3562-3565. Oleksy A, Barton H, Devedjiev Y, Purdy M, Derewenda U, Otlewski J, Derewenda ZS. 2004. Preliminary crystallographic analysis of the complex of the human GTPase RhoA with the DH/PH tandem of PDZ-RhoGEF. Acta Crystallogr D Biol Crystallogr 60 : 740-742. Phillips RA, Hunter JL, Eccleston JF, Webb MR. 2003. The mechanism of Ras GTPase activation by neurofibromin. Biochemistry 42 : 3956-3965. Remmers AE, Posner R, Neubig RR. 1994. Fluorescent guanine nucleotide analogs and G protein activation. J Biol Chem 269 : 13771-13778. Sacco E, Metalli D, Busti S, Fantinato S, D'Urzo A, Mapelli V, Alberghina L, Vanoni M. 2006. Catalytic competence of the Ras-GEF domain of hSos1 requires intra-REM domain interactions mediated by phenylalanine 577. FEBS Lett 580 : 6322-6328. Scheidig AJ, Franken SM, Corrie JE, Reid GP, Wittinghofer A, Pai EF, Goody RS. 1995. X-ray crystal structure analysis of the catalytic domain of the oncogene product p21H-ras complexed with caged GTP and mant dGppNHp. J Mol Biol 253 : 132-150. Sondermann H, Soisson SM, Boykevisch S, Yang SS, Bar-Sagi D, Kuriyan J. 2004. Structural analysis of autoinhibition in the Ras activator Son of sevenless. Cell 119 : 393-405. Spessard GO. 1998. ACD Labs/LogP dB 3.5 and ChemSketch 3.5. Journal of Chemical Information and Computer Sciences 38 : 1250-1253. Tan YC, Wu H, Wang WN, Zheng Y, Wang ZX. 2002. Characterization of the interactions between the small GTPase RhoA and its guanine nucleotide exchange factors. Anal Biochem 310 : 156-162. Yu Y, Li S, Xu X, Li Y, Guan K, Arnold E, Ding J. 2005. Structural basis for the unique biological function of small GTPase RHEB. J Biol Chem 280 : 17093-17100. Zhang B, Zheng Y. 1998. Regulation of RhoA GTP hydrolysis by the GTPase-activating proteins p190, p50RhoGAP, Bcr, and 3BP-1. Biochemistry 37 : 5249-5257.
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CHAPTER 3
Identification of critical amino acids in Rheb GTP hydrolysis
This chapter has been reformatted from the original publication: Mazhab-Jafari MT, Marshall CB, Ishiyama N, Ho J, Di Palma V, Stambolic V, Ikura M. An autoinhibited noncanonical mechanism of GTP hydrolysis by Rheb maintains mTORC1 homeostasis. Structure. 2012 Sep 5;20(9):1528-39.
A link to the published paper can be found at: http://www.sciencedirect.com/science/article/pii/S096921261200247X
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3.1 Abstract: Rheb, an activator of mammalian target of rapamycin (mTOR), displays low intrinsic GTPase activity favoring the biologically activated, GTP-bound state. We identified a Rheb mutation (Y35A) that increases its intrinsic nucleotide hydrolysis activity ~10-fold, and solved structures of both its active and inactive forms, revealing an unexpected mechanism of GTP hydrolysis involving Asp65 in switch II and Thr38 in switch I. In the wild-type protein, this non-canonical mechanism is markedly inhibited by Tyr35, which constrains the active site conformation, restricting the access of the catalytic Asp65 to the nucleotide-binding pocket. Rheb-Y35A mimics the enthalpic and entropic changes associated with GTP hydrolysis elicited by the GTPase activating protein (GAP) TSC2, and is insensitive to further TSC2 stimulation. Overexpression of Rheb-Y35A impaired the regulation of mTORC1 signaling by growth factor availability. We demonstrate that the opposing functions of Tyr35 in the intrinsic and GAP- stimulated GTP catalysis are critical for optimal mTORC1 regulation.
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3.2 Introduction: Small GTPases act as molecular switches to regulate diverse cellular functions. When bound to guanosine trisphosphate (GTP), they adopt an ‘on’ conformation that elicits a biological response. GTP hydrolysis is accompanied by a conformational change into a GDP-bound ‘off’ conformation. Cycling between the active and inactive states of each GTPase is a result of the intrinsic nucleotide hydrolysis and exchange rates, and regulatory proteins that catalyze these processes. GTPase activating proteins (GAPs) stimulate GTP hydrolysis, whereas guanine nucleotide exchange factors (GEFs) mediate the displacement of GDP, allowing a new GTP molecule to bind (Bos et al. 2007). GTPase proteins possess either complete or partial catalytic machinery for hydrolysis of GTP. In most cases, an electronegative group is used for stabilization/polarization of the hydrolytic water for in-line nucleophilic attack of the γ-phosphate (Maegley et al. 1996; Li and Zhang 2004). In most Ras and Rho subfamily GTPases, this is achieved by the carboxamide oxygen of a conserved Gln in a dynamic loop called switch II. Ras and Rho GAPs work by stabilizing this Gln in a catalytic conformation, while an Arg residue referred to as an “Arginine finger” neutralizes the developing negative charge on the α- and β-phosphates of GTP (Scheffzek et al. 1997). In other systems, such as Rap-RapGAP, a catalytic asparagine is provided in trans by the GAP (Scrima et al. 2008).
Ras homolog enriched in brain (Rheb) is a key regulator of the mTOR complex 1 (mTORC1) signaling pathway (Inoki et al. 2003; Dunlop et al. 2009). Rheb-GTP promotes phosphorylation of mTORC1 targets, resulting in enhanced protein translation and cellular growth (Garami et al. 2003). Rheb has an unusually slow intrinsic GTPase activity, which is regulated by the GAP activity of tuberous sclerosis complex 2 (TSC2), a tumor suppressor frequently inactivated in human patients with the tumor predisposition syndrome tuberous sclerosis (Garami et al. 2003; Tee et al. 2003). Rheb overexpression has been observed in certain cancer cell lines (Im et al. 2002; Eom et al. 2008; Nardella et al. 2008) and constitutively activated Rheb mutants can induce oncogenic transformation in cell culture (Jiang and Vogt 2008). The low intrinsic GTPase activity of Rheb has been attributed to the catalytically incompetent conformation of Gln64 (Yu et al. 2005), which is homologous to Ras Gln61, but does not participate in GTP hydrolysis (Li et al. 2004; Marshall et al. 2009). TSC2GAP is thought to utilize Asn1643 to promote GTP hydrolysis by substituting for Gln64 in an “Asn thumb”-type mechanism (Inoki et al. 2003; Marshall et al. 2009) similar to that of RapGAP (Scrima et al. 2008).
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Here, utilizing site-directed mutagenesis, crystallography and real-time NMR-based GTPase assays, we discovered that Rheb Tyr35, a residue that is highly conserved across the small GTPase superfamily (Wennerberg et al. 2005), maintains the high activation state of Rheb by inhibiting intrinsic GTP hydrolysis. Mutation of this residue substantially accelerated intrinsic nucleotide hydrolysis through a catalytic mechanism that did not require Gln64, but also conferred resistance to the activity of TSC2. Crystal structures of RhebY35A led us to identify the backbone carbonyl of Thr38 and side chain of Asp65 as candidate residues that contribute to the intrinsic GTPase activity. Mutagenesis studies confirm that Asp65 contributes significantly to the intrinsic GTPase activity of both wild-type Rheb and the Y35A mutant. Further, Asp65 was absolutely essential for the sensitivity of Rheb to the GAP activity of TSC2, whereas Gln64 was dispensable. Consistent with the in vitro data, expression of Rheb Y35A and D65A mutants in mammalian cells affected transduction of growth factor signals to mTORC1. Taken together, our observations reveal an efficient non-canonical mechanism of GTP hydrolysis by Rheb, and suggest that autoinhibition of catalysis maintains Rheb in its highly activated state upon growth factor stimulation, which is necessary for the proper signal transduction to mTORC1.
3.3 Results: 3.3.1 Rheb Tyr35 inhibits intrinsic GTPase activity: We previously showed that fluorescent-tagged nucleotides can alter the hydrolysis and exchange rates governing the GTPase cycle (Mazhab-Jafari et al. 2010). The most striking example we observed was that 2'-/3'-O-(N'- Methylanthraniloyl) (mant)GTP was hydrolyzed by Rheb ~10-fold faster than GTP. This is not an intrinsic property of the modified nucleotide as the mant moiety inhibited GTP hydrolysis by RhoA and did not affect hydrolysis by Ras. The rate of mantGTP hydrolysis by Rheb is similar to that of Ras (Figure 3.1a), indicating that Rheb has a latent capacity for efficient catalysis. Interestingly however, the rapid hydrolysis of mantGTP was independent of Rheb Gln64 (Mazhab-Jafari et al. 2010). The position of the fluorophore in a structure of Ras bound to a non-hydrolyzable analog of mantGTP (Scheidig et al. 1995) suggested it may interact with the phenol ring of Tyr35 in switch I of Rheb. Remarkably, mutation of Tyr35 to Ala recapitulated the mant effect, increasing the rate of GTP hydrolysis by an order of magnitude (Figure 3.1b). Furthermore, the mant tag had no further effect on the catalytic activity of Rheb Y35A, suggesting that the mutation and the fluorophore stimulate hydrolysis through the same mechanism (Figure 3.1b). These observations indicate that Tyr35 auto-inhibits the intrinsic GTPase activity of Rheb.
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Figure 3.1 Rapid hydrolysis of mantGTP by Rheb is related to autoinhibitory role of Tyr35. a) Hydrolysis of GTP or mantGTP by Rheb (black and green, respectively) and Ras (red and blue, respectively). Reaction rates derived by curve fitting are presented in the insets. b) Hydrolysis of GTP by wild-type Rheb (black), and GTP and mantGTP by Rheb Y35A (green and red respectively).
3.3.2 Structural basis for the Tyr35 auto-inhibitory function: We crystallized GDP-bound Rheb Y35A in the presence of excess GMPPNP (a non-hydrolyzable analog of GTP) and to our surprise, the asymmetric unit contained two molecules of Rheb, one bound to GDP and one to GMPPNP (Figure 3.2a-c). The overall protein fold is very similar to WT Rheb (Yu et al. 2005) (backbone RMSD of 0.44 Å) with a few key differences. The nucleotide-binding pocket is completely solvent exposed in the GMPPNP-bound structure of Rheb Y35A, whereas in the WT protein the triphosphate group of the
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Figure 3.2 Structure and dynamics of Rheb Y35A. (a) Asymmetric unit and electron density of nucleotide substrates. The asymmetric unit of the RhebY35A crystal containing one GDP-bound (cyan) and one GMPPNP-bound (green) Rheb molecule is shown in the center. 2F o-Fc electron density maps at 1.5 σ of the nucleotide binding site with GMPPNP (left) fitted into one Rheb Y35A molecule and GDP (right) in the second molecule of the crystal asymmetric unit. (b) Ribbon model of GMPPNP-bound Rheb Y35A. (c) Ribbon model of GDP-bound Rheb Y35A in the same orientation as b. Panels d, e, f and g show overlays of GMPPNP- or GDP-bound Rheb Y35A (colored as above) and WT Rheb in
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complex with GMPPNP (1XTR) (magenta) or GDP (1XTQ) (gray), as indicated. d) Mutation of Tyr35 affects the position of the catalytic water (spheres) and γ-phosphate with respect to the carbonyl of Thr38. e) Minor conformational change of Ala35 in the Rheb mutant upon GTP hydrolysis. The Ala35 C α and C β translocation distances from the GMPPNP-bound form to the GDP-bound form are shown. f) Major conformational rearrangement of WT Rheb Tyr35 upon GTP hydrolysis, with translocations indicated as in e. g) Position of switch II residues relative to the nucleotide binding site in the activated form of WT Rheb versus that of the Y35A mutant. The backbone of N-terminal switch II residues Gly63-Ser68 and side chains of Asp65 and Glu66 are shown. Two conformations were observed for the Asp65 side chain. h) 1H-15 N HSQC spectra illustrating cross-peaks from switch II residues in WT Rheb (black) and Rheb Y35A (red) in complex with GTP. The panel showing Ser68 is illustrated at a higher contour level for clarity. The reduction in height of the peak from the mutant relative to the wild-type peak is indicated as a percentage at the bottom of each panel in which it is measurable. The full spectra are shown in figure 3.7a.
nucleotide is shielded from the solvent by the phenol ring of Tyr35, which forms a hydrogen bond with the γ-phosphate. In addition, the γ-phosphate is 0.5 Å closer to Thr38 in the absence of Tyr35 (Figure 3.2d), which in the WT structure “pulls” the γ-phosphate toward the middle of switch I. Interestingly, the hydrolytic water is closer to the backbone carbonyl of Thr38 in the mutant (2.7 Å versus 3.8 Å in the WT protein) (Figure 3.2d), placing it in a more electron-rich environment that may enhance its polarization for an in-line nucleophilic attack to the γ-phosphate. It has been proposed that the corresponding backbone carbonyl of Ras (Thr35) contributes to the stabilization/activation of the catalytic water during intrinsic GTP hydrolysis (Frech et al. 1994; Buhrman et al. 2010). Comparison of our structure with that of wild-type Rheb indicates that Tyr35 pulls the γ-phosphate and catalytic water away from the Thr38 carbonyl, thus reducing its catalytic contribution.
Switch I of Rheb Y35A does not undergo any substantial conformational change upon nucleotide hydrolysis, whereas this region of the WT protein exhibits a large structural change mediated by an interaction between Tyr35 and the γ-phosphate (Yu et al. 2005) (Figure 3.2e&f). It was hypothesized that a similar nucleotide-dependent rearrangement of Rap Tyr32 would be energetically unfavourable to the GTPase reaction (Cherfils et al. 1997), consistent with our observation that nucleotide hydrolysis is accelerated by a mutation that disrupts this conformational change.
3.3.3 Identification of a catalytic residue for GTP hydrolysis: Previous work has shown that Gln64, corresponding to the catalytic Gln61 of Ras, is not involved in GTP hydrolysis by WT Rheb (Inoki et al. 2003; Li et al. 2004; Marshall et al. 2009). Likewise, Gln64 remains in a non-catalytic conformation in the structure of Rheb Y35A (Figure 3.3a) and is not required for the accelerated hydrolysis of GTP by
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Figure 3.3 Mutagenic analysis of potential catalytic residues in Rheb Y35A. a) Position in the structure of GMPPNP-bound Rheb Y35A of potential catalytic residues selected for mutagenesis,. b-e) Intrinsic GTPase assays for hydrolysis of GTP or mantGTP by WT Rheb and mutants as indicated: Hydrolysis of (b) GTP by Rheb Y35A and the double mutant Y35A, S16A, (c) mantGTP by WT Rheb and Rheb D36A, (d) GTP by Rheb Y35A and the double mutant Y35A, Q64L, (e) GTP by Rheb Y35A and the double mutant Y35A, R15G. Hydrolysis of mantGTP by Rheb Y35A is shown in Figure 3.1b, and hydrolysis of GTP by additional Rheb mutants is shown in Figures 3.4, 3.5 and 3.9. f) Multiple conformations of Arg15, Asp65, and Ser68 in the structure of Rheb Y35A in complex with GMPPNP.
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The 2F o-Fc electron density map at 1.0 σ is shown for the three aforementioned residues with double- headed arrows indicating the movement of the side chains.
Rheb Y35A (Figure 3.3d and 3.5a). Since the catalytic residues of other small GTPase superfamily members are found in the N-terminus of switch II, we examined this region for residues with electronegative side chains that may contribute to the hydrolytic reaction. Immediately downstream of Gln64 are two residues with acidic side chains, Asp65 and Glu66 (Figure 3.2g). The crystal structure of Rheb Y35A shows that the backbone of the N-terminal loop of switch II of this mutant is displaced by an average of 1 Å toward the nucleotide binding pocket relative to the wild type, which brings the side- WT chain carboxylate of Asp65 closer to the nucleotide by 1 Å (average Asp65O δ1,2 - average Y35A Asp65O δ1,2 ) (Figure 3.2g). Mutation of Asp65 to Ala reduced the intrinsic hydrolysis of Rheb Y35A by more than 60% and that of wild type by 30% (Figure 3.4a), as did the conservative substitution of Asp65 by Asn (Figure 3.5b). On the other hand, mutations of Glu66 had no effect on intrinsic GTPase activity (Figure 3.5c), consistent with its perpendicular orientation away from the nucleotide (Figure 3.2g). We also tested all other residues found within 10 Å of the hydrolytic water in the Rheb Y35A structure that could potentially provide (i) a negative charge to activate this water molecule, or (ii) a positive charge to stabilize the β- and γ-phosphates in the transition state for hydrolysis (Figure 3.3). There was no change in the rate of intrinsic nucleotide hydrolysis associated with R15G, S16A, or D36A mutations (Figure 3.3b, c, e). The only other charged residues within 10 Å of the hydrolytic water are Lys19 and Asp60 of the highly conserved G1 and G3 box motifs, respectively. The Rheb K19A mutant failed to express, presumably due to impaired nucleotide binding, and D60A was highly unstable and could not be loaded with GTP, consistent with the role of this residue in Mg ++ coordination (Yu et al. 2005). These data strongly suggest that Asp65 is the sole candidate for a catalytic residue in Rheb. Notably, carboxylates are more potent nucleophiles than carboxamides, and consistently, the Q61E substitution increased the GTPase activity of Ras (Frech et al. 1994).
In the structure of wild-type Rheb, the carboxylate of Asp65 is 12 Å (average Asp65O δ1,2 ) from the γ- phosphate in a single conformation, whereas the electron density of Rheb Y35A indicates that Asp65 exists in two conformations, 11.0 and 12.0 Å from the γ-phosphate, respectively (Figure 3.3f). By comparison, the catalytic carboxamide of Ras (Gln61O ε) has been found at distances varying from 4.7 to 12.2 Å from the γ-phosphate (median distance of 8.1Å) (Figure 3.6a) in available crystallographic snapshots, consistent with the dynamic nature of switch II determined by NMR studies (Ito et al. 1997).
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Figure 3.4 Role of Asp65 in intrinsic and GAP-mediated GTP hydrolysis by Rheb. a) Hydrolysis of GTP by wild-type Rheb (black), the mutants D65A and Y35A (blue and green, respectively), as well as the double mutant Y35A-D65A (red). Reaction rates derived by curve fitting are presented in the insets. b) Sensitivity of WT Rheb and Asp65 mutants to TSC2GAP-stimulated GTP hydrolysis. WT, WT+GAP, D65A+GAP, D65E+GAP, and D65N+GAP are shown with black, blue, green, yellow, and red respectively.
Thus, despite its established role as a catalytic residue (Frech et al. 1994), Gln61 is rarely found in a catalytically competent conformation in Ras crystal structures, presumably because this state is transient and energetically unfavorable (Grant et al. 2009; Fraser et al. 2011). Similarly, our Y35A structure and
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the previous wild-type Rheb structure (Yu et al. 2005) both appear to be energetically stable states, with the conformations of Asp65 stabilized primarily by ionic and polar interactions with the Arg15 and Ser68 side chains, which are also found in two alternate conformations in our structure (Figure 3.3f). Interestingly, comparison of WT and Y35A 1H-15 N heteronuclear single quantum coherence (HSQC) spectra revealed increased line broadening for residues in the P-loop and the N-terminus of switch II of GTP-bound Rheb Y35A (Figure 3.2h & 3.7a), suggesting elevated dynamics in µs-ms time scale. This
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Figure 3.5 Effect on Rheb GTPase activity of mutations of acidic and electronegative residues in switch II. a) Intrinsic GTPase assays for hydrolysis of mantGTP by WT Rheb (black), Rheb D65A (green), and Rheb Q64L (red). b) Intrinsic GTPase assays for hydrolysis of GTP by WT Rheb (black) and Rheb D65N (green). c) Mutation of Glu66 impairs TSC2 GAP-catalyzed but not intrinsic GTPase activity of Rheb. Intrinsic GTP hydrolysis by WT and E66A Rheb are shown in black and green, respectively. TSC2GAP-mediated GTP hydrolysis by Rheb WT and E66A are shown in blue and red, respectively. Note that the GTPase activity of Rheb E66A is modestly stimulated by TSC2GAP, but this mutant exhibits reduced sensitivity to GAP activity.
could allow the N-terminus of switch II to sample alternate conformations closer to the nucleotide and the catalytic water. The elevated dynamics of the N-terminal region of switch II and its proximity to the nucleotide binding site in Rheb Y35A is consistent with the greater impact on catalysis of Asp65 mutations in the Y35A mutant than in wild-type Rheb (Figure 3.4a). Hence, in addition to affecting the orientation of the nucleotide and hydrolytic water, Tyr35 may reduce the intrinsic GTPase activity of Rheb by restricting the dynamics of switch II and displacing it from the nucleotide binding site. Relative to Ras, the catalytic Gln residues of Rho subfamily GTPases were found closer to the γ-phosphate (median distance of 5.5Å) (Figure 3.6a and c), which may contribute to their faster intrinsic nucleotide hydrolysis rate (Mazhab-Jafari et al. 2010). On the other hand Gln63, which was recently proposed to be a non-canonical catalytic residue of Rap in GAP1 IP4BP -mediated GTP hydrolysis (Sot et al. 2010), is found with a median distance of 11.8Å from the γ-phosphate in structures of free Rap (Figure 3.6a), consistent with the slow nucleotide hydrolysis of this GTPase.
In Ras, Gly12, Gly13 and Gln61 are the major sites of oncogenic mutations. Mutation of Ras Gly12 to any other residue hinders GTP hydrolysis by sterically occluding access of the catalytic residue Gln61 to the hydrolytic water and nucleotide (Krengel et al. 1990). However, Rheb has an Arg in this position and its mutation to Gly (R15G) does not increase the catalytic activity of Rheb Y35A (Figure 3.3e) or WT (Yamagata et al. 1994; Im et al. 2002; Li et al. 2004; Marshall et al. 2009). The distinctive impact of P-loop residues on the activities of Ras and Rheb lends further support to the different molecular mechanisms of action of these two closely related GTPase homologs.
3.3.4 Involvement of Rheb’s Asp65 and Tyr35 in TSC2GAP-mediated GTP hydrolysis: Mutation of the solvent exposed residue Asp65 to Ala (D65A) did not perturb the structure of Rheb, on the basis of minimal and localized chemical shift perturbations in the 1H 15 N HSQC spectra that were mainly confined to switch II (Figure 3.8), but totally abolished the susceptibility of Rheb to the GAP activity of
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Figure 3.6 Structure-function analysis of the position of putative catalytic residues and the conserved switch I Tyrosine in small GTPases. a) Crystallographic ensemble of interatomic distances between the γ-phosphate of GTP (or analogue) and the proposed catalytic residues of Ras, Rheb, Rho, and Rap GTPases. Histogram of distances measured from the γ-phosphate (P γ) to Ras Gln61O ε (blue), Rheb average Asp65O δ1,2 (red), Rho Gln63O ε (green), and Rap Gln63O ε (purple) from crystal structures of free protein in complex with GTP and non-hydrolyzable GTP analogs. All available PDB-archived structures of Ras with wild-type GTPase activity where Q61 is resolved were included, [PDB code] (distance in Å): [5P21] (6.1), [6Q21] (6.3, 7.0, 6.8, 7.6), [1QRA] (7.8, 6.7), [1CTQ] (6.7), [1GNP] (9.7),
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[3K8Y] (5.9), [3K9N] (11.7), [1P2S] (6.3), [1P2V] (6.7), [1PLK] (4.7), [2CL0] (12.2), [2CL7] (10.4), [2CLC] (10.3), [121P] (8.1), [3PIR] (9.0), [3PIT] (9.8), [3I3S] (7.2). Some structures contain more than one Ras molecule in the asymmetric unit, in which case the distance was measured for each molecule separately. 1GNP and 3K9N are structures of WT-Ras in complex with mantGMPPNP and Ras Y32F in complex with GMPPNP, respectively, both of which have the same intrinsic nucleotide hydrolysis rate as WT Ras (Yamasaki et al. 1994; Mazhab-Jafari et al. 2010). 2CL0, 2CLC and 2CL7 are structures of Ras bearing a fluorescent tag on switch I (with Y32C mutation) in complex with GMPPNP or GTP (Klink et al. 2006). 3PIR, 3PIT, and 3I3S are structures of Ras D41E and T50I, mutations that are solvent exposed and far away from switch II. For Rheb, distances were measured for WT Rheb- GMPPNP [1XTR] (12.0), WT Rheb-GTP [1XTS] (12.1) and two separate measurements were made for Rheb Y35A-GMPPNP, in which Asp65 exists in two conformations (11.0, 12.0). The distances for Rho subfamily GTPases (Rac1, TC10/RhoQ, RhoC, Rac3, Cdc42) were measured using the following structures: [1MH1] (5.7), [2ATX] (6.8, 7.4), [2GCO] (5.7, 5.7), [2GCP] (5.6), [2IC5] (4.8), [2QRZ] (4.4, 3.8). 1MH1 is structure of Rac1 M1P-F78S double mutant, both of which are far away from nucleotide binding site. Finally, the distances for Rap were from structures of Rap2A: [2RAP] (12.7), [3RAP] (10.4, 12.2). b) Curves showing the intrinsic GTP hydrolysis rate of WT RhoA (black) and the Y34A mutant (green). c) The positions of the Tyr34, Gln63 and the non-hydrolyzable nucleotide GTP γS in RhoA G14V mutant (PDB code: 1A2B). d) Curves showing the intrinsic GTP hydrolysis rate of WT Ras (black) and the Y32A mutant (green). e) The positions of the Tyr32, Gln61 and the non- hydrolyzable nucleotide GMPPNP in Ras (PBD code: 5P21).
TSC2 (Figure 3.4b). Furthermore, even conservative mutations of Asp65 (D65E/N) rendered Rheb totally insensitive to the activity of TSC2 GAP. The strict requirement for the geometry and charge of this side chain suggest that it might be a critical catalytic residue for the GAP-mediated hydrolysis reaction. We also tested the sensitivity of the GTPase activity of Rheb Y35A to the action of TSC2GAP and found that the GTPase activity of this mutant was not further stimulated by the addition of the GAP domain of TSC2 (Figure 3.9a). An analagous mutation (Y32A), impaired the sensitivity of Rap GTPase to the function of RapGAP (Brinkmann et al. 2002; Scrima et al. 2008), however a conservative mutation (Y32F) was tolerated. Interestingly, the Y35F mutation was sufficient to render Rheb insensitive to the function of the TSC2GAP (Figure 3.9b), highlighting differences in the details of molecular recognition in these two homologous systems.
3.3.5 Thermodynamic basis for the Tyr35 auto-inhibitory function: To better understand the energetic basis of Tyr35 auto-inhibition, we analyzed the thermodynamics of the GTP hydrolysis reaction using an Arrhenius plot (Figure 3.10). This powerful technique allows one to extract energetic parameters, such as enthalpy, entropy and free energy, from the highly unstable and low populated transition state of an enzymatic reaction. The increased catalytic activity of Rheb Y35A was associated with a large reduction in the activation enthalpy for GTP hydrolysis (Figure 3.10, Table 3.1). However, the
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Figure 3.7 Perturbation of Rheb HSQC spectrum by Tyr35 mutation. a) HSQC spectrum of Rheb Y35A-GTP (red) overlaid with WT Rheb-GTP (black). Resonances that are present in the wild-type
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spectrum but exhibit large chemical shift changes or severe broadening in the spectrum of the mutant are circled. Resonances showing minor chemical shift changes due to the mutation are indicated by double headed arrows. Note that in the GTP-bound form there are no extra peaks in the Y35A mutant, indicating that most circled peaks correspond to resonances broadened beyond detection in the mutant. b) HSQC spectrum of Y35A-GDP (red) overlaid with WT Rheb-GDP (black). Resonances that are unique to the wild-type spectrum are circled and those unique to the mutant spectrum are highlighted by squares. Note that in the GDP-bound form, the total number of observable resonances remains constant between WT Rheb and the Y35A mutant (circles ≈ squares), indicating that most of these resonances undergo long range chemical shift changes.
activation entropy was also reduced (unfavorable contribution), resulting in a modest decrease in the overall activation free energy of the nucleotide hydrolysis reaction in the mutant. Because there is a build-up of negative charge on the β-γ bridging oxygen during GTP hydrolysis (Cepus et al. 1998; Du et al. 2000; Allin et al. 2001), the proximity of the electron rich phenol ring of Rheb Tyr35 could destabilize the transition state, which is consistent with the reduction in activation enthalpy associated with mutation of this residue. Interestingly, the Arg fingers of Ras- and Rho-GAPs accelerate nucleotide hydrolysis of their cognate GTPases by providing positive charge in a position equivalent to that of Rheb Tyr35. Another contribution to the enthalpic term may come from the strengthened hydrogen bond between the Thr38 carbonyl in the mutant and the repositioned catalytic water, which may be more reactive toward the γ-phosphate (Frech et al. 1994).
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Figure 3.8 Minimal chemical shift perturbation associated with mutation of Rheb Asp65. HSQC spectrum of Rheb D65A-GTP (red) overlaid with WT Rheb-GTP (black). Resonances that are strongly perturbed by the mutation (severe broadening or large chemical shift change) are circled and those showing minor chemical shift changes are indicated by double headed arrows.
The larger negative value of S‡ for Rheb Y35A indicates that formation of the transition state requires the mutant to undergo a larger increase in “order” than the wild-type protein. In the crystal structure of WT Rheb-GMPPNP, a hydrogen bond between the hydroxyl of Tyr35 and the γ-phosphate of GMPPNP stabilizes switch I, contributing to the order of the ground state. Disruption of this contact by mutation of Tyr35 increases the disorder in switch I, as illustrated by partial spectral broadening of peaks from residues 27-30 of GTP-bound Rheb Y35A (Figure 3.7). Thus assembly of the ordered transition state from the more flexible Rheb Y35A ground state would be more entropically unfavourable. The conservative mutation Y35F increased intrinsic hydrolysis almost as much as Y35A with similar thermodynamic effects (Figure 3.10, Table 3.1), suggesting that the H-bond between the hydroxyl of Tyr35 and the γ-phosphate is critical for the auto-inhibition of Rheb’s GTPase activity. It is very interesting to note that the thermodynamic landscape of intrinsic GTP hydrolysis in the Y35A mutant
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Figure 3.9 Tyr35 hydroxyl is required for TSC2GAP-assisted GTP hydrolysis. a) Intrinsic and GAP-catalyzed GTP hydrolysis by Rheb Y35A. b) Intrinsic and GAP-catalyzed GTP hydrolysis by Rheb Y35F. In both graphs the GTPase activity of mutant Rheb with and without TSC2GAP are shown in black and green, respectively, and the TSC2GAP-catalyzed GTP hydrolysis by WT Rheb is shown in blue.
(reduced activation enthalpy with an entropic penalty) is similar to that reported for TSC2GAP-mediated GTP hydrolysis in WT Rheb (Marshall et al. 2009), suggesting that TSC2GAP may promote hydrolysis in part by disrupting the electrostatic contact between Tyr35 and the γ-phosphate. Consistent with this hypothesis, the increased rate of GTP hydrolysis by the Rheb Y35A/F mutants is not further accelerated by the addition of the GAP (Figure 3.9). The larger reduction of the activation enthalpy by TSC2GAP- mediated catalysis compared to Y35A mutation suggests the GAP provides additional stimulatory electrostatic contributions to GTP hydrolysis, perhaps via complementation of the intrinsic catalytic machinery by the Asn thumb. On the other hand the larger unfavorable reduction in entropy of the GAP- mediated reaction could be due to complex formation between Rheb and the GAP domain of TSC2.
Figure 3.10 Effect of Tyr35 and Asp65 mutations on the thermodynamic activation parameters for GTP hydrolysis by Rheb. Arrhenius plots for intrinsic GTP hydrolysis by Rheb WT (black), Y35A (green), Y35F (brown), Y35A-D65A (blue) and D65A (red). Each data point represents a rate
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determined from a representative GTPase assay consisting of 25 time points performed at a given temperature. Error bars represent standard error associated with derivation of the rate by curve fitting.
Mutation of Asp65 substantially impairs the stimulatory effect of the Y35A mutation on intrinsic hydrolysis, hence we measured the thermodynamic parameters of the transition state for the Rheb double mutant Y35A-D65A (Table 3.1). Mutation of Asp65 increased the activation enthalpy ( H‡ ) of Rheb Y35A, indicating that the negatively charged carboxylic acid side chain of Asp65 stabilizes the transition state since the enthalpic term originates primarily from electrostatic interactions (Kötting and Gerwert 2004). In Ras, the enthalpic contribution to hydrolysis was attributed to the charge shift from the γ- toward the β-phosphate (Kötting and Gerwert 2004). We propose that electrostatic interactions between Rheb Asp65 and the nucleotide similarly shift charge in the transition state to promote hydrolysis. Interestingly, Tyr35 reduces the enthalpic contribution of Asp65 to GTP hydrolysis, H‡(Y35A-Y35A,D65A) > H‡(WT-D65A) (Table 3.1), which is consistent with our kinetic data (Figure 3.4a).
Table 3.1 Summary of thermodynamic activation parameters. [free energy of activation ( G‡), activation enthalpy ( H‡), and activation entropy (T S‡) in kJ/mol] calculated for GTP hydrolysis by Rheb WT and mutants. T is set to 298 K in the equation; G‡ = H‡ - T S‡.
Protein WT Y35A Y35F Y35A- D65A TSC2GAP* D65A H‡ 86.0 52.3 52.7 55.6 87.0 41.3
T S‡ -13.5 -43 -43.3 -41.6 -13.3 -51.8