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The Role of Conformational Dynamics in Isocyanide Hydratase Catalysis

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The Role of Conformational Dynamics in Isocyanide Hydratase Catalysis University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses and Dissertations in Biochemistry Biochemistry, Department of Spring 4-15-2020 THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS Medhanjali Dasgupta University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biochemdiss Part of the Biochemistry Commons, Biophysics Commons, Microbiology Commons, and the Structural Biology Commons Dasgupta, Medhanjali, "THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS" (2020). Theses and Dissertations in Biochemistry. 29. https://digitalcommons.unl.edu/biochemdiss/29 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses and Dissertations in Biochemistry by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS by Medhanjali Dasgupta A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Biochemistry Under the Supervision of Professor Mark A. Wilson Lincoln, Nebraska May 2020 THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS Medhanjali Dasgupta, Ph.D. University of Nebraska, 2020 Advisor: Dr. Mark. A. Wilson Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics, which in turn, affects catalysis, remains poorly understood. Here we use X-ray crystallography, computer simulations, site directed mutagenesis and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in the enzyme, isocyanide hydratase (ICH), affects the protein conformational ensemble during catalysis. Our results suggest that cysteine modification may be a common and likely underreported means for regulating protein conformational dynamics. This thesis will also include ongoing work with ICH homologs, showing that Cys covalent modification-gated helical dynamics in Cys dependent enzymes is common to enzymes of this family. ii Copyright: Medhanjali Dasgupta iii Dedication To my wonderful husband, Karl Francis Joseph, & To my emotional support cat, Scoopy Noopers. iv Acknowledgements I would like to extend my gratitude towards my advisor, Dr. Mark A. Wilson for his support and guidance throughout my entire doctoral studies. I would also like to take this opportunity to thank my wonderful committee members, Drs. Melanie Simpson, Joe Barycki, Donald Becker, David Berkowitz for their valuable mentoring, guidance, support and help. Of course, none of my learning would be complete without my helpful lab mates, Madison, Lin, Nate, Peter and Ekta. I also thank the collaborators who made all this work possible, Henry van den Bedem (SSRL), Mike Wall (LANL), Aina Cohen (SSRL), Ray Sierra (LCLS), Darya Marchany Rivera, Ken Nickerson (UNL), Javier Seravalli (UNL), Virendra Tiwari (UNL), Dominik Budday, Saulo de Oliveira, Brandon Hayes, Sebastian Boutet, Mark Hunter, Ruberto Alonso Mori, Alexander Batyuk, Jennifer Wierman, Artem Lyubimov, Aaron Brewster, Nicholas Sauter, Gregory Applegate, Michael Thompson, and James Fraser. v Funding This work was supported by Nebraska Tobacco Settlement Biomedical Research Development Fund. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02- 76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (including P41GM103393). Use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. Use of BioCARS was also supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number R24GM111072. vi Table of Contents CHAPTER 1: Introduction: Isocyanides as natural products. 1.1.1 Terrestrial isocyanides …………………… 3 1.1.1.a Biosynthesis of terrestrial isocyanides …………………… 3 1. 1.1.b Identification of IsnA/B homolog gene clusters …………………… 5 1.1.1.c Biological targets of terrestrial isocyanides …………………… 13 1.1.1.d Types of terrestrial isocyanides …………………… 19 Xanthocillin type …………………… 19 Cyclopentyl type …………………… 25 Assorted others …………………… 30 1.1.2 Non terrestrial isocyanides …………………… 32 1.1.2 A Types of non terrestrial isocyanides …………………… 32 Monoterpenoid type …………………… 33 Diterpenoid type …………………… 37 Sesquiterpenoid type …………………… 38 1.1.3 Degradation of isocyanides via Isocyanide hydratase …………………… 42 (ICH) CHAPTER 2: Introduction: The relationship between internal enzyme conformational dynamics and catalysis 2.1 How internal protein motions effect the catalytic mechanism …………………… 45 of enzyme action CHAPTER 3: Introduction: Biochemistry of reactive cysteine residues in enzymes. 3.1 The relationship between cysteine covalent modification ………………… 52 gated enzyme dynamics and catalysis. 3.2 Cysteine covalent modification and internal enzyme ………………… 53 dynamics 3.3. Cysteine covalent modification and internal enzyme ………………… 64 dynamics vii CHAPTER 4: Mix and Inject Serial Femtosecond Crystallography at XFEL reveals gated conformational dynamics during ICH catalysis. 4.1 Abstract ………………… 68 4.2 Introduction ………………… 69 4.3 Materials and Methods ………………… 71 4.4 Results ………………… 81 4.5 Discussion ………………… 96 CHAPTER 5: Purification, Kinetics and Structural Characterization of novel ICH homolog, RsICH from Ralstonia solanacearum GMI1000. 5.1 Abstract ………………… 102 5.2 Introduction ………………… 103 5.3 Materials and Methods ………………… 104 5.4 Results ………………… 110 5.5 Discussion ………………… 119 Works cited. ………………… 120 viii List of Tables Table 1: Pseudomonas ICH Enzyme kinetic parameters ……………… ix Table 2: Pseudomonas ICH Crystallographic Data Statistics ……………… x Table 3: Pseudomonas ICH crystallographic Refinement Statistics ……………… xi Table 4: Ralstonia ICH Enzyme kinetic parameters ……………… xii Table 5: Ralstonia ICH Crystallographic Refinement Statistics ……………… xiii Table 6: Ralstonia ICH Crystallographic Refinement Statistics ……………… xiv ix List of Multimedia Objects Table 1: Pseudomonas ICH Enzyme kinetic parameters *measured at 160 μM p-NPIC and [enzyme]=50 nM. Standard deviations are derived from the fit; data measured n≥3 PfICH Enzyme WT G150A G150T Steady State Kinetics -1 kcat (sec ) 0.248±0.031 0.025±0.002 0.046±0.003 KM (μM) 9.262±3.250 1.208 ±0.6134 8.892±1.529 -1 -1 4 4 3 kcat/KM (M sec ) 2.68x10 2.07x10 5.21x10 Stopped Flow mixing Burst rate constant (sec-1)* 11.395±0.120 11.882±0.071 4.255±0.187 Second order rate constant for 4.85x104±943 5.51x104±557 1.11x104±999 burst (M-1 sec-1) -1 * Steady state rate kobs (sec ) 0.268±0.001 0.046±0.002 0.095±0.003 x Table 2: Pseudomonas ICH Crystallographic Data Statistics Values for the highest resolution bins are shown in parenthesis WT ICH WT ICH G150A G150T WT ICH WT ICH WT ICH WT ICH RT1 RT1 (more ICH ICH XFEL: XFEL: 15 XFEL: 5 cryo Sample (less oxidized) Apo1 sec min1 oxidized) Thioimida te1 Diffraction SSRL SSRL SSRL SSRL LCLS LCLS LCLS APS source 12-2 7-1 12-2 7-1 MFX MFX MFX 14BM-C Wavelength 0.827 0.975 0.827 0.975 1.305 1.305 1.305 0.900 (Å) Temperature 274 277 274 277 298 298 298 100 (K) Rayonix Rayonix Rayonix ADSC ADSC ADSC Detector Pilatus 6M Pilatus 6M MX170- MX170- MX170- Q315 Q315 Q315 HS HS HS Space group P21 P21 P21 C2 P21 P21 P21 P21 57.24 57.15 57.04 72.11 56.88 56.77 56.81 56.58 a, b, c (Å) 58.03 57.97 57.90 59.74 57.68 57.42 57.64 56.47 69.09 69.09 69.11 56.13 68.78 68.79 68.76 68.23 90.00 90.00 90.00 90.00 90.00 90.00 90.00 90.00 α, β, γ (°) 112.83 112.77 112.55 115.86 112.74 112.74 112.74 112.49 90.00 90.00 90.00 90.00 90.00 90.00 90.00 90.00 Mosaicity (°) 0.08 0.08 0.08 0.07 N/A5 N/A5 N/A5 0.27 Resolution 39.04-1.20 42.87-1.15 38.96-1.30 35.45-1.10 20.13-1.55 20.09-1.55 20.1-1.55 37-1.05 range (Å) (1.22-1.20) (1.17-1.15) (1.32-1.30) (1.12-1.10) (1.57-1.55) (1.57-1.55) (1.57-1.55) (1.09-1.05) Total no. of 363112 517060 327591 224032 3032726 3185312 2648001 1077211 observations (16358) (15585) (13542) (2017) (18818) (16342) (38049) (79769) No. of unique 126373 145885 100249 84423 60075 60053 60082 179423 observations (5922) (6657) (4568) (1216) (2983) (2970) (2988) (17341) Completeness 97.4 (92.7) 98.9 (91.2) 98.1 (90.1) 97.2 (95.9) 99.9 (99.8) 99.9 (99.4) 99.9 (100) 97.1 (94.2) (%) Multiplicity 2.9 (2.8) 3.5 (2.3) 3.3 (3.0) 2.7 (2.0) 50.5 (6.3) 53.0 (5.5) 44.1 (12.7) 6.0 (4.6) 〈I/σ(I)〉 10.4(1.8) 12.5 (0.8) 9.1 (1.2) 9.7 (1.4) 60.5 (2.0) 58.4 (1.8) 73.1 (3.4) 22.8 (2.1) 2 0.991 0.999 0.996 0.999 0.962 0.963 0.937 4 CC1/2 N/A (0.225) (0.488) (0.318) (0.690) (0.16) (0.14) (0.36) Rmeas (Rsplit for 0.072 0.059 0.066 0.045 0.196 0.197 0.232 0.07 (0.70) XFEL data)3 (1.689) (0.959) (1.513) (0.545) (0.862) (0.905) (0.658) 1 RT, Room temperature synchrotron radiation collection; XFEL, X-ray free electron laser 2 CC1/2 (31) was used to determine the high resolution cutoff.
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