Signature of Hydrophobic Hydration in a Single Polymer

Total Page:16

File Type:pdf, Size:1020Kb

Signature of Hydrophobic Hydration in a Single Polymer Signature of hydrophobic hydration SEE COMMENTARY in a single polymer Isaac T. S. Li and Gilbert C. Walker1 Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6 Edited by Robert Baldwin, Stanford University, Stanford, CA, and approved August 4, 2011 (received for review April 12, 2011) Hydrophobicity underpins self-assembly in many natural and syn- thetic molecular and nanoscale systems. A signature of hydro- phobicity is its temperature dependence. The first experimental evaluation of the temperature and size dependence of hydration free energy in a single hydrophobic polymer is reported, which tests key assumptions in models of hydrophobic interactions in protein folding. Herein, the hydration free energy required to ex- tend three hydrophobic polymers with differently sized aromatic side chains was directly measured by single molecule force spectro- scopy. The results are threefold. First, the hydration free energy per monomer is found to be strongly dependent on temperature and does not follow interfacial thermodynamics. Second, the temperature dependence profiles are distinct among the three hydrophobic polymers as a result of a hydrophobic size effect at the subnanometer scale. Third, the hydration free energy of a monomer on a macromolecule is different from a free monomer; corrections for the reduced hydration free energy due to hydro- CHEMISTRY phobic interaction from neighboring units are required. ydrophobic hydration involves the minimization of the free Henergies of water molecules near nonpolar surfaces. Hydro- phobic hydration of macromolecules is central to understanding Fig. 1. The role of hydrophobic collapse in the folding of three polymers protein folding (1–6) and advancing materials science and bio- with decreasing hydrophobicities: hydrophobic homopolymer, copolymer, technologies (7–9). A detailed methodology has been developed and protein (from top to bottom), plotting global free energy vs. radius of to study hydrophobic hydration by the mechanical unfolding of a gyration. Starting from an extended conformation in water, both protein collapsed single hydrophobic polymer (10). Typically, the hydra- and polymer chains are entropically reduced to random coils with reduced tion free energy (ΔGhyd) is assumed to scale with the solvent radii of gyration (red). When a random coil is compacted such that the accessible surface area (SASA) of molecules according to macro- chain can make frequent contact with itself, hydrophobic collapse (yellow) occurs to further reduce the global free energy and the radius of gyration. scopic interfacial thermodynamics, which is supported by the lin- If the hydrophobic units are sparser on the chain, hydrophobic collapse ear correlation between the SASA and the free energy to transfer occurs later during entropic coiling. For proteins, specific interactions (blue) hydrocarbons from a hydrophobic solvent (such as hexadecane) such as hydrogen bonds and salt bridges bring the protein to an energy to water (11). Despite a strong correlation, the experimentally minimum with the most compact structure. Hydrophobic polymers do not measured small hydrocarbon ΔGhyd is smaller than that predicted have such specific interactions and remain as compact random coils. by the calculated SASA (12), showing the breakdown of macro- scopic interfacial thermodynamics at the microscopic scale and Theoretical studies of hydrophobic hydration relied on experi- suggesting that the origin of the correlation goes beyond SASA. mental measurements of small molecule solubilities in water and In addition, the temperature dependence of ΔGhyd (the signature their transfer free energies from organic solvents to water. It is of hydrophobic hydration) varies according to the size of the usually assumed that these small molecule ΔGhyd can be directly solute; such temperature dependence cannot be explained simply applied to hydrophobic side chains in polymers and proteins. How- by the macroscopic interfacial free energy. In an earlier attempt ever, this assumption has not been experimentally tested due to the to address these issues, Tolman (13) developed a thermodynamic lack of a suitable experimental model system and the difficulty of treatment that lowers the surface tension of water at the solute- studying hydrophobic macromolecules insoluble in water. Hydro- water interface by taking into account the cavity curvature. Later phobic homopolymers provide simple models of the hydrophobic developments included temperature dependence of the Tolman hydration and collapse of proteins and other linear biological length using simulations to address the temperature dependence molecules (Fig. 1). Preceding hydrophobic collapse, an initially ex- of ΔGhyd (14, 15). However, it was argued that the correction to the effective surface tension to maintain the correlation between tended hydrophobic polymer in water undergoes entropic coiling ΔGhyd and SASA at small length scales lacked a clear physical meaning (16). Instead of depending on a scaling relation with Author contributions: I.T.S.L. and G.C.W. designed research; I.T.S.L. performed research; SASA, theories and simulations were developed predicting that G.C.W. contributed new reagents/analytic tools; I.T.S.L. and G.C.W. analyzed data; and ΔGhyd has nontrivial size dependence: Below approximately 1 nm I.T.S.L. and G.C.W. wrote the paper. radius, ΔGhyd of a spherical solute scales roughly with the solute The authors declare no conflict of interest. volume; whereas above this value, ΔGhyd scales with SASA and This article is a PNAS Direct Submission. asymptotically approaches the behavior described by macroscopic See Commentary on page 16491. interfacial thermodynamics (6, 17–28). These treatments cor- 1To whom correspondence should be addressed. E-mail: [email protected]. ΔGhyd rectly predict the trend for the temperature dependence of This article contains supporting information online at www.pnas.org/lookup/suppl/ for small molecules. doi:10.1073/pnas.1105450108/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1105450108 PNAS ∣ October 4, 2011 ∣ vol. 108 ∣ no. 40 ∣ 16527–16532 Downloaded by guest on September 29, 2021 that reduces the tension along the chain to a point where the coil- that free monomer ΔGhyd cannot be directly applied to calculate globule transition can occur. The onset of this transition depends the hydration free energy of a hydrophobic macromolecule. on the overall hydrophobicity of the polymer such that the transi- tion begins at higher tension and radius of gyration for a hydro- Results phobic homopolymer than for a mixed hydrophobic/hydrophilic Single Polymer Force Plateau Marks Hydrophobic Hydration. Using polymer such as a protein (Fig. 1). Similar to a protein, a hydro- AFM, a single polymer chain can be pulled from a naturally phobic homopolymer collapses in an aqueous environment into a collapsed state to a hydrated, extended state as illustrated in compact globule that is largely disordered. This collapse captures Fig. 2A. It has been predicted theoretically and shown in simula- the essential physics governing the hydrophobic hydration of a tions that forced hydration of a collapsed hydrophobic polymer protein and is illustrated in Fig. 1. Ensemble studies of hydropho- produces a constant force-distance profile. (29–31) Force-exten- bic polymers are not viable because of their insolubility in water sion curves of single hydrophobic polymers such as polystyrene and limited experimental access to different conformational states (PS), poly(4-tert-butylstyrene) (PtBS), and poly(4-vinylbiphenyl) (e.g., extended and collapsed). However, by way of single molecule (PVBP) show characteristic constant force plateaus correspond- force spectroscopy using atomic force microscopy (AFM), the ing to single-chain hydration (10, 32–34), followed by entropic conformation of a single hydrophobic polymer can be changed elastic stretching before the chain detaches from the AFM can- from collapsed globule to extended coil (Fig. 2A)andΔGhyd in this B B tilever or the Si substrate (Fig. 2 ). Statistical analysis of the force process can be estimated (Fig. 2 ). A previous study provides a plateau magnitudes from thousands of independent molecular detailed description of the control experiments undertaken here pulling events at a given temperature for a given polymer shows for the mechanical unfolding of a collapsed single hydrophobic a quantized distribution (Fig. S1), which suggests that the lowest polymer in aqueous solvents (10). This report presents the effect of temperature on hydrophobic hydration of several polymers and force plateau results from hydration of a single polymer chain. Furthermore, when normalized to the same contour length, the how the size of side chains affects their temperature dependence. A The result shows that a phenomenological model using SASA and force curves can be superimposed on top of one another (Fig. 3 ), macroscopic interfacial thermodynamics cannot account for the showing that the polymer chains have the same persistence length observed temperature dependence of macromolecular hydropho- and that the physics behind the forced hydration is length inde- bic hydration. The observed temperature dependence shows the pendent within the range of polymer sizes accessible to our ex- turnover behavior typically seen in the hydration of small hydro- periment (hundreds of nanometers) The constant force profile phobic molecules. Moreover, individual monomers along the chain is
Recommended publications
  • How Fast Is Protein Hydrophobic Collapse?
    How fast is protein hydrophobic collapse? Mourad Sadqi*, Lisa J. Lapidus†‡, and Victor Mun˜ oz*§ *Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742; and †Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 Edited by Michael Levitt, Stanford University School of Medicine, Stanford, CA, and approved August 18, 2003 (received for review June 21, 2003) One of the most recurring questions in protein folding refers to the Equilibrium FRET Experiments. Equilibrium FRET experiments interplay between formation of secondary structure and hydro- were performed at 25 ␮M concentration in citrate buffer at pH phobic collapse. In contrast with secondary structure, it is hard to 3.0 in an Applied Photophysics (Surrey, U.K.) PiStar instrument. isolate hydrophobic collapse from other folding events. We have Efficiency of energy transfer between naphtyl-alanine (donor) directly measured the dynamics of protein hydrophobic collapse in and dansyl-lysine (acceptor) was determined from the fluores- the absence of competing processes. Collapse was triggered with cence quantum yield of the donor by using the equation: laser-induced temperature jumps in the acid-denatured form of a Qda simple protein and monitored by fluorescence resonance energy E ϭ 1 Ϫ . [1] transfer between probes placed at the protein ends. The relaxation Qd time for hydrophobic collapse is only Ϸ60 ns at 305 K, even faster than secondary structure formation. At higher temperatures, as the The intrinsic quantum yield of the donor (Qd) was measured by protein becomes increasingly compact by a stronger hydrophobic exciting at 288 nm in the protein labeled at the N terminus with naphtyl-alanine and nonlabeled at the C terminus and using force, we observe a slowdown of the dynamics of collapse.
    [Show full text]
  • Translation and Folding of Single Proteins in Real Time PNAS PLUS
    Translation and folding of single proteins in real time PNAS PLUS Florian Wrucka,1, Alexandros Katranidisb,2, Knud H. Nierhausc,3, Georg Büldtb,d, and Martin Hegnera,2 aCentre for Research on Adaptive Nanostructures and Nanodevices, School of Physics, Trinity College Dublin, Dublin 2, Ireland; bInstitute of Complex Systems ICS-5, Forschungszentrum Jülich, 52425 Jülich, Germany; cInstitute for Medical Physics and Biophysics, Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany; and dLaboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia Edited by George H. Lorimer, University of Maryland, College Park, MD, and approved April 21, 2017 (received for review October 27, 2016) Protein biosynthesis is inherently coupled to cotranslational pro- ensemble methods. Optical tweezers have been used to observe tein folding. Folding of the nascent chain already occurs during stepping of motor proteins (19–23), DNA–protein complexes (24), synthesis and is mediated by spatial constraints imposed by the as well as unfolding and refolding of RNA molecules and proteins ribosomal exit tunnel as well as self-interactions. The polypeptide’s (25, 26). This powerful single-molecule method has provided in- vectorial emergence from the ribosomal tunnel establishes the possi- formation on (i) the translation machinery by reporting on the ble folding pathways leading to its native tertiary structure. How strength of interactions between the ribosome and mRNA (27), cotranslational protein folding and the rate of synthesis are linked (ii) its translocation along a short hairpin-forming mRNA mole- to a protein’s amino acid sequence is still not well defined. Here, we cule (28), as well as (iii) the release of an arrested nascent chain follow synthesis by individual ribosomes using dual-trap optical twee- (7).
    [Show full text]
  • Cell-Penetrating Peptides: Design Strategies Beyond Primary Structure and Amphipathicity
    molecules Review Cell-Penetrating Peptides: Design Strategies beyond Primary Structure and Amphipathicity Daniela Kalafatovic 1 and Ernest Giralt 1,2,* 1 Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain; [email protected] 2 Department of Inorganic and Organic Chemistry, University of Barcelona, Marti i Franques, 1-5, 08028 Barcelona, Spain * Correspondence: [email protected]; Tel.: +34-93-40-37125 Received: 26 September 2017; Accepted: 4 November 2017; Published: 8 November 2017 Abstract: Efficient intracellular drug delivery and target specificity are often hampered by the presence of biological barriers. Thus, compounds that efficiently cross cell membranes are the key to improving the therapeutic value and on-target specificity of non-permeable drugs. The discovery of cell-penetrating peptides (CPPs) and the early design approaches through mimicking the natural penetration domains used by viruses have led to greater efficiency of intracellular delivery. Following these nature-inspired examples, a number of rationally designed CPPs has been developed. In this review, a variety of CPP designs will be described, including linear and flexible, positively charged and often amphipathic CPPs, and more rigid versions comprising cyclic, stapled, or dimeric and/or multivalent, self-assembled peptides or peptido-mimetics. The application of distinct design strategies to known physico-chemical properties of CPPs offers the opportunity to improve their penetration efficiency and/or internalization kinetics. This led to increased design complexity of new CPPs that does not always result in greater CPP activity. Therefore, the transition of CPPs to a clinical setting remains a challenge also due to the concomitant involvement of various internalization routes and heterogeneity of cells used in the in vitro studies.
    [Show full text]
  • Inversion of the Balance Between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation
    Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation Anthony W. Fitzpatrick, Tuomas P. J. Knowles, Christopher A. Waudby, Michele Vendruscolo, Christopher M. Dobson* Department of Chemistry, University of Cambridge, Cambridge, United Kingdom Abstract Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer’s disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side- chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions. Citation: Fitzpatrick AW, Knowles TPJ, Waudby CA, Vendruscolo M, Dobson CM (2011) Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation. PLoS Comput Biol 7(10): e1002169. doi:10.1371/journal.pcbi.1002169 Editor: Vijay S. Pande, Stanford University, United States of America Received December 5, 2010; Accepted July 6, 2011; Published October 13, 2011 Copyright: ß 2011 Fitzpatrick et al.
    [Show full text]
  • Jacqueline L. Warren, Peter A. Dykeman-Bermingham, and Abigail S
    Jacqueline L. Warren, Peter A. Dykeman-Bermingham, and Abigail S. Knight* Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States ABSTRACT: While methods for polymer synthesis have proliferated, their functionality pales in comparison to natural biopolymers – strategies are limited for building the intricate network of noncovalent interactions necessary to elicit complex, protein-like functions. Using a bioinspired diphenylalanine acrylamide (FF) monomer, we explored the impact of various non-covalent interactions in generating ordered assembled structures. Amphiphilic copolymers were synthesized that exhibit β-sheet-like secondary structure upon collapsing into single-chain assemblies in aqueous environments. Systematic analysis of a series of amphiphilic copolymers illustrated that the collapse is primarily driven by hydrophobic forces. Hydrogen-bonding and aromatic interactions stabilize local structure, as β-sheet-like interactions were identified via circular dichroism and thioflavin T fluorescence. Similar analysis of phenylalanine (F) and alanine-phenylalanine acrylamide (AF) copolymers found that distancing the aromatic residue from the polymer backbone is sufficient to induce β-sheet-like secondary structure akin to the FF copolymers; however, the interactions between AF subunits are less stable than those formed by FF. Further, hydrogen-bond donating hydrophilic monomers disrupt internal structure formed by FF within collapsed assemblies. Collectively, these results illuminate design principles for the facile incorporation of multiple facets of protein-mimetic, higher-order structure within folded synthetic polymers. INTRODUCTION Confined to a limited pool of natural amino acid monomers, proteins have evolved primary structures that yield canonical structure hierarchy: quaternary structures of multiple polypeptide chains, tertiary structure that defines the three-dimensional morphology, and local rigid regions dictated by secondary structure.
    [Show full text]
  • Solvent Coarse-Graining and the String Method Applied to the Hydrophobic Collapse of a Hydrated Chain
    Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain Thomas F. Miller III†, Eric Vanden-Eijnden‡, and David Chandler†§ †Department of Chemistry, University of California, Berkeley, CA 94720; and ‡Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 Contributed by David Chandler, June 25, 2007 (sent for review February 14, 2007) With computer simulations of >100,000 atoms, the mechanism for tWC have previously reported simulations of an idealized hy- the hydrophobic collapse of an idealized hydrated chain was ob- drophobic chain solvated by a coarse-grained model of liquid water tained by tiling space with (0.2 nm)3 cubes and projecting the (4). For this model, they found that the key step in the collapse atomistic water molecule positions onto this grid. With the coarse- dynamics is a collective solvent density fluctuation that is nucleated grained field thus defined, the string method in collective variables at the hydrophobic surface of the chain. However, it was not clear was used to compute a minimum free-energy pathway (MFEP) for the whether this mechanism was an artifact of their coarse-grained collapsing chain. These calculations provide a proof of principle for a model of water. Atomistic simulations are needed to resolve the coarse-grained description of water solvent. Furthermore, the calcu- issue. lated MFEP characterizes the mechanism for the collapse of the Previous efforts to characterize the mechanism of hydrophobic hydrated chain by providing a path of maximum likelihood for collapse using atomistic computer simulations neither confirm nor dynamical trajectories.
    [Show full text]
  • Role of Water in Mediating the Assembly of Alzheimer Amyloid-# A#16#22 Protofilaments Mary Griffin Krone, Lan Hua, Patricia Soto, Ruhong Zhou, B
    Subscriber access provided by Columbia Univ Libraries Article Role of Water in Mediating the Assembly of Alzheimer Amyloid-# A#16#22 Protofilaments Mary Griffin Krone, Lan Hua, Patricia Soto, Ruhong Zhou, B. J. Berne, and Joan-Emma Shea J. Am. Chem. Soc., 2008, 130 (33), 11066-11072 • DOI: 10.1021/ja8017303 • Publication Date (Web): 29 July 2008 Downloaded from http://pubs.acs.org on November 18, 2008 More About This Article Additional resources and features associated with this article are available within the HTML version: • Supporting Information • Links to the 1 articles that cite this article, as of the time of this article download • Access to high resolution figures • Links to articles and content related to this article • Copyright permission to reproduce figures and/or text from this article Journal of the American Chemical Society is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published on Web 07/29/2008 Role of Water in Mediating the Assembly of Alzheimer Amyloid- A16-22 Protofilaments Mary Griffin Krone,† Lan Hua,§ Patricia Soto,† Ruhong Zhou,§,| B. J. Berne,§,| and Joan-Emma Shea*,†,‡ Department of Chemistry and Biochemistry, UniVersity of California, Santa Barbara, California 93106, Department of Physics, UniVersity of California, Santa Barbara, California 93106, Department of Chemistry, Columbia UniVersity, New York, New York 10027, and Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598 Received March 7, 2008; E-mail: [email protected] Abstract: The role of water in promoting the formation of protofilaments (the basic building blocks of amyloid fibrils) is investigated using fully atomic molecular dynamics simulations.
    [Show full text]
  • Hydrophobic Collapse In
    Computational Biology and Chemistry 30 (2006) 255–267 Hydrophobic collapse in (in silico) protein folding Michal Brylinski a,b, Leszek Konieczny c, Irena Roterman a,d,∗ a Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Krakow, Poland b Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland c Institute of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31 034 Krakow, Poland d Faculty of Physics, Jagiellonian University, Reymonta 4, 30-060 Krakow, Poland Received 19 December 2005; received in revised form 6 April 2006; accepted 6 April 2006 Abstract A model of hydrophobic collapse, which is treated as the driving force for protein folding, is presented. This model is the superposition of three models commonly used in protein structure prediction: (1) ‘oil-drop’ model introduced by Kauzmann, (2) a lattice model introduced to decrease the number of degrees of freedom for structural changes and (3) a model of the formation of hydrophobic core as a key feature in driving the folding of proteins. These three models together helped to develop the idea of a fuzzy-oil-drop as a model for an external force field of hydrophobic character mimicking the hydrophobicity-differentiated environment for hydrophobic collapse. All amino acids in the polypeptide interact pair-wise during the folding process (energy minimization procedure) and interact with the external hydrophobic force field defined by a three-dimensional Gaussian function. The value of the Gaussian function usually interpreted as a probability distribution is treated as a normalized hydrophobicity distribution, with its maximum in the center of the ellipsoid and decreasing proportionally with the distance versus the center.
    [Show full text]
  • Entropy-Enthalpy Compensations Fold Proteins in Precise Ways
    International Journal of Molecular Sciences Article Entropy-Enthalpy Compensations Fold Proteins in Precise Ways Jiacheng Li 1,†, Chengyu Hou 2,†, Xiaoliang Ma 1,†, Shuai Guo 1,†, Hongchi Zhang 1, Liping Shi 1, Chenchen Liao 2, Bing Zheng 3 , Lin Ye 4, Lin Yang 1,4,* and Xiaodong He 1,5,* 1 National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; [email protected] (J.L.); [email protected] (X.M.); [email protected] (S.G.); [email protected] (H.Z.); [email protected] (L.S.) 2 School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; [email protected] (C.H.); [email protected] (C.L.) 3 Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education), School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China; [email protected] 4 School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] 5 Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China * Correspondence: [email protected] (L.Y.); [email protected] (X.H.); Tel.: +86-13163437675 (L.Y.); +86-0451-86412513 (X.H.) † These authors contributed equally to this work. Abstract: Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy Citation: Li, J.; Hou, C.; Ma, X.; equation and the change in enthalpy.
    [Show full text]
  • Hydrophobic Forces and the Length Limit of Foldable Protein Domains
    Hydrophobic forces and the length limit of foldable protein domains Milo M. Lin and Ahmed H. Zewail1 Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125 Contributed by Ahmed H. Zewail, May 2, 2012 (sent for review March 28, 2012) To find the native conformation (fold), proteins sample a subspace folds, we demonstrate that hydrophobic collapse together with that is typically hundreds of orders of magnitude smaller than their hydrophobic/hydrophilic residue segregation lead to realistic full conformational space. Whether such fast folding is intrinsic folding time scales for globular proteins and protein domains, or the result of natural selection, and what is the longest foldable which are independently folding subunits that constitute larger protein, are open questions. Here, we derive the average confor- proteins (12), thus quantitatively resolving the paradox. We also mational degeneracy of a lattice polypeptide chain in water and find an upper limit, of approximately 200 amino acids, on the quantitatively show that the constraints associated with hydro- length of protein domains for which such hydrophobic packing phobic forces are themselves sufficient to reduce the effective constraints would allow the native state to be identified within conformational space to a size compatible with the folding of a biologically reasonable timescale through a hypothetical ex- proteins up to approximately 200 amino acids long within a biolo- haustive search. By comparing to the experimental distribution gically reasonable amount of time. This size range is in general of protein domain lengths, we find that most protein fall below agreement with the experimental protein domain length distribu- this “hydrophobic length limit,” although it can be exceeded due tion obtained from approximately 1,200 proteins.
    [Show full text]
  • Lactalbumin Molten Globule (Protein Folding͞hydrophobic Interaction͞disulfide Bond͞proteolysis)
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 14314–14319, December 1997 Biochemistry Hydrophobic sequence minimization of the a-lactalbumin molten globule (protein foldingyhydrophobic interactionydisulfide bondyproteolysis) LAWREN C. WU AND PETER S. KIM* Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142 Contributed by Peter S. Kim, October 24, 1997 ABSTRACT The molten globule, a widespread protein- tamine, leucine, and arginine can form helical oligomers, folding intermediate, can attain a native-like backbone topol- although their detailed structures are unknown (19, 20). ogy, even in the apparent absence of rigid side-chain packing. Interestingly, proteins with cores of predominantly one amino Nonetheless, mutagenesis studies suggest that molten globules acid form folded structures with varying degrees of order are stabilized by some degree of side-chain packing among (21–24). In one case, a well packed native structure is formed, specific hydrophobic residues. Here we investigate the impor- of which a high resolution structure has been determined by tance of hydrophobic side-chain diversity in determining the x-ray crystallography (23). overall fold of the a-lactalbumin molten globule. We have Here we use the molten globule formed by the helical replaced all of the hydrophobic amino acids in the sequence of domain of a-lactalbumin (a-LA) as a model system to inves- the helical domain with a representative amino acid, leucine. tigate the role of specific hydrophobic amino acids in deter- Remarkably, the minimized molecule forms a molten globule mining backbone topology. a-LA is a two-domain protein that that retains many structural features characteristic of a native forms one of the most widely studied molten globules (25–32).
    [Show full text]
  • Polypeptide Chain Collapse and Protein Folding ⇑ Jayant B
    Archives of Biochemistry and Biophysics 531 (2013) 24–33 Contents lists available at SciVerse ScienceDirect Archives of Biochemistry and Biophysics journal homepage: www.elsevier.com/locate/yabbi Review Polypeptide chain collapse and protein folding ⇑ Jayant B. Udgaonkar National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India article info abstract Article history: Polypeptide chain collapse is an integral component of a protein folding reaction. In this review, exper- Available online 19 October 2012 imental characterization of the interplay of polypeptide chain collapse, secondary structure formation, consolidation of the hydrophobic core and the development of tertiary interactions, is scrutinized. In par- Keywords: ticular, the polypeptide chain collapse reaction is examined in the context of the three phenomenological Unfolded state dynamics models of protein folding – the hydrophobic collapse model, the framework model and the nucleation Polypeptide chain collapse condensation model – which describe different ways by which polypeptide chains are able to fold in bio- Molten globule logically relevant time-scales. Folding mechanisms Ó 2012 Elsevier Inc. All rights reserved. Hydrophobic collapse Introduction examines the results of experimental studies of the collapse reac- tion in the context of phenomenological models of protein folding. In the unfolded state, a polypeptide chain appears to be describ- able as a statistical random coil. The radius of gyration (R )ofan g The unfolded state unfolded polypeptide chain that is N residues long, scales as N0.6 [1] similar to the scaling (N0.6) expected for a homopolymer in Chain contraction and expansion in the unfolded state good solvent [2]. The low density of a typical random coil polypep- tide chain makes it improbable that distant segments of the chain Protein folding reactions are best studied experimentally start- will make contact with each other.
    [Show full text]