Abstract
It is now well established that in order to execute specific biological functions proteins must adopt well defined three dimensional structures.1,2 The diverse biological demands placed on proteins are probably the reason why one observes seemingly large classes of protein structures. However, the process by which proteins acquire their three dimensional structure remains an unsolved problem in biochemistry and molecular biology. The text book description of the folding of proteins follows the classic work of Anfinsen on the spontaneous in vitro refolding of ribonuclease.3 This work suggests that the protein folding is a self-assembly process which means that all the information needed for folding is contained in the various solvent induced interactions between the amino acids comprising a protein molecule. The self-assembly process does not require additional input of energy or other constraints. Since many proteins have been made to fold in vitro it follows that the major principles of protein folding can be formulated without the need to involve extra cellular components. It therefore follows that the protein folding problem reduces to a statistical mechanical description of finite sized branched heteropolymers.
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References
R. Jaenicke, “Protein Structure and Protein Engineering”, (Mossbach Colloq. 39, Springer-Verlag, Berlin, 1988).
R. Jaenicke, “Protein Folding: Local Structures, Domains, Subunits, and Assemblies”, Biochemistry 30:3147 (1991).
C.B. Anfinsen, Principles that Govern the Folding of Protein Chains, Science 181:223 (1973).
C. Levinthal in “Mossbauer Spectroscopy in Biological Systems” (Proceedings of a meeting held in Allerton House, Monticello, Illinois, University of Illinois, Press, 1969).
J.D. Honeycutt and D. Thirumalai, Metastability of the Folded States of Globular Proteins, Proc. Natl. Acad. Sci. (USA) 87:3526 (1990).
R.J. Ellis and S.M. Van der Vies, “Molecular Chaperones”, Ann. Rev. Biochem 60: 321 (1991).
R.B. Freedman in “Protein Folding”, Edited by T. E. Creighton 455 (W. H. Freeman and Co., New York, 1992).
J.D. Bryngelson and P.G. Wolynes, Spin Glasses and the Statistical Mechanics of Protein Folding, Proc. Natl. Acad. Sci. 84:7524 (1987); Intermediates and Barrier Crossing in a Random Energy Model (with Applications to Protein Folding), J. Phys. Chem. 93:6902 (1989).
M.S. Friedrichs and P.G. Wolynes, Toward Protein Tertiary Structure Recognition by Means of Associative Memory Hamiltonian, Science 246:371 (1989).
T. Garel and H. Orland, Mean Field Model for Protein Folding, Europhys. Lett. 6:307 (1988).
T. Garel and H. Orland, Chemical Sequence and Spatial Structure in Simple Models of Biopolymers Europhys. Lett. 8:327 (1988).
J. Bascle, T. Garel, and H. Orland, Some Physical Approaches to Protein Folding, J. Phys. I (France), 3:259 (1993).
E.I. Shakhnovich and A.M. Gutin, Frozen States of Disordered Heteropolymers. J. Phvs. A22:1647 (1989).
E.I. Shakhnovich and A. M. Gutin, Implication of Thermodynamics of Protein Folding for Evolution of Primary Sequences Nature 346:773 (1990).
E.J. Shakhnovich, G. Farztdinov, A.M. Gutin, and M. Karplus, Protein Folding Bottlenecks: A Lattice Monte Carlo Simulation, Phys. Rev. Lett. 67:1665 (1991).
H.S. Chan and K.A. Dill, Origins of Structure in Globular Proteins, Proc. Natl. Acad. Sci. (USA) 87:6388 (1990).
H.S. Chan and K.A. Dill, Compact Polymers Macromolecules 22:4559 (1989).
K.M. Fiebig and K.A. Dill, Protein Cone Assembly Processes, J, Chem. Phys. 98:3475 (1993).
J. Skolnick and A. Kolinski, Simulations of the Folding of a Globular Protein, Science 250:1121 (1990).
J. Skolnick, A. Kolinski, and R. Yaris, Monte Carlo Simulations of the Folding of Beta Barrel Globular Proteins, Proc. Natl. Acad. Sci. (USA) 86:5057 (1988).
D.G. Garrett, K. Kastella, and D.M. Ferguson, New Results on Protein Folding From Simulated Annealing, J. Am. Chem. Soc. 114:6555 (1992).
P. Leopold, M. Montai, and J.N. Onuchic, Protein Folding Funnels: A Kinetic Approach to the Sequence-Structure Relationship, Proc. Natl. Acad. Sci. (USA) 89:8721 (1991).
G. Iori, E. Marinari, and G. Parisi, Random Self-Interacting Chains: A Mechanism for Protein Folding, J. Phys. A24:5439 (1991).
D.G. Covell and R.L. Jernigan, Conformations of Folded Proteins in Restricted Spans, Biochemistry 29:3287 (1990).
J.D. Honeycutt and D. Thirumalai, The Nature of Folded States of Globular Proteins, Biopolymers 32:695 (1992).
K. A. Dill, Dominant Forces in Protein Folding, Biochemistry 29:7133 (1990).
M. Levitt and R. Sharon, Accurate Simulation of Protein Dynamics in Solution, Proc. Natl. Acad. Sci. USA, 85:8557 (1988).
H. Taketomi, Y. Ueda, and N. Go, Studies on Protein Folding, Unfolding and Fluctuations by Computer Simulation, Int. J. Peptide Protein Res. 7:445 (1975).
M. Levitt and A. Warshel, Computer Simulation of Protein Folding, Nature 253:694 (1975).
C.J. Camacho and D. Thirumalai, Kinetics and Thermodynamics of Folding in Model Proteins, Proc. Natl. Acad. Sci. (USA) 90:6369 (1993).
Z. Guo and D. Thirumalai, Kinetics of Helix Formation, Preprint.
A. Rey and J. Skolnick, Comparison of Lattice Monte Carlo Dynamics Brownian Dynamics Folding Pathways of Alpha-Helical Hairpins, Chem. Phys. 158:199 (1991).
H.C. Andersen, Rattle: A “Velocity” Version of the Shake Algorithm for Molecular Dynamics Calculations, J. Comp. Phys. 52:24 (1983).
S. Kirkpatrick, C. D. Gelatt, and M. P. Vecchi, Optimization by Simulated Annealing, Science 220:671 (1983).
Z. Guo, D. Thirumalai, and J.D. Honeycutt, Folding Kinetics of Proteins: A Model Study, J. Chem. Phys. 97:525 (1992).
Z. Guo and D. Thirumalai, Kinetics of Protein Folding: Time Scales and Pathways, Preprint.
H.S. Chan and K.A. Dill, Energy Landscapes and Collapse Dynamics of Homopolymers, J. Chem. Phys. 99:2116 (1993).
Y. Ueda, H. Taketomi, and N. Go, Studies on Protein Folding, Unfolding, and Fluctuations by Computer Simulation II. A Three Dimensional Lattice Model of Lysozyme, Biopolymers 17:1531 (1978).
C.M. Jones, E.R. Henry, Y. Hu, C.-K. Chan, S.D. Luck, A. Bhuyan, H. Roder, J. Hofrichter, and W.A. Eaton, Fast Events in Protein Folding Initiated by Nanosecond Laser Photolysis, Preprint.
P.G. de Gennes, Kinetics of Collapse for a Flexible Coil, J. Physique Lett. 46:L639 (1985).
J.P. Hendrick and F.-U. Harti, Molecular Chaperone Functions of Heat Shock Proteins, Ann. Rev. Biochem. 62:349 (1993).
E.A. Craig, Chaperones: Helpers Along Pathways to Protein Folding, Science 260:1902 (1993).
D.A. Agard, To Fold or Not to Fold. Science 260:1903 (1993).
J.N. Israelachvili in “Intermolecular and Surface Forces”, (Academic Press, London, 1991).
R.P. Beckman, L.A. Mizzan, and W.J. Welch, Interaction of Hsp70 with Newly Synthesized Proteins: Implications for Protein Folding and Assembly Science 248:850 (1990).
M.Y. Cheng, F.-U. Hartl, J. Martin, R.A. Pollock, F. Kalousek, W. Neupert, E.M. Hallberg, R.L. Hallberg, and A.L. Horwich, Mitochondrial Heat-Shock Protein Hsp60 is Essential for Assembly of Proteins Imported into Yeast Mitochondria Nature 337:620 (1989).
T. Langer, C. Lu, H. Echols, J. Flanagan, M.K. Hayer, and F.-U. Hartl, Successive Action of Dnak, Dnaj and GroEl along the Pathway of Chaperone-Mediated Protein Folding Nature 356:683 (1992).
P.V. Viitanen, A.A. Gatenby, and G.H. Lorimer, Purified Chaperonin 60 (GroEl) Interacts with the Non-Native States of a Multitude of Escherichia coli Proteins, Protein Sci. 1:363 (1992).
P.G. de Gennes in “Scaling Concepts in Polymer Physics”:, (Cornell University Press, Ithaca, New York, 1985).
D.H. Napper in “Polymeric Stabilization of Colloidal Dispersions”, (Academic Press, New York, 1983).
D. Thirumalai, Interaction Between Chaperone Bound Protein Complexes, Preprint.
G.H. Lorimer, M.J. Todd, and P. Viitanen, Chaperonins and Protein Folding: Unity and Disunity of Mechanisms, Phil. Trans. R. Soc. Lond. B 339:297 (1993).
D. Sarid in “Scanning Force Microscopy with Applications to Electric, Magnetic, and Atomic Forces”, (Oxford University Press, Cambridge, 1993).
R.E. Elber and M. Karplus, Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Proteins, Science 235:318 (1987).
H. Frauenfelder, S. Sligar, and P.G. Wolynes, The Energy Landscapes and Motions of Proteins, Science 254:1598 (1991).
J.E. Straub and D. Thirumalai, Exploring the Energy Landscape in Proteins, Proc. Natl. Acad. Sci. (USA) 90:809 (1993).
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Thirumalai, D. (1994). Theoretical Perspectives on In Vitro and In Vivo Protein Folding. In: Doniach, S. (eds) Statistical Mechanics, Protein Structure, and Protein Substrate Interactions. NATO ASI Series, vol 325. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1349-4_12
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DOI: https://doi.org/10.1007/978-1-4899-1349-4_12
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