On potential energy surfaces and relaxation to the global minimum

By analyzing the dynamics of model potential energy surfaces we systematically investigate the processes involved in passing from a high energy state to the global minimum and how the probability of reaching the global minimum depends upon the topography and topology of the potential energy surface (PES). Relaxation to the global minimum is easiest for PES’s consisting of a single funnel (a set of convergent pathways which lead to the global minimum) with low barriers and a significant potential energy gradient towards the global minimum. The presence of additional funnels on the surface can severely reduce the rate of relaxation to the global minimum. Such secondary funnels act most efficiently as kinetic traps when they terminate at a low energy minimum, have a steep potential energy gradient and are wide (i.e., have a large configurational entropy) compared to the primary funnel. Indeed, it is even possible to construct PES’s for which the system relaxes to the minimum at the bottom of a secondary funn...

[1]  L. Wille,et al.  Computational complexity of the ground-state determination of atomic clusters , 1985 .

[2]  Berry,et al.  Coexistence in finite systems. , 1994, Physical review letters.

[3]  Frank H. Stillinger,et al.  Supercooled liquids, glass transitions, and the Kauzmann paradox , 1988 .

[4]  D. Wales,et al.  From Topographies to Dynamics on Multidimensional Potential Energy Surfaces of Atomic Clusters , 1996, Science.

[5]  J. Doye,et al.  The Structure and Stability of Atomic Liquids: From Clusters to Bulk , 1996, Science.

[6]  J T Ngo,et al.  Computational complexity of a problem in molecular structure prediction. , 1992, Protein engineering.

[7]  J. Onuchic,et al.  DIFFUSIVE DYNAMICS OF THE REACTION COORDINATE FOR PROTEIN FOLDING FUNNELS , 1996, cond-mat/9601091.

[8]  J. Onuchic,et al.  Navigating the folding routes , 1995, Science.

[9]  G. Lorimer,et al.  Dynamics of the chaperonin ATPase cycle: implications for facilitated protein folding. , 1994, Science.

[10]  D. Nelson,et al.  Polytetrahedral Order in Condensed Matter , 1989 .

[11]  K. Kelton Crystal Nucleation in Liquids and Glasses , 1991 .

[12]  J. C. Schön,et al.  Studying the energy hypersurface of continuous systems - the threshold algorithm , 1996 .

[13]  R. Stephen Berry,et al.  Statistical interpretation of topographies and dynamics of multidimensional potentials , 1995 .

[14]  M. Karplus,et al.  Kinetics of protein folding , 1995, Nature.

[15]  Eberhard R. Hilf,et al.  The structure of small clusters: Multiple normal-modes model , 1993 .

[16]  Bernd Hartke,et al.  Global geometry optimization of (Ar)n and B(Ar)n clusters using a modified genetic algorithm , 1996 .

[17]  P. Stein,et al.  Mobile reactive centre of serpins and the control of thrombosis , 1991, Nature.

[18]  L. Piela,et al.  Molecular Dynamics on Deformed Potential Energy Hypersurfaces , 1995 .

[19]  Jonathan P. K. Doye,et al.  An order parameter approach to coexistence in atomic clusters , 1995 .

[20]  C. Dobson,et al.  The folding of hen lysozyme involves partially structured intermediates and multiple pathways , 1992, Nature.

[21]  Pieter Rein ten Wolde,et al.  Numerical calculation of the rate of crystal nucleation in a Lennard‐Jones system at moderate undercooling , 1996 .

[22]  Berry,et al.  Multiple phase coexistence in finite systems. , 1994, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[23]  K. Dill,et al.  Transition states and folding dynamics of proteins and heteropolymers , 1994 .

[24]  E. Shakhnovich,et al.  Engineering of stable and fast-folding sequences of model proteins. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[25]  B. L. Chen,et al.  Low-temperature unfolding of a mutant of phage T4 lysozyme. 1. Equilibrium studies. , 1989, Biochemistry.

[26]  J. Rose,et al.  KCl) 32 and the possibilities for glassy clusters , 1993 .

[27]  M. Karplus,et al.  How does a protein fold? , 1994, Nature.

[28]  J. Northby,et al.  Structure of Charged Argon Clusters Formed in a Free Jet Expansion , 1984 .

[29]  J. Onuchic,et al.  Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.

[30]  D. Thirumalai,et al.  Kinetics of protein folding: Nucleation mechanism, time scales, and pathways , 1995 .

[31]  D. Danley,et al.  Expression of human plasminogen activator inhibitor type-1 (PAI-1) in Escherichia coli as a soluble protein comprised of active and latent forms. Isolation and crystallization of latent PAI-1. , 1990, Biochimica et biophysica acta.

[32]  Olof Echt,et al.  Magic Numbers for Sphere Packings: Experimental Verification in Free Xenon Clusters , 1981 .

[33]  K. Ho,et al.  Structural optimization of Lennard-Jones clusters by a genetic algorithm , 1996 .

[34]  P. Alexander,et al.  Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G. , 1992, Biochemistry.

[35]  F. Frank Supercooling of liquids , 1952, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[36]  Ho,et al.  Molecular geometry optimization with a genetic algorithm. , 1995, Physical review letters.

[37]  P. Wolynes,et al.  Spin glasses and the statistical mechanics of protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[38]  J. Onuchic,et al.  Toward an outline of the topography of a realistic protein-folding funnel. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[39]  E. Shakhnovich,et al.  Proteins with selected sequences fold into unique native conformation. , 1994, Physical review letters.

[40]  Peter Salamon,et al.  Emergent Hierarchical Structures in Complex-System Dynamics. , 1993 .

[41]  N. Shimamoto,et al.  Identification and characterization of the direct folding process of hen egg-white lysozyme. , 1982, Biochemistry.

[42]  A. Mackay A dense non-crystallographic packing of equal spheres , 1962 .

[43]  Crystallization in curved three-dimensional space , 1984 .

[44]  H. Roder,et al.  Early hydrogen-bonding events in the folding reaction of ubiquitin. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[45]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[46]  Thomas L. Beck,et al.  Solid–liquid phase changes in simulated isoenergetic Ar13 , 1986 .

[47]  K Gulukota,et al.  Statistical mechanics of kinetic proofreading in protein folding in vivo. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[48]  J. Rose,et al.  Freezing, melting, nonwetting, and coexistence in (KCl)32 , 1993 .

[49]  H. Frauenfelder,et al.  Conformational substates in proteins. , 1988, Annual review of biophysics and biophysical chemistry.

[50]  J. Onuchic,et al.  KINETICS OF PROTEINLIKE MODELS : THE ENERGY LANDSCAPE FACTORS THAT DETERMINE FOLDING , 1995 .

[51]  T. Sosnick,et al.  The barriers in protein folding , 1994, Nature Structural Biology.

[52]  Andreoni,et al.  Melting of small gold particles: Mechanism and size effects. , 1991, Physical review letters.

[53]  D. C. Tardy,et al.  Theory of Unimolecular Reactions , 1973 .

[54]  Harold A. Scheraga,et al.  MONTE CARLO SIMULATION OF A FIRST-ORDER TRANSITION FOR PROTEIN FOLDING , 1994 .

[55]  Eugene I. Shakhnovich,et al.  Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations , 1994 .

[56]  Jeffery G. Saven,et al.  Kinetics of protein folding: The dynamics of globally connected rough energy landscapes with biases , 1994 .

[57]  R. Lynden-Bell Landau free energy, Landau entropy, phase transitions and limits of metastability in an analytical model with a variable number of degrees of freedom , 1995 .

[58]  John E. Straub,et al.  FOLDING MODEL PROTEINS USING KINETIC AND THERMODYNAMIC ANNEALING OF THE CLASSICAL DENSITY DISTRIBUTION , 1995 .

[59]  D A Agard,et al.  Kinetics versus thermodynamics in protein folding. , 1994, Biochemistry.

[60]  R. Zwanzig,et al.  Levinthal's paradox. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[61]  W. Baase,et al.  Low-temperature unfolding of a mutant of phage T4 lysozyme. 2. Kinetic investigations. , 1989, Biochemistry.

[62]  D. Thirumalai,et al.  From Minimal Models to Real Proteins: Time Scales for Protein Folding Kinetics , 1995 .

[63]  D Thirumalai,et al.  Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Jianpeng Ma,et al.  Simulated annealing using the classical density distribution , 1994 .

[65]  Nulton,et al.  Statistical mechanics of combinatorial optimization. , 1988, Physical review. A, General physics.

[66]  Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique , 1995, chem-ph/9507003.

[67]  Jonathan P. K. Doye,et al.  Coexistence and phase separation in clusters: From the small to the not‐so‐small regime , 1995 .

[68]  J. Doye,et al.  The effect of the range of the potential on the structures of clusters , 1995 .

[69]  E. Shakhnovich,et al.  Simulations of chaperone-assisted folding. , 1996, Biochemistry.

[70]  J. Doye,et al.  Magic numbers and growth sequences of small face-centered-cubic and decahedral clusters , 1995 .

[71]  David J. Wales,et al.  Coexistence in small inert gas clusters , 1993 .

[72]  Klimov,et al.  Criterion that determines the foldability of proteins. , 1996, Physical review letters.

[73]  J. Onuchic,et al.  Protein folding funnels: a kinetic approach to the sequence-structure relationship. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[74]  T. Kiefhaber,et al.  Kinetic traps in lysozyme folding. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[75]  P. Wolynes,et al.  Intermediates and barrier crossing in a random energy model , 1989 .

[76]  R. Whetten,et al.  Statistical thermodynamics of the cluster solid-liquid transition. , 1990, Physical review letters.

[77]  Jonathan P. K. Doye,et al.  Calculation of thermodynamic properties of small Lennard‐Jones clusters incorporating anharmonicity , 1995 .

[78]  N. Kampen,et al.  Stochastic processes in physics and chemistry , 1981 .

[79]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[80]  David J. Wales,et al.  Free energy barriers to melting in atomic clusters , 1994 .

[81]  Thirumalai,et al.  Minimum energy compact structures of random sequences of heteropolymers. , 1993, Physical review letters.