Simulations of protein folding

Reviews in Computational Chemistry

Volumn 22, Issue , 2006, Pages 169-228

  Shea, Joan Emma ^a   Friedel, Miriam R ^a   Baumketner, Andrij ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INSTITUTE FOR CONDENSED MATTER PHYSICS   (Ukraine)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33750029744     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Review

References (196)

1. C. Chothia, Nature, 357, 543 (1992). One Thousand Families for the Molecular Biologist.
2. E. Haber and C. B. Anfinsen, J. Biol. Chem., 237, 1839 (1962). Side-chain Interactions Governing the Pairing of Half-cystine Residues in Ribonuclease.
3. C. B. Anfinsen, E. Haber, M. Sela, and F. H. White, Jr., Proc. Natl. Acad. Sci. USA, 47, 1309 (1961). The Kinetics of Formation of Native Ribonuclease during Oxidation of the Reduced Polypeptide Chain.
4. C. B. Anfinsen, Science, 181, 223 (1973). Principles that Govern the Folding of Protein Chains.
5. C. Levinthal, J. Chimie Physique et de Phisio-Chemie Biologique, 65, 44 (1968). Are There Pathways for Protein Folding?
6. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. USA, 84, 7524 (1987). Spin Glasses and the Statistical Mechanics of Protein Folding.
7. J. D. Bryngelson and P. G. Wolynes, J. Phys. Chem., 93, 6902 (1989). Intermediates and Barrier Crossing in a Random Energy Model (with Applications to Protein Folding).
8. J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem., 48, 545 (1997). Theory of Protein Folding: The Energy Landscape Perspective.
9. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, Protein Sci., 4, 561 (1995). Principles of Protein Folding-a Perspective from Simple Exact Models.
10. M. Karplus and D. L. Weaver, Nature, 260, 404 (1976). Protein Folding Dynamics.
11. M. Karplus and D. L. Weaver, Protein Sci., 3, 650 (1994). Protein Folding Dynamics: Diffusion-collision Model and Experimental Data.
12. P. S. Kim and R. L. Baldwin, Annu. Rev. Biochem., 51, 459 (1982). Specific Intermediates in the Folding Reactions of Small Proteins and the Mechanism of Protein Folding.
13. W. Kauzmann, Adv. Protein Chem., 14, 1 (1959). Some Factors in the Interpretation of Protein Denaturation.
14. O. Ptitsyn, Nature Struct. Biol., 3, 488 (1996). How Molten is the Molten Globule?
15. D. B. Wetlaufer, Proc. Natl. Acad. Sci. USA, 70, 697 (1973). Nucleation, Rapid Folding, and Globular Intrachain Regions in Proteins.
16. D. B. Wetlaufer, Trends Biochem. Sci., 15, 414 (1990). Nucleation in Protein Folding-Confusion of Structure and Process.
17. A. R. Fersht, Curr. Opin. Struct. Biol., 7, 3 (1997). Nucleation Mechanisms in Protein Folding.
18. J.-E. Shea and C. L. Brooks, III, Annu. Rev. Phys. Chem., 52, 499 (2001). From Folding Theories to Folding Proteins: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding.
19. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. N. Teller, and E. Teller, J. Chem. Phys., 21, 1087 (1953). Equation of State Calculations by Fast Computing Machines.
20. K. Binder and A. P. Young, Rev. Mod. Phys., 58, 801 (1986). Spin Glasses: Experimental Facts, Theoretical Concepts and Open Questions.
21. E. Gardner and B. Derrida, J. Stat. Phys. 39, 267 (1985). Zero Temperature Magnetization of a One-dimensional Spin Glass.
22. B. Derrida, Physica D, 107, 186 (1997). From Random Walks to Spin Glasses.
23. P. W. Anderson, J. Less-Common Metals, 62, 291 (1978). The Concept of Frustration in Spin Glasses.
24. M. Mezard, G. Parisi, and M. A. Virasoro, Spin Glass Theory and Beyond, World Scientific, Singapore, 1987.
25. J. D. Bryngelson, J. N. Onuchic, N. D. Socci, and P. G. Wolynes, Proteins, 21, 167 (1995). Funnels, Pathways, and the Energy Landscape of Protein Folding: A Synthesis.
26. B. Derrick, Phys. Rev. B, 24, 2613 (1981). Random-Energy Model: An Exactly Solvable Model of Disordered Systems.
27. B. Derrida, Phys. Rev. Lett., 45, 79 (1980). Random-Energy Model: Limit of a Family of Disordered Models.
28. T. Garel and H. Orland, Europhys. Lett., 6, 307 (1988). Mean-field Model for Protein Folding.
29. E. I. Shakhnovich and A. M. Gutin, Biophys. Chem., 34, 187 (1989). Formation of Unique Structure in Polypeptide Chains. Theoretical Investigation with the Aid of a Replica Approach.
30. P. E. Leopold, M. Montal, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA, 89, 8721 (1992). Protein Folding Funnels: A Kinetic Approach to the Sequence-Structure Relationship.
31. J.-E. Shea, J. N. Onuchic, and C. L. Brooks, III, Proc. Natl. Acad. Sci. USA, 96, 12512 (1999). Exploring the Origins of Topological Frustration: Design of a Minimally Frustrated Model of Fragment B of Protein A.
32. J.-E. Shea, J. N. Onuchic, and C. L. Brooks, III, J. Chem. Phys., 113, 7663 (2000). Energetic Frustration and the Nature of the Transition State in Protein Folding.
33. C. Clementi, H. Nymeyer, and J. N. Onuchic, J. Mol. Biol., 298, 937 (2000). Topological and Energetic Factors: What Determines the Structural Details of the Transition State Ensemble and "en-route" Intermediates for Protein Folding? An Investigation for Small Globular Proteins.
34. E. Rhoades, E. Gussakovsky, and G. Haran, Proc. Natl. Acad. Sci. USA, 100, 3197 (2003). Watching Proteins Fold one Molecule at a Time.
35. E. A. Lipman, B. Schuler, O. Bakajin, and W. A. Eaton, Science, 301, 1233 (2003). Single-Molecule Measurement of Protein Folding Kinetics.
36. B. Schuler, E. A. Lipman, and W. A. Eaton, Nature, 419, 743 (2002). Probing the Free-energy Surface for Protein Folding with Single-molecule Fluorescence Spectroscopy.
37. K. A. Dill, Protein Sci., 8, 1166 (1999). Polymer Principles and Protein Folding.
38. M. Gruebele, Curr. Opin. Str. Biol., 12, 161 (2002). Protein Folding: The Free Energy Surface.
39. C. M. Dobson and P. J. Hore, Nature Struct. Biol., 5, 504 (1998). Kinetic Studies of Protein Folding Using NMR Spectroscopy.
40. S. E. Jackson, Folding Design, 3, R81 (1998). How do Small Single-domain Proteins Fold?
41. A. R. Fersht, Structure and Mechanism in Protein Science, W. H. Freeman and Company, New York, 1999.
42. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
43. B. A. Berg and T. Neuhaus, Phys. Rev. Lett., 68, 9 (1992). Multicanonical Ensemble: A New Approach to Simulate First-Order Phase Transition.
44. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys., 96, 1776 (1992). New Approach to Monte Carlo Calculation of the Free Energy: Method of Expanded Ensembles.
45. E. Marinari and G. Parisi, Europhys. Lett., 19, 451 (1992). Simulated Tempering: A New Monte Carlo Scheme.
46. B. Hesselbo and R. B. Stinchcombe, Phys. Rev. Lett., 74, 2151 (1995). Monte Carlo Simulation and Global Optimization without Parameters.
47. D. D. Frantz, D. L. Freeman, and J. D. Doll, J. Chem. Phys., 74, 2769 (1990). Reducing Quasi-ergodic Behavior in Monte Carlo Simulations by J-walking: Applications to Atomic Clusters.
48. C. Tsallis, J. Stat. Phys., 52, 479 (1988). Possible Generalization of Boltzmann-Gibbs Statistics.
49. U. H. E. Hansmann, Physica A, 242, 250 (1997). Simulated Annealing with Tsallis Weights-A Numerical Comparison.
50. I. I. Andricioaei and J. E. Straub, Phys. Rev. E., 53, R3055 (1996). Generalized Simulated Annealing Algorithms using Tsallis Statistics: Application to Conformational Optimization of a Tetrapeptide.
51. F. Wang and D. P. Landau, Phys. Rev. Lett., 86, 2050 (2001). Efficient, Multiple-range Random Walk Algorithm to Calculate the Density of States.
52. R. H. Swendsen and J. S. Wang, Phys. Rev. Lett., 57, 2607 (1986). Replica Monte Carlo Simulation of Spin Glasses.
53. M. C. Tesi, E. J. J. van Rensberg, E. Orlandi, and S. G. Whittington, J. Stat. Phys., 82, 155 (1996). Monte Carlo Study of the Interacting Self-avoiding Walk Model in Three Dimensions.
54. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn., 65, 1604 (1996). Exchange Monte Carlo Method and Application to Spin Glass Simulations.
55. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers, 60, 96 (2001). Generalized-ensemble Algorithms for Molecular Simulations of Biopolymers.
56. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett., 63, 1195 (1989). Optimized Monte Carlo Data Analysis.
57. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett., 61, 2635 (1988). New Monte Carlo Technique for Studying Phase Transitions.
58. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem., 13, 1011 (1992). The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. I. The Method.
59. A. Šali, E. Shakhnovich, and M. Karplus, Nature, 369, 248 (1994). How Does a Protein Fold?
60. N. D. Socci and J. N. Onuchic, J. Chem. Phys., 101, 1519 (1994). Folding Kinetics of Proteinlike Heteropolymers.
61. A. Kolinski, M. Milik, and J. Skolnick, J. Chem. Phys., 94, 3978 (1991). Static and Dynamic Properties of a New Lattice Model of Polypeptide Chains.
62. N. Gō and H. Taketomi, Proc. Natl. Acad. Sci. USA, 75, 559 (1975). Respective Roles of Short and Long Range Interactions in Protein Folding.
63. H. Taketomi, Y. Ueda, and N. Gō, Int. J. Pept. Protein Res., 7, 445 (1975). Studies on Protein Folding, Unfolding and Fluctuations by Computer Simulation. I. The Effect of Specific Amino Acid Sequence Represented by Specific Inter-unit Interactions.
64. H. Nymeyer, A. E. Garcia, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA, 95, 5921 (1998). Folding Funnels and Frustration in Off-lattice Minimalist Protein Landscapes.
65. R. Du, V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. I. Shakhnovich, J. Chem. Phys., 108, 334 (1998). On the Transition Coordinate for Protein Folding.
66. K. F. Lau and K. A. Dill, Macromolecules, 22, 3986 (1989). A Lattice Statistical Mechanics Model of the Conformational and Sequence Spaces of Proteins.
67. H. S. Chan and K. A. Dill, J. Chem. Phys., 92, 3118 (1990). The Effects of Internal Constraints on the Configuration of Chain Molecules.
68. H. S. Chan and K. A. Dill, Annu. Rev. Biophys. Biophys. Chem., 20, 447 (1991). Polymer Principles in Protein Structure and Stability.
69. H. S. Chan and K. A. Dill, J. Chem. Phys., 95, 3775 (1991). "Sequence Space Soup" of Proteins and Copolymers.
70. H. S. Chan and K. A. Dill, J. Chem. Phys., 99, 2116 (1993). Energy Landscapes and the Collapse Dynamics of Homopolymers.
71. H. S. Chan and K. A. Dill, J. Chem. Phys., 100, 9238 (1994). Transition States and the Folding Dynamics of Proteins and Heteropolymers.
72. C. J. Camacho and D. Thirumalai, Proc. Natl. Acad. Sci. USA, 90, 6369 (1993). Kinetics and Thermodynamics of Folding in Model Proteins.
73. E. I. Shakhnovich and A. M. Gutin, Proc. Natl. Acad. Sci. USA, 90, 7195 (1993). Engineering of Stable and Fast-folding Sequences of Model Proteins.
74. A. Sali, E. Shakhnovich, and M. Karplus, J. Mol. Biol., 235, 1614 (1994). Kinetics of Protein Folding. A Lattice Model Study of the Requirements for Folding to the Native State.
75. N. D. Socci and J. N. Onuchic J. Chem. Phys., 103, 4372 (1995). Kinetic and Thermodynamic Analysis of Proteinlike Heteropolymers: Monte Carlo Histogram Technique.
76. J. Skolnick and A. Kolinski, J. Mol. Biol., 221, 499 (1991). Dynamic Monte Carlo Simulations of a New Lattice Model of Globular Protein Folding, Structure and Dynamics.
77. A. Godzik, J. Skolnick, and A. Kolinski, Proc. Natl. Acad. Sci. USA, 89, 2629 (1992). Simulations of the Folding Pathway of Triose Phosphate Isomerase-type Alpha/Beta Barrel Proteins.
78. A. Kolinski, L. Jaroszweski, P. Rotkiewicz, and J. Skolnick, J. Phys. Chem. B, 102, 4628 (1998). An Efficient Monte Carlo Model of Protein Chains. Modeling the Short-Range Correlations Between Side Group Centers of Mass.
79. A. Kolinski, P. Rotkiewicz, B. Ilkowski, and J. Skolnick, Proteins, 37, 592 (1999). A Method for the Improvement of Threading-based Protein Models.
80. A. Kolinski, B. Ilkowski, and J. Skolnick, Biophys. J., 77, 2942 (1999). Dynamics and Thermodynamics of Beta-hairpin Assembly: Insights from Various Simulation Techniques.
81. A. Kolinski and J. Skolnick, Polymer, 45, 511 (2004). Reduced Models of Proteins and their Applications.
82. Y. Zhou and M. Karplus, Proc. Natl. Acad. Sci. USA, 94, 14429 (1997). Folding Thermodynamics of a Model Three-helix Bundle Protein.
83. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. USA, 87, 3526 (1990). Meta-stability of the Folded States of Globular Proteins.
84. Z. Guo, D. Thirumalai, and J. D. Honeycutt, J. Chem. Phys., 97, 525 (1992). Folding Kinetics of Proteins: A Model Study.
85. J. D. Honeycutt and D. Thirumalai, Biopolymers, 32, 695 (1992). The Nature of Folded States of Globular Proteins.
86. Z. Guo and D. Thirumalai, Biopolymers, 36, 83 (1994). Kinetics of Protein Folding: Nucleation Mechanism, Time Scales and Pathways.
87. Z. Guo and C. L. Brooks, III, Biopolymers, 42, 745 (1997). Thermodynamics of Protein Folding: A Statistical Mechanical Study of a Small All-beta Protein.
88. J.-E. Shea, Y. D. Nochomovitz, Z. Guo, and C. L. Brooks, III, J. Chem. Phys., 109, 2895 (1998). Exploring the Space of Protein Folding Hamiltonians: The Balance of Forces in a Minimalist Beta-barrel Model.
89. S. Takada, Z. Luthey-Schulten, and P. G. Wolynes, J. Chem. Phys., 110, 11616 (1999). Folding Dynamics with Nonadditive Forces: A Simulation Study of a Designed Helical Protein and a Random Heteropolymer.
90. A. V. Smith and C. K. Hall, J. Mol. Biol., 312, 187 (2001). Protein Refolding versus Aggregation: Computer Simulations on an Intermediate-resolution Protein Model.
91. D. K. Klimov and D. Thirumalai, Proc. Natl. Acad. Sci. USA, 97, 2544 (2000). Mechanisms and Kinetics of Beta-hairpin Formation.
92. F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, J. Mol. Biol., 324, 851 (2002). Molecular Dynamics Simulation of the SH3 Domain Aggregation Suggests a Generic Amyloidogenesis Mechanism.
93. M. S. Cheung, J. M. Finke, B. Callahan, and J. N. Onuchic, J. Phys. Chem. B, 107, 11193 (2003). Exploring the Interplay Between Topology and Secondary Structural Formation in the Protein Folding Problem.
94. J. Shimada and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA, 99, 11175 (2002). The Ensemble Folding Kinetics of Protein G From an All-atom {Monte Carlo} Simulation.
95. C. Clementi, A. E. Garcia, and J. N. Onuchic, J. Mol. Biol., 326, 933 (2003). Interplay Among Tertiary Contacts, Secondary Structure Formation and Side-chain Packing in the Protein Folding Mechanism: All-atom Representation Study of Protein L.
96. M. S. Cheung, A. E. Garcia, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA, 99, 685 (2002). Protein Folding Mediated by Solvation: Water Expulsion and Formation of the Hydrophobic Core Occur After the Structural Collapse.
97. A. M. Fernandez-Escamilla, M. S. Cheung, M. C. Vega, M. Wilmanns, J. N. Onuchic, and L. Serrano, Proc. Natl. Acad. Sci. USA, 101, 2834 (2004). Solvation in Protein Folding Analysis: Combination of Theoretical and Experimental Approaches.
98. J. Karanicolas and C. L. Brooks, III, Proc. Natl. Acad. Sci. USA, 100, 3954 (2003). The Structural Basis for Biphasic Kinetics in the Folding of the WW Domain From a Formin-binding Protein: Lessons for Protein Design?
99. J. M. Sorenson and T. Head-Gordon, Folding and Design, 3, 523 (1998). The Importance of Hydration for the Kinetics and Thermodynamics of Protein Folding: Simplified Lattice Models.
100. L. Verlet, Phys. Rev., 159, 98 (1967). Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules.
101. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, D. J. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1982). CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations.
102. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc., 117, 5179 (1995). A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules.
103. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984). A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins.
104. W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc., 110, 1657 (1988). The OPLS Potential Function for Proteins - Energy Minimizations for Crystals of Cyclic-peptides and Crambin.
105. W. R. P. Scott, P. H. Hunenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Kruger, and W. F. van Gunsteren, J. Phys. Chem. A, 103, 3596 (1999). The GROMOS Biomolecular Simulation Program Package.
106. D. Bashford and D. A. Case, Ann. Ref. Phys. Chem., 51, 129 (2000). Generalized Born Models of Macromolecular Solvation Effects.
107. M. S. Lee, F. R. J. Salsbury, and C. L. Brooks, III, J. Chem. Phys., 116, 10606 (2002). Novel Generalized Born Methods.
108. M. S. Lee, M. Feig, F. R. J. Salsbury, and C. L. Brooks, III, J. Comput. Chem., 24, 1348 (2003). New Analytical Approximation to the Standard Molecular Volume Definition and its Application to Generalized Born Calculations.
109. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys., 23, 327 (1977). Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular Dynamics of N-alkanes.
110. L. Duan, L. Wang, and P. A. Kollman, Proc. Natl. Acad. Sci. USA, 95, 9897 (1998). The Early Stage of Folding of Villin Headpiece Subdomain Observed in a 200-Nanosecond Fully Solvated Molecular Dynamic Simulation.
111. L. Duan and P. A. Kollman, Science, 282, 740 (1998). Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution.
112. E. M. Boczko and C. L. Brooks, III, Science, 269, 393 (1995). First Principles Calculation of the Folding Free Energy of a Three-helix Bundle Protein.
113. Z. Guo, E. M. Boczko, and C. L. Brooks, III, Proc. Natl. Acad. Sci. USA, 94, 10161 (1997). Exploring the Folding Free Energy Surface of a Three-helix Bundle Protein.
114. D. O. V. Alonso and V. Daggett, Proc. Natl. Acad. Sci. USA, 97, 133 (2000). Staphylococcal Protein A: Unfolding Pathways, Unfolded States, and Differences Between the B and E Domains.
115. A. E. Garcia and J. N. Onuchic, Proc. Natl. Acad. Sci. USA, 100, 13898 (2003). Folding a Protein in a Computer: An Atomic Description of the Folding/Unfolding of Protein A.
116. A. Ghosh, R. Elber, and H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 99, 10394 (2002). An Atomically Detailed Study of the Folding Pathways of Protein A with the Stochastic Difference Equation.
117. S. Sato, T. L. Religa, V. Daggett, and A. R. Fersht, Proc. Natl. Acad. Sci. USA, 101, 6952 (2004). Testing Protein-Folding Simulations by Experiment: B Domain of Protein A.
118. Y. Bai, A. Karimi, H. J. Dyson, and P. E. Wright, Protein Sci., 6, 1449 (1997). Absence of a Stable Intermediate on the Folding Pathway of Protein A.
119. S. Bottomley, A. Popplewell, M. Scawen, T. Wan, B. Sutton, and M. Gore, Protein Eng., 7, 1463 (1994). The Stability and Unfolding of an IgG Binding Protein Based Upon the B Domain of Protein A from Staphylococcus Aureus Probed by Tryptophan Substitution and Fluorescence Spectroscopy.
120. R. Elber, A. Ghosh, and A. E. Cardenas, Acc. Chem. Res., 35, 396 (2002). Long Time Dynamics of Complex Systems.
121. A. E. Cardenas and R. Elber, Proteins Struct. Funct. Genet., 51, 245 (2003). Kinetics of Cytochrome C Folding: Atomically Detailed Simulations.
122. G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, Chem. Phys. Lett., 246, 122 (1995). Pairwise Solute Descreening of Solute Charges from a Dielectric Medium.
123. A. R. Dinner and M. Karplus, J. Mol. Biol., 292, 403 (1999). Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis.
124. J. Tsai, M. Levitt, and D. Baker, J. Mol. Biol., 291, 215 (1999). Hierarchy of Structure Loss in MD Simulations of src-SH3 Domain Unfolding.
125. A. Li and V. Daggett, Proc. Natl. Acad. Sci. USA, 91, 10430 (1994). Characterization of the Transition State of Protein Unfolding by Use of Molecular Dynamics: Chymotrypsin Inhibitor 2.
126. A. Li and V. Daggett, J. Mol. Biol., 257, 412 (1996). Identification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics Simulations.
127. T. Lazaridis and M. Karplus, Science, 278, 1928 (1997). New View of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations.
128. M. Levitt, M. Hirshberg, R. Sharon, and V. Daggett, Comput. Phys. Commun., 91, 215 (1995). Potential Energy Function and Parameters for Simulations of the Molecular Dynamics of Proteins and Nucleic Acids in Solution.
129. F. B. Sheinerman and C. L. Brooks, III, J. Mol. Biol., 278, 439 (1998). Calculations on Folding of Segment B1 of Streptococcal Protein G.
130. W. Guo, S. Lampoudi, and J.-E. Shea, Biophys. J., 85, 61 (2003). Posttransition State Desolvation of the Hydrophobic Core of the src-SH3 Protein Domain.
131. W. Guo, S. Lampoudi, and J.-E. Shea, Proteins Struct. Funct. Genet., 55, 395 (2004). Temperature Dependence of the Free Energy Landscape of the src-SH3 Protein Domain.
132. J.-E. Shea, J. N. Onuchic, and C. L. Brooks, III, Proc. Natl. Acad. Sci. USA, 99, 16064 (2002). Probing the Folding Free Energy Landscape of the src-SH3 Protein Domain.
133. B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol., 7, 181 (1997). Novel Methods of Sampling Phase Space in the Simulation of Biological Systems.
134. Y. Sugita and Y. Okamoto, Chem. Phys. Lett., 314, 141 (1999). Replica-Exchange Molecular Dynamics Method for Protein Folding.
135. J. W. Pitera and W. Swope, Proc. Natl. Acad. Sci. USA, 100, 7587 (2003). Understanding Folding and Design: Replica-exchange Simulations of "Trp-cage" Miniproteins.
136. A. E. Garcia and K. Y. Sanbonmatsu, Proteins, 42, 345 (2001). Exploring the Energy Landscape of a Beta Hairpin in Explicit Solvent.
137. R. Zhou, Proc. Natl. Acad. Sci. USA, 100, 13280 (2003). Trp-cage: Folding Free Energy Landscape in Explicit Water.
138. M. Oliveberg, Curr. Opin. Struct. Biol., 11, 94 (2001). Characterization of the Transition States for Protein Folding: Towards a New Level of Mechanistic Detail in Protein Engineering Analysis.
139. V. Daggett and A. Fersht, Nat. Rev. Mol. Cell Biol., 4, 497 (2003). The Present View of the Mechanism of Protein Folding.
140. G. Hummer, J. Chem. Phys., 120, 516 (2004). From Transition Paths to Transition States and Rate Coefficients.
141. Z. Guo and D. Thirumalai, Folding Design, 2, 377 (1997). The Nucleation-Collapse Mechanism in Protein Folding: Evidence for the Non-uniqueness of the Folding Nucleus.
142. N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, J. Mol. Biol., 296, 1183 (2000). Identifying the Protein Folding Nucleus Using Molecular Dynamics.
143. M. Vendruscolo, E. Paci, C. M. Dobson, and M. Karplus, Nature, 409, 641 (2001). Three Key Residues from a Critical Contact Network in a Protein Folding Transition State.
144. R. Davis, C. M. Dobson, and M. Vendruscolo, J. Chem. Phys., 117, 9510 (2002). Determination of the Structures of Distinct Transition State Ensembles for a Beta-sheet Peptide with Parallel Folding Pathways.
145. E. Paci, J. Clarke, A. Steward, M. Vendruscolo, and M. Karplus, Proc. Natl. Acad. Sci. USA, 100, 394 (2003). Self-consistent Determination of the Transition State for Protein Folding: Application to a Fibronectin Type III Domain.
146. P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys., 62, 251 (1990). Reaction-rate Theory: Fifty Years After Kramers.
147. A. Baumketner and Y. Hiwatari, Phys. Rev. E, 66, 011905 (2002). Diffusive Dynamics of Protein Folding Studied by Molecular Dynamics Simulations of an Off-lattice Model.
148. P. G. Bolhuis, C. Dellago, and D. Chandler, Proc. Natl. Acad. Sci. USA, 97, 5877 (2000). Reaction Coordinates of Biomolecular Isomerization.
149. N. D. Socci, J. N. Onuchic, and P. G. Wolynes, J. Chem. Phys., 104, 5860 (1996). Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels.
150. J. Kubelka, J. Hofrichter, and W. A. Eaton, Curr. Opin. Struct. Biol., 14, 76 (2004). The Protein Folding 'Speed Limit'.
151. A. Baumketner, J.-E. Shea, and Y. Hiwatari, J. Chem. Phys., 121, 1114 (2004). Improved Theoretical Description of Protein Folding Kinetics from Rotations in the Phase Space of Relevant Order Parameters.
152. M.M. Klosek, B. J. Matkowsky, and Z. Schuss, Ber. Bunsenges Phys. Chem., 95, 331 (1991). The Kramers Problem in the Turnover Regime: The Role of the Stochastic Separatrix.
153. A. R. Dinner and M. Karplus, J. Phys. Chem. B, 103, 7976 (1999). The Thermodynamics and Kinetics of Protein Folding: A Lattice Model Analysis of Multiple Pathways with Intermediates.
154. D. K. Klimov and D. Thirumalai, Proteins Struct. Fund. Genet., 43, 465 (2001). Multiple Protein Folding Nuclei and the Transition State Ensemble in Two-state Proteins.
155. J. Gsponer and A. Caflisch, Proc. Natl. Acad. Sci. USA, 99, 6719 (2002). Molecular Dynamics Simulations of Protein Folding from the Transition State.
156. L. Li and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA, 98, 13014 (2001). Constructing, Verifying, and Dissecting the Folding Transition State of Chymotrypsin Inhibitor 2 with All-atom Simulations.
157. F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, Biophys. J., 83, 3525 (2002). Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble.
158. J. Gsponer and A. Caflisch, J. Mol. Biol., 309, 285 (2001). Role of Native Topology Investigated by Multiple Unfolding Simulations of Four SH3 Domains.
159. C. Clementi, P. A. Jennings, and J. N. Onuchic, J. Mol. Biol., 311, 879 (2001). Prediction of Folding Mechanism for Circular-permuted Proteins.
160. H. Nymeyer, N. D. Socci, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA, 97, 634 (2000). Landscape Approaches for Determining the Ensemble of Folding Transition States: Success and Failure Hinge on the Degree of Frustration.
161. N. V. Dokholyan, L. Li, F. Ding, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA, 99, 13014 (2002). Topological Determinants of Protein Folding.
162. V. Daggett, Acc. Chem. Res., 35, 422 (2002). Molecular Dynamics Simulations of the Protein Unfolding/Folding Reaction.
163. D. De Jong, R. Riley, D. O. V. Alonso, and V. Daggett, J. Mol. Biol., 319, 229 (2002). Probing the Energy Landscape of Protein Folding/Unfolding Transition States.
164. D. K. Klimov and D. Thirumalai, J. Mol. Biol., 282, 471 (1998). Lattice Models for Proteins Reveal Multiple Folding Nuclei for Nucleation-collapse Mechanism.
165. D. K. Klimov and D. Thirumalai, Chem. Phys., 307, 251 (2004). Progressing From Folding Trajectories to Transition State Ensemble in Proteins.
166. I. A. Hubner, M. Oliveberg, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA, 101, 8354 (2004). Simulation, Experiment, and Evolution: Understanding Nucleation in Protein S6 Folding.
167. D. K. Klimov and D. Thirumalai, J. Mol. Biol., 315, 721 (2002). Stiffness of the Distal Loop Restricts the Structural Heterogeneity of the Transition State Ensemble in SH3 Domains.
168. C. Dellago, P. G. Bolhuis, and D. Chandler, in Advances in Chemical Physics, I. Prigogine and S. A. Rice, Eds., Wiley, New York, 2002, pp. 1-78. Transition Path Sampling.
169. G. M. Torrie and J. P. Valleau, J. Comput. Phys., 23, 187 (1977). Nonphysical Sampling Distributions in Monte Carlo Free-energy Estimation: Umbrella Sampling.
170. P. G. Bolhuis, C. Dellago, P. L. Geissler, and D. Chandler, J. Phys.: Condens. Matter, 12, A147 (2000). Transition Path Sampling: Throwing Ropes Over Mountains in the Dark.
171. A. R. Fersht, A. Matouschek, and L. Serrano, J. Mol. Biol., 224, 771 (1992). The Folding of an Enzyme. I. Theory of Protein Engineering Analysis of Stability and Pathway of Protein Folding.
172. J. N. Onuchic, H. Nymeyer, A. E. Garcia, J. Chahine, and N. D. Socci, Adv. Prot. Chem., 53, 87 (2000). The Energy Landscape Theory of Protein Folding: Insights into Folding Mechanisms and Scenarios.
173. E. Paci, M. Vendruscolo, and M. Karplus, Proteins, 47, 379 (2002). Native and Non-native Interactions Along Protein Folding and Unfolding Pathways.
174. M. Vendruscolo and E. Paci, Curr. Opin. Str. Biol., 13, 82 (2003). Protein Folding: Bringing Theory and Experiment Closer Together.
175. C. M. Dobson, Trends Biochem. Sci., 24, 329 (1999). Protein Misfolding, Evolution and Disease.
176. R. Tycko, Curr. Opin. Chem. Biol., 4, 500 (2000). Solid-State NMR as a Probe of Amyloid Fibril Structure.
177. A. Clark, S. B. Charge, M. K. Badman, D. A. MacArthur, and E. J. de Koening, Biochem. Soc. Trans., 24, 594 (1996). Islet Amyloid Polypeptide: Actions and Role in the Pathogenesis of Diabetes.
178. S. B. Prusiner, Science, 252, 245 (1991). Molecular Biology of Prion Disease.
179. D. M. Walsh, D. M. Hartley, Y. Kusumoto, Y. Fezoui, M. M. Condron, A. Lomakin, G. B. Bebdek, D. J. Selkoe, and D. B. Teplow, J. Biol. Chem., 274, 25945 (1999). Amyloid Beta-protein Fibrillogenesis: Structure and Biological Activity of Protofibrillar Intermediates.
180. F. U. Hartl and M. Hayer-Hartl, Science, 295, 1852 (2002). Molecular Chaperones in the Cytosol: From Nascent Chain to Folded Protein.
181. M. Friedel, D. J. Sheeler, and J.-E. Shea, J. Chem. Phys., 118, 8106 (2003). Effects of Confinement and Crowding on the Thermodynamics and Kinetics of Folding of a Minimalist Beta-barrel Protein.
182. B. Ma and R. Nussinov, Protein Sci., 11, 2335 (2002). Molecular Dynamics Simulations of Alanine Rich Beta-sheet Oligomers: Insight into Amyloid Formation.
183. J. Gsponer, U. Haberthur, and A. Caflisch, Proc. Natl. Acad. Sci. USA, 100, 5154 (2003). The Role of Side-chain Interactions in the Early Steps of Aggregation: Molecular Dynamics Simulations of an Amyloid-froming Peptide from the Yeast Prion Sup35.
184. M. Friedel and J.-E. Shea, J. Chem. Phys., 120, 5809 (2004). Self-assembly of Peptides into a Beta-barrel Motif.
185. H. D. Nguyen and C. K. Hall, Proc. Natl. Acad. Sci. USA, 101, 16180 (2004). Molecular Dynamics Simulations of Spontaneous Fibril Formation by Random-Coil Peptides.
186. R. I. Dima and D. Thirumalai, Protein Sci., 11, 1036 (2002). Exploring Protein Aggregation and Self-propagation Using Lattice Models: Phase Diagram and Kinetics.
187. D. K. Klimov and D. Thirumalai, Structure, 11, 295 (2003). Dissecting the Assembly of Aβ 16-22 Amyloid Peptides into Antiparallel β-sheets.
188. F. Massi and J. E. Straub, Proteins, 42, 217 (2001). Energy Landscape Theory for Alzheimer's Amyloid β-peptide Fibril Elongation.
189. A. I. Jewett, A. Baumketner, and J.-E. Shea, Proc. Natl. Acad. Sci. USA, 101, 13192 (2004). Accelerated Folding in the Weak Hydrophobic Environment of a Chaperonin Cavity: Creation of an Alternate Fast Folding Pathway.
190. A. Baumketner, A. I. Jewett, and J.-E. Shea, J. Mol. Biol., 332, 710 (2003). Effects of Confinement in Chaperonin Assisted Protein Folding: Rate Enhancement by Decreasing the Roughness of the Folding Energy Landscape.
191. K. Gulukota and P. G. Wolynes, Proc. Natl. Acad. Sci. USA, 91, 9292 (1994). Statistical Mechanics of Kinetic Proofreading in Protein Folding in Vivo.
192. H. S. Chan and K. A. Dill, Proteins Struct. Funct. Genet., 24, 345 (1996). A Simple Model of Chaperonin-mediated Protein Folding.
193. C. D. Sfatos, A. M. Gutin, V. I. Abkevich, and E. Shakhnovich, Biochemistry, 35, 334 (1996). Simulations of Chaperone-assisted Folding.
194. M. Betancourt and D. Thirumalai, J. Mol. Biol., 287, 627 (1999). Exploring the Kinetic Requirements for Enhancement of Protein Folding Rates in the GroEL Cavity.
195. D. Gorse, Biopolymers, 59, 411 (2001). Global Minimization of an Off-lattice Potential Energy Function Using a Chaperone-based Refolding Method.
196. D. Gorse, Biopolymers, 64, 146 (2002). Application of a Chaperone-based Refolding Method to Two-and Three-dimensional Off-lattice Protein Models.