The energy computation paradox and ab initio protein folding

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Faver, John C ^a   Benson, Mark L ^a   He, Xiao ^a   Roberts, Benjamin P ^a   Wang, Bing ^a   Marshall, Michael S ^b   Sherrill, C David ^b   Merz Jr , Kenneth M ^a  

^a UNIVERSITY OF FLORIDA   (United States)

^b Georgia Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ACCURACY; ARTICLE; CONTROLLED STUDY; PREDICTION; PROBABILITY; PROTEIN FOLDING; PROTEIN STRUCTURE; SCORING SYSTEM; BIOLOGICAL MODEL; CHEMISTRY; METABOLISM; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

PROTEIN;

DATABASES, PROTEIN; MODELS, BIOLOGICAL; PROBABILITY; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 79955552707     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018868     Document Type: Article

References (56)

1. Anfinsen CB, (1961) Influences of 3-Dimensional Configuration on Chemical Reactivity and Stability of Proteins. Journal of Polymer Science 49: 31-49.
2. Dill KA, Ozkan SB, Shell MS, Weikl TR, (2008) The protein folding problem. Annual Review of Biophysics 37: 289-316.
3. Anfinsen CB, (1973) Principles That Govern Folding of Protein Chains. Science 181: 223-230.
4. Sohl JL, Jaswal SS, Agard DA, (1998) Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature 395: 817-819.
5. Baker D, Agard DA, (1994) Kinetics Versus Thermodynamics in Protein-Folding. Biochemistry 33: 7505-7509.
6. Duan Y, Kollman PA, (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282: 740-744.
7. Liwo A, Khalili M, Scheraga HA, (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proceedings of the National Academy of Sciences of the United States of America 102: 2362-2367.
8. Zagrovic B, Snow CD, Shirts MR, Pande VS, (2002) Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology 323: 927-937.
9. Snow CD, Nguyen N, Pande VS, Gruebele M, (2002) Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420: 102-106.
10. Li ZQ, Scheraga HA, (1987) Monte-Carlo-Minimization Approach to the Multiple-Minima Problem in Protein Folding. Proceedings of the National Academy of Sciences of the United States of America 84: 6611-6615.
11. Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA, (2007) The protein folding problem: when will it be solved? Current Opinion in Structural Biology 17: 342-346.
12. Kryshtafovych A, Fidelis K, Moult J, (2009) CASP8 results in context of previous experiments. Proteins-Structure Function and Bioinformatics 77: 217-228.
13. Kim DE, Blum B, Bradley P, Baker D, (2009) Sampling Bottlenecks in De novo Protein Structure Prediction. Journal of Molecular Biology 393: 249-260.
14. Levinthal C, (1968) Are There Pathways for Protein Folding. Journal De Chimie Physique Et De Physico-Chimie Biologique 65: 44-45.
15. Leopold PE, Montal M, Onuchic JN, (1992) Protein Folding Funnels- a Kinetic Approach to the Sequence Structure Relationship. Proceedings of the National Academy of Sciences of the United States of America 89: 8721-8725.
16. Dill KA, Chan HS, (1997) From Levinthal to pathways to funnels. Nature Structural Biology 4: 10-19.
17. Ghosh K, Ozkan SB, Dill KA, (2007) The ultimate speed limit to protein folding is conformational searching. Journal of the American Chemical Society 129: 11920-11927.
18. Levitt M, Lifson S, (1969) Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure. Journal of Molecular Biology 46: 269-&.
19. Dill KA, (1997) Additivity principles in biochemistry. Journal of Biological Chemistry 272: 701-704.
20. Freddolino PL, Liu F, Gruebele M, Schulten K, (2008) Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal 94: L75-L77.
21. Freddolino PL, Park S, Roux B, Schulten K, (2009) Force Field Bias in Protein Folding Simulations. Biophysical Journal 96: 3772-3780.
22. Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, et al. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78: 1950-1958.
23. Bixon M, Lifson S, (1967) Potential Functions and Conformations in Cycloalkanes. Tetrahedron 23: 769-&.
24. Warshel A, Levitt M, Lifson S, (1970) Consistent Force Field for Calculation of Vibrational Spectra and Conformations of Some Amides and Lactam Rings. Journal of Molecular Spectroscopy 33: 84-&.
25. Merz KM, (2010) Limits of Free Energy Computation for Protein-Ligand Interactions. Journal of Chemical Theory and Computation 6: 1769-1776.
26. Faver JC, Benson ML, He X, Roberts BP, Wang B, et al. (2010) Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes. Journal of Chemical Theory and Computation.
27. Taylor JR, (1997) An introduction to error analysis: the study of uncertainties in physical measurements Sausalito, Calif. University Science Books pp. xvii, 327.
28. Helgaker T, Klopper W, Tew DP, (2008) Quantitative quantum chemistry. Molecular Physics 106: 2107-2143.
29. Mark AE, Vangunsteren WF, (1994) Decomposition of the Free-Energy of a System in Terms of Specific Interactions- Implications for Theoretical and Experimental Studies. Journal of Molecular Biology 240: 167-176.
30. Baum B, Muley L, Smolinski M, Heine A, Hangauer D, et al. (2010) Non-additivity of Functional Group Contributions in Protein Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry. Journal of Molecular Biology 397: 1042-1054.
31. Vijaykumar S, Bugg CE, Cook WJ, (1987) Structure of Ubiquitin Refined at 1.8 a Resolution. Journal of Molecular Biology 194: 531-544.
32. Case DA, Darden TA, Cheatham I TE, Simmerling CL, Wang J, et al. (2010) AMBER 11. University of California, San Francisco.
33. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins-Structure Function and Bioinformatics 65: 712-725.
34. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF chimera- A visualization system for exploratory research and analysis. Journal of Computational Chemistry 25: 1605-1612.
35. Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA, (2004) Development and testing of a general amber force field. Journal of Computational Chemistry 25: 1157-1174.
36. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong GM, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry 24: 1999-2012.
37. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP, (1985) AM1: A New General Purpose Quantum Mechanical Molecular Model. J Am Chem Soc 107: 3902-3909.
38. Stewart JJP, (1989) Optimization of Parameters for Semiempirical Methods I. Method. J Comp Chem 10: 209-220.
39. Stewart JJP, (2007) Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements. Journal of Molecular Modeling 13: 1173-1213.
40. Repasky MP, Chandrasekhar J, Jorgensen WL, (2002) PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods. Journal of Computational Chemistry 23: 1601-1622.
41. Korth M, Pitonak M, Rezac J, Hobza P, (2010) A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. Journal of Chemical Theory and Computation 6: 344-352.
42. Grimme S, (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. Journal of Computational Chemistry 27: 1787-1799.
43. Zhao Y, Truhlar DG, (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoretical Chemistry Accounts 120: 215-241.
44. Wang B, Truhlar DG, (2010) Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm. Journal of Chemical Theory and Computation 6: 359-369.
45. Halkier A, Helgaker T, Jorgensen P, Klopper W, Koch H, et al. (1998) Basis-set convergence in correlated calculations on Ne, N-2, and H2O. Chemical Physics Letters 286: 243-252.
46. Molnar LF, He X, Wang B, Merz KM, (2009) Further analysis and comparative study of intermolecular interactions using dimers from the S22 database. Journal of Chemical Physics 131: 065102.
47. Berka K, Laskowski RA, Hobza P, Vondrasek J, (2010) Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins. Journal of Chemical Theory and Computation 6: 2191-2203.
48. Jurecka P, Sponer J, Cerny J, Hobza P, (2006) Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Physical Chemistry Chemical Physics 8: 1985-1993.
49. (2010) Macromodel version 9.8 New York, NY Schrodinger, LLC.
50. Dixon SL, van der Vaart A, Gogonea V, Vincent JJ, Brothers EN, et al. (1999) DIVCON99 The Pennsylvania State University.
51. Stewart JJP, (2008) MOPAC2009 Colorado Springs, CO Stewart Computational Chemistry.
52. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, et al. (2009) Gaussian 09 Wallingford, CT Gaussian, Inc.
53. Werner H-J, Knowles PJ, Lindh R, Manby FR, Schütz M, et al. (2009) MOLPRO. pp.see Available: http://www.molpro.net. Accessed 2010 Apr 05.
54. Kendall RA, Apra E, Bernholdt DE, Bylaska EJ, Dupuis M, et al. (2000) High performance computational chemistry: An overview of NWChem a distributed parallel application. Computer Physics Communications 128: 260-283.
55. Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, et al. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins-Structure Function and Genetics 53: 76-87.
56. Cooper S, Khatib F, Treuille A, Barbero J, Lee J, et al. (2010) Predicting protein structures with a multiplayer online game. Nature 466: 756-760.