Toward correct protein folding potentials

Journal of Biological Physics

Volumn 30, Issue 2, 2004, Pages 171-185

  Chhajer, M ^a   Crippen, G M ^b  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

barnase; decoys; denatured state; protein folding; thermodynamic stability

Indexed keywords

PROTEIN;

MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR STABILITY; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; THERMODYNAMICS; VALIDATION PROCESS;

EID: 4043173536     PISSN: 00920606     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:JOBP.0000035854.68334.dd     Document Type: Review

References (46)

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E.: The Protein Data Bank, Nucl. Acids Res. 28 (2000), 235-242.
2. Chhajer, M. and Crippen, G.M.: A Protein Folding Potential that Places the Native States of a Large Number of Proteins near a Local Minimum, BMC Struct. Biol. 2 (2002), 4.
3. Clementi, C., Vendruscolo, M., Maritan, A. and Domany, E.: Folding Lennard-Jones Proteins by a Contact Potential, Proteins 37 (1999), 544-553.
4. CPLEX Version 6.6. ILOG, Inc. (2000), 〈http://www.ilog.com〉.
5. Crippen, G.M. and Ohkubo, Y.Z.: Statistical Mechanics of Protein Folding by Exhaustive Enumeration, Proteins 32 (1998), 425-437.
6. Crippen, G.M.: Enumeration of Cubic Lattice Walks by Contact Class, J. Chem. Phys. 112 (2000), 11065-11068.
7. Crippen, G.M.: A Gaussian Statistical Mechanical Model for the Equilibrium Thermodynamics of Barnase Folding, J. Mol. Biol. 306 (2001), 565-573.
8. Crippen, G.M.: Constructing Smooth Potential Functions for Protein Folding. J. Mol. Graph. Mod. 19 (2001), 87-93.
9. Dill, K.A., Phillips, A.T. and Rosen, J.B.: Protein Structure and Energy Landscape Dependence on Sequence using a Continuous Energy Function, J. Comput. Biol. 4 (1997), 227-239.
10. Dombkowski, A.A. and Crippen, G.M.: Disulfide Recognition in an Optimized Threading Potential, Protein Enging. 13 (2000), 679-689.
11. Freund, S.M.V., Wong, K.-B. and Fersht, A.R.: Initiation Sites of Protein Folding by NMR Analysis, Proc. Natl. Acad. Sci. USA 93 (1996), 10600-10603.
12. Godzik. A., Kolnski, A. and Skolnick, J.: Are Proteins Ideal Mixtures of Amino Acids? Analysis of Energy Parameter Sets, Protein Sci. 4 (1995), 2107-2117.
13. Goldstein, R.A., Luthey-Shulten, Z. and Wolynes, P.G.: Protein Tertiary Structure Recognition using Optimized Hamiltonians with Local Interactions, Proc. Natl. Acad. Sci. USA 89 (1992), 9029-9033.
14. Guerois, R., Nielsen, J.E. and Serrano, L.: Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of more than 1000 Mutations, J. Mol. Biol. 320 (2002), 369-387. 〈http://fold-x.embl- heidelberg.de〉
15. Hammerstrom, P. and Carlsson, U.: Is the Unfolded State the Rosetta Stone of the Protein Folding Problem?, Biochem. Biophys. Res. Commun. 276 (2000), 393-398.
16. Hinds, D.A. and Levitt, M.: Exploring Conformational Space with a Simple Lattice Model for Protein Structure, J. Mol. Biol. 243 (1994), 668-682.
17. Huang, E.S., Subbiah, S., Tsai, J. and Levitt, M.: Using a Hydrophobic Contact Potential to Evaluate Native and Near-Native Folds Generated by Molecular Dynamics Simulations, J. Mol. Biol. 257 (1996), 716-725.
18. Kabsch, W.: A Discussion of the Solution of the Best Rotation to relate Two Sets of Vectors, Acta Cryst. A34 (1978), 827-828.
19. Kocher, J.-P.A., Rooman, M.J. and Wodak, S.J.: Factors Influencing the Ability of Knowledge-Based Potentials to Identify Native Sequence-Structure Matches, J. Mol. Biol. 235 (1994), 1598-1613.
20. Lazaridis, T. and Karplus, M.: Effective Energy Functions for Protein Structure Prediction, Curr. Opin. Struct. Biol. 10 (2000), 139-145.
21. Maiorov, V.N. and Crippen, G.M.: Contact Potential that Recognizes the Correct Folding of Globular Proteins, J. Mol. Biol. 227 (1992), 876-888.
22. Maiorov, V.N. and Crippen, G.M.: Size-Independent Comparison of Protein 3-Dimensional Structures, Proteins 22 (1995), 273-283.
23. Micheletti, C., Seno, F., Banavar, J.R. and Maritan, A.: Learning Effective Amino Acid Interactions through Interactive Stochastic Techniques, Proteins 42 (2001), 422-431.
24. Mirny, L.A. and Shakhnovich, E.I.: How to Derive a Protein Folding Potential? A New Approach to an Old Problem, J. Mol. Biol. 264 (1996), 1164-1179.
25. Miyazawa, S. and Jernigan, R.L.: Estimation of Effective Contact Energies from Protein Crystal Structures: Quasi-Chemical Approximation, Macromolecules 18 (1985), 534-552.
26. Miyazawa, S. and Jernigan, R.L.: Residue-Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term, for Simulation and Threading, J. Mol. Biol. 256 (1996), 623-644.
27. Ohkubo, Y.Z. and Crippen, G.M.: Potential Energy Function for Continuous State Model of Globular Proteins, J. Comput. Biol. 7 (2000), 363-379.
28. Park, B. and Levitt, M.: Energy Functions that Discriminate X-ray and Near Native Folds from Well-Constructed Decoys, J. Mol. Biol. 258 (1996), 367-392.
29. Park, B.H., Huang, E.S. and Levitt, M.: Factors Affecting the Ability of Energy Functions to Discriminate Correct from Incorrect Folds, J. Mol. Biol. 266 (1997), 831-846.
30. Park, K., Vendruscolo, M. and Domany, E.: Towards an Energy Function for the Contact Map Representation of Proteins, Proteins 40 (2000), 237-248.
31. Reith, D., Huber, T., Muller-Plathe, F. and Torda, A.E.: Free Energy Approximations in Simple Lattice Proteins, J. Chem. Phys. 114 (2001), 4998-5005.
32. Samudrala, R. and Moult, J.: An All-Atom Distance Dependent Conditional Probability Discriminatory Function for Protein Structure Prediction, J. Mol. Biol. 275 (1998), 895-916.
33. Serrano, L., Kellis, J.T., Cann, P., Matouschek, A. and Fersht A.R.: The Folding of an Enzyme II. Substructure of Bamase and the Contribution of Different Interactions to Protein Stability, J. Mol. Biol. 224 (1992), 783-804.
34. Shakhnovich, E.I.: Proteins with Selected Sequences Fold into Unique Native Conformation, Phys. Rev. Lett. 72 (1994), 3907-3910.
35. Shanno, D.F. and Phua, K.H.: Remark on Algorithm 500: Minimization of Unconstrained Multi-Variate Function [E4], ACM Trans. Math. Software 6 (1980), 618-622.
36. Sippl, M.J.: Boltzmann's Principle, Knowledge-Based Mean Fields and Protein Folding. An Approach to the Computational Determination of Protein Structures, J. Comput-Aided Mol. Design 7 (1993), 473-501.
37. Skolnick, J., Jaroszewski, L., Kolinski, A. and Godzik A.: Derivation and Testing of Pair Potentials for Protein Folding. When is the Quasichemical Approximation Correct?, Protein Sci. 6 (1997), 676-688.
38. Takei, J., Chu, R.-A. and Bai, Y.: Absence of Stable Intermediates on the Folding Pathway of Barnase, Proc. Natl. Acad. Sci. USA 97 (2000), 10796-10801.
39. Thomas, P.D. and Dill, K.A.: An Interactive Method for Extracting Energy-like Quantities from Protein Structure, Proc. Natl. Acad Sci. USA 93 (1993), 11628-11633.
40. Thomas, P.D. and Dill, K.A.: Statistical Potentials Extracted from Protein Structures: How Accurate are They?, J. Mol. Biol. 257 (1996), 457-469.
41. Tobi, D. and Elber, R.: Distance-Dependent, Pair Potential for Protein Folding: Results from Linear Optimization, Proteins 41 (2000), 40-46.
42. Tobi, D., Shafran, G., Linial, N. and Elber, R.: On the Design and Analysis of Protein Folding Potentials, Proteins 40 (2000), 71-85.
43. Vendruscolo, M. and Domany, E.: Pairwise Contact Potentials are Unsuitable for Protein Folding, J. Chem. Phys. 109 (1998), 11101-11108.
44. Vendruscolo, M., Najmanovich, R. and Domany, E.: Can a Pairwise Contact Potential Stabilize Native Protein Folds against Decoys Obtained by Threading?, Proteins 38 (2000), 134-148.
45. Wang, Y., Zhang, H., Li, W. and Scott, R.A.: Discriminating Compact Nonnative Structures from the Native Structure of Globular Proteins, Proc. Natl. Acad. Sci. USA 92 (1995), 709-713.
46. Zagrovic, B., Snow, C.D., Shirts, M.R. and Pande, V.S.: Simulation of Folding of a Small Alpha-Helical Protein in Atomistic Detail using Worldwide-Distributed Computing, J. Mol. Biol. 323 (2002), 927-937.