Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix

Proteins: Structure, Function and Genetics

Volumn 49, Issue 3, 2002, Pages 403-412

  Li, Hao ^a   Tang, Chao ^a   Wingreen, Ned S ^a  

^a NEC LABORATORIES AMERICA   (United States)

Author keywords

Alphabet; Designability; Lattice models; Miyazawa Jernigan matrix; Protein folding; Statistical potential

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; CRYSTAL STRUCTURE; HYDROPHOBICITY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THERMODYNAMICS;

AMINO ACIDS; HYDROPHOBICITY; MODELS, THEORETICAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; THERMODYNAMICS;

EID: 0037110580     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10239     Document Type: Article

References (46)

1. Anfinsen C. Principles that govern the folding of protein chains. Science 1973;181:223-230.
2. Richardson JS. Handedness of crossover connections in β-sheets. Proc Natl Acad Sci USA 1976;73:2619-2623.
3. Richardson JS. The anatomy and taxonomy of protein structures. Adv Protein Chem 1981;34:167-339.
4. Levitt M, Chothia C. Structural patterns in globular proteins. Nature 1976;261:552-558.
5. Chothia C. One thousand families for the molecular biologist. Nature 1992;357:543-544.
6. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: A structural classification of protein database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
7. Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature 1994;372:631-634.
8. Finkelstein AV, Ptitsyn OB. Why do globular proteins fit the limited set of folding patterns? Prog Biophys Mol Biol 1987;50:171-190.
9. Finkelstein AV, Gutin AM, Badretdinov AY. Why are the same protein folds used to perform different functions? FEBS Lett 1993;325:23-28.
10. Finkelstein AV, Badretdinov AY, Gutin AM. Why do protein architectures have Boltzmann-like statistics? Proteins 1995;23: 142-150.
11. Yue K, Dill KA. Forces of tertiary structural organization in globular proteins. Proc Natl Acad Sci USA 1995;92:146-150.
12. Govindarajan S, Goldstein RA. Searching for foldable protein structures using optimized energy functions. Biopolymers 1995;36: 43-51.
13. Govindarajan S, Goldstein RA. Why are some protein structures so common? Proc Natl Acad Sci USA 1996;93:3341-3345.
14. Li H, Helling R, Tang C, Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science 1996;273: 666-669.
15. Li H, Tang C, Wingreen NS. Are protein folds atypical? Proc Natl Acad Sci USA 1998;95:4987-4990.
16. Mélin R, Li H, Wingreen NS, Tang C. Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study. J Chem Phys 1999;110:1252-1262.
17. Tang C. Simple models of the protein folding problem. Physica A 2000;288:31-48.
18. Wang T, Miller J, Wingreen NS, Tang C, Dill KA. Symmetry and designability for lattice protein models. J Chem Phys 2000;113: 8329-8336.
19. Cejtin H, Edler J, Gottlieb A, Helling R, Li H, Philbin J, Wingreen N, Tang C. Fast tree search for enumeration of a lattice model of protein folding. J Chem Phys 2002;116:352-359.
20. Miller J, Zeng C, Wingreen NS, Tang C. Emergence of highly- designable protein-backbone conformations in an off-lattice model. Proteins 2002;47:506-512.
21. Borman S. Protein folding model focuses on "designability." Chem Eng News 1996;74:36.
22. Shakhnovich EI. Protein design: A perspective from simple tractable models. Fold Design 1998;3:R45-R58.
23. Buchler NEG, Goldstein RA. Effect of alphabet size and foldability requirements on protein structure designability. Proteins 1999;34: 113-124.
24. Buchler NEG, Goldstein RA. Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus. J Chem Phys 2000;112:2533-2547.
25. Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 1985;18:534-552.
26. Li H, Tang C, Wingreen NS. Nature of driving force for protein folding: A result from analyzing the statistical potential. Phys Rev Lett 1997;79:765-768.
27. Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996;256: 623-644.
28. Miyazawa S, Jernigan RL. Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins 1999;34:49-68.
29. Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
30. Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Optimal protein-folding codes from spin-glass theory. Proc Natl Acad Sci USA 1992;89:4918-4922.
31. Shakhnovich EI, Gutin AM. Enumeration of all compact conformations of copolymers with random sequence of links. J Chem Phys 1990;93:5967-5971.
32. Shakhnovich EI, Gutin AM. Implications of thermodynamics of protein folding for evolution of primary sequences. Nature 1990; 346:773-775.
33. Sali A, Shakhnovich E, Karplus M. How does a protein fold. Nature 1994;369:248-251.
34. Klimov DK, Thirumalai D. Factors governing the foldability of proteins. Proteins 1996;26:411-441.
35. Shahrezaei V, Ejtehadi MR. Geometry selects highly designable structures. J Chem Phys 2000;113:6437-6442.
36. Lau KF, Dill KA. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules 1989;22:3986-3997.
37. Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH. Protein design by binary patterning of polar and nonpolar amino acids. Science 1993;262:1680-1685.
38. Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D. Functional rapidly folding proteins from simplified amino acid sequences. Nature Struct Biol 1997;4:805-809.
39. Wolynes PG. As simple as can be? Nature Struct Biol 1997;4:871-874.
40. Wang J, Wang W. A computational approach to simplifying the protein folding alphabet. Nature Struct Biol 1999;6:1033-1038.
41. Chan HS. Folding alphabets. Nature Struct Biol 1999;6:994-996.
42. Skorobogatiy M, Guo H, Zuckermann MJ. A deterministic approach to protein design problem. Macromolecules 1997;30:3403-3410.
43. Ejtehadi MR, Hamedani N, Seyed-Allaei H, Shahrezaei V, Yahyanejad M. Stability of preferable structures for a hydrophobic-polar model of protein folding. Phys Rev E 1998;57:3298-3301.
44. Ejtehadi MR, Hamedani N, Seyed-Allaei H, Shahrezaei V, Yahyanejad M. Highly designable protein structures and inter-monomer interactions. J Phys A 1998;31:6141-6155.
45. Ejtehadi MR, Hamedani N, Shahrezaei V. Geometrically reduced number of protein ground state candidates. Phys Rev Lett 1999;82: 4723-4726.
46. Kussell EL, Shakhnovich EI. Analytic approach to the protein design problem. Phys Rev Lett 1999;83:4437-4440.