Self-consistently optimized statistical mechanical energy functions for sequence structure alignment

Protein Science

Volumn 5, Issue 6, 1996, Pages 1043-1059

  Koretke, K K ^a   Luthey Schulten, Z ^a   Wolynes, P G ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

homologous modeling; protein sequence alignment; protein structure prediction; statistical mechanical energy functions

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DATA BASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; STRUCTURE ACTIVITY RELATION;

EID: 0029895539     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050607     Document Type: Article

References (52)

1. Abad-Zapaiero C, Griffith J, Sussman J, Rossmann M. 1987. Refined crystal structure of dogfish m4 apo-lactace dehydrogenase. J Mol Biol 198:445.
2. Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J. 1987. Protein Data Bank, in: Allen FH, Bergerhoff G, Sievers R, eds. Crystallographic databases - Information content, software systems, scientific applications. Bonn/Cambridge/Chester: Data Commission of the International Union of Crystallography, pp 107-132.
3. Antholine W, Kastrau D, Steffens G, Buse G, Zumft W, Kroneck P. 1992. A comparative epr investigation of the multicopper proteins nitrous-oxide reductase and cytochrome-c oxidase. Eur J Biochem 209:875-881.
4. Bairoch A, Boeckmann B. 1994. Nucleic Acid Res 22:3578-3580
5. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kermard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
6. Bolin J, Filman D, Mathhews D, Hamlin R, Kraut J. 1982. Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 angstroms resolution. J Biol Chem 257:13650.
7. Bowie J, Luthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-112.
8. Brünger AT. 1987. X-PLOR version 3.1. A system for X-ray crystallography and WMR. New Haven, Connecticut: Yale University Press.
9. Bryngelson J, Onuchic J, Socci N, Wolynes P. 1995. Funnels, pathways and the energy landscape of protein folding: A synthesis. Proteins Struct Funct Genet 27:167-195.
10. Bryngelson J, Wolynes P. 1987. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 84:7524-7528.
11. Church W, Guss J, Potter J, Freeman H. 1986. The crystal structure of mercury-substituted poplar piasiocyanin at 1.9 angstroms resolution. J Biol Chem 267:234.
12. Dill K, Bromberg S, Yue K, Fiebig K, Yee D, Thomas P, Chan H. 1995. Principles of protein folding - A perspective from simple exact models. Protein Sci 4:561-602.
13. Dill K, Stigter D. 1995. Modeling protein stability as heteropolymer collapse, vol 46. New York: Academic Press, Inc. pp 59-104.
14. Epp O, Lattman E, Schiffer M, Huber R, Palm W. 1975. The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein rei refined at 2.0 angstroms resolution. Biochemistry 14:4943.
15. Farrar J, Lappalamen P, Saraste M, Thomson A. 1995. Spectroscopic and mutagenesis studies on the cu-a centre from the cytochrome-c oxidase complex of Paracoccus denitrificans. Eur J Biochem 232:294-303.
16. Ferrin TE, Huang CC, Jarvis LE, Langridge R. 1988. The midas display system. J Mol Graphics 6:13-27.
17. Garrett T, Saper M, Bjorkman P, Strominger J, Wiley D. 1989. Specificity pockets for the side chains of peptide antigens m hla-aw68. Nature 342:692.
18. Godzik A, Kolinski A, Skolnick J. 1992. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 227:227-238.
19. Goldstein R, Luthey-Schulten Z, Wolynes P. 1992a. Optimal protein-folding codes from spin-glass theory. Proc Natl Acad Sci USA 89(11):4918-4922.
20. Goldstein R, Luthey-Schulten Z, Wolynes P. 1992b Protein tertiary structure recognition using optimized hamiltonians with local interactions. Proc Natl Acad Sci USA 89:9029-9033.
21. Goldstein R, Luthey-Schulten Z, Wolynes P. 1994. A Bayesian approach to sequence structure alignment algorithms for protein structure recognition. In: Proceedings of the 27th Hawaii International Conference on System Sciences. Los Alamitos, California: IEEE Computer Society P'ress. pp 306-315.
22. Goldstein R, Luthey-Schulten Z, Wolynes P. 1995. The statistical mechanical basis of sequence alignment algorithms for protein structure recoginition. In: Elber R, ed. New developments in theoretical studies of proteins. Singapore: World Scientific.
23. Gribskov, Burgess. 1986. Sigma factors from E. coli, B. subtilis, phage sp01 and phage t4 are homologous proteins. Nucleic Acids Res 14(16):6745-6763.
24. Han J, Adman E, Beppu T. 1991. Resonance ramon spectra of plastocyanin and pseudoazurin: Evidence for conserved cysteine ligand conformation in cupredoxins (blue copper proteins). Biochemistry 30:1-904-13.
25. Holmgren A, Soderberg BO, Eklund H, Branden CI. 1990. Crystal structure of thioredoxin from Escherichia coli at 1.68 angstroms resolution. J Mol Biol 212:161.
26. Iwata S, Ostermeier C, Ludwig B, Michel H. 1995. Structure at 2.8 angstroms resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 570:660-669.
27. Ji X, Sesay MA, Dickert L, Prassad SM, Johnson WW, Ammon HL, Armstrong RN, Gilliland GL. 1994. Structure and function of the xenobiotic substrate binding site of a glutathione S-transferase as revealed by X-ray crystallographic analysis of product complexes with the diastereomers of 9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene. Biochemistry 33:I043.
28. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2571-2631.
29. Kelly M, Lappalamen P, Talbo G, Haltia T, van der Oost J, Saraste M. 1993. Two cysteines, two histidines and one methionine are ligands of a binuclear purple copper center. J Biol Chem 268:16781-16787.
30. Maiorov V, Crippen G. 1994. Learning about protein folding via potential functions. Proteins Struct Funct Genet 20:167-173.
31. Mathews F, Bethge P, Czerwinski E. 1975. The structure of cytochrome b562 from Escherichia coli at 2.5 angstroms resolution. J Biol Chem 254:1699.
32. McTigue M, Davies J, Kaufman B. 1993. Crystal structure of chicken liver dihydrofolate reductase complexes with nadp+ and bipterin. Biochemistry 32:6855-6862.
33. McTigue MA, Bernstein SL, Williams DR, Tainer JA. 1995. Purification and crystallization of a schistosomal glutathione S-transferase. Proteins Struct Funct Genet 22:55-57.
34. Miyazawa S, Jernigan RL. 1985. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 15:534-552.
35. Murzin A, Brenner SE, Hubbard TJP, Chothia C. 1995. Scop - Structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
36. Needleman S, Wunsch C. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48.443-453.
37. Nishikawa K, Matsuo Y. 1993. Development of pseudoenergy potentials for assessing protein 3-d-1-d compatibility and detecting weak homologies. Protein Eng 6(8):811-820.
38. Padian E, Silvenon E, Sheriff S, Cohen G, Smith-Gill S, Davies D. 1989. Structure of an antibody-antigen complex. Crystal structure of the hy/hel-10 fab-lysozyme complex. Proc Natl Acad Sci USA 56:5938.
39. Quiocho F, Vyas N. 1984. Novel stereospecificity of L-arabinose-binding protein. Nature 310:381-386.
40. Richards FM. 1977. Areas, volumes, packing, and protein structure. Annu Rev Biophys Bioeng 5:151-176.
41. Sasai M, Wolynes P. 1990. Molecular theory of associative memory hamiltonian models of protein folding. Phys Rev Lett 65:2740-2743.
42. Sippl M. 1993. Boltzmann principle, knowledge-based mean fields and protein folding - An approach to the computational determination of protein structures. J Comput-Aided Mol Design 7(4):473-501.
43. Smith W, Burnett R, Darling G, Ludwig M. 1977. Structure of the semiquinone form of flavodoxin from Clostridium sp. extension of 1.8 angstroms resolution and some comparisons with the oxidized state and reduced forms. J Mol Biol 117:195.
44. Srinivasan R, Rose G. 1995. Linus: A hierarchic procedure to predict the fold of a protein. Proreins Struct Funct Genet 22:81-99.
45. Steffens G, Soulimane T, Wolff G, Buse G. 1993. Stoichiometry and redox behavior of metals in cytochrome c oxidase. Eur J Biochem 213:1149-1157.
46. Stenkamp R, Sieker L, Jensen L, McQueen J. 1978. Structure of methhemerythnn at 2.8 antgstroms resolution. Computer graphics fit of an averaged electron density map. Biochemistry 77:2499.
47. Takano T. 1977. Structure of myoglobin refined at 2.0 angstroms resolution. Structure of deoxymyoglobin from sperm whale. J Mol Biol 110:569.
48. van der Cost J et al. 1992. EMBO J 11:3209-3217.
49. Vyas NK, Vyas MN, Quiocho FA. 1988. Surgar and signal transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242:1290.
50. Watenpaugh K, Sieker L, Jensen L, Legall J, Dubourdieu M. 1972. Structure of the oxidized form of a flavodoxin at 2.5-angstroms resolution. Resolution of the phase ambiguity by anomalous scattering. Proc Natl Acad Sci USA 59:3185.
51. Weber P, Bartsch R, Cusanovich M, Hamlin R, Howard A, Jordan S, Kamen M, Meyer T, Weatherford D, Xuong N, Salemme F. 1980. Structure of cytochrome c prime. A dimeric, high-spin haem protein. Nature 286:302.
52. Zuker M. 1991. Suboptimal sequence alignment in molecular biology alignment with error analysis. J Mol Biol 221(2):403.