Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of β-sheet formation in proteins

Protein Science

Volumn 8, Issue 2, 1999, Pages 326-342

  Zhu, Hongyao ^a   Braun, Werner ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Self correcting distance geometry calculations; Statistical potentials; Tertiary structure; strand alignment recognition; strand pairing

Indexed keywords

APROTININ; TRIPEPTIDE; TRYPSIN INHIBITOR;

AMINO ACID SEQUENCE; ARTICLE; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

EID: 0033003903     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.2.326     Document Type: Article

References (50)

1. Beasley JR, Hecht MH. 1997. Protein design: The choice of de novo sequences. J Biol Chem 272:2031-2034.
2. Bernstein FC, Koetzle TF, Williams GJ, Meyer EFJ, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur J Biochem 80:319-324.
3. Bowie JU, Luthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170.
4. Bryant SH, Lawrence CE. 1991. The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions. Proteins 9:108-119.
5. Bryant SH, Lawrence CE. 1993. An empirical energy function for threading protein sequence through the folding motif. Proteins 16:92-112.
6. Chou PY, Fasman GD. 1978. Empirical predictions of protein conformation. Ann Rev Biochem 47:251-276.
7. Creighton TE, Darby NJ, Kemmink J. 1996. The roles of partly folded intermediates in protein folding. FASEB J 10:110-118.
8. Dahiyat BI, Mayo SL. 1997. De novo protein design: Fully automated sequence selection. Science 278:82-87.
9. Finkelstein AV, Badretdinov AY, Gutin AM. 1995. Why do protein architectures have Boltzmann-like statistics? Proteins 23:142-150.
10. Finkelstein AV, Gutun AM, Badretdinov AY. 1993. Why are the same protein folds used to perform different functions? FEBS Lett 325:23-28.
11. Finkelstein AV, Reva BA. 1996. Search for the most stable folds of protein chains: I. Application of a self-consistent molecular field theory to a problem of protein three-dimensional structure prediction. Protein Eng 9:387-397.
12. Godzik A, Kolinski A, Skolnick J. 1992. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 227:227-238.
13. Hänggi G, Braun W. 1994. Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin. FEBS Lett 344:147-153.
14. Harrison PM, Sternberg MJE. 1996. The disulphide β-cross: From cystine geometry and clustering to classification of small disulphide-rich protein folds. J Mol Biol 264:603-623.
15. Hecht MH. 1994. De novo design of β-sheet proteins. Proc Natl Acad Sci USA 91:8729-8730.
16. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
17. Kamimura M, Takahashi Y. 1994. Phi-psi conformational pattern clustering of protein amino acid residues using the potential function method. CABIOS 10:163-169.
18. Kim CA, Berg JM. 1993. Thermodynamic β-sheet propensities measured using a zinc-finger host peptide. Nature 362:267-270.
19. Kim CA, Berg JM. 1996. A 2.2 A resolution crystal structure of a designed zinc-finger protein bound to DNA. Nature Struct Biol 3:940-945.
20. Kocher JP, Rooman MJ, Wodak SJ. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235:1598-1613.
21. Levitt M. 1978. Conformational preferences of amino acids in globular proteins. Biochemistry 17:4277-4285.
22. Lifson S, Sander C. 1980. Specific recognition in the tertiary structure of betasheets of proteins. J Mol Biol 139:627-639.
23. Maiorov VN, Crippen GM. 1992. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 227:876-888.
24. Minor DLJ, Kim PS. 1994a. Measurement of the β-sheet-forming propensities of amino acids. Nature 367:660-663.
25. Minor DLJ, Kim PS. 1994b. Context is a major determinant of β-sheet propensity. Nature 371:264-267.
26. Mirny LA, Shakhnovich EI. 1996. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 264:1164-1179.
27. Miyazawa S, Jernigan RL. 1985. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
28. Miyazawa S, Jernigan RL. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-644.
29. Mumenthaler C, Braun W. 1995. Predicting the helix packing of globular proteins by self-correcting distance geometry. Protein Sci 4:863-871.
30. Munoz V, Serrano L. 1994. Intrinsic secondary structure propensities of the amino acids, using statistical φ-ψ matrices: Comparison with experimental scales. Proteins 20:301-311.
31. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
32. Orengo CA, Flores TP, Taylor WR, Thornton JM. 1993. Identification and classification of protein fold families. Protein Eng 6:485-500.
33. Otzen DE, Fersht AR. 1995. Side-chain determinants of β-sheet stability. Biochemistry 34:5718-5724.
34. Park B, Levitt M. 1996. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 258:367-392.
35. Reva BA, Finkelstein AV. 1996. Search for the most stable folds of protein chains: II. Computation of stable architectures of β-proteins using a self-consistent molecular field theory. Protein Eng 9:399-411.
36. Richardson JS. 1981. The anatomy and taxonomy of protein structure. Adv Protein Chem 34:167-339.
37. Seckler R, Jaenicke R. 1992. Protein folding and protein refolding. FASEB J 6:2545-2554.
38. Sippl MJ. 1990. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213:859-883.
39. Sippl MJ. 1993. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput-Aid Mol Des 7:473-501.
40. Sippl MJ. 1995. Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229-235.
41. Skolnick J, Jaroszewski L, Kolinski A, Godzik A. 1997. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 6:676-688.
42. Smith CK, Regan L. 1995. Guidelines for protein design: The energetics of beta sheet side chain interactions. Science 270:980-982.
43. Smith CK, Regan L. 1997. Construction and design of β-sheets. Acc Chem Res 30:153-161.
44. Smith CK, Withka JM, Regan L. 1994. A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 33:5510-5517.
45. Tanaka S, Scheraga HA. 1976. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structure proteins. Macromolecules 9:945-950.
46. Widmer H, Widmer A, Braun W. 1993. Extensive distance geometry calculations with different NOE calibrations. New criteria for structure selection applied to Sandostatin and BPTI. J Biomol NMR 3:307-324.
47. Williams RW, Chang A, Juretic D, Loughran S. 1987. Secondary structure predictions and medium range interactions. Biochim Biophys Acta 916:200-204.
48. Wouters MA, Curmi PM. 1995. An analysis of side chain interactions and pair correlations within antiparallel β-sheets: The differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs. Proteins 22:119-131.
49. Wüthrich K, Wagner G, Richarz R, Braun W. 1980. Correlation between internal mobility and stability of globular proteins. Biophys J 32:549-560.
50. Yang AS, Honig B. 1995. Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets. J Mol Biol 252:366-376.