Predicting protein structure from long-range contacts

Biophysical Chemistry

Volumn 105, Issue 1, 2003, Pages 11-21

  Chen, Jin ^a   Zhang, Linxi ^a   Jing, Li ^a   Wang, Youxing ^a   Jiang, Zhouting ^a   Zhao, Delu ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b INSTITUTE OF CHEMISTRY   (China)

Author keywords

Protein structural class; Protein structure; Short range and long range contact

Indexed keywords

AMINO ACID; ARGININE; ASPARAGINE; ASPARTIC ACID; CYSTEINE; GLUTAMIC ACID; GLUTAMINE; ISOLEUCINE; LYSINE; PHENYLALANINE; PROTEIN; TRYPTOPHAN; TYROSINE; VALINE;

ARTICLE; CALCULATION; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 0043161980     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(03)00033-4     Document Type: Article

References (22)

1. Tanaka S., Scheraga H.A. Model of protein folding: inclusion of short-, medium-, and long-range interactions. Proc. Natl. Acad. Sci. 72:1975;3802-3805.
2. Bahar I., Kaplan M., Jernigan R.L. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins. 29:1997;292-308.
3. Zhang C., Cornette J.L., Delisi C. Consistency in structural energetics of protein folding and peptide recognition. Protein Sci. 6:1997;1057-1064.
4. Gottfried D.S., Haas E. Nonlocal interactions stabilize compact folding intermediates in reduced unfolded bovine pancreatic trypsin inhibitor. Biochemistry. 31:1992;12353-12362.
5. Gromiha M.M., Selvaraj S. Influence of medium and long range contacts in TIM barrel proteins. J. Biol. Phys. 23:1997;209-217.
6. Gromiha M.M., Selvaraj S. Importance of long range interactions in protein folding. Biophys. Chem. 77:1999;49-68.
7. Gromiha M.M., Selvaraj S. Important amino acid properties for determining the transition state structures of two-state protein mutants. FEBS Lett. 526:2002;129-134.
8. Gromiha M.M., Selvaraj S. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long range order to folding rate prediction. J. Mol. Biol. 310:2001;27-32.
9. Levitt M., Chothia C. Structural patterns in globular proteins. Nature. 261:1976;552-554.
10. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Brice M.D., Rodgers J.R., et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
11. Hubbard T.J.P., Ailey B., Brenner S.E., Murzin A.G., Chothia C. SCOP: a structural classification of proteins database. Nucl. Acids Res. 27:1999;254-257.
12. Orengo C.A., Pearl F.M.G., Bray J.E., Todd A.E., Martin A.C., Loconte L., et al. The CATH database provides insights into protein structure/function relationships. Nucl. Acids Res. 27:1999;275-279.
13. Gromiha M.M. Prediction of secondary structures in globular and membrane proteins. Recent Res. Dev. Protein Eng. 2:2001;161-178.
14. Gromiha M.M., Selvaraj S. Inter-residue interactions in the structure, folding and stability of proteins. Recent Res. Dev. Biophys. Chem. 1:2000;1-14.
15. Miyazawa S., 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.
16. Miyazawa S., Jernigan R.L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:1985;534-552.
17. Crippen G.M., Kollman P.A. Distance geometry methods for protein structure calculations. Biopolymers. 18:1979;939-957.
18. Zhouting J., Linxi Z., Jin C., Agen X., Delu Z. Effect of amino acid on forming residue-residue contacts in proteins. Polymer. 43:2002;6037-6047.
19. Kamtekar S., Schiffer J.M., Xiong H., Babik J.M., Hecht M. Protein design by binary patterning of polar and nonpolar amino acids. Science. 262:1993;1680-1682.
20. Lau K.F., Dill K.A. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules. 22:1989;3986-3997.
21. Dill K.A., Bromberg S., Yue S., Fiebig K., Yee K.M., Thomas D.P., et al. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4:1995;561-602.
22. Fauchere J.L., Pliska V. Hydrophobic parameters of amino acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. 18:1983;369-375.