Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease

Biophysical Journal

Volumn 85, Issue 2, 2003, Pages 853-863

  Kurt, Nese ^a   Haliloglu, Turkan ^a   Schiffer, Celia A ^b,c  

^a BOGAZICI UNIVERSITY   (Turkey)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; PEPTIDE DERIVATIVE; POL PROTEIN; PROTEINASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; DRUG TARGETING; DYNAMICS; ENERGY; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME SPECIFICITY; ENZYME SUBSTRATE; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SEQUENCE HOMOLOGY;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0042344862     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74525-1     Document Type: Article

References (26)

1. Altuvia, Y., O. Schueler, and H. Margalit. 1995. Ranking potential binding peptides to MHC molecules by a computational threading approach. J. Mol. Biol. 249:244-250.
2. Altuvia, Y., A. Sette, J. Sidney, S. Southwood, and H. Margalit. 1997. A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets. Hum. Immunol. 58:1-11.
3. Ayers, D. J., P. R. Gooley, A. W. Cooper, and A. E. Torda. 1999. Enhanced protein fold recognition using secondary structure information from NMR. Protein Sci. 8:1127-1133.
4. Bahar, I., B. Erman, T. Haliloglu, and R. L. Jernigan. 1997b. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry. 36:13512-13532.
5. Bahar, I., M. Kaplan, and R. L. Jernigan. 1997a. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins. 29:292-308.
6. Bahar, I., and R. L. Jernigan. 1997. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separations. J. Mol. Biol. 266:195-214.
7. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
8. Bernstein, F. C., T. F. Koetzle, G. J. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
9. Chou, K. C. 1996. Prediction of human immunodeficiency virus protease cleavage sites in proteins. Anal. Biochem. 233:1-14.
10. Covell, D. G., and R. L. Jernigan. 1990. Conformations of folded proteins in restricted spaces. Biochemistry. 29:3287-3294.
11. Goldstein, R. A., Z. A. Luthey-Schulten, and P. G. Wolynes. 1992. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc. Natl. Acad. Sci. USA. 89:9029-9033.
12. Haliloglu, T., and I. Bahar. 1998. Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin. Proteins. 31:271-281.
13. Haliloglu, T. 1999. Characterization of internal motions of Escherichia coli ribonuclease H by Monte Carlo simulation. Proteins. 34:533-539.
14. Jernigan, R., and I. Bahar. 1996. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6:195-209.
15. Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
16. Keskin, O., and I. Bahar. 1998. Packing of sidechains in low-resolution models for proteins. Fold. Des. 3:469-479.
17. Kurt, N., and T. Haliloglu. 1999. Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations. Proteins. 37:454-464.
18. Madden, D. R., D. N. Garboczi, and D. C. Wiley. 1993. The antigenic identity of peptide/MHC complexes, a comparison of the conformations of five viral peptides presented by HLA-A2. Cell. 75:693-708.
19. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. J. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
20. Miyazawa, S., and R. L. Jernigan. 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.
21. Prabu-Jeyabalan, M., E. Nalivaika, and C. A. Schiffer. 2002. Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure. 10:369-381.
22. Prabu-Jeyabalan, M., E. Nalivaika, and C. A. Schiffer. 2000. How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J. Mol. Biol. 301:1207-1220.
23. Rost, B., R. Schneider, and C. Sander. 1997. Protein fold recognition by prediction-based threading. J. Mol. Biol. 270:471-480.
24. Russell, R. B., R. R. Copley, and G. J. Barton. 1996. Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259:349-365.
25. Schueler-Furman, O., Y. Altuvia, S. Alessandro, and H. Margalit. 2000. Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles. Protein Sci. 9:1838-1846.
26. Sippl, M. J. 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.