Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK

Proteins: Structure, Function and Genetics

Volumn 40, Issue 2, 2000, Pages 185-192

  Kasper, Patrik ^a   Christen, Philipp ^a   Gehring, Heinz ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

DnaK; Energy calculation of peptide binding; Molecular dynamics simulations; Poisson Boltzmann electrostatics; Protein peptide interactions

Indexed keywords

CHAPERONE; PROTEIN DNAK;

ARTICLE; BINDING AFFINITY; CALCULATION; COMPLEX FORMATION; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

BINDING SITES; ENTROPY; ESCHERICHIA COLI PROTEINS; HSP70 HEAT-SHOCK PROTEINS; KINETICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CHAPERONES; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 0034257127     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000801)40:2<185::AID-PROT20>3.0.CO;2-X     Document Type: Article

References (18)

1. Ellis RJ, van der Vies SM. Molecular chaperones. Annu Rev Biochem 1991;60:321-347.
2. Hartl FU. Molecular chaperones in cellular protein folding. Nature 1996;381:571-579.
3. Zhu X, Zhao X, Burkholder WF, et al. Structural analysis of substrate binding by the molecular chaperone DnaK. Science 1996;272:1606-1614
4. Froloff N, Windemuth A, Honig B. On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions. Protein Sci 1997;6:1293-1301.
5. Novotny J, Bruccoleri RE, Davis M, Sharp KA. Empirical free energy calculations: a blind test and further improvements to the method. J Mol Biol 1997;268:401-411.
6. Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature 1974;248:338-339.
7. Nicholls A, Honig B. A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem 1991;12:435-445.
8. Novotny J, Bruccoleri RE, Saul FA. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry 1989; 28:4735-4749.
9. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971; 55:379-400.
10. Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988;4:7-18.
11. Harvey SC. Treatment of electrostatic effects in macromolecular modeling. Proteins 1989;5:78-92.
12. Pickett SD, Sternberg MJ. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 1993;231:825-839.
13. Hubbard SJ, Thornton JM. 'NACCESS', Computer Program. Department of Biochemistry and Molecular Biology, University College London.1993.
14. Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free-energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.
15. Flynn G, Pohl J, Flocco T, Rothman J. Peptide-binding specificity of the molecular chaperone BiP. Nature 1991;353:726-730.
16. Schmid D, Baici A, Gehring H, Christen P. Kinetics of molecular chaperone action. Science 1994;263:971-973.
17. Pierpaoli EV, Gisler SM, Christen P. Sequence-specific rates of interaction of target peptides with the molecular chaperones DnaK and DnaJ. Biochemistry 1998;37:16741-16748.
18. Gragerov A, Zeng L, Zhao X, Burkholder W, Gottesman ME. Specificity of DnaK-peptide binding. J Mol Biol 1994;235:848-854.