Protein hot spots: The Islands of stability

Journal of Molecular Biology

Volumn 415, Issue 2, 2012, Pages 419-428

  Kuttner, Yosef Y ^a   Engel, Stanislav ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

backbone compliance; protein hot spots; protein ligand interaction; protein protein interaction; steered molecular dynamics simulation

Indexed keywords

CYCLINE; INTERLEUKIN 2; MOUSE DOUBLE MINUTE PROTEIN 2; PROTEIN DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; ENERGY; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN METABOLISM; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; SIGNAL TRANSDUCTION; SIMULATION;

EID: 84855757866     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.11.009     Document Type: Article

References (31)

1. Schreiber G., Haran G., and Zhou H.X. Fundamental aspects of protein-protein association kinetics Chem. Rev. 109 2009 839 860
2. Moreira I.S., Fernandes P.A., and Ramos M.J. Hot spots-a review of the protein-protein interface determinant amino-acid residues Proteins 68 2007 803 812 (Pubitemid 47434705)
3. Young L., Jernigan R.L., and Covell D.G. A role for surface hydrophobicity in protein-protein recognition Protein Sci. 3 1994 717 729 (Pubitemid 24139897)
4. Sheinerman F.B., Norel R., and Honig B. Electrostatic aspects of protein-protein interactions Curr. Opin. Struct. Biol. 10 2000 153 159 (Pubitemid 30198940)
5. Thorn K.S., and Bogan A.A. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions Bioinformatics 17 2001 284 285 (Pubitemid 32288219)
6. Ma B., Shatsky M., Wolfson H.J., and Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations Protein Sci. 11 2002 184 197 (Pubitemid 34075781)
7. Wells J.A., and McClendon C.L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces Nature 450 2007 1001 1009 (Pubitemid 350273630)
8. Yin H., and Hamilton A.D. Strategies for targeting protein-protein interactions with synthetic agents Angew. Chem., Int. Ed. 44 2005 4130 4163 (Pubitemid 40982718)
9. Li X., Keskin O., Ma B., Nussinov R., and Liang J. Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking J. Mol. Biol. 344 2004 781 795 (Pubitemid 39469220)
10. Eyrisch S., and Helms V. Transient pockets on protein surfaces involved in protein-protein interaction J. Med. Chem. 50 2007 3457 3464 (Pubitemid 47195455)
11. Thanos C.D., Randal M., and Wells J.A. Potent small-molecule binding to a dynamic hot spot on IL-2 J. Am. Chem. Soc. 125 2003 15280 15281 (Pubitemid 37532159)
12. DeLano W.L., Ultsch M.H., de Vos A.M., and Wells J.A. Convergent solutions to binding at a protein-protein interface Science 287 2000 1279 1283 (Pubitemid 30112152)
13. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., and Villa E. Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
14. Arkin M.R., Randal M., DeLano W.L., Hyde J., Luong T.N., and Oslob J.D. Binding of small molecules to an adaptive protein-protein interface Proc. Natl Acad. Sci. USA 100 2003 1603 1608 (Pubitemid 36254494)
15. Stauber D.J., Debler E.W., Horton P.A., Smith K.A., and Wilson I.A. Crystal structure of the IL-2 signaling complex: paradigm for a heterotrimeric cytokine receptor Proc. Natl Acad. Sci. USA 103 2006 2788 2793
16. Braisted A.C., Oslob J.D., Delano W.L., Hyde J., McDowell R.S., and Waal N. Discovery of a potent small molecule IL-2 inhibitor through fragment assembly J. Am. Chem. Soc. 125 2003 3714 3715 (Pubitemid 36512355)
17. Uhrinova S., Uhrin D., Powers H., Watt K., Zheleva D., and Fischer P. Structure of free MDM2 N-terminal domain reveals conformational adjustments that accompany p53-binding J. Mol. Biol. 350 2005 587 598 (Pubitemid 40828916)
18. Chen J., Marechal V., and Levine A.J. Mapping of the p53 and mdm-2 interaction domains Mol. Cell. Biol. 13 1993 4107 4114 (Pubitemid 23187639)
19. Kussie P.H., Gorina S., Marechal V., Elenbaas B., Moreau J., Levine A.J., and Pavletich N.P. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain Science 274 1996 948 953 (Pubitemid 26398409)
20. Allen J.G., Bourbeau M.P., Wohlhieter G.E., Bartberger M.D., Michelsen K., and Hungate R. Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2-tumor protein 53 protein-protein interaction J. Med. Chem. 52 2009 7044 7053
21. Kontopidis G., Wu S.Y., Zheleva D.I., Taylor P., McInnes C., and Lane D.P. Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design Proc. Natl Acad. Sci. USA 102 2005 1871 1876 (Pubitemid 40261979)
22. Warbrick E. The puzzle of PCNA's many partners BioEssays 22 2000 997 1006
23. Maga G., and Hübscher U. Proliferating cell nuclear antigen (PCNA): a dancer with many partners J. Cell Sci. 116 2003 3051 3060 (Pubitemid 37038954)
24. WAF1/CIP1 complexed with human PCNA Cell 87 1996 297 306 (Pubitemid 26359007)
25. Bruning J.B., and Shamoo Y. Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-δ p66 subunit and flap endonuclease-1 Structure 12 2004 2209 2219 (Pubitemid 39593198)
26. Brown S.P., and Hajduk P.J. Effects of conformational dynamics on predicted protein druggability ChemMedChem 1 2006 70 72 (Pubitemid 44104979)
27. Fuller J.C., Burgoyne N.J., and Jackson R.M. Predicting druggable binding sites at the protein-protein interface Drug Discov. Today 14 2009 155 161
28. Spassov V.Z., Flook P.K., and Yan L. LOOPER: a molecular mechanics-based algorithm for protein loop prediction Protein Eng. Des. Sel. 21 2008 91 100 (Pubitemid 351301921)
29. MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., and Field M.J. All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616 (Pubitemid 128576688)
30. Darnell S.J., LeGault L., and Mitchell J.C. KFC Server: interactive forecasting of protein interaction hot spots Nucleic Acids Res. 36 2008 W265 W269
31. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics J. Mol. Graphics 14 1996 3327 3828