Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

Proceedings of the National Academy of Sciences of the United States of America

Volumn 104, Issue 3, 2007, Pages 808-813

  Young, Tom ^a   Abel, Robert ^a   Kim, Byungchan ^a   Berne, Bruce J ^a   Friesner, Richard A ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

Binding motifs; Dewetting; Hydrophobic effect; Streptavidin

Indexed keywords

BIOTIN; STREPTAVIDIN;

ARTICLE; BINDING AFFINITY; BINDING SITE; ENTHALPY; ENTROPY; HYDRATION; HYDROGEN BOND; HYDROPHOBICITY; LIGAND BINDING; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; SOLVATION; THERMODYNAMICS;

AMINO ACID MOTIFS; ANTIBODIES; BINDING SITES; CYCLOOXYGENASE 2; HIV PROTEASE; HYDROPHOBICITY; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; WATER;

EID: 33846524439     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0610202104     Document Type: Article

References (30)

1. Wang R, Lu Y, Fang X, Wang S (2004) J Chem Inf Comp Sci 44:2114-2125.
2. Murphy RB, Halgren TA, Friesner RA (2006) J Med Chem 49:6177-6196.
3. Lazaridis T (1998) J Phys Chem B 102:3531-3541.
4. Baranyai A, Evans D (1989) Phys Rev A 40:3817-3822.
5. Morita T, Hiroike K (1961) Prog Theor Phys 25:537-578.
6. Lazaridis T, Paulaitis ME (1992) J Phys Chem 96:3847-3855.
7. Rahman A, Stillinger F (1973) J Am Chem Soc 95:7943-7948.
8. Hyre D, Trong I, Merritt E, Eccleston J, Green N, Stenkamp R, Stayton P (2006) Protein Sci 15:459-467.
9. Chu V, Freitag S, Trong I, Stenkamp R, Stayton P (1998) Protein Sci 7:848-859.
10. Chilkoti A, Stayton P (1995) J Am Chem Soc 117:10622-10628.
11. Lazaridis T, Masunov A, Gandolfo F (2002) Proteins Struct Funct Genet 47:194-208.
12. Luo H, Sharp K (2002) Proc Natl Acad Sci USA 99:10399-10404.
13. Dixit S, Chipot C (2001) Proc Natl Acad Sci USA 105:9795-9799.
14. Wallqvist A, Gallicchio E, Levy RM (2001) J Phys Chem B 105:6745-6753.
15. Huang X, Margulis C, Berne B (2003) Proc Natl Acad Sci USA 100:11953-11958.
16. Sriraman S, Kevrekidis I, Hummer G (2005) Phys Rev Lett 95:13603.
17. Wolde P, Chandler D (2002) Proc Natl Acad Sci USA 99:6539-6543.
18. Collins M, Hummer G, Quillin M, Matthews B, Gruner S (2005) Proc Natl Acad Sci USA 102:16668.
19. Kurumbail RG, Stevens AM, Gierse JK, Joseph J McDonald RAS, Pak JY, Gildehaus D, iyashiro JM, Penning TD (1996) Nature 384:644-648.
20. Weber P, Ohlendorf D, Wendoloski J, Salemme F (1989) Science 243:859-863.
21. Kiefer J, Pawlitz J, Moreland K, Stegeman R, Hood W, Gierse J, Stevens A, Goodwin D, Rowlinson S, Marnett L, et al. (2000) Nature 405:97-101.
22. Arevalo J, Taussig M, Wilson I (1993) Nature 365:859-863.
23. Baldwin E, Bhat T, Gulnik S, Liu B, Topol I, Kiso Y, Mimoto T, Mitsuya H, Erickson J (1995) Structure (London) 3:581-590.
24. Tuckerman ME, Martyna GJ, Klein ML (1992) J Chem Phys 97:2635.
25. Andersen HC (1980) J Chem Phys 72:2384.
26. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001 ) J Phys Chem B 105:6474.
27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein M (1983) j Chem Phys 79:926.
28. Darden T, York D, Pedersen L (1993) J Chem Phys 98:10089.
29. Stern H, Berne BJ, Rittner F, Pavese M, Harder E, Xu H, Kim B (2001) SIM: Molecular Dynamics Simulation Program (Columbia University, New York).
30. Kuffner J (2004) Proc IEEE Int Conf Robot Automat (Inst Electric Electron Eng, Piscataway, NJ).