A simple atomic-level hydrophobicity scale reveals protein interfacial structure

Journal of Molecular Biology

Volumn 426, Issue 2, 2014, Pages 484-498

  Kapcha, Lauren H ^a   Rossky, Peter J ^a  

^a University of Texas at Austin   (United States)

Author keywords

biomolecule visualization; hydration; hydropathy; molecular recognition; protein binding

Indexed keywords

AMINO ACID; CARRIER PROTEIN;

ARTICLE; ATOM; HYDRATION; HYDROPHILICITY; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; SURFACE PROPERTY;

BIOMOLECULE VISUALIZATION; HYDRATION; HYDROPATHY; IL-1Β; INTERLEUKIN-1Β; MOLECULAR RECOGNITION; PDB; PF4; PLATELET FACTOR 4; PROTEIN BINDING; PROTEIN DATA BANK; SASA; SOLVENT-ACCESSIBLE SURFACE AREA;

HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEINS; WATER;

EID: 84891833933     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.09.039     Document Type: Article

References (44)

1. W. Kauzmann Some factors in the interpretation of protein denaturation Adv Protein Chem 14 1959 1 57
2. C. Tanford Contribution of hydrophobic interactions to the stability of the globular conformation of proteins J Am Chem Soc 84 1962 4240 4247
3. K.A. Dill Dominant forces in protein folding Biochemistry 29 1990 7133 7155
4. J. Kyte, and R.F. Doolittle A simple method for displaying the hydropathic character of a protein J Mol Biol 157 1982 105 132
5. K.M. Biswas, D.R. DeVido, and J.G. Dorsey Evaluation of methods for measuring amino acid hydrophobicities and interactions J Chromatogr A 1000 2003 637 655
6. Y. Nozaki, and C. Tanford The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions: establishment of a hydrophobicity scale J Biol Chem 246 1971 2211 2217
7. E.B. Leodidas, and A.T. Hatton Amino acids in AOT reversed micelles. 2. The hydrophobic effect and hydrogen bonding as driving forces for interfacial solubilization J Phys Chem 94 1990 6411 6420
8. B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J Mol Biol 55 1971 379 400
9. C. Chothia The nature of the accessible and buried surfaces in proteins J Mol Biol 105 1976 1 12
10. A.A. Aboderin An empirical hydrophobicity scale for α-amino acids and some of its applications Int J Biochem 2 1971 537 544
11. J.L. Meek Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition Proc Natl Acad Sci USA 77 1980 1632 1636
12. H.B. Bull, and K. Breese Surface tension of amino acid solutions: a hydrophobicity scale of the amino acid residues Arch Biochem Biophys 161 1974 665 670
13. D. Eisenberg, and A.D. McLachlan Solvation energy in protein folding and binding Nature 319 1986 199 203
14. M.H. Hecht, J.M. Sturtevant, and R.T. Sauer Effect of single amino acid replacements on the thermal stability of the NH2-terminal domain of phage lambda repressor Proc Natl Acad Sci USA 81 1984 5685 6589
15. K. Yutani, K. Ogasahara, T. Tsujita, and Y. Sugino Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit Proc Natl Acad Sci USA 84 1987 4441 4444
16. C. Carey, Y.-K. Cheng, and P.J. Rossky Hydration structure of the α-chymotrypsin substrate binding pocket: the impact of constrained geometry Chem Phys 258 2000 415 425
17. A.K. Ghose, and G.M. Crippen Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships I. Partition coefficients as a measure of hydrophobicity J Comput Chem 7 1986 565 577
18. G. Steinkellner, R. Rader, G.G. Thallinger, C. Kratky, and K. Gruber VASCo: computation and visualization of annotated protein surface contacts BMC Bioinformatics 10 2009 32 42
19. F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer, M.D. Brice, and J.R. Rodgers et al. The protein data bank: a computer-based archival file for macromolecular structures J Mol Biol 112 1977 535 542
20. W.L. Jorgenson, and J. Tirado-Rives The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin J Am Chem Soc 110 1988 1657 1666
21. A.D. MacKerell, D. Bashford, R.L. Dunbrack, J.D. Evanseck, M.J. Field, and S. Fischer et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins J Phys Chem B 102 1998 3586 3616
22. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J Mol Graphics 14 1996 33 38
23. G. Trinquier, and Y.-H. Sanejouand Which effective property of amino acids is best preserved by the genetic code? Protein Eng 11 1998 153 169
24. P.W. Snyder, J. Mecinovic, D.T. Moustakas, S.W. Thomas, M. Harder, and E.T. Mack et al. Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase Proc Natl Acad Sci USA 108 2011 17889 17894
25. L. Wang, B.J. Berne, and R.A. Friesner Ligand binding to protein-binding pockets with wet and dry regions Proc Natl Acad Sci USA 108 2011 1326 1330
26. R. Abel, T. Young, R. Farid, B.J. Berne, and R.A. Friesner Role of the active-site solvent in the thermodynamics of factor Xa ligand binding J Am Chem Soc 130 2008 2817 2831
27. T. Young, R. Abel, B. Kim, B.J. Berne, and R.A. Friesner Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding Proc Natl Acad Sci USA 104 2007 808 813
28. L. Hua, X. Huang, P. Liu, R. Zhou, and B.J. Berne Nanoscale dewetting transition in protein complex folding J Phys Chem 111 2007 9069 9077
29. T.C. Terwilliger, and D. Eisenberg The structure of melittin. I. Structure determination and partial refinement J Biol Chem 257 1982 6010 6015
30. T.C. Terwilliger, and D. Eisenberg The structure of melittin. II. Interpretation of the structure J Biol Chem 257 1982 6016 6022
31. R. St. Charles, D.A. Walz, and B.F.P. Edwards The three-dimensional structure of bovine platelet factor 4 at 3.0-Å resolution J Biol Chem 264 1989 2092 2099
32. J.S. Kavanaugh, P.H. Rogers, A. Arnone, H.L. Hui, A. Wierzba, and A. Deyoung et al. Intersubunit interactions associated with Tyr42α stabilize the quaternary-T-tetramer but are not major quaternary constraints in deoxyhemoglobin Biochemistry 44 2005 3806 3820
33. W. Blokzijl, and J.B.F.N. Engberts Hydrophobic effects. Opinions and facts Angew Chem Int Ed 32 1993 1545 1579
34. J. Walshaw, and J.M. Goodfellow Distribution of solvent molecules around apolar side-chains in protein crystals J Mol Biol 231 1993 392 414
35. P. Ball Water as an active constituent in cell biology Chem Rev 108 2008 74 108
36. S. Vaitheeswaran, H. Yin, J.C. Rasaiah, and G. Hummer Water clusters in nonpolar cavities Proc Natl Acad Sci USA 101 2004 17002 17005
37. M.L. Quillin, P.T. Wingfield, and B.W. Matthews Determination of solvent content in cavities in IL-1β using experimentally phased electron density Proc Natl Acad Sci USA 103 2006 19749 19753
38. B.C. Finzel, L.L. Clancy, D.R. Holland, S.W. Muchmore, K.D. Watenpaugh, and H.M. Einspahr Crystal structure of recombinant human interleukin-1β at 2.0 Å resolution J Mol Biol 209 1989 779 791
39. J.P. Priestle, H.P. Schär, and M.G. Grütter Crystallographic refinement of interleukin 1 beta at 2.0 Å resolution Proc Natl Acad Sci USA 86 1989 9667 9671
40. A.C. Treharne, D.H. Ohlendorf, P.C. Weber, J.J. Wendoloski, and F.R. Salemme X-ray structural studies of the cytokine interleukin 1-beta Prog Clin Biol Res 349 1990 309 319
41. B. Veerapandian, G.L. Gilliland, R. Raag, A.L. Svensson, Y. Masui, and Y. Hirai et al. Functional implications of interleukin-1β based on the three-dimensional structure Proteins 12 1992 10 23
42. H. Sui, B.-G. Han, J.K. Lee, P. Walian, and B.K. Jap Structural basis of water-specific transport through the AQP1 water channel Nature 414 2001 872 878
43. + channel-Fab complex at 2.0 Å resolution Nature 414 2001 43 48
44. + conduction and selectivity Science 280 1998 69 77