The solvation interface is a determining factor in peptide conformational preferences

Journal of Molecular Biology

Volumn 356, Issue 1, 2006, Pages 248-256

  Sorin, Eric J ^a   Rhee, Young Min ^c   Shirts, Michael R ^d   Pande, Vijay S ^a,b  

^a STANFORD UNIVERSITY   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

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

Author keywords

Distributed computing; Explicit solvent; Hydrophobicity; Molecular dynamics; Protein folding

Indexed keywords

ALANINE; BIOPOLYMER; WATER;

ARTICLE; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR DYNAMICS; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SOLVATION;

EID: 30344484542     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.11.058     Document Type: Article

References (49)

1. G.D. Rose, and R. Wolfenden Hydrogen bonding, hydrophobicity, packing, and protein folding Annu. Rev. Biophys. Biomol. Struct. 22 1993 381 415
2. P.R. ten Wolde, and D. Chandler Drying-induced hydrophobic polymer collapse Proc. Natl Acad. Sci. USA 99 2002 6539 6543
3. M.S. Cheung, A.E. Garcia, and J.N. Onuchic Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse Proc. Natl Acad. Sci. USA 99 2002 685 690
4. J.E. Shea, J.N. Onuchic, and C.L. Brooks Probing the folding free energy landscape of the src-SH3 protein domain Proc. Natl Acad. Sci. USA 99 2002 16064 16068
5. R. Zhou, X. Huang, C.J. Margulis, and B.J. Berne Hydrophobic collapse in multidomain protein folding Science 305 2004 1605 1609
6. R. Zhou, B.J. Berne, and R. Germain The free energy landscape for beta hairpin folding in explicit water Proc. Natl Acad. Sci. USA 98 2001 14931 14936
7. R. Zhou Free energy landscape of protein folding in water: explicit vs. implicit solvent Proteins: Struct. Funct. Genet. 53 2003 148 161
8. E.J. Sorin, Y.M. Rhee, and V.S. Pande Does water play a structural role in the folding of small nucleic acids? Biophys. J. 88 2005 2516 2524
9. Y.M. Rhee, E.J. Sorin, G. Jayachandran, E. Lindahl, and V.S. Pande Simulations of the role of water in the protein-folding mechanism Proc. Natl Acad. Sci. USA 101 2004 6456 6461
10. H. Nymeyer, and A.E. Garcia Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent Proc. Natl Acad. Sci. USA 100 2003 13934 13939
11. G. Hummer, A.E. Garcia, and S. Garde Helix nucleation kinetics from molecular simulations in explicit solvent Proteins: Struct. Funct. Genet. 42 2001 77 84
12. A.E. Garcia, and K.Y. Sanbonmatsu α-Helical stabilization by side chain shielding of backbone hydrogen bonds Proc. Natl Acad. Sci. USA 99 2001 2782 2787
13. A.E. Garcia, and K.Y. Sanbonmatsu Exploring the energy landscape of a beta-hairpin in explicit solvent Proteins: Struct. Funct. Genet. 42 2001 345 354
14. V. Makarov, B.M. Pettitt, and M. Feig Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment Accts Chem. Res. 35 2002 376 384
15. Y. Duan, and P.A. Kollman Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution Science 282 1998 740 744
16. V.S. Pande, I. Baker, J. Chapman, S. Elmer, S. Kaliq, and S. Larson Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing Biopolymers 68 2003 91 109
17. E.J. Sorin, and V.S. Pande Exploring the helix-coil transition via all-atom equilibrium ensemble simulations Biophys. J. 88 2005 2472 2493
18. E.J. Sorin, and V.S. Pande Empirical force field assessment: the interplay between backbone torsions and non-covalent term scaling J. Comput. Chem. 26 2005 682 690
19. B. Zagrovic, E.J. Sorin, and V. Pande β-Hairpin folding simulations in atomistic detail using an implicit solvent model J. Mol. Biol. 313 2001 151 169
20. B.H. Zimm, and J.K. Bragg Theory of the phase transition between helix and random coil in polypeptide chains J. Chem. Phys. 31 1959 526 535
21. S. Lifson, and A. Roig Theory of helix-coil transition in polypeptides J. Chem. Phys. 34 1961 1963 1974
22. M.M. Lopez, D.-H. Chin, R.L. Baldwin, and G.I. Makhatadze The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metalbinding to induce helix formation Proc. Natl Acad. Sci. USA 99 2002 1298 1302
23. E.J. Spek, C.A. Olson, Z. Shi, and N.R. Kallenbach Alanine is an intrinsic α-helix stabilizing amino acid J. Am. Chem. Soc. 121 1999 5571 5572
24. S. Marqusee, V.H. Robbins, and R.L. Baldwin Unusually stable helix formation in short alanine based peptides Proc. Natl Acad. Sci. USA 86 1989 5286 5290
25. A.-S. Yang, and B. Honig Free energy determinants of secondary structure formation. I. α-Helices J. Mol. Biol. 252 1995 351 365
26. R.N.A.H. Lewis, Y.-P. Zhang, R.S. Hodges, W.K. Subczynski, A. Kusumi, and C.R. Flach A polyalanine-based peptide cannot form a stable transmembrane α-helix in fully hydrated phospholipid bilayers Biochemistry 40 2001 12103 12111
27. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
28. M.R. Shirts, and V.S. Pande Solvation free energies of amino acid side chain analogs for common molecular mechanics water models J. Chem. Phys. 122 2005 134508
29. Y. Sun, and P.A. Kollman Hydrophobic solvation of methane and nonbond parameters of the TIP3P water model J. Comput. Chem. 16 1995 1164 1169
30. M. Mezei, P.J. Fleming, R. Srinivasan, and G.D. Rose Polyproline II helix is the preferred conformation for unfolded polyalanine in water Proteins: Struct. Funct. Genet. 55 2004 502 507
31. S. Williams, T.P. Causgrove, R. Gilmanshin, K.S. Fang, R.H. Callender, W.H. Woodruff, and R.B. Dyer Fast events in protein folding: helix melting and formation in a small peptide Biochemistry 35 1996 691 697
32. H. Qian, and J.A. Schellman Helix-coil theories: a comparative study for finite length polypeptides J. Phys. Chem. 96 1992 3987 3994
33. E. Lindahl, B. Hess, and D. van der Spoel GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Mod. 7 2001 306 317
34. F. Eisenhaber, P. Lijnzaad, P. Argos, C. Sander, and M. Scharf The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies J. Comput. Chem. 16 1995 273 284
35. 6 J. Phys. Chem. B 104 2000 10080 10086
36. 10-helix and α-helix in ala-rich peptides: a hydrogen exchange and high field NMR study J. Mol. Biol. 267 1997 963 974
37. 10-, and π-helix in helix-coil transitions Protein Sci. 12 2003 1145 1157
38. Z. Shi, C.A. Olson, G.D. Rose, R.L. Baldwin, and N.R. Kallenbach Polyproline II structure in a sequence of seven alanine residues Proc. Natl Acad. Sci. USA 99 2002 9190 9195
39. A.E. Garcia Characterization of non-alpha helical conformations in Ala peptides Polymer 45 2004 669 676
40. S.A. Asher, A.V. Mikhonin, and S. Bykov UV Raman demonstrates that α-helical polyalanine peptides melt to polyproline II conformations J. Am. Chem. Soc. 126 2004 8433 8440
41. A.N. Drozdov, A. Grossfield, and R.V. Pappu Role of solvent in determining conformational preferences of alanine dipeptide in water J. Am. Chem. Soc. 126 2003 2574 2581
42. A. Kentsis, M. Mezei, T. Gindin, and R. Osman Unfolded state of polyalanine is a segmented polyproline II helix Proteins: Struct. Funct. Genet. 55 2004 493 501
43. C.F. Weise, and J.C. Weisshaar Conformational analysis of alanine dipeptide from dipolar couplings in a water-based liquid crystal J. Phys. Chem. B 107 2003 3265 3277
44. B. Zagrovic, J. Lipfert, E.J. Sorin, I.S. Millett, W.F. Van Gunsteren, S. Doniach, and V.S. Pande Unusual compactness of a polyproline type II structure Proc. Natl Acad. Sci. USA 102 2005 11698 11703
45. H.J.C. Berendsen, J.P.M. Postma, W.F. Van Gunsteren, A. Dinola, and J. Haak Molecular-dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
46. P.A. Thompson, W.A. Eaton, and J. Hofrichter Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model Biochemistry 36 1997 9200 9210
47. A. Ianoul, A. Mikhonin, I.K. Lednev, and S.A. Asher UV resonance Raman study of the spatial dependence of α-helix unfolding J. Phys. Chem. A 106 2002 3621 3624
48. B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comput. Chem. 18 1997 1463 1472
49. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637