Explicit and implicit water simulations of a β-hairpin peptide

Proteins: Structure, Function and Genetics

Volumn 37, Issue 1, 1999, Pages 73-87

  Ma, Buyong ^a   Nussinov, Ruth ^a,b,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

hairpin peptide; Conformational energy; Continuum solvation model; Explicit water model; Free energy simulation; Hydrophobic interaction; Peptide conformation; Vibrational entropy

Indexed keywords

HYDROGEN; PEPTIDE; WATER;

ARTICLE; ENTROPY; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; SIMULATION; SOLVATION; VIBRATION;

COMPUTER SIMULATION; ENTROPY; HYDROGEN BONDING; MODELS, MOLECULAR; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; VIBRATION; WATER;

EID: 0033214430     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991001)37:1<73::AID-PROT8>3.0.CO;2-Z     Document Type: Article

References (33)

1. Constantine KL, Mueller L, Anderson NH, Tong H, Wandder CF, Friederichs MS, Bruccoleri RE. Structural and dynamic properties of a β-hairpin-forming linear peptide: 1. Modeling using ensemble-averaged constraints [see references cited therein]. J Am Chem Soc 1995;117:10841-10854.
2. 13C NMR relaxation analysis. J Am Chem Soc 1995;117:10855-10864.
3. Edinger SR, Cortis C, Shenkin PS, Friesner RA. Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation. J Phys Chem B 1997;101:1190-1197.
4. Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringalda MN, Sitkoff D, Honig B. New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short range hydrogen bonding effects. J Phys Chem 1996;100:11775-11788.
5. Bashford D, Case DA, Choi C, Gippert GP. A computational study of the role of solvation effects in reverse turn formation in the tetrapeptides APGD and APGN. J Am Chem Soc 1997;119:4964-4971.
6. Demchuk E, Bashford D, Gipert GP, Case DA. Thermodynamics of a reverse turn motif: solvent effects and side-chain packing. J Mol Biol 1997;270:305-317.
7. Blanco F, Ramirez-Alvarado M, Serrano L. Formation and stability of β-hairpin structure in polypeptides. Curr Opin Struct Biol 1998;8:107-111.
8. Evans JS, Mathiowetz AM, Chan SI, Goddard WA III. De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology. Protein Sci 1995;4:1203-1216.
9. Möhley K, Gubmann M, Hofmann H-J. Structural and energetic relations between β turns. J Comp Chem 1997;18:1415-1430.
10. Prévost M, Ortmans I. Refolding simulations of an isolated fragments of Barnase into a native like β-hairpin: evidence for compactness and hydrogen bonding as concurrent stabilizing factors. Proteins 1997;29:212-227.
11. Yang A-S, Hitz B, Honig B. Free energy determinants of secondary structure formation III. β-turns and their role in protein folding. J Mol Biol 1996;259:873-882.
12. Viguera AR, Jiménez MA, Rico M, Serrano L. Conformational analysis of peptides corresponding to β-hairpin and a β-sheet that represent the entire sequence of the α-spectrin SH3 domain. J Mol Biol 1996;255:507-521.
13. Ramirez-Alvarado M, Blanco FJ, Serrano L. De novo design and structural analysis of a model β-hairpin peptide system. Nature Struct Biol 1996;3:604-612.
14. Muñoz V, Thompson PA, Hofrichter J, Eaton WA. Folding dynamics and mechanism of β-hairpin formation. Nature 1997;390:196-199.
15. 13C-NMR relaxation. Protein Sci 1998;7:720-729.
16. de Alba E, Jiménez MA, Rico M. Turn residue sequence determines β-hairpin conformation in designed peptides. J Am Chem Soc 1997;119:175-183.
17. de Alba E, Jiménez MA, Rico M, Nieto JL. Conformational investigation of designed short linear peptides able to fold into β-hairpin structures in aqueous solution. Fold Des 1996;1:133-144.
18. de Alba E, Rico M, Jiménez MA. Cross-strand side-chain interactions versus turn conformation in β-hairpins. Protein Sci 1997;6: 2548-2560.
19. Jayaram B, Sharp KA, Honig B. The electrostatic potential of B-DNA. Biopolymers 1989;28:975-993.
20. Gilson MK, Sharp KA, Honig BH. Calculating the electrostatic potential of molecules in solution: method and error assessment. J Comput Chem 1988;9:327-335.
21. Biosys/MSI. Discover user guide, part 1. Biosys/MSI; 1995.
22. Maple JR, Hwang MJ, Jalkanen KJ, Stockfisch TP, Hagler AT. Derivation of class II force fields: V. quantum force field for amides, peptides, and related compounds. J Comput Chem 1998; 19:430-458.
23. Tsai C-J, Nussinov R. Hydrophobic folding units derived from dissimilar monomer structures and their interactions. Protein Sci 19997;6:24-42.
24. Kollman PA. Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 1993;93:2395-2417.
25. Kollman PA. Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Acc Chem Res 1996;29:461-469.
26. Israelachvili J, Wennerström H. Role of hydration and water structure in biological and colloidal interactions. Nature 1996;379: 219-225.
27. Hagler AT, Stern PS, Sharon R, Becker JM, Naider F. Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results. J Am Chem Soc 1979;101:6842-6852.
28. Tidor B, Karplus M. The contribution of vibrational entropy to molecular association. The dimerization of insulin. J Mol Biol 1994;238:405-414.
29. Scarsi M, Apostolakis J, Caflish A. Comparison of GB solvation model with explicit solvent simulations: potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane. J Phys Chem B 1998;102:3637-3641.
30. Reddy MR, Erion MD, Agarwal A, Viswanadham VN, McDonald DQ, Still WC. Solvation free energies calculated using the GB/SA model: sensitivity of results on charge sets, protocols, and force fields. J Comp Chem 1998;19:769-780.
31. Samuelson S, Tobias DJ, Martyna GJ. Modern computational methodology applied to the simulation of blocked trialanine peptide in vacuo, water clusters, and bulk water. J Phys Chem B 1997;101:7592-7603.
32. Qiu D, Shenkin PS, Hollinger FD, Still WC. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii. J Phys Chem A 1997;101: 3005-3014.
33. Schaefer M, Bartels C, Karplus M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol 1998;284:835-848.