Hydrogen Bonds In Molecular Mechanics Force Fields

Advances in Protein Chemistry

Volumn 72, Issue , 2005, Pages 105-119

  Hermans, Jan ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN;

CHEMICAL BOND; CHEMICAL REACTION; DECOMPOSITION; DERIVATIZATION; ENERGY TRANSFER; FORCE; HYDROGEN BOND; MACROMOLECULE; MATHEMATICAL ANALYSIS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; PARTICLE SIZE; PRIORITY JOURNAL; PROTEIN FOLDING; QUANTUM MECHANICS; REACTION ANALYSIS; REVIEW; SIMULATION; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR DYNAMICS;

HYDROGEN; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE;

EID: 33645861085     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3233(05)72004-0     Document Type: Review

References (31)

1. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B. (Ed). "Intermolecular Forces" (1981), Reidel, Dordrecht, Holland 331-342
2. Chelli R., Schettino V., and Procacci P. Comparing polarizable force fields to ab initio calculations reveals nonclassical effects in condensed phases. J. Chem. Phys. 122 (2005) 234107-1-7.
3. Cornell W.D., Cieplak P., Bayly C., Gould I.R., Merz K.M.J., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A second generation force field for the simulation of proteins and nucleic acids. J. Am. Chem. Soc. 117 (1995) 5179-5197
4. Cui Q., Elstner M., Kaxiras E., Frauenheim T., and Karplus M. A QM/MM implementation of the self-consistent-charge density functional tight binding (SCC-DFTB) method. J. Phys. Chem. B 105 (2001) 569-585
5. Elstner M., Frauenheim T., Kaxiras E., Seifert G., and Suhai S. A self-consistent charge density-functional based tight-binding scheme for large biomolecules. Phys. Status Solidi. B. 217 (2000) 357-376
6. Elstner M., Porezag D., Jungnickel G., Elsner J., Haugk M., Frauenheim T., Suhai S., and Seifert G. Self-consistent charge density functional tight-binding method for simulation of complex material properties. Phys. Rev. B 58 (1998) 7260-7268
7. Ferro D., and Hermans J. Nonbonded interatomic potential functions and crystal structure: Non hydrogen bonded organic molecules. In: Johnson J.F., and Porter R. (Eds). "Liquid Crystals and Ordered Fluids" (1970), Plenum, New York 259-275
8. Friesner R.A. Modeling polarization in proteins and protein-ligand complexes: Methods and preliminary results. Adv. Protein Chem. 72 (2006) 80-104
9. Hagler A.T., Dauber P., and Lifson S. Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 3. The C:O...H-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids. J. Am. Chem. Soc. 101 (1979) 5131-5141
10. Hagler A.T., Lifson S., and Dauber P. Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields. J. Am. Chem. Soc. 101 (1979) 5122-5130
11. Hermans J., Berendsen H.J.C., van Gunsteren W.F., and Postma J.P.M. A consistent empirical potential for water-protein interactions. Biopolymers 23 (1984) 1513-1518
12. Hu H., Elstner M., and Hermans J. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins: Struct. Funct. Genet. 50 (2003) 451-463
13. Jorgensen W.L. OPLS force fields. In: Schleyer P.v.R. (Ed). "Encyclopedia of Computational Chemistry" (1998), Wiley, New York
14. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
15. Jorgensen W.L., and Tirado-Rives J. Potential functions for atomic-level simulations of water and organic and biomolecular systems. Proc. Natl. Acad. Sci. USA 102 (2005) 6665-6670
16. Kaminski G., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA forcefield for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 105 (2001) 6474-6487
17. Kortemme T., Morozov A.V., and Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326 (2003) 1239-1259
18. Lifson S., Hagler A.T., and Dauber P. Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides, and the C:O...H- hydrogen bonds. J. Am. Chem. Soc. 101 (1979) 5111-5121
19. Liu H., Elstner M., Kaxiras E., Frauenheim T., Hermans J., and Yang W. Quantum mechanics simulation of protein dynamics on long time scale. Proteins: Struct. Funct. Genet. 44 (2001) 484-489
20. MacKerell A.D., Bashford D., Bellott M., Dunbrack Jr. R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiórkiewicz-Kuczera J., Yin D., and Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102 (1998) 3586-3616
21. MacKerell A.D., Feig J.M., and Brooks C.L. Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 126 (2004) 698-699
22. Mahoney M.W., and Jorgensen W.L. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112 (2000) 8910-8922
23. Maple J.R., Hwang M.-J., Jalkanen K.J., Stockfisch T.P., and Hagler A.T. Derivation of class II force fields. V. Quantum force field for amides, peptides, and related compounds. J. Comput. Chem. 19 (1998) 430-458
24. Morozov A.V., and Kortemme T. Potential functions for hydrogen bonds in protein structure prediction and design. Adv. Protein Chem. 72 (2006) 1-38
25. Morozov A.V., Kortemme T., Tsemekhman K., and Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc. Natl. Acad. Sci. USA 101 (2004) 6946-6951
26. Scheraga H.A. Calculations of conformations of polypeptides. Adv. Phys. Org. Chem. 6 (1968) 103-184
27. Stillinger F.H., and Rahman A. Improved simulation of liquid water by molecular dynamics. J. Chem. Phys. 60 (1974) 1545-1557
28. van Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., Krüger P., Mark A.E., Scott W.R.P., and Tironi I.G. "Biomolecular Simulation: The GROMOS96 Manual and User Guide." (1996), Vdf Hochschulverlag AG an der ETH Zürich, Zürich
29. Weinhold F. Resonance character of hydrogen-bonding interactions in water and other H-bonded species. Adv. Protein Chem. 72 (2006) 121-153
30. Wernet P., Nordlund D., Bergmann U., Cavalleri M., Odelius M., Ogasawara H., Näslund L.A., Hirsch T.K., Ojamäe L., Glatzel P., Pettersson L.G.M., and Nilsson A. The structure of the first coordination shell in liquid water. Science 304 (2004) 995-999
31. Williams D.E. Nonbonded potential parameters derived from crystalline hydrocarbons. J. Chem. Phys. 47 (1967) 4680-4684