Abstract
Molecular dynamics simulation on BPTI (biovine pancreatic trypsin inhibitor) aqueous solution has been performed for the first time in terms of the atom-bond electronegativity equalization method fused with molecular mechanics (ABEEM/MM). The simulated parameters including ABEEM parameters and force field parameters have been tested. Some structural properties including root-mean-square deviations of atomic coordinates and radial distribution functions were studied by ABEEM/MM fluctuating charge method. The results demonstrate that this model can obtain reasonable structural properties compared with experimental crystal data. The radial distribution functions indicate that ABEEM/MM method can well embody the electrostatic polarizations between protein molecule and its surrounding solvent waters.
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References
Kim B, Young T, Harder E, et al. Structure and dynamics of the solvation of biovine pancreatic trypsin inhibitor in explicit water: A comparative study of the effects of solvent and protein polarizability. J Phys Chem B, 2005, 109: 16529–16538
Yang Z Z, Wang C S. Atom-bond electronegativity equalization method. 1. Calculation of the charge distribution in large molecules. J Phys Chem A, 1997, 101: 6315–6321
Cong Y, Yang Z Z. General atom-bond electronegativity equalization method and its application in prediction of charge distributions in polypeptide. Chem Phys Lett, 2000, 316: 324–329
Wu Y, Yang Z Z. Atom-bond electronegativity equalization method fused into molecular mechanics. II. A seven-site fluctuating charge and flexible body water potential function for liquid water. J Phys Chem A, 2004, 108: 7563–7576
Zhang Q, Yang Z Z. An investigation of alkane conformations based on the ABEEM/MM model. Chem Phys Lett, 2005, 403: 242–247
Yang Z Z, Zhang Q. Study of peptide conformation in terms of the ABEEM/MM method. J Comput Chem, 2006, 27: 1–10
Yang Z Z, Qian P. A study of N-methylacetamide in water clusters: Based on atom-bond electronegativity equalization method fused into molecular mechanics. J Chem Phys, 2006, 125: 064311
Li X, Yang Z Z. Hydration of Li+-ion in atom-bond electronegativity equalization method-7P water: A molecular dynamics simulation study. J Chem Phys, 2005, 122: 084514
Zhang Q, Yang, Z. Z. Application of the ABEEM/MM model to simulate molecule of protein (Crambin). Chem J of Chin Univ (in Chinese), 2005, 26(12): 2345–2347
Zhang Q, Zhang X, Yang, Z. Z. Modeling of cyclic peptides by the ABEEM/MM fluctuating charge force field. Acta Phys-Chim Sin (in Chinese), 2006, 22(10): 1243–1247
Kaminski G A, Friesner R A, Tirado-Rives J, et al. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B, 2001, 105: 6474–6487
Vrbka L, Jungwirth P, Bauduin P, et al. Specific ion effects at protein surfaces: A molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions. J Phys Chem B, 2006, 110: 7036–7043
MacKerell Jr A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B, 1998, 102: 3586–3616
Allinger N L, Yuh Y H, Lii J H. Molecular mehanics: The MM3 force field for hydrocarbons. 1. J Am Chem Soc, 1989, 111: 8551–8566
Lii J H, Allinger N L. Directional hydrogen bonding in the MM3 force field: II. J Comput Chem, 1998, 19: 1001–1016
Langley C H, Allinger N L. Molecular mechanics (MM4) and ab initio study of amide-amide and amide-water dimers. J Phys Chem A, 2003, 107: 5208–5216
Kang Y K. Which functional form is appropriate for hydrogen bond of amides? J Phys Chem B, 2000, 104: 8321–8326
Vargas R, Garza J, Friesner R A, et al. Strength of the N-H⋯O=C and C-H⋯O=C bonds in formamide and N-Methylacetamide dimmers. J Phys Chem A, 2001, 105: 4963–4968
No K T, Kwon O, Kim Y. A simple functional representation of angular-sependent hydrogen-bonded systems. 1. Amide, carboxylic acid, and amide-carboxylic acid pairs. J Phys Chem, 1995, 99: 3478–3486
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Supported by the National Natural Science Foundation of China (Grant Nos. 20633050 and 20403007)
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QingMei, G., BaoQiu, C., DongXia, Z. et al. Molecular dynamics study on BPTI aqueous solution by ABEEM/MM fluctuating charge model. Chin. Sci. Bull. 53, 1171–1174 (2008). https://doi.org/10.1007/s11434-007-0493-5
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DOI: https://doi.org/10.1007/s11434-007-0493-5