Molecular dynamics study on BPTI aqueous solution by ABEEM/MM fluctuating charge model |
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Authors: | Guan QingMei Cui BaoQiu Zhao DongXia Gong LiDong Yang ZhongZhi |
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Institution: | (1) Department of Chemistry, Liaoning Normal University, Dalian, 116029, China |
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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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Keywords: | ABEEM/MM fluctuating charge model BPTI aqueous solution root-mean-square deviation radial distribution function |
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