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dc.contributor.authorWu, Ruibo
dc.contributor.authorLu, Zhenyu(NYU, Dept Chem)
dc.contributor.authorCao, Zexing
dc.contributor.author曹泽星
dc.contributor.authorZhang, Yingkai(NYU, Dept Chem)
dc.date.accessioned2012-03-18T06:08:12Z
dc.date.available2012-03-18T06:08:12Z
dc.date.issued2010-12-23
dc.identifier.citationJOURNAL OF CHEMICAL THEORY AND COMPUTATION,2011,7(2):433-443zh_CN
dc.identifier.issn1549-9618
dc.identifier.urihttp://dx.doi.org/doi:10.1021/ct100525r
dc.identifier.uriWOS:000287049200017
dc.identifier.urihttps://dspace.xmu.edu.cn/handle/2288/11787
dc.description.abstractHerein we introduce a novel practical strategy to overcome the well-known challenge of modeling the divalent zinc cation in metalloproteins. The main idea is to design short-long effective functions (SLEF) to describe charge interactions between the zinc ion and all other atoms. This SLEF approach has the following desired features: (1) It is pairwise, additive, and compatible with widely used atomic pairwise force fields for modeling biomolecules; (2) It only changes interactions between the zinc ion and other atoms and does not affect force field parameters that model other interactions in the system; (3) It is a nonbonded model that is inherently capable to describe different zinc ligands and coordination modes. By optimizing two SLEF parameters as well as zinc van der Weals parameters through force matching based on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations, we have successfully developed the first SLEF force field (SLEF1) to describe zinc interactions. Extensive MD simulations of seven zinc enzyme systems with different coordination ligands and distinct chelation modes (four-, five-, and six-fold), including a binuclear zinc active site, yielded zinc coordination numbers and binding distances in good agreement with the corresponding crystal structures as well as ab initio QM/MM MD results. This not only demonstrates the transferability and adequacy of the new SLEF1 force field in describing a variety of zinc proteins but also indicates that this novel SLEF approach is a promising direction to explore for improving force field description of metal ion interactions.zh_CN
dc.description.sponsorshipNIH[R01-GM079223]; NSF[CHE-CAREER-0448156]; China Scholarship Councilzh_CN
dc.language.isoenzh_CN
dc.publisherAMER CHEMICAL SOCzh_CN
dc.titleA Transferable Nonbonded Pairwise Force Field to Model Zinc Interactions in Metalloproteinszh_CN
dc.typeArticlezh_CN


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