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A simulation method of combinding boundary element method with generalized Langevin dynamics

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Chinese Science Bulletin 2000年第24期45卷 2227-2231页

作者： chen weizu LU Benzhuo WANG Cunxin Center tor Biomedical Engineering Beijing Polytechnic UniversityBeijing 100022China School of Life Science University of Science and Technology of ChinaHefei 230026China

A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as the mean force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model is taken for the friction kernel. A simulation study has been performed on the cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dynamics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.

关键词： potential of mean force of solvent boundary element method friction memory function generalized Langevin dynamics.

A holistic molecular docking approach for predicting protein-protein complex structure

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Science China(Life Sciences) 2010年第9期53卷 1152-1161页

作者： GONG XinQi LIU Bin CHANG Shan LI ChunHua chen weizu WANG CunXin College of Life Science and Bioengineering Beijing University of TechnologyBeijing 100124China

A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure *** article explains the detailed steps and applications for CAPRI Target *** CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

关键词： protein-protein complex structure prediction binding site molecular docking CAPRI

Salt and pH-dependent properties of native and mutant insulin

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Chinese Science Bulletin 2002年第6期47卷 464-466页

作者： MA Xiaohui LI Chunhua LU Benzhuo chen weizu WANG Cunxin XU Xiaojie Center for Biomedical Engineering Beijing Polytechnic UniversityBeijing 100022China Department of Astronomy and Applied Physics University of Science and Technology of ChinaHeifei 230026China College of Chemistry&Molecular Engineering Peking UniversityBeijing 100871China

A fast and effective model for predicting the salt and pH dependent properties of protein complexes is presented. It is based on the formal charge parameter sets of ionizable groups and applied in conjunction with the finite difference Poisson-Boltzmann (FDPB) method to calculate the electrostatic interactions. All simulations were performed on the native 2Zn insulin and its fast-acting mutants such as B9D (B9Ser→Asp), B9E (B9Aer→Glu), B9EB10D (B9Ser→ Glu, B10His→Asp), and B10D (B10His→Asp). The salt and pH dependent properties of these dimers were analyzed from the aspect of electrostatic interaction, and the theoretical basis of the fast-acting behavior of these mutants was explained. It is found that the results agree well with experimental observations.

关键词： formal charge electrostatic interaction insulin Pois-son-Boltzmann equation.

Development of a high-throughput assay for the HIV-1 integrase disintegration reaction

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Science China(Life Sciences) 2010年第2期53卷 241-247页

作者： HE HongQiu,LIU Bin,ZHANG XiaoYi,chen weizu & WANG CunXin College of Life Science and Bioengineering,Beijing University of Technology,Beijing 100124,China 1. College of Life Science and Bioengineering Beijing University of Technology Beijing 100124 China

Both HIV-1 integrase (IN) and the central catalytic domain of IN (IN-CCD) catalyze the disintegration reaction in *** this study,IN and IN-CCD proteins were expressed and purified,and a high-throughput format enzyme-linked immunosorbent assay (ELISA) was developed for the disintegration *** exhibited a marked preference for Mn2+ over Mg2+ as the divalent cation cofactor in ***,a known IN inhibitor,was found to be an IN-CCD *** assay is sensitive and specific for the study of disintegration reaction as well as for the in vitro identification of antiviral drugs targeting IN,especially targeting IN-CCD.

关键词： HIV-1 integrase IN-CCD disintegration high-throughput assay

Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

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Science China Chemistry 2007年第5期50卷 665-674页

作者： HU JianPing1,2, CHANG Shan1, chen weizu1 & WANG CunXin1 1 College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China 2 Department of Chemistry & Life Sciences, Leshan Normal University, Leshan 614004, China College of Life Science and Bioengineering Beijing University ofTechnologyBeijing 100022China Department of Chemistry & Life Sciences Leshan NormalUniversityLeshan 614004China

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2+ ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.

关键词： molecular docking, MD simulation, HIV-1 IN, drug design

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胰岛素六聚体在水溶液中的稳定性研究

化学学报 2002年第12期60卷 2129-2134页

作者：王维宴卢本卓陈慰祖王存新北京工业大学生物医学工程中心北京100022

用分子动力学(MD)模拟方法设计了两个模拟时间为 60 0ps的对比计算机模拟实验,研究了R6态的胰岛素六聚体在水溶液中的稳定性以及苯酚和锌离子对结构稳定性的影响.通过对MD模拟所得到的轨迹的分析发现,在维系胰岛素六聚体稳定性的因素中... 详细信息

用分子动力学(MD)模拟方法设计了两个模拟时间为 60 0ps的对比计算机模拟实验,研究了R6态的胰岛素六聚体在水溶液中的稳定性以及苯酚和锌离子对结构稳定性的影响.通过对MD模拟所得到的轨迹的分析发现,在维系胰岛素六聚体稳定性的因素中,静电相互作用和氢键起着主要的作用.对于包含锌离子和苯酚的体系,胰岛素六聚体的稳定性得到了增强;对不含锌离子和苯酚的体系,胰岛素六聚体的稳定性明显减弱,在这种情况下,胰岛素六聚体还表现出解聚的倾向.

关键词：水溶液胰岛素六聚体分子动力学模拟结构稳定性

Prediction of PK-specific phosphorylation site based on information entropy

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Science China(Life Sciences) 2008年第1期51卷 12-20页

作者： WANG MingHui, LI ChunHua, chen weizu & WANG CunXin College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China 1. College of Life Science and Bioengineering Beijing University of Technology Beijing 100022 China

Phosphorylation is a crucial way to control the activity of proteins in many eukaryotic organisms in vivo. Experimental methods to determine phosphorylation sites in substrates are usually restricted by the in vitro condition of enzymes and very intensive in time and labor. Although some in silico methods and web servers have been introduced for automatic detection of phosphorylation sites, sophisticated methods are still in urgent demand to further improve prediction performances. Protein primary se-quences can help predict phosphorylation sites catalyzed by different protein kinase and most com-putational approaches use a short local peptide to make prediction. However, the useful information may be lost if only the conservative residues that are not close to the phosphorylation site are consid-ered in prediction, which would hamper the prediction results. A novel prediction method named IEPP (Information-Entropy based Phosphorylation Prediction) is presented in this paper for automatic de-tection of potential phosphorylation sites. In prediction, the sites around the phosphorylation sites are selected or excluded by their entropy values. The algorithm was compared with other methods such as GSP and PPSP on the ABL, MAPK and PKA PK families. The superior prediction accuracies were ob-tained in various measurements such as sensitivity (Sn) and specificity (Sp). Furthermore, compared with some online prediction web servers on the new discovered phosphorylation sites, IEPP also yielded the best performance. IEPP is another useful computational resource for identification of PK-specific phosphorylation sites and it also has the advantages of simpleness, efficiency and con-venience.

关键词： phosphorylation prediction information entropy bioinformatics

Molecular dynamics simulation of the transmembrane subunit of BtuCD in the lipid bilayer

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Science China(Life Sciences) 2010年第5期53卷 620-630页

作者： SUN TingGuang1,2,LIU Ming1,chen weizu1 & WANG CunXin1 1College of Life Science and Bioengineering,Beijing University of Technology,Beijing 100124,China 2Department of Biological and Chemical Engineering,Guangxi University of Technology,Liuzhou 545006,China 1. College of Life Science and Bioengineering Beijing University of Technology Beijing 100124 China2. Department of Biological and Chemical Engineering Guangxi University of Technology Liuzhou 545006 China

Based on the crystal structure of the vitamin B12 transporter protein of Escherichia coli(BtuCD) a system consisting of the BtuCD transmembrane domain(BtuC) and the palmitoyloleoyl phosphatidylcholine(POPC) lipid bilayer was constructed in silica,and a more-than-57-nanosecond molecular dynamics(MD) simulation was performed on it to reveal the intrinsic functional motions of *** results showed that a stable protein-lipid bilayer was obtained and the POPC lipid bilayer was able to adjust its thickness to match the embedded BtuC which underwent relatively complicated *** results may help to understand the mechanism of transmembrane substrate transport at the atomic level.

关键词： BtuCD POPC functional motion principal component analysis

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材料法向光谱发射率测量方法研究

红外研究(A辑) 1987年第6期6卷 431-436页

作者：陈诗伟章卫祖中国科学院上海技术物理研究所

本文报道利用红外分光光度计和微机系统,采用二次测量技术,测量材料表面法向光谱发射率的基本原理和测试方法。推导出光谱发射率的计算公式,对引起测量误差的诸因素进行讨论,并实测了几种材料法向光谱发射率曲线。

关键词：黑体空腔加热炉热处理炉法向光谱发射率光辐射标准器黑体炉有效发射率测量方法