PSBC model and its application in the folding

(第一九四期) PSBC model and its application in the folding of α-helices and β-sheets Prof. Dawei Zhang Henan University of Science and Technology 2018年 7月24日(周二) 上午 10: 00 -11: 30 新波谱楼M-1017报告厅 报告人简介：张大为于1993年毕业于南开大学化学 系，1996年在南开大学新能源材料化学研究所获得 硕士学位后留校任教。1999年赴美留学，2005年在 美国纽约大学化学系获得博士学位。之后在美国纽 约大学医学院从事博士后研究，2006至 2008年在纽 约大学任职助理研究员。2008年应聘到新加坡南洋 理 大学任教。2016年回国，就职于河南科技大学 物理 程学院。主要研究方向是蛋白质折叠模拟， 蛋白质-配体相互作用以及用于蛋白质模拟的极化力 场。 Abstract： In this presentation, a new charge model named polarized structurespecific backbone charge (PSBC) model will be introduced. In the model, two alanine molecules conforming to geometries of backbone hydrogen bonds formed in α-helix, parallel, and anti-parallel β-sheet are subjected respectively to obtain functional forms that defines a relationship between hydrogen bond length and charge transferred between hydrogen bond donor and acceptor during formation. Both hydrogen bond length and type of secondary structure are considered together to determine whether to prompt charge update and which formula is going to be applied. This factor renders PSBC a structure-specific polarization model which may be useful in improving the efficiency of folding simulations for proteins with multiple secondary structures. By periodically updating the charges of atoms involved in backbone hydrogen bonding during molecular dynamics simulation, the polarization of intraprotein hydrogen bond can be included to some extent. Benchmark tests have been done to check the performance of the PSBC model in the folding of helical peptides with different helical propensities, trp-zippers, and a mixed-fold protein with ββα configuration. The application of the PSBC model in the study of prion protein will be also introduced. 主办单位: 武汉物数所理论与交叉研究部