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计算机辅助酶设计—基于酶催化循环的软件工具介绍

嘉宾:蒲中机 博士,大连理工大学
主持人:汤文
摘要:
酶作为理想的催化剂,显示出显著的反应速率、高立体化学和区域选择性以及温和的反应条件,使其成为工业应用的理想选择。进化显示了酶的可塑性,但较大的序列空间使得酶的设计和工程化成为瓶颈。随着人们对酶的作用机理的了解,开发一种虚拟筛选酶突变库的方法成为可能,就像虚拟筛选药物一样。酶催化循环分为三个过程:底物结合、化学反应和产物释放。对于底物结合:使用flex_ddg、alchemical free energy(TI)、MMPBSA/MMGBSA和前反应构象数等评估突变后底物亲和力的变化。对于化学反应:从过渡态理论的观点来看,一个关键的挑战是能垒的计算,酶的相对活性依赖于限速步骤步骤的能垒。主要有两种方法来降低限速步骤的能垒,去稳基态和稳定过渡态。因此,有必要制定一种快速、准确的protocol来对限速步骤的能垒进行排序。对于产物释放:通过CAVER等通道分析软件,结合加速采样分子动力学模拟,确定产物释放路径、瓶颈残基和关键相互作用的氨基酸残基。本报告主要介绍围绕酶催化循环进行计算机辅助设计酶(鉴定热点残基)或者计算机直接进化酶(突变库虚拟筛选)的软件工具和方法协议,突破设计和工程化酶的瓶颈。

作者: 蒲中机

中机是大连理工大学在读博士,擅长生物体系分子模拟领域,精通软件Amber,Gromacs,autodock,ledock,modeller ...;目前运营微信公众号生物研究生,搜索公众号shengwuyanjiusheng,可关注



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