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。
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