Side-chain dynamics analysis of KE07 series

详细信息    查看全文

• 作者：Xin Geng^a ; ^{gengxin_1986@163.com} ; Jiaogen Zhou^b ; ^{zhoujg@isa.ac.cn} ; Jihong Guan^a ; ^{jhguan@tongji.edu.cn}
• 关键词：Molecular dynamics ; Conformational entropy ; Generalized order parameter ; Protein design
• 刊名：Computational Biology and Chemistry
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：65
• 期：Complete
• 页码：148-153
• 全文大小：328 K
• 卷排序：65

文摘

The significant improvement of KE07 series in catalytic activities shows the great success of computational design approaches combined with directed evolution in protein design. Understanding the protein dynamics in the evolutionary optimization process of computationally designed enzyme will provide profound implication to study enzyme function and guide protein design. Here, side chain squared generalized order parameters and entropy of each protein are calculated using 50 ns molecular dynamics simulation data in both apo and bound states. Our results show a correlation between the increase of side chain motion amplitude and catalytic efficiency. By analyzing the relationship between these two values, we find side chain squared generalized order parameter is linearly related to side chain entropy, which indicates the computationally designed KE07 series have similar dynamics property with natural enzymes.