Side-chain dynamics analysis of KE07 series.
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 50ns 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.
Department of Computer Science and Technology, Tongji University, Shanghai 201804, China. Electronic address: gengxin_1986@163.com.
Xin
X
Geng
The Institute of Subtropical Agriculture, China Academy of Sciences, Changsha 410125, China. Electronic address: zhoujg@isa.ac.cn.
Jiaogen
J
Zhou
Department of Computer Science and Technology, Tongji University, Shanghai 201804, China. Electronic address: jhguan@tongji.edu.cn.
Jihong
J
Guan
D002384:Catalysis; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
Conformational entropy; Generalized order parameter; Molecular dynamics; Protein design