Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production

Mingyu Wu; Yu Sun; Meiru Zhu; Laiyu Zhu; Junhong Lü; Feng Geng

doi:10.1021/acsomega.1c00798

Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production

ACS Omega. 2021 Apr 15;6(16):10975-10983. doi: 10.1021/acsomega.1c00798. eCollection 2021 Apr 27.

Authors

Mingyu Wu¹, Yu Sun¹, Meiru Zhu¹, Laiyu Zhu¹, Junhong Lü^{1

2}, Feng Geng¹

Affiliations

¹ School of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China.
² Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China.

Abstract

Allosteric proteins are considered as one of the most critical targets to design cell factories via synthetic biology approaches. Here, we proposed a molecular dynamics-based allosteric prediction method (MBAP) to screen indirect-binding sites and potential mutations for protein re-engineering. Using this MBAP method, we have predicted new sites to relieve the allosteric regulation of threonine dehydrogenase (TD) by isoleucine. An obtained mutation P441L has been verified with the ability to significantly reduce the allosteric regulation of TD in vitro assays and with the fermentation application in vivo for amino-acid production. These findings have proved the MBAP method as an effective and efficient predicting tool to find new positions of the allosteric enzymes, thus opening a new path to constructing cell factories in synthetic biology.