Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques

Jinyin Zha; Mingyu Li; Ren Kong; Shaoyong Lu; Jian Zhang

doi:10.1016/j.jmb.2022.167481

Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques

J Mol Biol. 2022 Sep 15;434(17):167481. doi: 10.1016/j.jmb.2022.167481. Epub 2022 Feb 4.

Authors

Jinyin Zha¹, Mingyu Li¹, Ren Kong², Shaoyong Lu³, Jian Zhang⁴

Affiliations

¹ Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
² Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China.
³ Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China. Electronic address: lushaoyong@yeah.net.
⁴ Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China. Electronic address: Jian.zhang@sjtu.edu.cn.

PMID: 35131258
DOI: 10.1016/j.jmb.2022.167481

Abstract

Allostery is a phenomenon that the protein activity is regulated when a non-functional site on it is bounded. This phenomenon is important in life process and disease therapy. However, it is difficult to study allostery due to the lack of knowledge. Facing this demand, we have created Allosteric Database (ASD) 10 years before to collect numerous kinds of allosteric data. In this review, we will introduce the 4 categories of data in ASD. For each category, we further reviewed how researchers applied ASD data to conduct studies. We focused on their research topics, analytical methods and conclusions. Several discoveries of new drug targets and allosteric modulators driven by ASD are also summarized. We hope this review could inspire researchers with new utilities of ASD data.

Keywords: allosteric drug; allosteric mechanism; allosteric site; machine learning; protein sequence.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Allosteric Regulation
Allosteric Site
Databases, Protein*
Humans
Molecular Targeted Therapy*
Proteins* / chemistry

Substances

Proteins