The Identification of Metal Ion Ligand-Binding Residues by Adding the Reclassified Relative Solvent Accessibility.

Xiuzhen Hu,Zhenxing Feng,Xiaojin Zhang,Shan Wang,Liu Liu

doi:10.3389/fgene.2020.00214

Abstract

Many proteins realize their special functions by binding with specific metal ion ligands during a cell’s life cycle. The ability to correctly identify metal ion ligand-binding residues is valuable for the human health and the design of molecular drug. Precisely identifying these residues, however, remains challenging work. We have presented an improved computational approach for predicting the binding residues of 10 metal ion ligands (Zn2+, Cu2+, Fe2+, Fe3+, Co2+, Ca2+, Mg2+, Mn2+, Na+, and K+) by adding reclassified relative solvent accessibility (RSA). The best accuracy of fivefold cross-validation was higher than 77.9%, which was about 16% higher than the previous result on the same dataset. It was found that different reclassification of the RSA information can make different contributions to the identification of specific ligand binding residues. Our study has provided an additional understanding of the effect of the RSA on the identification of metal ion ligand binding residues.

Highlights

Proteins act as an indispensable material in the life process
The predicted results did not change much by adding other parameters. It indicated that the relative solvent accessibility (RSA) played an important role in the whole parameters for identifying the metal ion ligand-binding residues
We found that the predicted results of the same metal ion ligand were different for the four general prediction models, and the optimal predicted results of ten metal ion ligand-binding residues were from the differently specific prediction model

Summary

Introduction

Proteins act as an indispensable material in the life process. Many special functions of protein are realized by binding with specific ligands, and more than one-third of the proteins need to bind with metal ion ligands. Depending on the interaction between the metal ion ligands and specific binding residues, many metal ion ligands can affect the special protein functions (Caspers et al, 1990; Supek et al, 1997; Selvarengan and Kolandaivel, 2005). The basic principle of molecular drug design is that the interaction between the receptor and ligand must conform to the “Lock and Key Model,” and the interaction between the protein and ion ligands we studied conforms to the “Lock and Key Model.”. In the experiment of molecular drug design, protein crystallization, structure The basic principle of molecular drug design is that the interaction between the receptor and ligand must conform to the “Lock and Key Model,” and the interaction between the protein and ion ligands we studied conforms to the “Lock and Key Model.” In the experiment of molecular drug design, protein crystallization, structure

Methods

Results

Conclusion