Predicting DNA‐binding protein and coronavirus protein flexibility using protein dihedral angle and sequence feature. Issue 4 (9th November 2022)

• Record Type: Journal Article
• Authors: Wang, Wei; Su, Xili; Liu, Dong; Zhang, Hongjun; Wang, Xianfang; Zhou, Yun
• Is Part Of: Proteins. Volume 91:Issue 4(2023)
• Page Start: 497
• Page End: 507
• Publication Date: 2022-11-09
• Subjects: B‐factor -- protein dihedral angle -- protein flexibility -- protein structure -- support vector machine; Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.26443
• Languages: English
• ISSNs: 0887-3585

Abstract

Abstract: The flexibility of protein structure is related to various biological processes, such as molecular recognition, allosteric regulation, catalytic activity, and protein stability. At the molecular level, protein dynamics and flexibility are important factors to understand protein function. DNA‐binding proteins and Coronavirus proteins are of great concern and relatively unique proteins. However, exploring the flexibility of DNA‐binding proteins and Coronavirus proteins through experiments or calculations is a difficult process. Since protein dihedral rotational motion can be used to predict protein structural changes, it provides key information about protein local conformation. Therefore, this paper introduces a method to improve the accuracy of protein flexibility prediction, DihProFle (Prediction of DNA‐binding proteins and Coronavirus proteins flexibility introduces the calculated dihedral Angle information). Based on protein dihedral Angle information, protein evolution information, and amino acid physical and chemical properties, DihProFle realizes the prediction of protein flexibility in two cases on DNA‐binding proteins and Coronavirus proteins, and assigns flexibility class to each protein sequence position. In this study, compared with the flexible prediction using sequence evolution information, and physicochemical properties of amino acids, the flexible prediction accuracy based on protein dihedral Angle information, sequence evolution information and physicochemical properties of amino acids improved by 2.2% and 3.1% in the nonstrict and strict conditions, respectively. And DihProFle achieves better performance than previous methods for protein flexibility analysis. In addition, we further analyzed the correlation of amino acid properties and protein dihedral angles with residues flexibility. The results show that the charged hydrophilic residues have higher proportion in the flexible region, and the rigid region tends to be in the angular range of the protein dihedral angle (such as the ψ angle of amino acid residues is more flexible than rigid in the range of 91°–120°). Therefore, the results indicate that hydrophilic residues and protein dihedral angle information play an important role in protein flexibility.