InPrNa: A Tool for Insight Into Protein–Nucleic Acids Interaction Information

Wei Wang,Hongjun Zhang,Keliang Li,Hehe Lv,Yuan Zhao,Shiguang Zhang

doi:10.1109/access.2019.2943748

Abstract

Protein-nucleic acids bindings play key roles in many biological processes. However, the biological mechanisms underlying these interactions are not fully understood. Understanding the interface features between protein and nucleic acids may offer insights into how proteins are coupled with nucleic acids. There is a lack of tools that insight into the features of interface in a protein at present. In this work, we developed the InPrNa tool, a graphical tool for protein-nucleic acids complexes that works seamlessly within the PyMOL and gives quick results including 3D visualization for the residue's structure. InPrNa provides three distinct visualization modes to highlight interface, detecting interface residues with different distance between protein and nucleic acid, marking physicochemical properties of the interface residues, and displaying three spatial structures of the interface residues. We also demonstrate the effectiveness of InPrNa's algorithm by contrast DNA binding proteins (DBPs) and RNA binding proteins (RBPs). These results show that DBPs and RBPs have significant differences in amino acids distribution and structural distribution. InPrNa may help for analysis the interface characteristics of proteins-nucleic acids in PyMOL, and can be particularly useful in rapidly pinpointing the interaction mode of proteins-nucleic acids interface. Availability: Freely available at https://github.com/HNUBioinformatics.

Highlights

Nucleic acids binding proteins (NBPs) are a type of proteins that are composed of amino acids binding domains and have specific or general affinities for either
In this work, we have developed the InPrNa tool, an easy-to-use PyMOL plugin that can analyze the physicochemical properties of NBPs and present them in an easy to understand manner
The users can visually observe some of the physicochemical properties of these proteins by InPrNa, which will help researchers to understand in depth how this specific identification occurs

Summary

Introduction

Nucleic acids binding proteins (NBPs) are a type of proteins that are composed of amino acids binding domains and have specific or general affinities for either. The proteins are essential and ubiquitous proteins involved in many biological processes, such as nucleic acids replication, transcription, nucleic acids repair and gene expression [1]. That the specific DNA sequences or certain nucleobases can be identified and bound by nucleic acids binding proteins. Since the structure and biological mechanism is not fully understood, the interface of the proteins needs further analysis. The analysis and visualization of protein interface are used to find protein-nucleic acids binding features, and can help to explain the interaction mechanism of protein and nucleic acids

Methods

Conclusion