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

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.

Keywords

• Protein-nucleic acids
• interaction information
• protein structure