Title

Salt-Bridges in the Microenvironment of Stable Protein Structures

Authors

Amal Kumar Bandyopadhyay^{1, $,*}, Rifat Nawaz Ul Islam^1,2,$, & Niladri Hazra²

Affiliation

¹Department of Biotechnology, University of Burdwan, West Bengal, India; ²Department of Zoology, University of Burdwan, West Bengal, India

Email

^$Equally contributed; Amal Kumar Bandyopadhyay - E-mail: akbanerjee@biotech.buruniv.ac.in; *Corresponding author

Article Type

Research Article

Date

Received October 10, 2020; Revised October 23, 2020; Accepted October 23, 2020; Published November 30, 2021

Salt-bridges (sb) play an important role in the folding and stability of proteins. This is deduced from the evaluation of net energy in the microenvironments (ME, residues that are 4Å away from positive and negative partners of salt-bridge and interact with them). ME’s act as a determinant of net-energy due to the intrinsic features by the sequence. The stability of extremophilic proteins is due to the presence of favorable residues at the ME without any unfavorable residues. We studied a dataset of four structures from the pdb and a homology model (PDB ID: 1HM5) to gain insights on this issue. Data shows that the presence of isolated charges and polar residues in the core of extremophilic proteins helps in the formation of stable salt-bridges with reduced desolvation. Thus, site-specific mutations with favorable residues at the ME will help develop thermo stable proteins with strong salt bridges.

Keywords

Salt-Bridges, microenvironment, Stable Protein Structures

Citation

Bandyopadhyay et al. Bioinformation 16(11): 900-909 (2020)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.