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Salt-Bridges in the Microenvironment of Stable Protein Structures


Amal Kumar Bandyopadhyay1, $,*, Rifat Nawaz Ul Islam1,2,$, & Niladri Hazra2



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



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


Article Type

Research Article



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 4 away from positive and negative partners of salt-bridge and interact with them). MEs 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.



Salt-Bridges, microenvironment, Stable Protein Structures



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


Edited by

P Kangueane






Biomedical Informatics



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.