Abstract
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 Å 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 in 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 protein data bank (PDB) and a homology model (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 to develop thermo stable proteins with strong salt bridges.
Highlights
The tertiary structure of a protein is made up of contributing and compromising weak forces [1] derived from the underlying amino acid sequence [2]
We studied a dataset of four structures from the protein data bank (PDB) and a homology model (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
Summary
The tertiary structure of a protein is made up of contributing and compromising weak forces [1] derived from the underlying amino acid sequence [2]. When conditions are recreated in the laboratory in which a protein is functional in the environment (high-temperature, high-salt, etc.), its primary sequence forms the same functional state [3, 4, 5]. These intrinsic codes of protein folding embedded in the primary sequence [2], which determines tertiary structure through the interconnection and interplay of weak forces and secondary structures [6]. The evolutionary pressures of the environment are responsible for the divergence of the primary sequence's codes in the orthologous set, which causes functional convergence in the related environment in tertiary structures [7]. Salt-bridge is a specific electrostatic interaction whose importance especially in protein structure specific binary design (core vs surface, local vs long-ranged, etc.), ISSN 0973-2063 (online) 0973-8894 (print)
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