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Bioinformation. 2019 Mar 15;15(3):214-225. doi: 10.6026/97320630015214. eCollection 2019.

Analysis of salt-bridges in prolyl oligopeptidase from Pyrococcus furiosus and Homo sapiens.

Author information

1
Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India.
2
Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India.
3
Department of Biological Sciences, ISI, Kolkata, West Bengal, India.

Abstract

Hyper thermophilic archaea not only tolerate high temperature but also operate its biochemical machineries, normally under these conditions. However, the structural signatures in proteins that answer for the hyper thermo-stability relative to its mesophilic homologue remains poorly understood. We present comparative analyses of sequences, structures and salt-bridges of prolyl-oligopeptidase from Pyrococcus furiosus (pfPOP - PDB ID: 5T88) and human (huPOP - PDB ID: 3DDU). A similar level of hydrophobic and hydrophilic residues in pfPOP and huPOP is observed. A low level of interactions between shell-waters and atom-types in pfPOP indicated hyper thermophilic features are negligible. Salt-bridge-forming-residues (sbfrs) are high in pfPOP's core and surface (pfPOP). Increased sbfrs largely indicate specific-electrostatic is important for thermo stability in pfPOP. Four classes of sbfrs are found namely positionally non-conservative (PNCS), conservative (PCS), unchanged (PU) and interchanged (PIC) type of substitutions. PNCS-sbfrs constitutes 28% and it is associated with the topology of pfPOP at high temperature. PCS helps to increase the salt-bridge population. It is also found that PU maintains similar salt-bridges at the active site and other binding sites while PIC abolishes mesophilic patterns.

KEYWORDS:

Thermo stability; electrostatics; prolyl oligo peptidase; salt bridge; salt bridge design

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