Title

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

Authors

Amal Kumar Bandyopadhyay^*,1, Rifat Nawaz Ul Islam^2,$, Debanjan Mitra^1,$, Sahini Banerjee^3,$ and
Arunava Goswami³

Affiliation

¹Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India; ²Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India; ³Department of Biological Sciences, ISI, Kolkata, West Bengal, India; ^$equal contribution;

Email

Amal Kumar Bandyopadhyay – E-mail: akbanerjee@biotech.buruniv.ac.in; *corresponding author

Article Type

Research Article

Date

Received January 9, 2019; Revised March 9, 2019; Accepted March 11, 2019; Published March 15, 2019

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 a 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 thermo-philic
features are negligible. Salt-bridge-forming-residues (sbfrs) are high in pfPOP 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; salt bridge; salt bridge design; electrostatics; prolyl oligo peptidase

Citation

Bandyopadhyay et al. Bioinformation 15(3): 214-225 (2019)

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.