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Pyrococcus abyssi‘s Methionine-tRNA Synthetase Exhibits Hyperthermophilic Signatures in Its Weak Forces and Cavities

Sahini Banerjee
Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India

Amal Kumar Bandyopadhyay
Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
OrchideID Icon https://orcid.org/0000-0003-3499-5491

Published online:30th November, 2024

DOI: https://doi.org/10.52756/lbsopf.2024.e03.008

Keywords: Salt-bridge and microenvironment, energetics, weak forces, interior cavity

Abstract:

Weak forces, including the salt-bridge and the inner cavity, are of particular importance in protein folding and functioning in extreme environments. A comparative study on these may reveal insights into the intrinsic protein thermostability.  Here, we study salt-bridge energetics and its microenvironment, other weak interactions, and interior cavity properties of Methionine-tRNA synthetase from hyperthermophilic, Pyrococcus abyssi (PMRS) and mesophilic, E. coli (EMRS). Results show that PMRS, which is more hydrophilic, is uniquely distinct from EMRS. PMRS’s complete and domain-specific sequences are favorable for more salt-bridges and other weak interactions than EMRS’s. In the former, the recruitment of excess networked, long-ranged, and inter-domain salt bridges with energetically advantageous pairs and ME around them suggests that these properties originate from the underlying sequence. The fact that the net stability (ΔΔGnet) per salt bridge of PMRS exceeds that of EMRS denotes a novel design in its salt bridge. Furthermore, compared to EMRS, an excess of hydrogen bonds (HyB), hydrophobic, and other electrostatic interactions in PMRS’s core and surface demonstrate that these also contribute to its thermostability. Notably, PMRS has a much lower level of water-mediated HyB than EMRS, pointing to an altered strategy. In addition, compared to EMRS, a lower and higher mostly empty interior cavities in PMRS’s core and surface, respectively, indicate that surface engineering is more prominent in PMRS. We think that these differences are indeed related to the thermostability of the PMRS, which would apply to other similar systems.

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Life as Basic Science: An Overview and Prospects for Future [Volume: 3]

How to Cite
Sahini Banerjee and Amal Kumar Bandyopadhyay (2024). Pyrococcus abyssi‘s Methionine-tRNA Synthetase Exhibits Hyperthermophilic Signatures in its Weak Forces and Cavities. © International Academic Publishing House (IAPH), Dr. Somnath Das, Dr. Jayanta Kumar Das, Dr. Mayur Doke and Dr. Vincent Avecilla (eds.), Life as Basic Science: An Overview and Prospects for the Future Volume: 3, pp. 180-208. ISBN: 978-81-978955-7-9.
DOI: https://doi.org/10.52756/lbsopf.2024.e03.008

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