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Insight into the Salt Bridge of Malate Dehydrogenase from Halobacterium salinarum and Escherichia coli



Amal Kumar Bandyopadhyay*,1, Rifat Nawaz Ul Islam2,$, Debanjan Mitra1,$, Sahini Banerjee3,$, Saba Yasmeen4,$ & Arunava Goswami3



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; 4Department of Botany and Microbiology, Acharya Nagarjun University, Nagarjun Nagar, Andra Pradesh, India; $equally contributed



Amal Kumar Bandyopadhyay - E-mail:; *corresponding author


Article Type

Research Article



Received January 3, 2019; Revised February 11, 2019; Accepted February 11, 2019; Published February 28, 2019



Halophilic proteins have greater abundance of acidic over basic residues in sequence. In structure, the surface is decorated by negative charges, with lower content of lysine residues. Using sequence BLOCK and 3D model of malate dehydrogenase from halophilic archaea (Halobacterium salinarum; hsMDH) and X-ray structure of mesophilic bacteria (E. coli; ecMDH), we show that not only acidic and basic residues have higher mean relative abundance (MRA) and thus, impart higher polarity to the sequences, but also show their presence in the surface of the structure of hsMDH relative to its mesophilic counterpart. These observations may indicate that both the acidic and the basic residues have a concerted role in the stability of hsMDH. Analysis on salt bridges from hsMDH and ecMDH show that in the former, salt bridges are highly intricate, newly engineered and global in nature. Although, these salt bridges are abundant in hsMDH, in the active site the design remains unperturbed. In high salt where hydrophobic force is weak, these salt bridges seem to play a major role in the haloadaptation of the tertiary structure of hsMDH. This is the first report in such an observation.



Malate dehydrogenase; Stability; Halophilic; Salt Bridge; Sequence; Homology model



Bandyopadhyay et al. Bioinformation 15(2): 95-103 (2019)


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.