Statistical and molecular dynamics (MD) simulation approach to investigate the role of intrinsically disordered regions
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ORIGINAL PAPER
Statistical and molecular dynamics (MD) simulation approach to investigate the role of intrinsically disordered regions of shikimate dehydrogenase in microorganisms surviving at different temperatures Damodaran Kamalesh1 · Aditya Nair2 · Jaya Sreeshma2 · Pattathil Sasikumar Arundhathi2 · Chinnappan Sudandiradoss2 Received: 6 March 2020 / Accepted: 3 September 2020 © Springer Japan KK, part of Springer Nature 2020
Abstract Hyperthermophiles, a subset of prokaryotes that thrive in adverse temperatures, potentially utilize the protein molecular biosystem for maintaining thermostability in a wide range of temperatures. Recent studies revealed that these organisms have smaller proportions of intrinsically disordered proteins. In this study, we performed sequence and structural analysis to investigate the maintenance of protein conformation and their stability at different temperatures. The sequence analysis reveals the higher proportion of charged amino acids are responsible for preventing the helix formation and, hence, become disordered regions. For structural analysis, we chose shikimate dehydrogenase from four species, namely Listeria monocytogenes, Escherichia coli, Thermus thermophilus, and Methanopyrus kandleri, and evaluated the protein adaptation at 283 K, 300 K, and 395 K temperatures. From this investigation, we found more residues of shikimate dehydrogenase prefer an order-to-disorder transition at 395 K only for hyperthermophilic species. The solvent-accessible surface area (SASA) and hydrogen-bond analysis revealed that the tertiary conformation and the number of hydrogen bonds for hyperthermophilic shikimate dehydrogenase are highly preserved at 395 K, compared to 300 K. Our simulation results conjointly provide shikimate dehydrogenase of hyperthermophile which resists high temperatures through stronger protein tertiary conformations. Keywords Thermophiles · Shikimate dehydrogenase · Intrinsically disorder regions · Molecular dynamics simulation
Introduction Discovering micro-fossils of prokaryotes demonstrates that the existence of life was about 3.5–3.9 billion years ago. Steadily, life has adapted from deep-sea hydrothermal vents to the height of Himalayas, from boiling waters of hot springs to the Communicated by M. Moracci. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00792-020-01198-6) contains supplementary material, which is available to authorized users. * Chinnappan Sudandiradoss [email protected] 1
Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
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cold spot areas (Razvi and Scholtz 2006). The survival power of bacteria in extreme cold and hot temperatures has been a puzzle to the scientific community for decades, resulting in constant scrutiny of molecular-level mechanisms in bacteria
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