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.
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The authors would like to acknowledge the management of Vellore Institute of Technology, Vellore for providing the facilities and encouragement to carry out this work.
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Supplementary file1 Supplementary figure 1: (A) Multiple sequence alignment of AroE_Ecoli, AroE_Lismo, Ar-oE_Thet8 and AroE_Metka. (B) Structural superimposition of AroE protein. Color scheme: Green—Lismo, Blue—Thet8, Magneta—Ecoli and Red—Metka. (C) Table describing structural similarity score and Root Mean Square Devi-ation score of backbone (RMSD) (PNG 320 kb)
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Supplementary file2 Supplementary figure 2: Number of hydrogen bonds. X-axis represents species name with temper-ature. Y-axis represents the number of hydrogen bonds. Color scheme: Red—300 K, Blue—283 K and Cyan—395 K (PNG 39 kb)
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Supplementary file3 Supplementary figure 3: Average bond length of hydrogen bond for each snapshots during the simulation. X-axis represents the name of the species and temperature. Y-axis represents the average hydrogen bond length (TIF 3281 kb)
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Kamalesh, D., Nair, A., Sreeshma, J. et al. Statistical and molecular dynamics (MD) simulation approach to investigate the role of intrinsically disordered regions of shikimate dehydrogenase in microorganisms surviving at different temperatures. Extremophiles 24, 831–842 (2020). https://doi.org/10.1007/s00792-020-01198-6
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DOI: https://doi.org/10.1007/s00792-020-01198-6