title: Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges.
abstract: BACKGROUND
  Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications.
  
  
  METHODS
  Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins.
  
  
  RESULTS
  Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ2 = 238.54, p<0.001) and Gly (χ2 = 73.35, p<0.001) are highly and Val moderately (χ2 = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ2~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of cis peptide, loop/ turn and outlier in thermophiles. Pearson's correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement.
  
  
  CONCLUSIONS
  Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.
authors.affiliation: Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India.
authors.forename: Anindya Sundar
authors.initials: AS
authors.lastname: Panja
authors.affiliation: Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India.
authors.forename: Bidyut
authors.initials: B
authors.lastname: Bandopadhyay
authors.affiliation: Post Graduate Department of Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India.
authors.forename: Smarajit
authors.initials: S
authors.lastname: Maiti
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011489:Protein Denaturation; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry*; D044366:Transition Temperature
chemical_list: D000596:Amino Acids; D011506:Proteins