Several organisms, specifically microorganisms survive in a wide range of harsh environments including extreme temperature, pH, and salt concentration. We analyzed systematically a large number of protein sequences with their structures to understand their stability and to discriminate extremophilic proteins from their non-extremophilic orthologs. our results highlighted that the strategy for the packing of the protein core was influenced by the environmental stresses through substitutive structural events through better ionic interaction. Statistical analysis showed that a significant difference in number and composition of amino acid exist among them. The negative correlation of pairwise sequence alignments and structural alignments indicated that most of the extremophile and non-extremophile proteins didn't contain any association for maintaining their functional stability. A significant numbers of salt bridges were noticed on the surface of the extremostable proteins. The Ramachandran plot data represented more occurrences of amino acids being present in helix and sheet regions of extremostable proteins. We also found that a significant number of small nonpolar amino acids and moderate number of charged amino acids like Arginine and Aspartic acid represented more nonplanar omega angles in their peptide bond. thus, extreme conditions may predispose amino acid composition including geometric variability for molecular adaptation of extremostable proteins against atmospheric variations and associated changes under natural selection pressure. the variation of amino acid composition and structural diversifications in proteins play a major role in evolutionary adaptation to mitigate climate change. Modifications in protein structures from organisms that have evolved under extreme environmental conditions differ in how they maintain optimum activity. For example, in the case of halophiles, their optimal growth is associated with their optimal metabolic functions. Heat tolerant organisms are classified as thermophiles, which have optimum growth temperature (OGT) in the range of 45 °C-80 °C and hyper thermophiles with OGT of above 80 °C. Psychrophiles are the organisms which grow on cold condition, that have OGT below 10 °C. Alkalophiles are found in an alkaline p H of more than 9. Alkalophiles and haloalkaliphiles are isolated from extremely alkaline-saline environments, alkaline soil and film such as the Western soda lakes of the United States and Rift valley lakes from East Africa, these are also available from natural environments 1,2. Most of the acidophilic microorganisms survive in low pH by modifying their intracellular protein along with their genome. Evolutionarily conserved protein structures and their sequences showed similarities in their functions but often they differ in their sequence pattern 3. Crystallographic and NMR structures sometimes differ from each other due to their specific experimental condition and retrieval oucome 4-7. The report revealed that proteins with >40% sequence identity may also ...

IntroductionProtein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications.MethodsPresently, 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.ResultsPresent results strongly suggest that nonpolar smaller volume amino acids Ala (χ 2 = 238.54, p<0.001) and Gly (χ 2 = 73.35, p<0.001) are highly and Val moderately (χ 2 = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ 2~20.0, 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.ConclusionsPresent 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 a...

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Green metal nanoparticles (NPs) have emerged as efficient biofilm inhibitors. Citrus macroptera (CM) fruit extract mediated iron (Fe) NPs, i. e., CM-FeNPs were thus synthesized for studying biofilm inhibition property. The shape (spherical), size (12 nm), and crystallinity (α-Fe 0 bcc) of the CM-FeNPs were confirmed by studying mainly Transmission Electron microscopy (TEM) and X-ray Diffractometer (X-RD) tools. The particles inhibit biofilm growth of a bacteria Pseudomonas aeruginosa (P. aeruginosa) by inhibiting the functions of extracellular polymeric substances (EPS) and virulence factors to ∼ 80 %. Scanning Electron microscopy (SEM) images of the bacteria in presence of the CM-FeNPs (4600 nM) in combination with azithromycin (AZI) evidence the inhibition of biofilm growth > 80 %. Molecular docking studies support experimental findings and result significant negative binding energies (e. g., isoplatydesmine/LasR: À 8.25 kcal/mole, isoplatydesmine/MvfR: À 7.56 kcal/mole) from bioactive molecules/biofilm proteins interactions. Thus, CM-FeNPs could be considered as potential biofilm inhibitors, and as an alternative to antibiotic drugs.

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