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Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges.

Panja AS, Bandopadhyay B, Maiti S - PLoS ONE (2015)

Bottom Line: 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 60% thermophiles are found with higher number of salt bridges in this study.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.

View Article: PubMed Central - PubMed

Affiliation: Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India.

ABSTRACT

Introduction: 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.

No MeSH data available.


Distribution and deviations of individual values of isoelectric point and charge of 50 thermophilic and their homologue mesophilic proteins are shown in dot plot and the average values (mean ± SE) of those are plotted in the inset as bar diagram.The backbone conformations of both types of proteins were verified by the Peptide Property Calculator server https://www.genscript.com/ssl-bin/site2/peptide_calculation.cgi. The level of significances of the difference of mean are calculated by Student’s t test and represented on the bar as “*”. *p<0.05 and **p<0.01.
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pone.0131495.g003: Distribution and deviations of individual values of isoelectric point and charge of 50 thermophilic and their homologue mesophilic proteins are shown in dot plot and the average values (mean ± SE) of those are plotted in the inset as bar diagram.The backbone conformations of both types of proteins were verified by the Peptide Property Calculator server https://www.genscript.com/ssl-bin/site2/peptide_calculation.cgi. The level of significances of the difference of mean are calculated by Student’s t test and represented on the bar as “*”. *p<0.05 and **p<0.01.

Mentions: Present results from 50 thermophilic and 50 mesophilic proteins suggest that hydrophobicity in a larger number of thermophilic proteins was consistently higher than their homologous mesophiles (Fig 2). Hydrophilicity, up to a certain level was lower in a greater number of thermophilic proteins, but at higher levels it was comparatively higher in these proteins. The number of proteins is also shown to be differentially segregated according to the ranges of their isoelectric points and charges (Fig 2). The segregation of an individual value of isoelectric point and charges from each of 50 thermophilic and 50 mesophilic proteins are presented in Fig 3. And the mean and SE values of these parameters presented in the inset. These data show a significantly lower isoelectric point (p<0.05) and charge (p<0.01) in thermophilic proteins. When the average charge in mesophiles is found to be a positive value (at neutral pH), the same is found to be negative in thermophiles (Fig 3).


Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges.

Panja AS, Bandopadhyay B, Maiti S - PLoS ONE (2015)

Distribution and deviations of individual values of isoelectric point and charge of 50 thermophilic and their homologue mesophilic proteins are shown in dot plot and the average values (mean ± SE) of those are plotted in the inset as bar diagram.The backbone conformations of both types of proteins were verified by the Peptide Property Calculator server https://www.genscript.com/ssl-bin/site2/peptide_calculation.cgi. The level of significances of the difference of mean are calculated by Student’s t test and represented on the bar as “*”. *p<0.05 and **p<0.01.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4503463&req=5

pone.0131495.g003: Distribution and deviations of individual values of isoelectric point and charge of 50 thermophilic and their homologue mesophilic proteins are shown in dot plot and the average values (mean ± SE) of those are plotted in the inset as bar diagram.The backbone conformations of both types of proteins were verified by the Peptide Property Calculator server https://www.genscript.com/ssl-bin/site2/peptide_calculation.cgi. The level of significances of the difference of mean are calculated by Student’s t test and represented on the bar as “*”. *p<0.05 and **p<0.01.
Mentions: Present results from 50 thermophilic and 50 mesophilic proteins suggest that hydrophobicity in a larger number of thermophilic proteins was consistently higher than their homologous mesophiles (Fig 2). Hydrophilicity, up to a certain level was lower in a greater number of thermophilic proteins, but at higher levels it was comparatively higher in these proteins. The number of proteins is also shown to be differentially segregated according to the ranges of their isoelectric points and charges (Fig 2). The segregation of an individual value of isoelectric point and charges from each of 50 thermophilic and 50 mesophilic proteins are presented in Fig 3. And the mean and SE values of these parameters presented in the inset. These data show a significantly lower isoelectric point (p<0.05) and charge (p<0.01) in thermophilic proteins. When the average charge in mesophiles is found to be a positive value (at neutral pH), the same is found to be negative in thermophiles (Fig 3).

Bottom Line: 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 60% thermophiles are found with higher number of salt bridges in this study.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.

View Article: PubMed Central - PubMed

Affiliation: Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India.

ABSTRACT

Introduction: 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.

No MeSH data available.