Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges

Bidyut Bandyopadhyay,Anindya S. Panja,Smarajit Maiti

doi:10.1038/s41598-020-58825-7

Bidyut Bandyopadhyay, Anindya S. Panja + Show 1 more

Open Access

https://doi.org/10.1038/s41598-020-58825-7

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Journal: Scientific Reports	Publication Date: Feb 4, 2020
Citations: 67	License type: open-access

Affiliation: Vidyasagar University

Abstract

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.

Highlights

Several organisms, microorganisms survive in a wide range of harsh environments including extreme temperature, pH, and salt concentration
In the current study we found more hydrophobicity (45–55%) in halophilic, 45–59% in acidic and 49–53% in alkaline with thermophilic proteins respectively[11] whereas, it was little higher in psychrophilic proteins
Number of glutamine are rich in halophilic protein it is little higher in acidic and alkaline stable proteins

Summary

Result

Physiochemical property along with amino acid composition of halophilic, acidophilic, alkalophilic, thermophilic, psychrophilic and their corresponding homologous normal protein. The hydrophobic neutral non polar amino acid valine was abundant (25%) in alkaline and halophilic proteins in their chain with >12% of abundance. Some higher amounts (Fig. S2) of polarity were shown by halophilic proteins to attract aqueous solvent for better interaction in their folding These properties may be a potential parameter to estimate protein’s functional and structural stability[42]. An increase in the proportion of hydrophobicity in the protein has indicated the presence of higher number of the smallest non polar amino acids like alanine, glycine and lyophilic valine, which was positively correlated with our result. Another acidic protein acetyl-xylan esterase (1BS9) exhibited sixteen non planar peptide bonds whereas non acidic protein (1QOZ) didn’t showed non planarity

Discussion and Conclusion

Findings

Materials and Methods