Higher peptide nonplanarity (ω) close to protein carboxy-terminal and its positive correlation with ψ dihedral-angle is evolved conferring protein thermostability

Maiti, Smarajit; Panja, Anindya Sundar; Bandopadhyay, Bidyut

doi:10.1016/j.pbiomolbio.2018.10.004

Progress in Biophysics and Molecular Biology

2019

DOI: 10.1016/j.pbiomolbio.2018.10.004

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Higher peptide nonplanarity (ω) close to protein carboxy-terminal and its positive correlation with ψ dihedral-angle is evolved conferring protein thermostability

Smarajit Maiti

Anindya Sundar Panja

Bidyut Bandopadhyay

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Cited by 3 publications

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“…During the verification attempt at ultrahigh resolution, protein structures were precisely analyzed and certain level of peptide nonplanarity was observed by Rosetta in 2013, but shorter peptide do not show no significant nonplanarity 36,37 . We also observed that the non-planarity is one of the major determinants in protein stability which is increasingly abundant in protein carboxy-terminal at increasing temperature 38 .…”

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

Panja

Maiti

Bandyopadhyay

2020

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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 ...

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confidence: 66%

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

Panja

Maiti

Bandyopadhyay

2020

Sci Rep

Self Cite

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The systematic codon usage bias has an important effect on genetic adaption in native species

Sundar Panja

2024

Gene

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Investigation of machine learning techniques on proteomics: A comprehensive survey

Sonsare¹,

Gunavathi

2019

Progress in Biophysics and Molecular Biology

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Higher peptide nonplanarity (ω) close to protein carboxy-terminal and its positive correlation with ψ dihedral-angle is evolved conferring protein thermostability

Cited by 3 publications

References 41 publications

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

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

The systematic codon usage bias has an important effect on genetic adaption in native species

Investigation of machine learning techniques on proteomics: A comprehensive survey

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