title: Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins.
abstract: Proteins belonging to the same class, having similar structures thus performing the same function are known to have different thermal stabilities depending on the source- thermophile or mesophile. The variation in thermo-stability has not been attributed to any unified factor yet and understanding this phenomenon is critically needed in several areas, particularly in protein engineering to design stable variants of the proteins. Toward this motive, the present study focuses on the sequence and structural investigation of a dataset of 373 pairs of proteins; a thermophilic protein and its mesophilic structural analog in each pair, from the perspectives of hydrophobic free energy, hydrogen bonds, physico-chemical properties of amino acids and residue-residue contacts. Our results showed that the hydrophobic free energy due to carbon, charged nitrogen and charged oxygen atoms was stronger in 65% of thermophilic proteins. The number of hydrogen bonds which bridges the buried and exposed regions of proteins was also greater in case of thermophiles. Amino acids of extended shape, volume and molecular weight along with more medium and long range contacts were observed in many of the thermophilic proteins. These results highlight the preference of thermophiles toward the amino acids with larger side chain and charged to make up greater free energy, better packing of residues and increase the overall compactness.
authors.affiliation: Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, India.
authors.forename: Dharma Rao
authors.initials: DR
authors.lastname: Tompa
authors.affiliation: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, ​Indian Institute of Technology Madras, Chennai 600036, India.
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
authors.affiliation: Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, India. Electronic address: sarabojik@gmail.com.
authors.forename: K
authors.initials: K
authors.lastname: Saraboji
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: Amino acid properties; Hydrophobic free energy; Thermal stability; Thermophilic proteins