Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins
[Display omitted] •Systematic structural study on larger dataset of thermophilic-mesophilic homologues.•Factors responsible for increased stability of thermophilic proteins are explored.•Hydrophobic free energy due to C, N+ and O atoms are stronger in thermophiles.•H-bonds in buried to exposed regio...
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Published in | Journal of molecular graphics & modelling Vol. 64; pp. 85 - 93 |
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Language | English |
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Elsevier Inc
01.03.2016
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Abstract | [Display omitted]
•Systematic structural study on larger dataset of thermophilic-mesophilic homologues.•Factors responsible for increased stability of thermophilic proteins are explored.•Hydrophobic free energy due to C, N+ and O atoms are stronger in thermophiles.•H-bonds in buried to exposed region, medium & long range contacts gives stability.•Large sidechain/charged residues results better free energy, packing and stability.
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. |
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AbstractList | [Display omitted]
•Systematic structural study on larger dataset of thermophilic-mesophilic homologues.•Factors responsible for increased stability of thermophilic proteins are explored.•Hydrophobic free energy due to C, N+ and O atoms are stronger in thermophiles.•H-bonds in buried to exposed region, medium & long range contacts gives stability.•Large sidechain/charged residues results better free energy, packing and stability.
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. 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. |
Author | Gromiha, M.Michael Tompa, Dharma Rao Saraboji, K. |
Author_xml | – sequence: 1 givenname: Dharma Rao surname: Tompa fullname: Tompa, Dharma Rao organization: Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, India – sequence: 2 givenname: M.Michael surname: Gromiha fullname: Gromiha, M.Michael organization: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India – sequence: 3 givenname: K. orcidid: 0000-0002-4876-4443 surname: Saraboji fullname: Saraboji, K. email: sarabojik@gmail.com, saraboji@scbt.sastra.edu organization: Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, India |
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Keywords | Thermophilic proteins Hydrophobic free energy Amino acid properties Thermal stability |
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•Systematic structural study on larger dataset of thermophilic-mesophilic homologues.•Factors responsible for increased stability of... Proteins belonging to the same class, having similar structures thus performing the same function are known to have different thermal stabilities depending on... |
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SubjectTerms | Amino acid properties Amino acids Amino Acids - chemistry Chains Charging Contact Free energy Hydrogen Bonding Hydrophobic and Hydrophilic Interactions Hydrophobic free energy Mathematical models Models, Molecular Protein Conformation Protein Stability Proteins Proteins - chemistry Thermal stability Thermodynamics Thermophiles Thermophilic proteins |
Title | Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins |
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