Comparative analysis of thermophilic and mesophilic proteins using Protein energy networks

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Vijayabaskar, MS ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE ANALYSIS; COMPARATIVE STUDIES; CONFORMATIONAL FLEXIBILITY; CONTRIBUTING FACTOR; FUNCTIONAL SIMILARITY; INTERACTION ENERGIES; NUMBER OF CLUSTERS; THERMOPHILIC PROTEINS;

AMINO ACIDS; STABILITY; BIOINFORMATICS;

PROTEINS;

PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; METHODOLOGY; PROTEIN CONFORMATION; TEMPERATURE; THERMODYNAMICS;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; TEMPERATURE; THERMODYNAMICS;

EID: 75149155238     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S49     Document Type: Article

References (17)

1. Vieille C, Zeikus GJ. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 2001, 65(1):1-43. 10.1128/MMBR.65.1.1-43.2001, 99017, 11238984.
2. Chakravarty S, Varadarajan R. Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 2002, 41(25):8152-8161. 10.1021/bi025523t, 12069608.
3. Szilagyi A, Zavodszky P. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure 2000, 8(5):493-504. 10.1016/S0969-2126(00)00133-7, 10801491.
4. Razvi A, Scholtz JM. Lessons in stability from thermophilic proteins. Protein Sci 2006, 15(7):1569-1578. 10.1110/ps.062130306, 2242557, 16815912.
5. Brinda KV, Vishveshwara S. A network representation of protein structures: implications for protein stability. Biophysical journal 2005, 89(6):4159-4170. 10.1529/biophysj.105.064485, 1366981, 16150969.
6. Kannan N, Vishveshwara S. Aromatic clusters: a determinant of thermal stability of thermophilic proteins. Protein engineering 2000, 13(11):753-761. 10.1093/protein/13.11.753, 11161106.
7. Greene LH, Higman VA. Uncovering network systems within protein structures. Journal of molecular biology 2003, 334(4):781-791. 10.1016/j.jmb.2003.08.061, 14636602.
8. Kumar S, Nussinov R. How do thermophilic proteins deal with heat?. Cell Mol Life Sci 2001, 58(9):1216-1233. 10.1007/PL00000935, 11577980.
9. Hollien J, Marqusee S. Structural distribution of stability in a thermophilic enzyme. Proceedings of the National Academy of Sciences of the United States of America 1999, 96(24):13674-13678. 10.1073/pnas.96.24.13674, 24123, 10570131.
10. Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. Journal of computational chemistry 2005, 26(16):1701-1718. 10.1002/jcc.20291, 16211538.
11. Ghosh A, Brinda KV, Vishveshwara S. Dynamics of lysozyme structure network: probing the process of unfolding. Biophysical journal 2007, 92(7):2523-2535. 10.1529/biophysj.106.099903, 1864820, 17208969.
12. Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics (Oxford, England) 2006, 22(8):1021-1023. 10.1093/bioinformatics/btl039, 16473872.
13. Ghosh A, Vishveshwara S. Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. Biochemistry 2008, 47(44):11398-11407. 10.1021/bi8007559, 18842003.
14. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nature reviews 2004, 5(2):101-113. 10.1038/nrg1272, 14735121.
15. Berezovsky IN, Shakhnovich EI. Physics and evolution of thermophilic adaptation. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(36):12742-12747. 10.1073/pnas.0503890102, 1189736, 16120678.
16. Robinson-Rechavi M, Alibes A, Godzik A. Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. Journal of molecular biology 2006, 356(2):547-557. 10.1016/j.jmb.2005.11.065, 16375925.
17. Sadeghi M, Naderi-Manesh H, Zarrabi M, Ranjbar B. Effective factors in thermostability of thermophilic proteins. Biophysical chemistry 2006, 119(3):256-270. 10.1016/j.bpc.2005.09.018, 16253416.