Distinct role of non-covalent interactions to the function and structural stability of glutaredoxins: A multifunctional redox protein

International Journal of Bioinformatics Research and Applications

Volumn 6, Issue 3, 2010, Pages 241-259

  Prasad, Vibhu Ranjan ^a   Tripathi, Bhumi Nath ^b   Sethumadhavan, Rao ^a  

^a VIT UNIVERSITY   (India)

^b BANASTHALI UNIVERSITY   (India)

Author keywords

Cation interaction; CH interaction; Glutaredoxins; Long range contacts; Redox proteins

Indexed keywords

GLUTAREDOXIN;

CHEMISTRY; MOLECULAR COMPUTER; OXIDATION REDUCTION REACTION; PROTEIN SECONDARY STRUCTURE; STRUCTURE ACTIVITY RELATION;

COMPUTERS, MOLECULAR; GLUTAREDOXINS; OXIDATION-REDUCTION; PROTEIN STRUCTURE, SECONDARY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77954547460     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2010.034073     Document Type: Article

References (44)

1. Anbarasu, A., Anand, S., Babu, M. M. and Sethumadhavan, R. (2007) 'Investigations on C-H⋯π interactions in RNA binding proteins', International Journal of Biological Macromolecules, Vol. 41, pp. 251-259.
2. Babu, M. M. (2003) 'NCI: A server to calculate non-canonical interactions in protein structures', Nucleic Acids Research, Vol. 31, pp. 3345-3348, doi:10.1093/nar/gkg528. (Pubitemid 37442155)
3. Bacik, J. P. and Hazes, B. (2007) 'Crystal structures of a poxviral glutaredoxin in the oxidized and reduced states show redox-correlated structural changes', Journal of Molecular Biology, Vol. 365, p. 1545. doi:10.1016/J. Jmb.2006.11.002
4. Berman, H. M., Westbrook, J. Z., Feng, G., Gilliland, T. N., Bhat, H., Weissig, I. N., Shindyalov I. N. and Bourne P. E (2000) 'The protein data bank', Nucleic Acids Research, Vol. 28, pp. 235-242.
5. Chakkaravarthi, S. and Gromiha, M. M. (2006) 'Analysis of cation-π interactions to the structural stability of RNA binding proteins', Polymer, Vol. 47, pp. 709-721.
6. Chakrabarti, P. and Samanta, U. (1995) 'CH/π interaction in the packing of the adenine ring in protein structures', Journal of Molecular Biology, Vol. 251, pp. 9-14. doi:10.1006/jmbi.1995.0411.
7. Chakravarthy, S. and Varadarajan, R. (2000) 'Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study', Biochemistry, Vol. 41, pp. 8152-8161.
8. Dougherty, D. A (1996) 'Cation-π interactions in chemistry and biology: a new view of benzene', Phe, Tyr and Trp, Science, Vol. 271, pp. 163-168.
9. Dougherty, D. A. and Stauffer, D. A (1990) 'Acetylcholine binding by a synthetic receptor: implications for biological recognition', Science, Vol. 250, pp. 1558-1560.
10. Fernandes, A. P. and Holmgren, A. (2004) 'Glutaredoxins: glutathione-dependent redox enzymes with functions far beyond a simple thioredoxin backup system', Antioxidants and Redox Signaling, Vol. 6, No. 1, pp. 63-74, doi:10.1089/152308604771978354.
11. Fraczkiewicz, R. and Braun, W. (1998) 'Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules', Journal of Computational Chemistry, Vol. 19, pp. 319-333.
12. Gallivan, J. P. and Dougherty, D. A. (1999) 'Cation-π interactions in structural biology', Proceedings of National Academy of Sciences, Vol. 96, No. 17, pp. 9459-9464.
13. Gallivan, J. P. and Dougherty, D. A. (2000) 'A computational study of cation-π interactions vs. salt bridges in aqueous media: implications for protein engineering', Journal of American Chemical Society, Vol. 122, pp. 870-874.
14. Gleason, F. K. and Holmgren, A. (1988) 'Thioredoxin and related proteins in prokaryotes', FEMS Microbiology Reviews, Vol. 4, No. 4, pp. 271-297.
15. Gromiha, M. M. (2003) 'Influence of cation-π interaction in different folding types of membrane proteins', Biophysical Chemistry, Vol. 103, pp. 251-258.
16. Gromiha, M. M. and Selvaraj, S. (Eds.) (2002) Recent Research Developments in Protein Folding, Stability and Design, Research Signpost, Trivandrum, India.
17. Gromiha, M. M. and Suwa, M. (2005) Structural analysis of residues involving cation-π interactions in different folding types of membrane proteins', International Journal of Biological Macromolecules, Vol. 35, pp. 55-62.
18. Gromiha, M. M., Santhosh, C. and Ahmad, S. (2004) 'Structural analysis of cation-π interactions in DNA binding proteins', International Journal of Biological Macromolecules, Vol. 34, pp. 203-211.
19. Gromiha, M. M., Thomas, S. and Santhosh, C. (2002) 'Role of cation-π interaction to the stability of thermophilic proteins', Preparative Biochemistry and Biotechnology, Vol. 32, pp. 355-362.
20. Holmgren, A. (1988) Thioredoxin and glutaredoxin: small multi-functional redox proteins with active-site disulphide bonds', Biochemical Society Transactions, Vol. 16, pp. 95-96.
21. Holmgren, A. (1989) 'Thioredoxin and glutaredoxin systems', Journal of Biological Chemistry, Vol. 264, pp. 13963-13966.
22. Jorgensen, W. L., Maxwell, D. S. and Tirado Rives, J. (1996) 'Development and testing of the OPLS all-atom force field on conformational energetic and properties of organic liquids', Journal of American Chemical Society, Vol. 118, pp. 11225-11236.
23. Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. and Ben-Tal, N. (2005) 'ConSurf: the projection of evolutionary conservation scores of residues on protein structures', Nucleic Acids Research, Vol. 33, pp. 299-302.
24. Matsui, I., Matsui, E., Sakai, Y., Kikuchi, H., Kawarabayasi, Y., Ura, H., Kawaguchi, S., Karamitsu, S. and Harata, K. (2000) 'The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii', The Journal of Biological Chemistry, Vol. 275, pp. 4871-4879, doi:10.1074/jbc.275.7.4871. (Pubitemid 30108880)
25. Mecozzi, S., West, A. P. and Dougherty, D. A. (1996) 'Cation-π interactions in aromatics of biological medicinal interest: electrostatic potential surfaces as a useful qualitative guide', Proceedings of National Academy of Sciences, Vol. 93, pp. 10566-10671.
26. Meyer, E. A., Castellano, R. K. and Deiderich, F. (2003) "Interactions with aromatic rings in chemical and biological recognition', Angewandte Chemie International Edition in English, Vol. 42, pp. 1210-1250, doi:10.1002/anie.200390319. (Pubitemid 36410287)
27. Muraki, M., Harata, K., Sugita, N. and Sato, K. I. (2000) 'Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling', Biochemistry, Vol. 39, pp. 292-299, doi:10.1021/bi991402q. (Pubitemid 30056462)
28. Nishio, M., Hirota, M. and Umezawa, Y. (Eds.) (1998) The CH/π interaction. Evidence, Nature and Consequences, Wiley-VCH, New York, Chapter 10.
29. Novotny, J., Bruccoleri, R. E. and Saul, F. A. (1989) 'On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3 and HyHEL-5', Biochemistry, Vol. 28, pp. 4735-4749.
30. Pellequer, J. L., Zhao, B., Kao, H. I., Bell, C. W., Li, K. and Li, Q. X. (2000) 'Stabilization of bound polycyclic aromatic hydrocarbons by a π-cation interaction', Journal of Molecular Biology, Vol. 302, pp. 691-699.
31. Reginald, G. and Charles, G. (1995) Biochemistry, Saunders College, Fort Worth, p. 893.
32. Ringer, A. L. (2009) From Small to Big: Understanding Non-Covalent Interactions in Chemical Systems from Quantum Mechanical Models, Chemistry and Biochemistry, GIT, Doctoral, 2009-03-23.
33. Rouhier, N., Couturier, J. and Jacquot, J. P. (2006) 'Genome-wide analysis of plant glutaredoxin systems', Journal of Experimental Botany, Vol. 281, No. 42, pp. 31736-31742, doi:10.1093/jxb/erl001. (Pubitemid 43992218)
34. Yu, J., Zhang, N. N., Yin, P. D., Cui, P. X. and Zhou, C. Z (2008) 'Glutathionylation-Triggered conformational changes Glutaredoxin Grx1 from the yeast Saccharomyces cerevisiae', Proteins, Vol. 72, No. 3, pp. 1077-1083.
35. Shanthi, V., Ramanathan, K. and Sethumadhavan, R. (2009) 'Exploring the role of CH⋯.π Interactions on the structural stability of single chain 'All-Alpha' proteins', Applied Biochemistry Biotechnology, doi:10.1007/s12010- 009-8584-1.
36. Shi, Z., Olson, C. A. and Kallenbach, N. R (2002) 'Cation-π interaction in model alpha helical peptides', Journal of American Chemical Society, Vol. 124, pp. 3284-3291.
37. Shimohigashi, Y., Maeda, I., Nose, T., Ikesue, K., Sakamoto, H., Ogawa, T., Ide, Y. and Kawahara, M. (1996) 'Chymotrypsin inhibitory conformation induced by amino acid side-chain side-chain intramolecular CH/π interaction', J. Chem. Soc., Perkin Trans., Vol. 1, pp. 2479-2485.
38. Shimohigashi, Y., Nose, T., Yamauchi, Y. and Maeda, I. (1999) Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/π interaction', Biopolymers, Vol. 51, pp. 9-17, doi:10.1002/(SICI) 1097-0282 (1999) 51:1<9::AID-BIP3>3.0. CO;2-5.
39. Steiner, T. (2002) 'The hydrogen bond in the solid state', Angewandte chemie International Edition in English, Vol. 41, pp. 48-76, doi:10.1002/1521-3773 (2002010) 41:1<48::AID-BIP3>3.0. CO;2-U.
40. Steiner, T. and Koellner, G. J. (2001) 'Hydrogen bonds with π-acceptors in proteins: frequencies and role in stabilizing local 3D structures', Journal of Molecular Biology, Vol. 305, pp. 535-557, doi:10.1006/jmbi.2000.4301. (Pubitemid 33032860)
41. Tamres, M. (1952) 'Aromatic molecules as donor molecules in hydrogen bonding', Journal of the American Chemical Society, Vol. 74, pp. 3375-3378, doi:10.1021/ja01133a047.
42. Tiwari, A. and Panigrahi, S. K. (2007) "HBAT: hydrogen bond analysis tool (HBAT 1.0) ', Silico Biology, Vol. 7, p. 0057.
43. Umezawa, Y. and Nishio, M. (1998a) 'CH/π Interactions as demonstrated in the crystal structure of guanine-nucleotide binding proteins, Src homology-2 domains and human growth hormone in complex with their specific ligands', Bioorganic and Medicinal Chemistry, Vol. 6, pp. 493-504, doi:10.1016/S0968-0896 (98) 00002-9.
44. Umezawa, Y. and Nishio, M. (1998b) 'CH/π interactions in the crystal structure of class I MHC antigens and their complexes with peptides', Bioorganic and Medicinal Chemistry, Vol. 6, pp. 2507-2515, doi:10.1016/S0968-0896 (98) 80024-2.