Molecular dynamics simulation studies on structural and conformational changes in tyrosine-67 nitrated cytochrome c

Molecular Simulation

Volumn 38, Issue 6, 2012, Pages 459-467

  Raja Singh, Sarkkarai ^a   Prakash, Subash ^a   Muneeswaran, Gurusamy ^a   Rajesh, Seenivasan ^a   Muthukumar, Kaliappan ^b   Vasu, Veerapandy ^c   Karunakaran, Chandran ^a  

^a VHNSN COLLEGE   (India)

^b GOETHE UNIVERSITY   (Germany)

^c MADURAI KAMARAJ UNIVERSITY   (India)

Author keywords

apoptosis; cyt c nitration; essential dynamics; MD simulation; nitrotyrosine; peroxynitrite

Indexed keywords

ACTIVE SITE; APOPTOTIC; CARBON ATOMS; CARDIO-VASCULAR DISEASE; CONFORMATIONAL CHANGE; CYTOCHROME C; ELECTRON TRANSFER; ESSENTIAL DYNAMICS; HYDROGEN BONDING INTERACTIONS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NEURODEGENERATIVE; NITROTYROSINE; PEROXYNITRITES; PLOT ANALYSIS; POST-TRANSLATIONAL MODIFICATIONS; RADIUS OF GYRATION; ROOM TEMPERATURE; ROOT-MEAN SQUARE DEVIATION; TYROSINE NITRATION; WILD TYPES;

AMINO ACIDS; CELL DEATH; DYNAMICS; HYDROGEN BONDS; MOLECULAR DYNAMICS; PORPHYRINS;

NITRATION;

EID: 84859172002     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2011.645597     Document Type: Article

References (44)

1. C. Szabo, Multiple pathways of peroxynitrite cytotoxicity, Toxicol. Lett. 140 (2003), pp. 105-112.
2. R. Radi, Nitric oxide, oxidants, and protein tyrosine nitration, Proc. Natl. Acad. Sci. USA 101 (2004), pp. 4003-4008.
3. S.A.B. Greenacre and H. Ischiropoulos, Tyrosine nitration: Localisation, quantification, consequences for protein function and signal transduction, Free Radic. Res. 34 (2001), pp. 541-581.
4. V. Nilakantan, H.L. Liang, S. Rajesh, J. Mortensen, and C. Karunakaran, Time-dependent protective effects of Manganese (III) tetraleis (1-methyl-4-pyridyl) porphyrin on mitochondrial function following renal ischemia-reperfusion injury, Free Radic. Res. 44 (2010), pp. 773-782.
5. I.V. Turko and F. Murad, Protein nitration in cardiovascular diseases, Pharmocol. Rev. 54 (2002), pp. 619-634.
6. B.A. Denicola, M. Freeman, and R. Trujillo, Radi. Peroxynitrite reaction with carbondioxide/bicarbonate: Kinetics and influence on peroxynitrite-mediated oxidation, Arch. Biochem. Biophys. 333 (1996), pp. 49-58.
7. C. Karunakaran, H. Zhang, J.P. Crow, W.E. Antholine, and B. Kalyanaraman, Direct probing of copper active site and free radical formed during bicarbonate-dependent peroxidase activity of bovine and human copper, zinc-superoxide dismutases. Lowtemperature electron paramagnetic resonance and electron nuclear double resonance studies, J. Biol. Chem. 279 (2004), pp. 32534-32540.
8. S. Beckman, Oxidative damage and tyrosine nitration from peroxynitrite, Chem. Res. Toxicol. 9 (1996), pp. 836-844.
9. R. Radi, A. Denicola, B. Alvarez, G. Ferrer-Sueta, and H. Rubbo, The biological chemistry of peroxynitrite, in Nitric Oxide Biology and Pathology, L.J. Ignarro, ed., Academic Press, San Diego, CA, 2000, pp. 57-82.
10. J.D. Lang Jr., P. Chumley, J.P. Eiserich, A. Estevez, T. Bamberg, A. Adhami, J. Crow, and B.A. Freeman, Hypercapnia induces injury to alveolar epithelial cells via a nitric oxide-dependent pathway, Am. J. Physiol. Lung Cell. Mol. Physiol. 279 (2000), pp. L994-L1002.
11. R. Radi, J.F. Turrens, and B.A. Freeman, Cytochrome c-catalyzed membrane lipid peroxidation by hydrogen peroxide, Arch. Biochem. Biophys. 288 (1991), pp. 118-125.
12. X. Hu, T. Ritz, A. Damjanovic, F. Autenrieth, and K. Schulten, Photosynthetic apparatus of purple bacteria, Quart. Rev. Biophys. 35 (2002), pp. 1-62.
13. J. Berg, J. Tymoczko, and L. Stryer, Biochemistry, W.H. Freeman and Company, New York, 2002.
14. H.B. Gray, Biological inorganic chemistry at the beginning of the 21st century, Proc. Natl. Acad. Sci. USA 100 (2003), pp. 3563-3568.
15. Y.A. Shi, Structural view of mitochondria-mediated apoptosis, Nat. Struct. Biol. 8 (2001), pp. 394-401.
16. C. Karunakaran, D. Aggarwal, R.Q. Migrino, J. Joseph, D. McAllister, E.A. Konorev, W.E. Antholine, J. Zielonka, S. Srinivasan, N.G. Aradhani, and B. Kalyanaraman, Doxorubicin inactivates myocardial cytochrome c oxidase in rats: Cardioprotection by Mito-Q, Biophys. J. 96 (2009), pp. 1388-1398.
17. C. Karunakaran, H. Zhang, J. Joseph, W.E. Antholine, and B. Kalyanaraman, Thiol oxidase activity of copper, zinc superoxide dismutase bicarbonate-dependent peroxidase activity: Intermediacy of carbonate anion radical, Chem. Res. Toxicol. 18 (2005), pp. 494-500.
18. A.M. Cassino, R. Hodara, J.M. Souza, L. Thomson, L. Castro, H. Ischiropoulos, B.A. Freeman, and R. Radi, Cytochrome c nitration by peroxynitrite, J. Biol. Chem. 275 (2000), pp. 21409-21415.
19. D. Nakagawa, Y. Ohshima, M. Takusagawa, N. Ikota, Y. Takahashi, S. Shimizu, and T. Ozawa, Functional modification of cytochrome c by peroxynitrite in an electron transfer reaction, Chem. Pharm. Bull. (Tokyo) 49 (2001), pp. 1547-1554.
20. M.J. Oursler, E.W. Bradley, S.L. Elfering, and C. Giulivi, Native, not nitrated, cytochrome c and mitochondria -derived hydrogen peroxide drive osteoclast apoptosis, Am. J. Physiol. Cell Physiol. 288 (2005), pp. C156-C168.
21. Y.T. Lai, C.S. Cheng, Y.N. Liu, Y.J. Lie, and P.C. Lyu, Effects of ligand binding on The dynamics of rice nonspecific lipid transfer protein 1: A model from molecular simulations, Proteins 72 (2008), pp. 1189-1198.
22. R. Pauli, A. Caceres, and W.F. de Azevedo, Jr, Molecular modeling and dynamics studies of shikimate kinase from Bacillus anthracis, Bioorg. Med. Chem. 16 (2008), pp. 8098-8108.
23. W.F. De Azevedo, Jr, Structure-based virtual screening, Curr. Drug Targets. 11(3) (2010), pp. 261-263.
24. W.F. De Azevedo, Jr, Molecular dynamics simulations of protein targets identified in Mycobacterium tuberculosis, Curr. Med. Chem. 18(9) (2011), pp. 1353-1366.
25. A.W. Schuttelkopf and D.M.F. van Aalten, PRODRG: A tool for high throughout crystallography of protein-ligand complexes, Acta Crystallogr. D Biol. Crystallogr. 60 (2004), pp. 1355-1363.
26. A. Amadei, A.B.M. Linssen, and H.J.C. Berendsen, Essential dynamics of proteins, Proteins Struct. Func. Genet. 17 (1993), pp. 412-425.
27. H.J.C. Berendsen, D. van der Spoel, and R. van Drunen, GROMACS: A message-passing parallel molecular dynamics implementation, Comput. Phys. Commun. 91 (1995), pp. 45-56.
28. E. Lindahl, B. Hess, and D. van der Spoel, GROMACS 3.0 a package for molecular simulation and trajectory analysis, J. Mol. Model. 7 (2001), pp. 306-317.
29. D. van der Spoel, E. Lindahl, B. Hess, A.R. van Buuren, E. Apol, P.J. Meulenhoff, D.P. Tieleman, A.L.T.M. Sijbers, A.K. Feenstra, R. van Druunen, and H.J.C. Berendsen, Groningnen machine for molecular simulations BIOSON research institute, GROMACS User Manual Version 3.2, Nijenborgh 4, 9747 AG Groningnen, The Netherlands, 2004. http://www.gromacs.org
30. W.F. van Gunstren, S.R. Billeter, A.A. Eising, P.H. Humberger, P. Kruger, A.E. Mark, W.R.P. Scott, and I.G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide, Hochschulverlag AG an der Zurich, Zurich, Switzerland, 1996.
31. G.W. Bushnell, G.V. Louie, and G.D. Brayer, High-resolution three dimensional structure of horse heart Cytochrome c, J. Mol. Biol. 214 (1990), pp. 585-595.
32. S.D. Conte and C.D. Boor, Elementary Numerical Analysis. An Algorthmic Approach, Mc Graw-Hill International Book Company, New York, 1982.
33. F. Autenrieth, E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten, Classical force field parameters for the heme prosthetic group of cytochrome c, J. Comput. Chem. 25 (2004), pp. 1613-1622.
34. H.J.C. Berendsen, J.D.M. Postman, and W.F. van Gunsteren, Intermol forces. Interaction models for water in relation to protein hydration, Dordrecht. D. Reidel, 1981, pp. 331-342.
35. H.J.C. Berendsen, J.D.M. Postman, W.F. van Gunsteren, A. Di Nola, and J.R. Haak, Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81 (1984), pp. 3684-3690.
36. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen, Numerical integration of the Cartesian equations of motions of systems with constraints: Molecular dynamics of n-Alkanes, J. Comput. Phys. 23 (1977), pp. 327-341.
37. S. Miyamoto and P.A. Kollman, SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water molecules, J. Comput. Chem. 13 (1992), pp. 952-962.
38. S. Raja Singh, S. Prakash, V. Vasu, and C. Karunakaran, Conformational flexibility decreased due to Y67F and F82H mutations in cytochrome c: Molecular dynamics simulation studies, J. Mol. Graph. Mod. 28 (2009), pp. 270-277.
39. B. Jang and S. Han, Biochemical properties of cytochrome c nitrated by peroxynitrite, Biochimie 88 (2006), pp. 53-58.
40. F. Yamakura, H. Taka, T. Fujimura, and K. Murayama, Inactivation of human manganese-superoxide dismutase by peroxynitrite is caused by exclusive nitration of tyrosine 34 to 3-nitrotyrosine, J. Biol. Chem. 273 (1998), pp. 14085-14089.
41. K. Yokoyama, U. Uhlin, and J. Stubbe, Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-Active tyrosines in ribonucleotide reductase, J. Am. Chem. Soc 132 (2010), pp. 8385-8397.
42. T. Takano, O.B. Kallai, R. Swanson, and R.E. Dickerson, The structure of ferrocytochrome c at 2.45 A ° resolution, J. Biol. Chem. 248 (1973), pp. 5234-5255.
43. E. Margoliash, S.F. Miller, J. Tullose, C.H. Kang, B.A. Feinberg, D.L. Brautigan, and M. Morrison, Separate intramolecular pathways for reduction and oxidation of cytochrome c in electron transport chain reactions, Proc. Natl. Acad. Sci. USA 70 (1973), pp. 3245-3249.
44. G.N. Ramachandran and V. Sasiskharan, Conformation of polypepdides and proteins, Adv. Protein Chem. 23 (1968), pp. 283-437.