The role of backbone stability near Ala44 in the high reduction potential class of rubredoxins

Proteins: Structure, Function and Genetics

Volumn 62, Issue 3, 2006, Pages 708-714

  Tan, Ming Liang ^a   Kang, ChulHee ^b   Ichiye, Toshiko ^a  

^a GEORGETOWN UNIVERSITY   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Backbone flexibility; Molecular dynamics; Reduction potential; Rubredoxin

Indexed keywords

ALANINE; MUTANT PROTEIN; RUBREDOXIN; SOLVENT; VALINE;

AMINO ACID SUBSTITUTION; ARTICLE; CLOSTRIDIUM PASTEURIANUM; CRYSTAL STRUCTURE; ENERGY; MOLECULAR DYNAMICS; MUTATION; NONHUMAN; OXIDATION REDUCTION POTENTIAL; PRIORITY JOURNAL; PROTEIN STABILITY; REDUCTION;

ALANINE; AMINO ACID SUBSTITUTION; COMPUTER GRAPHICS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DRUG STABILITY; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; OXIDATION-REDUCTION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; RUBREDOXINS;

CLOSTRIDIUM PASTEURIANUM; PYROCOCCUS FURIOSUS;

EID: 31944451358     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20806     Document Type: Article

References (24)

1. Bau R, Rees DC, Kurtz DM Jr, Scott RA, Huang H, Adams MWW, Eidsness MK. Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95 Å resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd: contributions of N-terminal interactions to thermostability. J Biol Inorg Chem 1998;3:484-493.
2. 4 coordination unit in a protein. Proc Natl Acad Sci USA 1996;93:8836-8840.
3. Humphrey W, Dalke A, Schulten K. VMD-visual molecular dynamics. J Mol Graphics 1996;14:33-38.
4. Swartz PD, Beck BW, Ichiye T. Structural origins of redox potential in iron-sulfur proteins: Electrostatic potentials of crystal structures. Biophys J 1996;71:2958-2969.
5. Eidsness MK, Richie KA, Burden AE, Kurtz DM Jr. Dissecting contributions to the thermostability of Pyrococcus furiosus rubredoxin: β-sheet chimeras. Biochemistry 1997;36:10406-10413.
6. 4 site in rubredoxin by the orientation of a peptide dipole. Biochemistry 1999;38:14803-14809.
7. Xiao Z, Maher MJ, Cross M, Bond CS, Guss JM, Wedd AG. Mutation of the surface valine residues 8 and 44 in the rubredoxin from Clostridium pasteurianum: Solvent access versus structural changes as determinants of reversible potential. J Biol Inorg Chem 2000;5:75-84.
8. Ergenekan CE, Thomas D, Fischer JF, Tan ML, Eidsness MK, Kang C, Ichiye T. Prediction of reduction potential changes in rubredoxin: a molecular mechanics approach. Biophys J 2003;85: 2818-2829.
9. 44 mutants of Clostridium pasteurianum rubredoxin: effects of side-chain size on reduction potential. Proteins 2004;57:618-625.
10. Watenpaugh K, Sieker LC, Jensen LH. Crystallographic refinement of rubredoxin at 1.2 Å resolution. J Mol Biol 1980;138:615-633.
11. Day MW, Hsu BT, Joshua-Tor L, Park J-B, Zhou ZH, Adams MWW, Rees DC. X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci 1992;1: 1494-1507.
12. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
13. Yelle RB, Park N-S, Ichiye T. Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: changes in structure and electrostatic potential during redox reactions. Proteins 1995; 22:154-167.
14. Steinbach PJ, Brooks BR. New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comp Chem 1994;15:667-683.
15. Tan M-L, Dolan EA, Ichiye T. Understanding intramolecular electron transfer in ferredoxin: a molecular dynamics study. J Phys Chem B 2004;108:20435-20441.
16. Molecular Simulations, Inc. QUANTA98, 98.1111 © 1986-1993. San Diego, CA: Biosym/MSI, Inc.
17. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
18. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
19. McCammon JA, Harvey SC. Dynamics of proteins and nucleic acids. New York: Cambridge University Press; 1987.
20. Min T, Ergenekan CE, Eidsness MK, Ichiye T, Kang C. Water gates and other structural modulators in the reduction of Clostridium pasteurianum rubredoxin. Protein Sci 2001;10:613-621.
21. Park IY, Youn B, Harley JL, Eidsness MK, Smith E, Ichiye T, Kang CH. The unique hydrogen bonded water in the reduced form of Clostridium pasteurianum rubredoxin and its possible role in electron transfer. J Biol Inorg Chem 2004;9:423-428.
22. Simonson T. Gaussian fluctuations and linear response in an electron transfer protein. Proc Natl Acad Sci USA 2002;99:6544-6549.
23. Simonson T, Archontis G, Karplus M. A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation. J Phys Chem 1999;103:6142-6156.
24. Stephens PJ, Jollie DR, Warshel A. Protein control of redox potentials of iron-sulfur proteins. Chem Rev 1996;96:2491-2513.