A comparative study of the single crystal X-ray determination and molecular modelling of the binding of oligomycin to ATP Synthase

Computational Biology and Chemistry

Volumn 33, Issue 3, 2009, Pages 189-195

  Green, Roderic C E ^a   Thumser, Alfred E ^a   Povey, David ^a   Saldanha, José W ^b   Potter, Brian S ^c   Palmer, Rex A ^c   Howlin, Brendan J ^a  

^a UNIVERSITY OF SURREY   (United Kingdom)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^c UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Antibiotic; ATP Synthase inhibitor; Modelling the oligomycin binding site; Oligomycin

Indexed keywords

ABSOLUTE CONFIGURATION; ATP SYNTHASE; ATP SYNTHASE INHIBITOR; BINDING MODES; COMPARATIVE STUDIES; COMPUTATIONAL DOCKING; HOMOLOGY MODELS; HYDROGEN BONDINGS; INDUCED FIT; MODELLING THE OLIGOMYCIN BINDING SITE; MOLECULAR MODELLING; OLIGOMYCIN; SINGLE CRYSTAL X-RAY DATA; THREE-DIMENSIONAL STRUCTURE; X-RAY SINGLE CRYSTAL; X-RAY STRUCTURE; X-RAY STUDIES;

ANTIBIOTICS; BINDING ENERGY; DOCKING; ENZYMES; ESCHERICHIA COLI; HYDROGEN; HYDROGEN BONDS; MODEL STRUCTURES; MOLECULAR MODELING; SINGLE CRYSTALS; X RAYS;

BINDING SITES;

ANTIINFECTIVE AGENT; OLIGOMYCIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATASE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; CONFORMATION; ENZYMOLOGY; ESCHERICHIA COLI; METABOLISM; PROTEIN BINDING; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ANTI-BACTERIAL AGENTS; BACTERIAL PROTON-TRANSLOCATING ATPASES; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR CONFORMATION; OLIGOMYCINS; PROTEIN BINDING; THERMODYNAMICS;

ESCHERICHIA COLI;

EID: 67249146354     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2009.01.001     Document Type: Article

References (20)

1. Altamura N., Capitanio N., Bonnefoy N., Papa S., and Dujardin G. The Saccharomyces cerevisiae OXA1 gene is required for the correct assembly of cytochrome c oxidase and oligomycin-sensitive ATP Synthase. FEBS Letters 382 1-2 (1996) 111-115
2. Arnold K., Bordoli L., Kopp J., and Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22 (2006) 195-201
3. Cho H.J., Balasubramanyam M., Chernaya G., Gardner J.P., Aviv A., Reeves J.P., Dargis P.G., and Christian E.P. Oligomycin inhibits store-operated channels by a mechanism independent of its effects on mitochondrial ATP. Biochemical Journal 324 (1997) 971-980
4. Cunningham C.C., and George D.T. The relationship between the bovine heart mitochondrial adenosine triphosphatase, lipophilic compounds, and oligomycin. The Journal of Biological Chemistry 250 (1975) 2035-2044
5. Devenish R.J., Prescott M., Boyle G.M., and Nagley P. The oligomycin axis of mitochondrial ATP Synthase: OSCP and the proton channel. Journal of Bioenergetics and Biomembranes 32 (2000) 507-515
6. Fossati G., Moulding D.A., Spiller D.G., Moots R.J., White M.R.H., and Edwards S.W. The mitochondrial network of human neutrophils: role in chemotaxis, phagocytosis, respiratory burst activation, and commitment to apoptosis. The Journal of Immunology 170 (2003) 1964-1972
7. Galanis M., Mattoon J.R., and Nagley P. Amino acid substitutions in mitochondrial ATP Synthase subunit 9 of Saccharomyces cerevisiae leading to venturicidin or ossamycin resistance. FEBS Letters 249 (1989) 333-336
8. + cations. Journal of Molecular Structure 738 (2005) 261-270
9. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. Journal of Molecular Graphics 14.1 (1996) 33-38
10. de Jonge M.R., Koymans L.H.M., Guillemont J.E.G., Koul A., and Andries K. A computational model of the inhibition of mycobacterium tuberculosis ATP Synthase by a New Drug Candidate R207910. Proteins: Structure, Function and Bioinformatics 67 (2007) 971-980
11. Lardy H.A. Antibiotic inhibitors of mitochondrial energy transfer. Pharmacology & Therapeutics 11 3 (1980) 649-660
12. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26 (1993) 283-291
13. Lorenson M.Y., and Jacobs L.S. Inhibitor studies with adenohypophyseal granule membrane ATPase. Evidence for a membrane environment which modulates sensitivity to inhibitors. Biochimica et Biophysica Acta - Biomembranes 769 (1984) 479-485
14. Palmer R.A., and Potter B.S. X-ray structures and absolute configurations of the antibiotics oligomycins A, B and C: inhibitors of ATP Synthase. Journal of Chemical Crystallography 38 (2008) 243-253
15. Przybylski P., Brzezinski B., and Bartl F. Oligomycin A complex structures with some divalent metal cations studied by ESI MS and PM5 semiempirical methods. Journal of Molecular Structure 830 (2007) 58-71
16. Rastogi V.K., and Girvin M.E. Structural changes linked to proton translocation by subunit c of the ATP synthase. Nature 402 (1999) 263-268
17. Schneider G., and Baringhaus K. Molecular design: concepts and applications (2008), Wiley-VCH
18. Van Dyke R.W., Steer C.J., and Scharschmidt B.F. Clathrin-coated vesicles from rat liver: enzymatic profile and characterization of ATP-dependent proton transport. PNAS 81 10 (1984) 3108-3112
19. Voet D., and Voet J.G. Biochemistry. 3rd ed. (2004), Wiley, Chichester
20. Wang J., Cieplak P., and Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. Journal of Computational Chemistry 21 (2000) 1049-1074