The unbinding of ATP from F1-ATPase

Biophysical Journal

Volumn 85, Issue 2, 2003, Pages 695-706

  Antes, Iris ^a   Chandler, David ^a   Wang, Hongyun ^b   Oster, George ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California Santa Cruz   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; MAGNESIUM; MOLECULAR MOTOR; PROTEIN SUBUNIT; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATASE;

ALPHA CHAIN; ARTICLE; BETA CHAIN; CATALYSIS; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; ELECTROCHEMICAL ANALYSIS; ENZYME STRUCTURE; ENZYME SUBUNIT; HYDROGEN BOND; HYDROLYSIS; MOLECULAR DYNAMICS; MOTOR COORDINATION; NONHUMAN; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; ENERGY TRANSFER; ENZYME ACTIVATION; PROTEIN BINDING; PROTEIN CONFORMATION;

ADENOSINE TRIPHOSPHATE; BINDING SITES; CATALYSIS; COMPUTER SIMULATION; ENERGY TRANSFER; ENZYME ACTIVATION; HYDROGEN BONDING; HYDROLYSIS; MAGNESIUM; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR MOTOR PROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN SUBUNITS; PROTON-TRANSLOCATING ATPASES;

EID: 0041843752     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74513-5     Document Type: Article

References (43)

1. 1-ATPase from bovine heart-mitochondria. Nature. 370:621-628.
2. 1-ATP synthase. Nat. Struct. Biol. 9:198-202.
3. Boyer, P. D. 1993. The binding change mechanism for ATP synthase some probabilities and possibilities. Biochim. Biophys. Acta. 1140:215-250.
4. Boyer, P. D. 1997. The ATP synthase - A splendid molecular machine. Annu. Rev. Biochem. 66:717-749.
5. Brooks, B. R., R. E. Buccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM - A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
6. Brooks, C. L., and M. Karplus. 1983. Deformable stochastic boundaries in molecular-dynamics. J. Chem. Phys. 79:6312-6325.
7. Eichinger, M., H. Heller, and H. Grubmüller. 2000. EGO - An efficient molecular dynamics program and its application to protein dynamics simulation. In Workshop on Molecular Dynamics on Parallel Computers. R. Esser, P. Grassberger, J. Grotendorst, and M. Lewerenz, editors. World Scientific Singapore. 154-174.
8. Elston, T., H. Wang, and G. Oster. 1998. Energy transduction in ATP synthase. Nature. 391:510-514.
9. 1-ATPase. Biochim. Biophys. Acta. 1458:310-325.
10. Futai, M., H. Omote, Y. Sambongi, and Y. Wada. 2000. ATP Synthase (H+ ATPase): coupling between catalysis, mechanical work, and proton translocation. Biochim. Biophys. Acta. 1458:276-288.
11. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: Visual molecular dynamics. J. Mol. Graph. 14:33-38.
12. Jaccucci, G., and A. Rahman. 1984. Comparing the efficiency of metropolis Monte-Carlo and molecular-dynamics methods for configuration space sampling. Nuovo Cimento. D4:341-356.
13. Jorgensen, W. L., R. W. Impey, J. Chandrasekhar, J. D. Madura, and M. L. Klein. 1990. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
14. Kraulis, P. J. 1991. MolScript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
15. Kinosita, K., R. Yasuda, H. Noji, and K. Adachi. 2000. A rotary molecular motor that can work at near 100% efficiency. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 355:473-490.
16. Le, N. P., H. Omote, Y. Wada, M. K. Al-Shawi, R. K. Nakamoto, and M. Futai. 2000. Escherichia coli ATP synthase a-subunit Arg-376: The catalytic site arginine does not participate in the hydrolysis/synthesis reaction but is required for promotion to the steady state. Biochemistry. 39:2778-2783.
17. 1ATPase, roles of three catalytic site residues. J. Biol. Chem. 6:3648-3656.
18. 1-ATPase. Structure. 10:921-931.
19. MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarth, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Chem. Phys. 102:3586-3616.
20. Massova, M., and P. Kollman. 1999. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121:8133-8143.
21. Mitchell, P. 1961. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature. 191:144-148.
22. 1-ATPase. Biochemistry. 38:7670-7677.
23. 1-ATPase residue a-Arg-376 for catalytic transition state stabilization. Biochemistry. 38:15493-15499.
24. Oster, G., and H. Wang. 2000a. Reverse engineering a protein: the mechanochemistry of ATP synthase. Biochim. Biophys. Acta. 1458:482-510.
25. 1 ATPase so high? J. Bioenerg. Biomembr. 32:459-469.
26. Pedersen, P., Y. Ko, and S. Hong. 2000. ATP synthases in the year 2000: evolving views about the structures of these remarkable enzyme complexes. J. Bioenerg. Biomembr. 32:325-332.
27. 1-type ATP synthases and ATPases. Adv. Enzymol. Relat. Areas Mol. Biol. 64:173-214.
28. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical-integration of cartesian equations of motion of a system with constraints molecular-dynamics of N-Alkanes. J. Comput. Phys. 23:327-341.
29. Sayle, R. A., and E. J. Milnerwhite. 1995. RASMOL - biomolecular graphics for all. Trends Biochem. Sci. 20:374-376.
30. Schlitter, J., M. Engels, and P. Krüger. 1994. Targeted molecular-dynamics - a new approach for searching pathways of conformational transitions. J. Mol. Graph. 12:84-89.
31. 1-ATPase. J. Bioenerg. Biomembr. 24:479-484.
32. 0-ATP synthase. J. Exp. Biol. 203:35-40.
33. 0-ATP synthase. Biochim . Biophys. Acta. 1553:188-211.
34. 1-ATPase. Eur. Biophys. J. In press.
35. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the α-subunits and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
36. 0-ATPase. Biochim. Biophys. Acta. 1458:221-510.
37. 1 motor of ATP synthase. Nature. 396:279-282.
38. 1-ATPase. Biochemistry. 37:608-614.
39. 1-ATPase. Biochim. Biophys. Acta. 1319:19-58.
40. Weber, J., and A. E. Senior. 2000. ATP synthase: what we know about ATP hydrolysis and what we do not know about ATP synthesis. Biochim. Biophys. Acta. 1458:300-309.
41. 1-ATPase is a highly efficient molecular motor that rotates with discrete 120° steps. Cell. 93:1117-1124.
42. 1-ATPase. Nature. 410:989-904.
43. Zhang, L., and J. Hermans. 1996. Hydrophilicity of cavities in proteins. Proteins. 24:433-438.