Combining Laue diffraction and molecular dynamics to study enzyme intermediates

Nature Structural Biology

Volumn 3, Issue 7, 1996, Pages 590-595

  Stoddard, Barry L ^a   Dean, Antony ^b   Bash, Paul A ^c  

^a Fred Hutchinson Cancer Research Center   (United States)

^b The Chicago Medical College   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOCITRATE DEHYDROGENASE;

ARTICLE; ENZYME CONFORMATION; FOURIER ANALYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ENZYMES; FOURIER ANALYSIS; ISOCITRATE DEHYDROGENASE; MODELS, MOLECULAR; MOLECULAR CONFORMATION; STOCHASTIC PROCESSES;

EID: 0029940466     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb0796-590     Document Type: Article

References (44)

1. Christianson, D.W., Lipscomb, W.N. X-ray crystallographic investigation of Substrate binding to carboxypeptidase A at subzero temperature. Proc. Natl. Acad. Sci. USA 83, 7568-7572 (1986).
2. Watt, W., Tulinsky, A., Swenson, R.P., Watenpaugh, K.D. Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures. J. Mol. Biol. 218, 195-208 (1991).
3. Chen, C.C.H., Herzberg, O. Inhibition of β-lactamase by clavulanate: trapped intermediates in cryocrystallographic studies. J. Mol. Biol. 224, 1103-1113 (1992).
4. Bartunik, H.D., Bartunik, L.J., Viemann, H. Time-resolved x-ray diffraction studies of enzymes under cryoconditions. Phil Trans R. Soc Lond [A] 340, 209-220 (1992).
5. Ding, X., Rasmussen, B.F., Petsko, G.A. & Ringe, D. (1994) Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase. Biochemistry 33, 9285-9293.
6. Teng, T.-Y., Srajer, V., Moffat, K. Photolysis-induced structural changes in single crystals of carbonmonoxymyoglobin at 4OK. Nature Struct. Biol. 1 (10) 701-705 (1994).
7. Schlichting, I., Berendzin, J., Phillips, G.N. Jr., & Sweet, R.M. Crystal structure of photolyzed carbonmonoxymyoblobin. Nature 371808-812 (1994).
8. Yennawar, N.H., Yennawar, H.P. & Farber, G.K. X-ray crystal structure of γ-chymotrypsin in hexane. Biochemistry33, 7326-7336 (1994).
9. Verschueren, K.H., Seljee, F., Rozeboom, H.J., Kalk, K.H. & Dijkstra, B.W. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature 363, 693-698 (1993).
10. Moffat, K., Szebenyi, D. & Bilderback, D. X-ray laue diffraction from protein crystals. Science 223, 1423-1425 (1984).
11. Helliwell, J.R. Synchrotron x-radiation protein crystallographyinstrumentation, methods, and applications. Rep. Prog. Phys. 47, 1403-1497 (1984).
12. Hajdu, J., Acharya, K.R., Stuart, D.I., McLaughlin, P.J., Barford, D., Klein, H. & Johnson, L.N. Time-resolved structural studies on catalysis in the crystal with glycogen phosphorylase Biochem. Soc. Trans. 14, 538-541 (1985).
13. Schilichting, I. et al. Time-resolved x-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis. Nature 345, 309 (1990).
14. Stoddard, B.L. et al. Observation of the light-triggered binding of pyrone to chymotrypsin by Laue x-ray crystallography. Proc. Natl, Acad. Sci. 88, 5503-5507 (1991).
15. Singer, P.A., Smalas, R.P., Carty, W.F., Mangel, W.F. & Sweet, R.M. The hydrolytic water molecule in trypsin, revealed by time-resolved Laue crystallography. Science 259, 669-673 (1993).
16. Fulop, V. et al. Laue diffraction study on the structure of cytochrome c peroxidase compound I. Structure 2, 201-208 (1994).
17. Bolduc, J.M. et al. Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase. Science 268, 1312-1318 (1995).
18. Moffat, K. Time-resolved macromolecular crystallograpyhy.Annu. Rev. Biophys. Biophys. Chem. 18, 309-332 (1989).
19. Hajdu, J. et al. On the limitations of the Laue method when applied to crystals of macromolecules. in Crystallographic Computing 5 (eds D. Moras, A.D. Podjarny & J.C. Thierry, Oxford University Press, New York 29-49, 1991).
20. Brooks, C.L. III, Karplus, M., Pettitt, B.M. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics (Adv. Chem. Phys. LXXI; John Wiley & Sons, 1988).
21. Venable, R.M., Zhang, Y., Hardy, B.J., Pastor, R. Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. Science 262, 223-226 (1993).
22. Becker, O. M., Karplus, M. Temperature echoes in molecular-dynamics simulations of proteins. Physical Review Letters 70, 3514-3517 (1993).
23. Weerasinghe, S., Smith, P.E., Mohan, V., Cheng, Y.-K. & Pettitt, B.M. Nanosecond dynamics and structure of a model DNA triple-helix in saltwater solution. J. Am. Chem. Soc. 117, 2147-2158 (1995).
24. Eriksson, M.A.L., Hard, T. & Nilsson, L. in NATO ASI Series (G. Wipff, ed.; 1993).
25. Woolf, T.B., Roux, B. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc. Natl. Acad. Sci. USA 91, 11631-11635 (1994).
26. Hurley, J.H., Dean, A.M., Koshland, D.E., Jr. & Stroud, R.M. Catalytic mechanism of NADP-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP complexes. Biochemistry 30, 8671(1991).
27. Stoddard, B.L. & Koshland, D.E. Jr. The Structure of Isocitrate Dehydrogenase complexed to α-ketoglutarate: A transient conformational change during catalysis. Biochemistry 32, 9317-9322 (1993).
28. Brooks, B. et al. CHARMM - A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187 (1983).
29. MacKerell, J.A.D., Wiorkiewicz-Kuczera, J., Karplus, M. An all-atom empirical energy function for the simulation of nucleic-acids. J. Am. Chem.Soc. 210, 68-72 (1995).
30. Brunger, A., Brooks, C.L. & Karplus, M. Active site dynamics of ribonuclease. Proc. Natl. Acad. Sci. 82, 8458 (1985).
31. Brooks C.L. III, Brūnger, A. & Karplus, M. Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. Biopolymers 24, 843 (1985).
32. Jorgensen, W.L, Chandrasekhar, J., Madura, J., Impey, R.W. & Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926 (1983).
33. Ramaswamy, S., Eklund, H. & Plapp, B. V. Structures of horse liver alcohol-dehydrogenase complexed with NAD(+) and substituted benzyl alcohols. Biochemistry 33, 5230 (1994).
34. Brünger, A., Kuriyan, J. & Karplus, M. Crystallographic R factor refinement by molecular dynamics. Science 235, 458 (1987).
35. Hurley, J.H., Dean, A.M., Sohl, J.L., Koshland, D.E. Jr. & Stroud, R.M. Regulation of an enzyme by phosphorylation at the active site. Science 249, 1012 (1990).
36. Stoddard, B.L., Dean, A.M. & Koshland, D.E. Jr. The 2.5 Å structure of isocitrate dehydrogenase with isocitrate, NADP, and calcium: A pseudo-Michaelis Ternary complex. Biochemistry 32, 9310-9316 (1993).
37. Hurley, J.H., Dean, A.M., Thorsness, P., Koshland, D.E. Jr. & Stroud, R.M. Regulation of isocitrate dehydrogenase by phosphorylation involves no long-range conformational change inthe free enzyme. J. Biol. Chem. 265, 3599-3602 (1990).
38. Dean, A.M. & Koshland, D. E. Jr. Electrostatic and steric contributions to regulation at the active site of isocitrate dehydrogenase. Science 249, 1044-1046 (1990).
39. Thorsness, P.E. & Koshland, D.E. Jr. The inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate., J. Biol. Chem. 262, 10422-10425 (1987).
40. Chen, R., Grobler, J.A., Hurley, J.H. & Dean, A.M. Second-site suppression of regulatory phosphorylation in Escherichi coli isocitrate dehydrogenase. Protein Science 5, 341-347 (1996).
41. Dean, A.M., Shiau, A.K. & Koshland, D.E. Jr. Determinants of performance in isocitrate dehydrogenase. Protein Science 5, 287-295 (1996).
42. Brünger, A.T. A unified approach to Crystallographic refinement and molecular replacement, in Crystallographic Computing 5 (eds D. Moras, A.D. Podjarny & J.C. Thierry) 382-391 (Oxford University Press, New York; 1991).
43. Gros, P. Time-averaged crystallographically restrained molecular dynamics, in Crystallographic Computing 5 (D. Moras, A. D. Podjarny and J. C. Thierry, eds) 2949 (Oxford University Press, New York; 1991).
44. Hehre, W.J., Radom, L., Scheyer, P., Pople, JA Ab initio molecular orbital theory. (John Wiley and Sons, New York, NY, 1981).