Simulation of diffusion time of small molecules in protein crystals

Structure

Volumn 14, Issue 3, 2006, Pages 393-400

  Geremia, Silvano ^a   Campagnolo, Mara ^a   Demitri, Nicola ^a   Johnson, Louise N ^b  

^a UNIVERSITY OF TRIESTE   (Italy)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTOGLOBULIN; ELASTASE; GLYCOGEN PHOSPHORYLASE B; ISOCITRATE DEHYDROGENASE; LIGAND; LYSOZYME; MALTODEXTRIN; RIBONUCLEASE; STEROID DELTA ISOMERASE;

ARTICLE; BINDING AFFINITY; CRYSTAL; DIFFUSION; EQUILIBRIUM CONSTANT; MOLECULE; PRIORITY JOURNAL; SIMULATION;

COMPUTER SIMULATION; CRYSTALLIZATION; DIFFUSION; MODELS, CHEMICAL; MURAMIDASE; NANOTECHNOLOGY; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS;

EID: 33644847519     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2005.12.007     Document Type: Article

References (31)

1. T. Alber, G.A. Petsko, and D. Tsernoglou Crystal structure of elastase-substrate complex at -55 degrees C Nature 263 1976 297 300
2. F.H. Batzold, A.M. Benson, D.F. Covey, C.H. Robinson, and P. Talalay The delta 5-3-ketosteroid isomerase reaction: catalytic mechanism, specificity and inhibition Adv. Enzyme Regul. 14 1976 243 267
3. J.J. Beintema, R.N. Campagne, and M. Gruber Rat pancreatic ribonuclease: I. Isolation and properties Biochim. Biophys. Acta 310 1973 148 160
4. W.H. Bishop, and F.M. Richards Properties of liquids in small pores: rates of diffusion of some solutes in cross-linked crystals of beta-lactoglobulin J. Mol. Biol. 38 1968 315 328
5. CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
6. Chemical Rubber Company CRC Handbook of Chemistry and Physics 83rd Edition 1995 CRC Press Cleveland, OH
7. J. Crank The Mathematics of Diffusion. 1956 Oxford University Press Oxford, UK
8. A. Cvetkovic, A.J. Straathof, D.N. Hanlon, S. van der Zwaag, R. Krishna, and L.A. van der Wielen Quantifying anisotropic solute transport in protein crystals using 3-D laser scanning confocal microscopy visualization Biotechnol. Bioeng. 86 2004 389 398
9. D. deBeer, P. Stoodley, and Z. Lewandowski Measurement of local diffusion coefficients in biofilms by microinjection and confocal microscopy Biotechnol. Bioeng. 53 1997 151 158
10. J.T. Edward Molecular volumes and the Stokes-Einstein equation J. Chem. Educ. 47 1970 261 270
11. A.L. Fink, and G.A. Petsko X-ray cryoenzymology Adv. Enzymol. Relat. Areas Mol. Biol. 52 1981 177 246
12. J. Garcia de la Torre, S. Navarro, M.C. Lopez Martinez, F.G. Diaz, and J.J. Lopez Cascales HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules Biophys. J. 67 1994 530 531
13. S. Geremia, M. Campagnolo, R. Schinzel, and L.N. Johnson Enzymatic catalysis in crystals of Escherichia coli maltodextrin phosphorylase J. Mol. Biol. 322 2002 413 423
14. J. Hajdu, K.R. Acharya, D.I. Stuart, P.J. McLaughlin, D. Barford, N.G. Oikonomakos, H. Klein, and L.N. Johnson Catalysis in the crystal: synchrotron radiation studies with glycogen phosphorylase b EMBO J. 6 1987 539 546
15. M.N. James, A.R. Sielecki, G.D. Brayer, L.T. Delbaere, and C.A. Bauer Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 A resolution: a model for serine protease catalysis J. Mol. Biol. 144 1980 43 88
16. L.N. Johnson Glycogen phosphorylase: control by phosphorylation and allosteric effectors FASEB J. 6 1992 2274 2282
17. L.N. Johnson, and J. Hajdu Synchrotron studies on enzyme catalysis in crystals S. Hasnian Synchrotron Radiation in Biophysics 1990 Ellis Horwood Ltd. Chichester, UK 142 155
18. H.W. Klein, M.J. Im, and D. Palm Mechanism of the phosphorylase reaction: utilization of D-gluco-hept-1-enitol in the absence of primer Eur. J. Biochem. 157 1986 107 114
19. M.E. Lee, D.H. Dyer, O.D. Klein, J.M. Bolduc, B.L. Stoddard, and D.E. Koshland Jr. Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli Biochemistry 34 1995 378 384
20. M.W. Makinen, and A.L. Fink Reactivity and cryoenzymology of enzymes in the crystalline state Annu. Rev. Biophys. Bioeng. 6 1977 301 343
21. K. Malek, T. Odijk, and M.O. Coppens Diffusion in protein crystals: a computer simulation Chemphyschem 5 2004 1596 1599
22. P. Mendes GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems Comput. Appl. Biosci. 9 1993 563 571
23. P. O'Hara, P. Goodwin, and B. Stoddard Direct measurement of diffusion rates in enzyme crystals by video absorbance spectroscopy J. Appl. Crystallogr. 28 1995 829 834
24. L.A. Sluyterman, and M.J. de Graaf The activity of papain in the crystalline state Biochim. Biophys. Acta 171 1969 277 287
25. B.L. Stoddard, and G.K. Farber Direct measurement of reactivity in the protein crystal by steady-state kinetic studies Structure 3 1995 991 996
26. M. Tomadakis, and S. Sotirchos Transport properties of random arrays of freely overlapping cylinders with various orientation distributions J. Chem. Phys. 98 1993 616 626
27. O.D. Velev, E.W. Kaler, and A.M. Lenhoff Surfactant diffusion into lysozyme crystal matrices investigated by quantitative fluorescence microscopy J. Phys. Chem. B 104 2000 9267 9275
28. K.A. Watson, C. McCleverty, S. Geremia, S. Cottaz, H. Driguez, and L.N. Johnson Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question EMBO J. 18 1999 4619 4632
29. E.M. Westbrook, and P.B. Sigler Enzymatic function in crystals of delta 5-3-ketosteroid isomerase: catalytic activity and binding of competitive inhibitors J. Biol. Chem. 259 1984 9090 9095
30. H.W. Wyckoff, M. Doscher, D. Tsernoglou, T. Inagami, L.N. Johnson, K.D. Hardman, N.M. Allewell, D.M. Kelly, and F.M. Richards Design of a diffractometer and flow cell system for X-ray analysis of crystalline proteins with applications to the crystal chemistry of ribonuclease-S J. Mol. Biol. 27 1967 563 578
31. H.W. Wyckoff, K.D. Hardman, N.M. Allewell, T. Inagami, D. Tsernoglou, L.N. Johnson, and F.M. Richards The structure of ribonuclease-S at 6 A resolution J. Biol. Chem. 242 1967 3749 3753