Intermediate trapping and laue X-ray diffraction: Potential for enzyme mechanism, dynamics, and inhibitor screening

Alber, 1976, Crystal structure of elastase-substrate complex at −55 °C, Nature, 263, 297, 10.1038/263297a0 Appelt, 1991, Design of enzyme inhibitors using iterative protein crystallographic analysis, J. Med. Chem., 34, 1925, 10.1021/jm00111a001 Bennett, 1980, Structure of a complex between yeast hexokinase A and glucose, J. Mol. Biol., 140, 211, 10.1016/0022-2836(80)90103-5 Bolduc, 1995, Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase, Science, 268, 1312, 10.1126/science.7761851 Brubaker, 1996, Synthesis, kinetics, and structural studies of a photolabile caged isocitrate: a catalytic trigger for isocitrate dehydrogenase, Biochemistry, 10.1021/bi951105v Campbell, 1986, Laue diffraction, Inf. Q. Protein Cryst., Daresbury Lab, 18, 23 Campbell, 1990, Calcium binding sites in tomato bushy stunt virus visualized by Laue crystallography, J. Mol. Biol., 214, 627, 10.1016/0022-2836(90)90278-T Chen, 1992, Inhibition of b-lactamase by clavulanate: trapped intermediates in cryocrystallographic studies, J. Mol. Biol., 224, 1103, 10.1016/0022-2836(92)90472-V Cherfils, 1991, Protein-protein recognition analyzed by docking simulation, Proteins Struc. Funct. Genet., 11, 271, 10.1002/prot.340110406 Christianson, 1986, X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature, 83, 7568 Cleland, 1979, Statistical analysis of enzyme kinetic data, Methods Enzymol., 63, 103, 10.1016/0076-6879(79)63008-2 Corrie, 1992, The development and application of photosensitive caged compounds to aid time-resolved structure determination of macromolecules, 65 Cruikshank, 1987, Multiplicity distribution of reflections in Laue diffraction, Acta Crystallogr., A 43, 656, 10.1107/S0108767387098763 Cruickshank, 1991, Angular distribution of reflections in Laue diffraction, Acta Crystallogr., A 47, 352, 10.1107/S0108767391000703 Ding, 1994, Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase, Biochemistry, 33, 9285, 10.1021/bi00197a032 Duke, 1994, Laue and monochromatic diffraction studies on catalysis in phosphorylase b crystals, Protein Sci., 3, 1178, 10.1002/pro.5560030804 Farber, 1995, It's show time, Curr. Biol., 5, 1088, 10.1016/S0960-9822(95)00217-X Farber, 1988, X-ray laue diffraction from crystals of xylose isomerase, 85, 112 Fauman, 1994, Water-mediated substrate/product discrimination: the product complex of thymidylate synthase at 1.83 Å, Biochemistry, 33, 1502, 10.1021/bi00172a029 Ferre-D'Amare, 1994, Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies, Structure, 2, 357, 10.1016/S0969-2126(00)00037-X Finer-Moore, 1993, Refined structures of substratebound and phosphate-bound thymidylate synthase from Lactobacillus casei, J. Mol. Biol., 232, 1101, 10.1006/jmbi.1993.1463 Fink, 1981, X-ray cryoenzymology, Adv. Enzymol., 52, 177 Fleischer, 1993, Antifolate analogs: mechanism of action, analytical methodology, and clinical efficacy, Ther. Drug Monit., 15, 521, 10.1097/00007691-199312000-00012 Fletterick, 1975, The structure of a yeast hexokinase monomer and its complexes with substrates at 2.7 Å resolution, 72, 38 Friedrich, 1912, Interferenzerscheinungen bei Rontgenstrahlen, 303 Fulop, 1994, Laue diffraction study on the structure of cytochrome c peroxidase compound I, Structure, 2, 201, 10.1016/S0969-2126(00)00021-6 Gerstein, 1994, Structural mechanisms for domain movements in proteins, Biochemistry, 33, 6739, 10.1021/bi00188a001 Goodford, 1985, A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, J. Med. Chem., 28, 849, 10.1021/jm00145a002 Goodsell, 1986, Isohelical analysis of DNA groove-binding drugs, J. Med. Chem., 29, 727, 10.1021/jm00155a023 Goodsell, 1990, Automated docking of substrates to proteins by simulated annealing, Proteins Struc. Funct. Genet., 8, 195, 10.1002/prot.340080302 Grissom, 1988, Isotope effect studies of the chemical mechanism of pig heart NADP isocitrate dehydrogenase, Biochemistry, 27, 2934, 10.1021/bi00408a040 Hadfield, 1993, A fast and portable microspectrophotometer for protein crystallography, J. Appl. Crystallogr., 26, 839, 10.1107/S0021889893005552 Hajdu, 1990, Progress with Laue diffraction studies on protein and virus crystals, Biochemistry, 29, 1669, 10.1021/bi00459a001 Hajdu, 1986, Time-resolved structural studies on catalysis in the crystal with glycogen phosphorylase, Biochem. Soc. Trans., 14, 538, 10.1042/bst0140538 Hajdu, 1987, Catalysis in the crystal: synchrotron radiation studies with glycogen phosphorylase b, EMBO J., 6, 539, 10.1002/j.1460-2075.1987.tb04786.x Hajdu, 1987, Millisecond x-ray diffraction and the first electron density map from Laue photographs of a protein crystal, Nature, 329, 115, 10.1038/329178a0 Hajdu, 1991, On the limitations of the laue method when applied to crystals of macromolecules, 29 Hardy, 1987, Atomic structure of thymidylate synthase: target for rational drug design, Science, 235, 448, 10.1126/science.3099389 Hedman, 1985, Protein microcrystal diffraction and the effects of radiation damage with ultra-high flux synchrotron radiation, 82, 7604 Helliwell, 1984, Synchrotron x-radiation protein crystallography-instrumentation, methods, and applications, Rep. Prog. Phys., 47, 1403, 10.1088/0034-4885/47/11/001 Helliwell, 1985, Protein crystallography with synchrotron radiation, J. Mol. Struct., 130, 63, 10.1016/0022-2860(85)85023-7 Helliwell, 1992 Helliwell, 1989, The recording and analysis of synchrotron x-radiation Laue diffraction photographs, J. Appl. Crystallogr., 22, 483, 10.1107/S0021889889006564 Howell, 1992, Activity of crystalline turkey egg white lysozyme, Proteins Struc. Funct. Genet., 12, 91, 10.1002/prot.340120111 Hurley, 1989, Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase, 86, 8635 Hurley, 1990, Regulation of an enzyme by phosphorylation at the active site, Science, 249, 1012, 10.1126/science.2204109 Hurley, 1990, Regulation of isocitrate dehydrogenase by phosphorylation involves no long-range conformational change in the free enzyme, J. Biol. Chem., 265, 3599, 10.1016/S0021-9258(19)39632-2 Hurley, 1991, Catalytic mechanism of NADP-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP complexes, Biochemistry, 30, 8671, 10.1021/bi00099a026 Joseph, 1990, Anatomy of a conformational change: hinged ‘Lid’ motion of the triosephosphate isomerase loop, Science, 249, 1425, 10.1126/science.2402636 Kalman, 1979, Derivation of integrated reflected energy formulas, Acta Crystallogr., A 35, 634, 10.1107/S0567739479001480 Kamb, 1992, Cofactor triggers the conformational change in thymidylate synthase: implications for an ordered binding mechanism, Biochemistry, 31, 12876, 10.1021/bi00166a024 Kirkpatrick, 1983, Optimization by simulated annealing, Science, 220, 671, 10.1126/science.220.4598.671 Kuntz, 1992, Structure-based strategies for drug design and discovery, Science, 257, 1078, 10.1126/science.257.5073.1078 Kuntz, 1982, A geometric approach to macromolecule-ligand interactions, J. Biol. Chem., 161, 269 Laskowski, 1993, PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Cryst., 26, 283, 10.1107/S0021889892009944 Laue, 1912, Eine quantitative prufung der theorie fur the interferenzerscheinungen bei Rontgenstrahlen, 363 Lolis, 1990, Structure of yeast triosephosphate isomerase at 1.9-Å resolution, Biochemistry, 29, 6609, 10.1021/bi00480a009 Makinen, 1977, Reactivity and cryoenzymology of enzymes in the crystalline state, Annu. Rev. Biophys. Bioeng., 6, 301, 10.1146/annurev.bb.06.060177.001505 Margaritondo, 1988 Matthews, 1968, Solvent content of protein crystals, J. Mol. Biol., 33, 491, 10.1016/0022-2836(68)90205-2 Matthews, 1990, Crystal structure of Escherichia coli thymidylate synthase containing bound 5-fluoro-2′-deoxyuridylate and 10-propargyl-5,8-dideazafolate, J. Mol. Biol., 214, 923, 10.1016/0022-2836(90)90346-N Matthews, 1990, Stereochemical mechanism of action for thymidylate synthase based on the x-ray structure of the covalent inhibitor ternary complex with 5-fluoro-2′-deoxyuridylate and 5,10-methylenetetrahydrofolate, J. Mol. Biol., 214, 937, 10.1016/0022-2836(90)90347-O Meng, 1992, Automated docking with grid-based energy evaluation, J. Comp. Chem., 13, 505, 10.1002/jcc.540130412 Moffat, 1989, Time-resolved macromolecular crystallography, Annu. Rev. Biophys. Biophys. Chem., 18, 309, 10.1146/annurev.bb.18.060189.001521 Moffat, 1984, X-ray laue diffraction from protein crystals, Science, 223, 1423, 10.1126/science.223.4643.1423 Moffat, 1986, Laue diffraction from biological samples, Nucl. Instrum. Methods, A246, 627, 10.1016/0168-9002(86)90164-6 Montfort, 1990, Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate, Biochemistry, 29, 6964, 10.1021/bi00482a004 Morris, 1993, The genetic toxicology of 5-fluoropyrimidines and 5-chlorouracil, Mutat. Res., 297, 39, 10.1016/0165-1110(93)90006-9 O'Hara, 1995, Direct measurement of diffusion rates in enzyme crystals by video absorbance spectroscopy, J. Appl. Crystallogr., 28, 829, 10.1107/S0021889895007722 Perry, 1990, Plastic adaptation toward mutations in proteins: structural comparison of thymidylate synthases, Proteins, 8, 315, 10.1002/prot.340080406 Rasmussen, 1992, Crystalline ribonuclease A loses function below the dynamic transition at 220K, Nature, 357, 423, 10.1038/357423a0 Reynolds, 1988, Preliminary study of a phasetransformation in insulin crystals using synchrotron radiation Laue diffraction, Acta Crystallogr., B 44, 512, 10.1107/S0108768188005956 Rodgers, 1994, Cryocrystallography, Structure, 2, 1135, 10.1016/S0969-2126(94)00116-2 Röntgen, 1898, Abdruck der 1. und 2. Originalmitteilung von 1895, uber eine neue art von strahlen, und der 3. Mitteilung von 1897, weitere beobachtungen uber die eigenschaften der x-strahlen, Ann. Phys. Chem., 64, 1, 10.1002/andp.18983000102 Schlichting, 1989, Biochemical and crystallogaphic characterization of a complex of c-Ha-ras p21 and caged GTP with flash photolysis, 86, 7687 Schlichting, 1990, Time-resolved x-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis, Nature, 345, 309, 10.1038/345309a0 Schlichting, 1994, Crystal structure of photolyzed carbonmonoxymyoglobin, Nature, 371, 808, 10.1038/371808a0 Shoichet, 1991, Protein docking and complementarity, J. Mol. Biol., 221, 327, 10.1016/0022-2836(91)80222-G Shoichet, 1993, Structure-based discovery of inhibitors of thymidylate synthase, Science, 259, 1445, 10.1126/science.8451640 Singer, 1992, The hydrolytic water molecule in trypsin, revealed by timeresolved Laue crystallography, Science, 259, 669, 10.1126/science.8430314 Stoddard, 1995, Direct measurement of reactivity in the protein crystal by steady-state kinetic studies, Structure, 3, 991, 10.1016/S0969-2126(01)00235-0 Stoddard, 1992, Prediction of the structure of a receptor-protein complex using a binary docking method, Nature, 358, 774, 10.1038/358774a0 Stoddard, 1990, Photolysis and deacylation of inhibited chymotrypsin, Biochemistry, 29, 8042, 10.1021/bi00487a008 Stoddard, 1990, Structure and activity of two photoreversible cinnamates bound to chymotrypsin, Biochemistry, 29, 4871, 10.1021/bi00472a017 Stoddard, 1991, Observation of the light-triggered binding of pyrone to chymotrypsin by Laue x-ray crystallography, 88, 5503 Szebenyi, 1988, Quantitative analysis of Laue diffraction patterns recorded with a 120 picosecond exposure from an x-ray undulator, Trans. Am. Crystallogr. Assoc., 24, 167 Teng, 1994, Photolysis-induced structural changes in single crystals of carbonmonoxymyoglobin at 40K, Nature Struct. Biol., 1, 701, 10.1038/nsb1094-701 Tilton, 1992, Effects of temperature on protein structure and dynamics: x-ray crystallographic studies of the protein ribonuclease A at nine different temperatures from 98 to 320 °K, Biochemistry, 31, 2469, 10.1021/bi00124a006 Varney, 1992, Crystal-structure-based design and synthesis of benz-[cd]indole-containing inhibitors of thymidylate synthase, J. Med. Chem., 35, 663, 10.1021/jm00082a006 Weichsel, 1995, Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancer drug 1843U89, Nature Struct. Biol., 2, 1095, 10.1038/nsb1295-1095 Wodak, 1978, Computer analysis of proteinprotein interaction, J. Mol. Biol., 124, 323, 10.1016/0022-2836(78)90302-9 Wyckoff, 1967, 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, 563, 10.1016/0022-2836(67)90059-9 Wyckoff, 1967, 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, 563, 10.1016/0022-2836(67)90059-9 Yennewar, 1994, X-ray crystal structure of γ-chymotrypsin in hexane, Biochemistry, 33, 7326, 10.1021/bi00189a038 Yennewar, 1995, A structural explanation for enzyme memory in nonaqueous solvents, J. Am. Chem. Soc., 117, 577, 10.1021/ja00107a001