Advances in kinetic protein crystallography.

Many proteins function in the crystalline state, making crystallography a tool that can address mechanism, as well as structure. By initiating biological turnover in the crystal, transient structural species form, which may be filmed by Laue diffraction or captured by freeze-trapping methods. Laue diffraction has now reached an unprecedented level of sophistication and has found a 'niche of excellence' in the study of cyclic, ultra-fast, light-triggered reactions. Trapping methods, on the other hand, are more generally applicable, but require care to avoid artifacts. New strategies have been developed and difficulties such as radiation damage have received particular attention. Complementary methods--mainly UV/visible single-crystal spectroscopy--have proven essential to design, interpret and validate kinetic crystallography experiments.

[1]  R. Neutze,et al.  Conformational regulation of charge recombination reactions in a photosynthetic bacterial reaction center , 2005, Nature Structural &Molecular Biology.

[2]  M. Delarue,et al.  Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals. , 2002, Acta crystallographica. Section D, Biological crystallography.

[3]  G. Nienhaus,et al.  Ligand migration and protein fluctuations in myoglobin mutant L29W. , 2005, Biochemistry.

[4]  K. Moffat,et al.  Time-resolved biochemical crystallography: a mechanistic perspective. , 2001, Chemical reviews.

[5]  P. Carey,et al.  Following ligand binding and ligand reactions in proteins via Raman crystallography. , 2004, Biochemistry.

[6]  K. Moffat,et al.  Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[7]  P. Wolynes,et al.  The energy landscapes and motions of proteins. , 1991, Science.

[8]  C. Townsend,et al.  The catalytic cycle of β-lactam synthetase observed by x-ray crystallographic snapshots , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  David van der Spoel,et al.  Potential impact of an X-ray free electron laser on structural biology , 2004 .

[10]  A. Mozzarelli,et al.  Microspectrophotometry for structural enzymology. , 2004, Current opinion in structural biology.

[11]  M. Delarue,et al.  Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway. , 2003, Journal of molecular biology.

[12]  G. Schneider,et al.  Snapshot of a key intermediate in enzymatic thiamin catalysis: Crystal structure of the α-carbanion of (α,β-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Keith Moffat,et al.  Photoexcited Structure of a Plant Photoreceptor Domain Reveals a Light-Driven Molecular Switch Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010475. , 2002, The Plant Cell Online.

[14]  G. Petsko,et al.  Observation of unstable species in enzyme-catalyzed transformations using protein crystallography. , 2000, Current opinion in chemical biology.

[15]  Marius Schmidt,et al.  Analysis of experimental time-resolved crystallographic data by singular value decomposition. , 2004, Acta crystallographica. Section D, Biological crystallography.

[16]  Axel T Brunger,et al.  Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. , 2004, Journal of molecular biology.

[17]  Karl Edman,et al.  Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin* , 2004, Journal of Biological Chemistry.

[18]  J. Hajdu,et al.  Structure of the Bound Dioxygen Species in the Cytochrome Oxidase Reaction of Cytochrome cd 1Nitrite Reductase* , 2001, The Journal of Biological Chemistry.

[19]  T. Terwilliger,et al.  Difference refinement: obtaining differences between two related structures. , 1995, Acta crystallographica. Section D, Biological crystallography.

[20]  D. Harrison,et al.  3-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time". , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Hajdu,et al.  Protein crystallography in a vapour stream: data collection, reaction initiation and intermediate trapping in naked hydrated protein crystals , 2002 .

[22]  S. Prigge,et al.  Dioxygen Binds End-On to Mononuclear Copper in a Precatalytic Enzyme Complex , 2004, Science.

[23]  I. Schlichting,et al.  Trapping intermediates in the crystal: ligand binding to myoglobin. , 2000, Current opinion in structural biology.

[24]  Marius Schmidt,et al.  A structural pathway for signaling in the E46Q mutant of photoactive yellow protein. , 2005, Structure.

[25]  Aleksandr V. Smirnov,et al.  Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography , 2003, Science.

[26]  B. Halle Biomolecular cryocrystallography: structural changes during flash-cooling. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Marius Schmidt,et al.  Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data. , 2003, Biophysical journal.

[28]  A. Miele,et al.  Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Sean McSweeney,et al.  The reaction mechanism of phospholipase D from Streptomyces sp. strain PMF. Snapshots along the reaction pathway reveal a pentacoordinate reaction intermediate and an unexpected final product. , 2004, Journal of molecular biology.

[30]  J. Sussman,et al.  Specific protein dynamics near the solvent glass transition assayed by radiation‐induced structural changes , 2001, Protein science : a publication of the Protein Society.

[31]  Karl Edman,et al.  Analyzing protein functions in four dimensions , 2000, Nature Structural Biology.

[32]  P. Nordlund,et al.  Displacement of the tyrosyl radical cofactor in ribonucleotide reductase obtained by single-crystal high-field EPR and 1.4-Å x-ray data , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[33]  D. H. Mellor,et al.  Real time , 1981 .

[34]  P. Hegemann,et al.  Crystal structures and molecular mechanism of a light-induced signaling switch: The Phot-LOV1 domain from Chlamydomonas reinhardtii. , 2003, Biophysical journal.

[35]  H. Sakamoto,et al.  CO-trapping site in heme oxygenase revealed by photolysis of its co-bound heme complex: mechanism of escaping from product inhibition. , 2004, Journal of molecular biology.

[36]  K. Hellingwerf,et al.  Initial Events in the Photocycle of Photoactive Yellow Protein* , 2004, Journal of Biological Chemistry.

[37]  J Berendzen,et al.  The catalytic pathway of cytochrome p450cam at atomic resolution. , 2000, Science.

[38]  S. Ealick,et al.  Observation of time-resolved structural changes by linear interpolation of highly redundant X-ray diffraction data. , 2004, Acta crystallographica. Section D, Biological crystallography.

[39]  Karl Edman,et al.  Bacteriorhodopsin: a high-resolution structural view of vectorial proton transport. , 2002, Biochimica et biophysica acta.

[40]  K. Moffat,et al.  Optical studies of a bacterial photoreceptor protein, photoactive yellow protein, in single crystals. , 1995, Biochemistry.

[41]  F. Parak,et al.  Proteins in action: the physics of structural fluctuations and conformational changes. , 2003, Current opinion in structural biology.

[42]  H. Eklund,et al.  Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron , 2003, Science.

[43]  K. Moffat,et al.  Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein. , 2004, Structure.

[44]  J. Hajdu,et al.  The catalytic pathway of horseradish peroxidase at high resolution , 2002, Nature.

[45]  Karl Edman,et al.  High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle , 1999, Nature.

[46]  N. Shibayama,et al.  Direct observation of photolysis-induced tertiary structural changes in hemoglobin , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  O. Carugo,et al.  When X-rays modify the protein structure: radiation damage at work. , 2005, Trends in biochemical sciences.

[48]  B. Stoddard,et al.  Laue crystallography: coming of age , 1999 .

[49]  F. Schotte,et al.  Picosecond time-resolved X-ray crystallography: probing protein function in real time. , 2004, Journal of structural biology.

[50]  Z. Ren,et al.  Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Mark Gerstein,et al.  MolMovDB: analysis and visualization of conformational change and structural flexibility , 2003, Nucleic Acids Res..

[52]  K. Moffat,et al.  Structural Heterogeneity of Cryotrapped Intermediates in the Bacterial Blue Light Photoreceptor, Photoactive Yellow Protein¶ , 2004, Photochemistry and photobiology.

[53]  M. Murakami,et al.  Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin. , 2002, Journal of molecular biology.

[54]  D. Bourgeois,et al.  Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals. , 2004, Biophysical journal.

[55]  Sean J. Johnson,et al.  Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Gerhard Hummer,et al.  Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[57]  K. Moffat,et al.  Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center. , 2004, Proceedings of the National Academy of Sciences of the United States of America.