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Reference Cryobench publications

Bourgeois D, Vernède X, Adam V, Fioravanti E, Ursby T. "A microspectrophotometer for UV-visible absorption and fluorescence studies of protein crystals" (2002) J. Appl. Crystallogr. 35, 319-326.

Royant A, Carpentier P, Ohana J, McGeehan J, Paetzold B, Noirclerc-Savoye M, Vernède X, Adam V, Bourgeois D. "Advances in spectroscopic methods for biological crystals. part 1 - Fluorescence lifetime measurements" (2007) J. Appl. Crystallogr. 40, 1105-1112.

Carpentier P, Royant A, Ohana J, Bourgeois D. "Advances in spectroscopic methods for biological crystals. part 2 - Raman spectroscopy" (2007) J. Appl. Crystallogr. 40, 1113-1122.

Cryobench publications [with spectroscopy in use]

2010

Experimental data

Faro AR, Adam V, Carpentier P, Darnault C, Bourgeois D, de Rosny E. "Low-temperature switching by photoinduced protonation in photochromic fluorescent proteins" (2010) Photochem. Photobiol. Sci. 9, 254-262. [UV-vis Absorption/Fluorescence]

2009

Experimental data

Adam V, Carpentier P, Violot S, Lelimousin M, Darnault C, Nienhaus GU, Bourgeois D. "Structural basis of X-ray-induced transient photobleaching in a photoactivatable green fluorescent protein" (2009) J. Am. Chem. Soc. 131, 18063-18065. [UV-vis Absorption/Fluorescence/Raman]

Barros T, Royant A, Standfuss J, Dreuw A, Kühlbrandt W. "Crystal structure of plant light-harvesting complex shows the active, energy-transmitting state." (2009) EMBO J. 28, 298-306. [UV-vis Absorption/Fluorescence/TCSPC]

Carpentier P, Violot S, Blanchoin L, Bourgeois D. "Structural basis for the phototoxicity of the fluorescent protein KillerRed." (2009) FEBS Lett. 583, 2839-42. [UV-vis Absorption/Fluorescence]

Durin G, Delaunay A, Darnault C, Heyes DJ, Royant A, Vernède X, Hunter CN, Weik M, Bourgeois D. “Simultaneous measurements of solvent dynamics and functional kinetics in a light-activated enzyme.” (2009) Biophys. J. 96, 1902-1910. [UV-vis Absorption/Fluorescence]

Howard-Jones AR, Adam V, Cowley A, Baldwin JE, Bourgeois D. “Cryophotolysis of a caged oxygen compound for use in low temperature biological studies.” (2009) Photochem. Photobiol. Sci. 8, 1150-1156. [UV-vis Absorption]

Lafaye C, Iwema T, Carpentier P, Jullian-Binard C, Kroll JS, Collet JF, Serre L. “Biochemical and structural study of the homologues of the thiol-disulfide oxidoreductase DsbA in Neisseria meningitidis.” (2009) J. Mol. Biol. 392, 952-966. [Raman]

Lelimousin M, Noirclerc-Savoye M, Lazareno-Saez C, Paetzold B, Le Vot S, Chazal R, Macheboeuf P, Field MJ, Bourgeois D, Royant A. “Intrinsic dynamics in ECFP and Cerulean control fluorescence quantum yield.” (2009) Biochemistry 48, 10038-10046 [UV-vis Absorption/Fluorescence/TCSPC]

Mailliet J, Psakis G, Schroeder C, Kaltofen S, Dürrwang U, Hughes J, Essen LO. "Dwelling in the dark: procedures for the crystallography of phytochromes and other photochromic proteins" (2009) Acta Cryst. D65, 1232-1235. [UV-vis Absorption]

Moldt J, Pokorny R, Orth C, Linne U, Geisselbrecht Y, Marahiel MA, Essen LO, Batschauer A. “Photoreduction of the folate cofactor in members of the photolyase family.” (2009) J. Biol. Chem. 284, 21670-82163. [UV-vis Absorption/Fluorescence]

Violot S, Carpentier P, Blanchoin L, Bourgeois D. “Reverse pH-dependence of chromophore protonation explains the large stokes shift of the red fluorescent protein mKeima.” (2009) J. Am. Chem. Soc. 131, 10356-10357. [UV-vis Absorption/Fluorescence/Raman]

Review or citation

Bourgeois D, Katona G, de Rosny E, Carpentier P. “Raman-assisted x-ray crystallography for the analysis of biomolecules.” (2009) Methods Mol. Biol. 544, 253-267.

Bourgeois D, Weik M. “Kinetic protein crystallography: a tool to watch proteins in action.” (2009) Crystallography Reviews 15, 87-118.

Garman EF, Nave C. “Radiation damage in protein crystals examined under various conditions by different methods.” (2009) J. Synchrotron Radiat. 16, 129-132.

Macedo S, Pechlaner M, Schmid W, Weik M, Sato K, Dennison C, Djinović-Carugo K. “Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?” (2009) J. Synchrotron Radiat. 16, 191-204.

McGeehan J, Ravelli RB, Murray JW, Owen RL, Cipriani F, McSweeney S, Weik M, Garman EF. “Colouring cryo-cooled crystals: online microspectrophotometry.” (2009) J. Synchrotron Radiat. 16, 163-172.

Owen RL, Pearson AR, Meents A, Boehler P, Thominet V, Schulze-Briese C. “A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source.” (2009) J. Synchrotron Radiat. 16, 173-182.

Pearson AR, Owen RL. “Combining X-ray crystallography and single-crystal spectroscopy to probe enzyme mechanisms.” (2009) Biochem. Soc. Trans. 37, 378-381.

2008

Experimental data

Adam V, Lelimousin M, Boehme S, Desfonds G, Nienhaus K, Field MJ, Wiedenmann J, McSweeney S, Nienhaus GU, Bourgeois D. “Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations.” (2008) Proc. Natl. Acad. Sci. USA 105 (47): 18343-18348. [UV-vis Absorption/Fluorescence]

Essen LO, Mailliet J, Hughes J. “The structure of a complete phytochrome sensory module in the Pr ground state.” (2008) Proc. Natl. Acad. Sci. USA 105, 14709-14714. [UV-vis Absorption]

Hersleth HP, Hsiao YW, Ryde U, Gorbitz CH, Andersson KK. “The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection.” (2008) Biochem. J. 412, 257-264. [UV-vis Absorption]

Review or citation

Coureux PD, Fan ZP, Stojanoff V, Genick UK. “Picometer-scale conformational heterogeneity separates functional from nonfunctional states of a photoreceptor protein.” (2008) Structure 16 (6): 863-872

Ellis MJ, Buffey SG, Hough MA, Hasnain SS. “On-line optical and X-ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states.” (2008) J. Synchrotron Radiat. 15, 433-439.

Hersleth HP, Hsiao YW, Ryde U, Görbitz CH, Andersson KK. “The influence of X-rays on the structural studies of peroxide-derived myoglobin intermediates.” (2008) Chem. Biodivers. 5, 2067-2089.

Merlino A, Sica F, Mazzarella L, Zagari A, Vergara A. “Correlation between Raman and X-ray crystallography data of (Pro-Pro-Gly)10.” (2008) Biophys. Chem. 137, 24-27.

Strange RW, Feiters MC. “Biological X-ray absorption spectroscopy (BioXAS): a valuable tool for the study of trace elements in the life sciences.” (2008) Curr. Opin. Struct. Biol. 18, 609-616.

2007

Experimental data

Carpentier P, Royant A, Ohana J, Bourgeois D. “Advances in spectroscopic methods for biological crystals. part 2 - Raman spectroscopy” (2007) J. Appl. Crystallogr. 40, 1113-1122. [Raman]

Colletier JP, Royant A, Specht A, Sanson B, Nachon F, Masson P, Zaccai G, Sussman JL, Goeldner M, Silman I, Bourgeois D, Weik M. “Use of a 'caged' analogue to study the traffic of choline within acetylcholinesterase by kinetic crystallography” (2007) Acta Crystallog. D63, 1115-1128. [UV-vis Absorption]

Katona G, Carpentier P, Nivière V, Amara P, Adam V, Ohana J, Tsanov N, Bourgeois D. “Raman-assisted crystallography reveals End-On peroxide intermediates in a nonheme iron enzyme” (2007) Science 316, 449-453. [Raman]

McGeehan JE, Carpentier P, Royant A, Bourgeois D, Ravelli RBG. “X-ray Radiation-induced damage in DNA monitored by online Raman” (2007) J. Synchrotron Radiat. 14, 97-108. [Raman]

Royant A, Carpentier P, Ohana J, McGeehan J, Paetzold B, Noirclerc-Savoye M, Vernède X, Adam V, Bourgeois D. “Advances in spectroscopic methods for biological crystals. part 1 - Fluorescence lifetime measurements” (2007) J. Appl. Crystallogr. 40, 1105-1112. [Fluorescence/TCSPC]

Schmidt M, Patel A, Zhao Y, Reuter W. “Structural basis for the photochemistry of alpha-phycoerythrocyanin” (2007) Biochemistry 46, 416-423. [UV-vis Absorption]

Review or citation

Beitlich T, Kuhnel K, Schulze-Briese C, Shoeman RL, Schlichting I. “Cryoradiolytic reduction of crystalline heme proteins: analysis by UV-Vis spectroscopy and X-ray crystallography” (2007) J. Synchrotron Radiat. 14, 11-23.

Bourgeois D, de Rosny E, Katona G. “La cristallographie cinétique : un outil pour filmer les protéines au travail” (2007) Biofutur 280, 48-51.

2006

Experimental data

Marcaida MJ, Schlarb-Ridley BG, Worrall JAR, Wastl J, Evans TJ, Bendall DS, Luisi BF, Howe CJ “Structure of cytochrome c_6A, a novel dithio-cytochrome of Arabidopsis thaliana, and its reactivity with plastocyanin: Implications for function.” (2006) J. Mol. Biol. 360, 968-977. [UV-vis Absorption]

Sainz G, Jakoncic J, Sieker LC, Stojanoff V, Sanishvili N, Asso M, Bertrand P, Armengaud J, Jouanneau Y. “Structure of a [2Fe-2S] ferredoxin from Rhodobacter capsulatus likely involved in Fe-S cluster biogenesis and conformational changes observed upon reduction.” (2006) J. Biol. Inorg. Chem. 11, 235-246. [UV-vis Absorption]

Vernède X, Lavault B, Ohana J, Nurizzo D, Joly J, Jacquamet L, Felisaz F, Cipriani F, Bourgeois D. “UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops.” (2006) Acta Crystallogr. D62, 253-261. [Fluorescence]

Williams P, Coates L, Mohammed F, Gill R, Erskine P, Bourgeois D, Wood SP, Anthony C, Cooper JB. “The 1.6 Å X-ray structure of the unusual c-type cytochrome, cytochrome c_L, from the methylotrophic bacterium Methylobacterium extorquens.” (2006) J. Mol. Biol. 357, 151-162. [UV-vis Absorption]

Review or citation

Klink BU, Goody RS, Scheidig AJ “A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction.” (2006) Biophys. J. 91, 981-992.

2005

Review or citation

Bourgeois D, Royant A. “Advances in kinetic protein crystallography.” (2005) Curr. Opin. Struct. Biol. 15, 538-547.

Bourgeois D, Weik M. “New perspectives in kinetic protein crystallography using caged compounds” (2005) in “Dynamic Studies in Biology: Phototriggers, Photoswitches and Caged Biomolecules”, edited by M. Goeldner & R. Givens, pp. 410–435. Weinheim: Wiley-VCH.

Johansson T, Oswald C, Pedersen A, Tornroth S, Okvist M, Karlsson BG, Rydstrom J, Krengel U. “X-ray structure of domain I of the proton-pumping membrane protein transhydrogenase from Escherichia coli.” (2005) J. Mol. Biol. 352, 299-312.

Judge RA, Swift K, Gonzalez C. “An ultraviolet fluorescence-based method for identifying and distinguishing protein crystals.” (2005) Acta Crystallogr. D61, 60-66.

2004

Experimental data

Adam V, Royant A, Niviere V, Molina-Heredia FP, Bourgeois D. “Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction.” (2004) Structure 12, 1729-1740. [UV-vis Absorption]

Dias JM, Alves T, Bonifácio C, Pereira AS, Trincão J, Bourgeois D, Moura I. Romão MJ. “Structural basis for the mechanism of Ca²⁺ activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617.” (2004) Structure 12, 961-973. [UV-vis Absorption]

Edman K, Royant A, Larsson G, Jacobson F, Taylor T, van der Spoel D, Landau EM, Pebay-Peyroula E, Neutze R. “Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin.” (2004) J. Biol. Chem. 279, 2147-2158. [UV-vis Absorption]

Jacquamet L, Ohana J, Joly J, Legrand P, Kahn R, Borel F, Pirocchi M, Charrault P, Carpentier P, Ferrer JL. “A new highly integrated sample environment for protein crystallography.” (2004) Acta Crystallogr. D60, 888-894. [Fluorescence]

Kort R, Hellingwerf KJ, Ravelli RBG. “Initial events in the photocycle of photoactive yellow protein” (2004) J. Biol. Chem. 279, 26417-26424. [UV-vis Absorption]

Kort R, Komori H, Adachi S, Miki K, Eker A. “DNA apophotolyase from Anacystis nidulans: 1.8 Å structure, 8-HDF reconstitution and X-ray-induced FAD reduction.” (2004) Acta Crystallogr. D60, 1205-1213. [UV-vis Absorption]

Weik M, Vernède X, Royant A, Bourgeois D. “Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals.” (2004) Biophys. J. 86, 3176-3185. [Fluorescence]

Review, or citation

Neutze R, Huldt G, Hajdu J, van der Spoel D. “Potential impact of an X-ray free electron laser on structural biology.” (2004) Rad. Phys. Chem. 71, 905-916.

Pearson AR, Mozzarelli A, Rossi GL. “Microspectrophotometry for structural enzymology.” (2004) Curr. Opin. Struct. Biol. 14, 656-662.

Powe AM, Fletcher KA, St Luce NN, Lowry M, Neal S, McCarroll ME, Oldham PB, McGown LB, Warner IM. “Molecular fluorescence, phosphorescence, and chemiluminescence spectrometry.” (2004) Anal. Chem. 76, 4614-4634.

2003

Experimental data

Aragão D, Macedo S, Mitchell EP, Romão CV, Liu MY, Frazão C, Saraiva LM, Xavier AV, LeGall J, van Dongen WMAM, Hagen WR, Teixeira M, Carrondo MA, Lindley P. “Reduced hybrid cluster proteins (HCP) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough): X-ray structures at high resolution using synchrotron radiation.” (2003) J. Biol. Inorg. Chem. 8, 540-548. [UV-vis Absorption]

Fioravanti E, Haouz A, Ursby T, Munier-Lehmann H, Delarue M, Bourgeois D. “Mycobacterium tuberculosis thymidylate kinase: Structural studies of intermediates along the reaction pathway.” (2003) J. Mol. Biol. 327,1077-1092. [Fluorescence]

Kort R, Ravelli RBG, Schotte F, Bourgeois D, Crielaard W, Hellingwerf K J, Wulff M. “Characterization of photocycle intermediates in crystalline photoactive yellow protein.” (2003) Photochem. Photobiol. 78, 131-137. [UV-vis Absorption]

2002

Experimental data

Bourgeois D, Vernède X, Adam V, Fioravanti E, Ursby T. “A microspectrophotometer for UV-visible absorption and fluorescence studies of protein crystals” (2002) J. Appl. Crystallogr. 35, 319-326. [UV-vis Absorption/Fluorescence]

Murray J, Garman E. “Investigation of possible free-radical scavengers and metrics for radiation damage in protein cryocrystallography.” (2002) J. Synchrotron Radiat. 9, 347-354. [UV-vis Absorption]

Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, Shichida Y. “Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.” (2002) Proc. Natl. Acad. Sci. USA 99, 5982-5987. [UV-vis Absorption]

Ursby T, Weik M, Fioravanti E, Delarue M, Goeldner M, Bourgeois D. “Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals.” (2002) Acta Crystallogr. D58, 607-614. [UV-vis Absorption]

Weik M, Berges J, Raves ML, Gros P, McSweeney S, Silman I, Sussman JL, Houée-Levin C, Ravelli RBG. “Evidence for the formation of disulfide radicals in protein crystals upon X-ray irradiation.” (2002) J. Synchrotron Radiat. 9, 342-346. [UV-vis Absorption]

Review or citation

Prasad GS, Wahlberg M, Sridhar V, Sundaresan V, Yamaguchi M, Hatefi Y, Stout CD “Crystal structures of transhydrogenase domain I with and without bound NADH.” (2002) Biochemistry 41, 12745-12754.

2001

Experimental data

Specht A, Ursby T, Weik M, Peng L, Kroon J, Bourgeois D, Goeldner M. “Cryophotolysis of ortho-nitrobenzyl derivatives of enzyme ligands for the potential kinetic crystallography of macromolecules.” (2001) Chembiochem 2, 845-848. [UV-vis Absorption]

2000

Experimental data

Royant A, Edman K, Ursby T, Pebay-Peyroula E, Landau EM, Neutze R. “Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin.” (2000) Nature 406, 645-648. [UV-vis Absorption]