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Institut de Biologie StructuraleGrenoble / France

Publications depuis 2015

La liste des publications du groupe parues dans des revues à comité de lecture depuis 2015, ainsi que les ouvrages et chapitres d’ouvrage, est consultable ici (données issues de HAL-IBS).

Publications jusqu’à 2014

Publications 2014

Adam V, Berardozzi R, Byrdin M, Bourgeois D
Phototransformable fluorescent proteins : future challenges
Current Opinion in Chemical Biology, in press

Adam V
Phototransformable fluorescent proteins : which one for which application ? Histochemistry and Cell Biology DOI : 10.1007/s00418-­‐014-­‐1190-­‐5

Aleksandrov A, Zverena E, Field MJ.
The Mechanism of Citryl-­‐Coenzyme A Formation Catalyzed by Citrate Synthase.
J Phys Chem B 118 : 4505–4513

Avilov S, Berardozzi R, Gunewardene MS, Adam V, Hess ST and Bourgeois D
In cellulo Evaluation of Phototransformation Quantum Yields in Fluorescent Proteins Used as Markers for Single-­‐Molecule Localization Microscopy.
PLoS One in press

Bhattacharjee A, Weiss AKH, Artero V, Field MJ, Hofer TS
Electronic Structure and Hydration of Tetramine Cobalt Hydride Complexes.
J Phys Chem B 118 : 5551–5561

Borshchevskiy V, Round E, Erofeev I, Weik M, Ishchenko A, Gushchin I, Mishin, A, Willbold D, Büldt G, Gordeliy, V
Low dose X-­‐ray radiation induces structural alterations in proteins.
Acta Cryst. D. (in press).

Brus B, Kosak U, Turk S, Pislar A, Coquelle N, Kos J, Stojan J, Colletier J-P, Gobec S.
Discovery, Biological Evaluation, and Crystal Structure of a Novel Nanomolar Selective Butyrylcholinesterase Inhibitor.
Journal of Medicinal Chemistry 57 : 8167-8179

Choudary OP, Paz A, Adelman JL, Colletier JP, Abramson J, Grabe M
Structure guided simulations illuminate the mechanism of ATP transport through VDAC1.
Nat Struct Mol Biol 21 : 626-­‐632

Crous W, Field MJ, Naidoo KJ.
Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary.
J Chem Theor Comput 10 : 1727–1738

Cupane A, Fomina M, Piazza I, Peters J, and Schirò G.
Experimental evidence for a liquid-liquid crossover in deeply cooled confined water.
Phys. Rev. Lett. 113 : 215701

Cupane A, Fomina M, and Schirò G.
The boson peak of deeply cooled confined water reveals the existence of a low-temperature liquid-liquid crossover.
Journal of Chemical Physics 141 : 18C510.

Duan C, Adam V, Byrdin M and Bourgeois D
Structural basis of photoswitching in fluorescent proteins
In Methods in Molecular Biology, vol. 1148 , pp 177-­‐202.

Falourd X, Natali F, Peters J, Foucat L.
Molecular mobility in Medicago truncatula seed during early stage of germination : Neutron Scattering and NMR investigations.
Chem. Phys. 428, 181 -­‐ 185.

Fron E, Sliwa M, Adam V, Michiels J, Rocha S, Dedecker P, Hofkens J, Mizuno H Excited state dynamics of photoconvertible fluorescent protein Kaede revealed by ultrafast spectroscopy.
Photochemical & Photobiological Sciences 13(6) : 867-­‐874

Gebhardt R, Teulon JM, Pellequer JL, Burghammer M, Colletier JP, Riekel C
Virus particle assembly into crystalline domains enabled by the coffee ring effect. Soft Matter 10 : 5458-­‐5462.

Gudmundsson M, Kim S, Wu M, Ishida T, Haddad Momeni M, Vaaje-­‐Kolstad G, Lundberg D, Royant A, Ståhlberg J, Eijsink VG, Beckham GT, Sandgren M
Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-­ray photo-­reduction.
Journal of Biological Chemistry 289, 18782–18792.

Jackson CJ, Coppin CW, Carr PD, Aleksandrov A, Wilding M, Sugrue E, Ubels J, Paks M, Newman J, Peat TS, Russell RJ, Field M, Weik M, Oakeshott JG, Scott C
Apoenzyme stabilization results in 300-­‐fold increased soluble production of the Zn2+-­‐dependent dechlorinase TrzN.
Applied and Environmental Microbiology, in press.

Jørgensen R, Batot G, Mannerstedt K, Imberty A, Breton C, Hindsgaul O, Royant A, Palcic MM
Structures of a human blood group glycosyltransferase in complex with a photo-­‐activatable UDP-­‐Gal derivative reveal two different binding conformations.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 70, 1015–1021.

Kliachyna M, Santoni G, Nussbaum V, Renou J, Sanson B, Colletier JP, Arboleas M, Loiodice M, Weik M, Jean L, Renard PY, Nachon F, Baati R
Design, synthesis and biological evaluation of novel tetrahydroacridine pyridine-­‐ aldoxime and ­‐amidoxime hybrids as efficient uncharged reactivators of nerve agent inhibited human acetylcholinesterase.
European Journal of Medicinal Chemistry 78 : 455-­‐467

Knoll W, Peters J, Kursula P, Gerelli Y, and Natali F.
Influence of myelin proteins on the structure and dynamics of a model membrane with emphasis on the low temperature regime.
Journal of Chemical Physics 141 : 205101.

Knoll W, Peters J, Kursula P, Gerelli Y, Ollivier J, Telling M, Kemner E, and Natali F. Structural and Dynamical Properties of Reconstituted Myelin Sheaths in Presence of Myelin Proteins MBP and P2 Studied by Neutron Scattering.
Soft Matter 10, 519-529.

Liu M, Wang Y, Chem Y, Field MJ, Gao J (2014). QM/MM Through the 1990s : The First Twenty Years of Method
Development and Applications .
Israel J Chem 54, sous presse.

Oueis E, Santoni G, Ronco C, Syzgantseva O, Tognetti V, Joubert L, Romieu A, Weik M, Jean L, Sabot C, Nachon F, Renard PY
Reaction site-­‐driven regioselective synthesis of AChE inhibitors.
Organic & Biomolecular Chemistry 12 : 156-­‐161

Peters J, Martinez N, Michoud G, Cario A, Franzetti B, Jebbar M, Oger P.
Deep sea microbes probed by incoherent neutron scattering under high hydrostatic pressure.
Z. Phys. Chem. 228 : 1121-1133.

Polovinkin V, Balandin T, Volkov O, Round E, Borshchevskiy V, Utrobin P, von Stetten D, Royant A, Willbold D, Arzumanyan G, Chupin V, Popot JL and Gordeliy V Nanoparticle Surface-­‐Enhanced Raman Scattering of Bacteriorhodopsin Stabilized by Amphipol A8-­‐35.
J Membr. Biol., in press.

Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier JP, Messerschmidt M, Boutet S, Kogli JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park HW, Federici BA, Sauter NK, Schlichting I and Eisenberg D.
Proceedings of the National Academy of Sciences, USA, in press.

Shaik MM, Bhattacharjee N, Bhattacharjee A, Field MJ, Zanotti G Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations.
Proteins : Structure, Function and Bioinformatics, sous presse.

Trapp M, Tehei M, Trovaslet M, Nachon F, Martinez N, Koza MM, Weik M, Masson P and Peters J
Correlation of the Dynamics of Native Human Acetylcholinesterase and its inhibited Huperzine A counterpart from sub-picoseconds to nanoseconds.
Journal of the Royal Society Interface 11, 20140372.

von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F, Juers DH, Flot D, Mueller-­‐Dieckmann C, Leonard GA, de Sanctis D, Royant A
In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF.
Acta Crystallographica Section D : Biological Crystallography, in press

Wickstrand C, Dods R, Royant A, Neutze R
Bacteriorhodopsin : would the real structural intermediates please stand up ? Biochimica et Biophysica Acta – General Subjects, in press

Wymore T, Field MJ, Langan P, Smith JC, Parks JM (2014). Hydrolysis of DFP and the Nerve Agent (S)-‐Sarin by DFPase
Proceeds along Two Different Reaction Pathways : Implications for Engineering Bioscavengers.
J Phys Chem B 118 : 4479–4489

Yu D, Gustafson WC, Han C, Lafaye C, Noirclerc-­‐Savoye M, Ge WP, Thayer DA, Huang H, Kornberg TB, Royant A, Jan LY, Jan YN, Weiss WA, Shu X
An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging.
Nature Communications 5:3626

Publications 2013

Aleksandrov A and Field M
Mechanism of activation of elongation factor Tu by ribosome : Catalytic histidine activates GTP by protonation.
Rna-a Publication of the Rna Society (2013) 19(9) : 1218-1225

Arantes GM, Bhattacharjee A and Field MJ
Homolytic cleavage of FeS bonds in rubredoxin under mechanical stress.
Angewandte Chemie-International Edition (2013) 52(31) : 8144-8146

Bachega JFR, Timmers LFSM, Assirati L, Bachega LR, Field MJ and Wymore T
GTKDynamo : A PyMOL plug-in for QC/MM hybrid potential simulations.
Journal of Computational Chemistry (2013) 34(25) : 2190-2196

Baggioli A, Crescenzi O, Field MJ, Castiglione F and Raos G
Computational 17O-NMR spectroscopy of organic acids and peracids : comparison of solvation models.
Physical Chemistry Chemical Physics (2013) 15(4) : 1130-1140

Bhattacharjee A, Andreiadis ES, Chavarot-Kerlidou M, Fontecave M, Field MJ and Artero V
A computational study of the mechanism of hydrogen evolution by cobalt(diimine-dioxime) catalysts.
Chemistry - A European journal (2013) 19(45) : 15166-15174

Canaguier S, Fourmond V, Perotto CU, Fize J, Pecaut J, Fontecave M, Field MJ and Artero V
Catalytic hydrogen production by a Ni-Ru mimic of NiFe hydrogenases involves a proton-coupled electron transfer step.
Chemical Communications (Camb) (2013) 49(44) : 5004-5006

Carletti E, Colletier JP, Schopfer LM, Santoni G, Masson P, Lockridge O, Nachon F and Weik M
Inhibition pathways of the potent organophosphate CBDP with cholinesterases revealed by X-ray crystallographic snapshots and mass spectrometry.
Chemical Research in Toxicology (2013) 26(2) : 280-289

Fron E, Van der Auweraer M, Moeyaert B, Michiels J, Mizuno H, Hofkens J and Adam V
Revealing the excited-state dynamics of the fluorescent protein dendra2.
Journal of Physical Chemistry B (2013) 117(8) : 2300-2313

Garman EF and Weik M
Radiation damage to biological macromolecules : some answers and more questions.
Journal of Synchrotron Radiation (2013) 20(Pt 1) : 1-6

Duan C, Adam V, Byrdin M, Ridard J, Kieffer-Jaquinod S, Morlot C, Arcizet D, Demachy I and Bourgeois D
Structural evidence for a two-regime photobleaching mechanism in a reversibly switchable fluorescent protein.
Journal of the American Chemical Society (2013) 135(42) : 15841-15850

Hamdane D, Bruch E, Un S, Field M and Fontecave M
Activation of a unique flavin-dependent tRNA-methylating agent.
_ Biochemistry (2013) 52(49) : 8949-8956

Jackson CJ, Liu JW, Carr PD, Younus F, Coppin C, Meirelles T, Lethier M, Pandey G, Ollis DL, Russell RJ, Weik M and Oakeshott JG
Structure and function of an insect alpha-carboxylesterase (alphaEsterase7) associated with insecticide resistance.
Proceedings of the National Academy of Sciences (2013) 110(25) : 10177-10182

Nachon F, Brazzolotto X, Trovaslet M and Masson P
Progress in the development of enzyme-based nerve agent bioscavengers.
Chemico-Biological Interactions (2013) 206(3) : 536–544

Nagy G, Kovacs L, Unnep R, Zsiros O, Almasy L, Rosta L, Timmins P, Peters J, Posselt D and Garab G
Kinetics of structural reorganizations in multilamellar photosynthetic membranes monitored by small-angle neutron scattering.
European Physical Journal E (2013) 36(7) : 69

Natali F, Gerelli Y, Stelletta C and Peters J
Anomalous proton dynamics of water molecules in neural tissue as seen by quasi-elastic neutron scattering. Impact on medical imaging techniques.
4th International Symposium on Slow Dynamics in Complex Systems (2013) 1518 : 551-557

Peters J, Giudici-Orticoni MT, Zaccai G and Guiral M
Dynamics measured by neutron scattering correlates with the organization of bioenergetics complexes in natural membranes from hyperthermophile and mesophile bacteria.
European Physical Journal E Soft Matter (2013) 36(7) : 78

Peters J and Kneller GR
Motional heterogeneity in human acetylcholinesterase revealed by a non-Gaussian model for elastic incoherent neutron scattering.
The Journal of Chemical Physics (2013) 139(16) : 165102

Rusevich L, Garcìa Sakai V, Franzetti B, Johnson M, Natali F, Pellegrini E, Peters J, Pieper J, Weik M and Zaccai G
Perspectives in biological physics : The nDDB project for a neutron Dynamics Data Bank for biological macromolecules
The European Physical Journal E - Soft Matter and Biological Physics (2013) 36 : 80

Sanchez-Martinez M, Marcos E, Tauler R, Field M and Crehuet R
Conformational compression and barrier height heterogeneity in the N-acetylglutamate kinase.
The Journal of Physical Chemistry B (2013) 117(46) : 14261-14272

Schiró G
Anharmonic onsets in polypeptides revealed by neutron scattering : Experimental evidences and quantitative description of energy resolution dependence.
Biophysical Chemistry (2013) 180–181 : 29-36

Theveneau P, Baker R, Barrett R, Beteva A, Bowler MW, Carpentier P, Caserotto H, de Sanctis D, Dobias F, Flot D, Guijarro M, Giraud T, Lentini M, Leonard GA, Mattenet M, McCarthy AA, McSweeney SM, Morawe C, Nanao M, Nurizzo D, Ohlsson S, Pernot P, Popov AN, Round A, Royant A, Schmid W, Snigirev A, Surr J and Mueller-Dieckmann C
The Upgrade Programme for the Structural Biology beam lines at the European Synchrotron Radiation Facility - High throughput sample evaluation and automation.
_Journal of Physics Conference Series (2013) 425 : 012001

Trovaslet M, Trapp M, Weik M, Nachon F, Masson P, Tehei M and Peters J
Relation between dynamics, activity and thermal stability within the cholinesterase family.
Chemico-Biological Interactions (2013) 203(1) : 14-18

Szalontai B, Nagy G, Krumova S, Fodor E, Pali T, Taneva SG, Garab G, Peters J and Der A
Hofmeister ions control protein dynamics.
Biochimica and Biophysica Acta-General Subjects (2013) 1830(10) : 4564-4572

Trapp M, Marion J, Tehei M, Deme B, Gutberlet T and Peters J
High hydrostatic pressure effects investigated by neutron scattering on lipid multilamellar vesicles.
Physical Chemistry Chemical Physics (2013) 15(48) : 20951-20956

Wood K, Gallat F-X, Otten R, van Heel AJ, Lethier M, van Eijck L, Moulin M, Haertlein M, Weik M and Mulder FAA
Protein surface and core dynamics show concerted hydration-dependent activation.
Angewandte Chemie International Edition (2013) 25(2) : 693-696

Publications 2012

Aleksandrov A and Field M
A hybrid elastic band string algorithm for studies of enzymatic reactions.
Physical Chemistry Chemical Physics (2012) 14(36) : 12544-12553

Amann-Winkel K, Low F, Handle PH, Knoll W, Peters J, Geil B, Fujara F and Loerting T
Limits of metastability in amorphous ices : the neutron scattering Debye-Waller factor.
Physical Chemistry Chemical Physics (2012) 14 : 16386-16391

Bajaj H, Tran QT, Mahendran KR, Nasrallah C, Colletier JP, Davin-Regli A, Bolla JM, Pagès JM and Winterhalter M
Antibiotic uptake through membrane channels : Role of Providencia stuartii omppst1 porin in carbapenem resistance.
Biochemistry (2012) 51(51) : 10244-10249

Bhattacharjee A, Chavarot-Kerlidou M, Andreiadis ES, Fontecave M, Field MJ and Artero V
Combined experimental-theoretical characterization of the hydrido-cobaloxime [HCo(dmgH)2(PnBu3)].
Inorganic Chemistry (2012) 51(13) : 7087-7093

Bhattacharjee A, Pribil AB, Randolf BR, Rode BM and Hofer TS
Hydration of Mg2+ and its influence on the water hydrogen bonding network via ab initio QMCF MD.
Chemical Physics Letters (2012) 536 : 39-44

Bourgeois D and Adam V
Reversible photoswitching in fluorescent proteins : A mechanistic view.
IUBMB Life (2012) 64(6) : 482-491

Colletier JP, Aleksandrov A, Coquelle N, Mraihi S, Mendoza-Barbera E, Field M and Madern D
Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions.
Molecular Biology and Evolution (2012) 29(6) : 1683-1694

Gallat FX, Brogan AP, Fichou Y, McGrath N, Moulin M, Hartlein M, Combet J, Wuttke J, Mann S, Zaccai G, Jackson CJ, Perriman AW and Weik M
A polymer surfactant corona dynamically replaces water in solvent-free protein liquids and ensures macromolecular flexibility and activity.
Journal of the American Chemical Society (2012) 134(32) : 13168-13171

Gallat FX, Laganowsky A, Wood K, Gabel F, van Eijck L, Wuttke J, Moulin M, Härtlein M, Eisenberg D, Colletier JP, Zaccai G and Weik M
Dynamical coupling of intrinsically disordered proteins and their hydration water : Comparison with folded soluble and membrane proteins.
Biophysical Journal (2012) 103(1) : 129-136

Goedhart J, Von Stetten D, Noirclerc-Savoye M, Lelimousin M, Joosen L, Hink MA, Van Weeren L, Gadella TWJ and Royant A
Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%.
Nature Communications (2012) 3 : n°1738

Masson P
Time dependent kinetic complexities in cholinesterase catalyzed reactions.
Biochemistry (Moscou) (2012) 77(10) : 1147-1161

Nagy G, Pieper J, Krumova SB, Kovacs L, Trapp M, Garab G and Peters J
Dynamic properties of photosystem II membranes at physiological temperatures characterized by elastic incoherent neutron scattering. Increased flexibility associated with the inactivation of the oxygen evolving complex.
Photosynthesis Research (2012) 111(1-2) : 113-124

Nasiri R, Field MJ, Zahedi M and Moosavi-Movahedi AA
Comparative DFT study to determine if alpha-oxoaldehydes are precursors for pentosidine formation.
Journal of Physical Chemistry A (2012) 116(11) : 2986-2996

Peters J, Trapp M, Hughes D, Rowe S, Demé B, Laborier JL, Payre C, Gonzales JP, Baudoin S, Belkhier N and Lelièvre-Berna E
High hydrostatic pressure equipment for neutron scattering studies of samples in solution.
High Pressure Research (2012) 32(1) : 97-102

Pieper J, Trapp M, Skomorokhov A, Natkaniec I, Peters J and Renger G
Temperature-dependent vibrational and conformational dynamics of photosystem II membrane fragments from spinach investigated by elastic and inelastic neutron scattering.
Biochimica et Biophysica Acta (BBA) - Bioenergetics (2012) 1817(8) : 1213–1219

Peters J, Trovaslet M, Trapp M, Nachon F, Hill F, Royer E, Gabel F, van Eijck L, Masson P and Tehei M
Activity and molecular dynamics relationship within the family of human cholinesterases.
Physical Chemistry Chemical Physics (2012) 14 : 6764-6770

Ronco C, Carletti E, Colletier JP, Weik M, Nachon F, Jean L and Renard PY
Huprine derivatives as sub-nanomolar human acetylcholinesterase inhibitors : From rational design to validation by X-ray crystallography.
ChemMedChem (2012) 7(3) : 400-405

Trapp M, Trovaslet M, Nachon F, Koza MM, van Eijck L, Hill F, Weik M, Masson P, Tehei M and Peters J
Energy landscapes of human acetylcholinesterase and its huperzine A-inhibited counterpart.
Journal of Physical Chemistry B (2012) 116(51) : 14744-14753

von Stetten D, Batot GO, Noirclerc-Savoye M and Royant A
Alteration of fluorescent protein spectroscopic properties upon cryoprotection.
Acta Crystallographica D Biological Crystallography (2012) 68(Pt 11) : 1578-1583

von Stetten D, Noirclerc-Savoye M, Goedhart J, Gadella TW, Jr. and Royant A
Structure of a fluorescent protein from Aequorea victoria bearing the obligate-monomer mutation A206K.
Acta Crystallographica Section F Structural Biology and Crystallization Communications (2012) 68(Pt 8) : 878-882

Wahlgren WY, Omran H, von Stetten D, Royant A, van der Post S and Katona G
Structural characterization of bacterioferritin from Blastochloris viridis.
PLoS One (2012) 7(10) : e46992

Publications 2011

Aleksandrov A and Field M
Efficient solvent boundary potential for hybrid potential simulations.
Physical Chemistry Chemical Physics (2011) 13 (22) : 10503-10509

Arcizet D, Adam V, Carpentier P, Faro A and Bourgeois D
Combining kinetic crystallography and optical spectroscopy for studying fluorescent proteins.
Actualité Chimique (2011) (356-57) : 78-83

Chaves I, Pokorny R, Byrdin M, Hoang N, Ritz T, Brettel K, Essen LO, Van Der Horst GTJ, Batschauer A and Ahmad M
The cryptochromes : Blue light photoreceptors in plants and animals.
Annual Review of Plant Biology (2011) 62 : 335-364

Colletier JP, Laganowsky A, Landau M, Zhao M, Soriaga AB, Goldschmidt L, Flot D, Cascio D, Sawaya MR and Eisenberg D
Molecular basis for amyloid-beta polymorphism.
Proceedings of the Nationall Academy of Sciences USA (2011) 108 (41) : 16938-16943

Fourmond V, Canaguier S, Golly B, Field MJ, Fontecave M and Artero V
A nickel-manganese catalyst as a biomimic of the active site of NiFe hydrogenases : a combined electrocatalytical and DFT mechanistic study.
Energy & Environmental Science (2011) 4 (7) : 2417-2427

Garman EF and Weik M
Macromolecular crystallography radiation damage research : what’s new ?
Journal of Synchrotron Radiation (2011) 18 (Pt 3) : 313-317

Juers DH and Weik M
Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin.
Journal of Synchrotron Radiation (2011) 18 (Pt 3) : 329-337

Masson P
Evolution of and perspectives on therapeutic approaches to nerve agent poisoning.
Toxicology Letters (2011) 206(1) : 5-13

McGeehan JE, Bourgeois D, Royant A and Carpentier P
Raman-assisted crystallography of biomolecules at the synchrotron : Instrumentation, methods and applications.
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics (2010) 1814 (6) : 750-759

Mikl C, Peters J, Trapp M, Kornmueller K, Schneider WJ and Prassl R
Softness of atherogenic lipoproteins : A comparison of very low density lipoprotein (VLDL) and low density lipoprotein (LDL) using elastic incoherent neutronscattering (EINS).
Journal of the American Chemical Society (2011) 133 (34) : 13213-13215

Nagy G, Posselt D, Kovacs L, Holm JK, Szabo M, Ughy B, Rosta L, Peters J, Timmins P and Garab G
Reversible membrane reorganizations during photosynthesis in vivo : revealed by small-angle neutron scattering.
Biochemical Journal (2011) 436 (2) : 225-230

Nasiri R, Field MJ, Zahedi M and Moosavi-Movahedi AA
Cross-linking mechanisms of arginine and lysine with alpha,beta-dicarbonyl compounds in aqueous solution.
Journal of Physical Chemistry A (2011) 115(46) : 13542-13555

Orru R, Dudek HM, Martinoli C, Torres Pazmino DE, Royant A, Weik M, Fraaije MW and Mattevi A
Snapshots of enzymatic baeyer-villiger catalysis : oxygen activation and intermediate stabilization.
Journal of Biological Chemistry (2011) 286 (33) : 29284-29291

Royant A and Noirclerc-Savoye M
Stabilizing role of glutamic acid 222 in the structure of Enhanced Green Fluorescent Protein.
Journal of Structural Biology (2011) 174 (2) : 385-290

Regis Faro A, Carpentier P, Jonasson G, Pompidor G, Arcizet D, Demachy I and Bourgeois D
Low-temperature chromophore isomerization reveals the photoswitching mechanism of the fluorescent protein padron.
Journal of the American Chemical Society (2011) 133 (41) : 16362-16365

Sage JT, Zhang Y, McGeehan J, Ravelli R, Weik M and van Thor JJ
Infrared protein crystallography.
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics (2011) 1814 (6) : 760-777

Sanson B, Colletier JP, Xu Y, Therese Lang P, Jiang H, Silman I, Sussman JL and Weik M
Backdoor opening mechanism in acetylcholinesterase based on X-ray crystallography and MD simulations.
Protein Science (2011) 20 (7) : 1114-1118

Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier J-P, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park H-W, Federici BA, Sauter NK, Schlichting I, Eisenberg DS.
Protein crystal structure obtained at 2.9 angstrom resolution from injecting bacterial cells into an X-ray free-electron laser beam.
Proceedings of the National Academy of Sciences of the United States of America 111 : 12769-12774

Smirnov I, Carletti E, Kurkova I, Nachon F, Nicolet Y, Mitkevich VA, Debat H, Avalle B, Belogurov AA, Kuznetsov N, Reshetnyak A, Masson P, Tonevitsky AG, Ponomarenko N, Makarov AA, Friboulet A, Tramontano A and Gabibov A
Reactibodies generated by kinetic selection couple chemical reactivity with favorable protein dynamics.
Proceedings of the National Academy of Sciences of the United States of America (2011) 108(38) : 15954-15959

Thiagarajan V, Byrdin M, Eker AP, Muller P and Brettel K
Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV.
Proceedings of the National Academy of Sciences (2011) 108(23) : 9402-9407

Wandhammer M, Carletti E, Van der Schans M, Gillon E, Nicolet Y, Masson P, Goeldner M, Noort D and Nachon F
Structural study of the complex stereoselectivity of human butyrylcholinesterase for the neurotoxic V-agents.
Journal of Biological Chemistry (2011) 286(19) : 16783-16789

Publications 2010

Adam V, Mizuno H, Grichine A, Hotta JI, Yamagata Y, Moeyaert B, Nienhaus GU, Miyawaki A, Bourgeois D and Hofkens J
Data storage based on photochromic and photoconvertible fluorescent proteins.
Journal of Biotechnology (2010) 149(4) : 289-298

Brettel K and Byrdin M
Reaction mechanisms of DNA photolyase.
Current Opinion in Structural Biology (2010) 20(6) : 693-701

Canaguier S, Field M, Oudart Y, Pecaut J, Fontecave M and Artero V
A structural and functional mimic of the active site of NiFe hydrogenases.
Chemical Communications (Camb) (2010) 46(32) : 5876-5878

Carletti E, Colletier JP, Dupeux F, Trovaslet M, Masson P and Nachon F
Structural evidence that human acetylcholinesterase inhibited by tabun ages through O-dealkylation.
J Med Chem (2010) 53(10) : 4002-4008

Carpentier P, Royant A, Weik M and Bourgeois D
Raman-assisted crystallography suggests a mechanism of X-ray-induced disulfide radical formation and reparation.
Structure (2010) 18(11) : 1410-1419

Faro AR, Adam V, Carpentier P, Darnault C, Bourgeois D and de Rosny E
Low-temperature switching by photoinduced protonation in photochromic fluorescent proteins.
Photochemistry and Photobiology Science (2010) 9(2) : 254-262

Hagiwara Y, Field MJ, Nureki O and Tateno M
Editing mechanism of aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst.
Journal of the American Chemical Society (2010) 132(8) : 2751-2758

Jasnin M, van Eijck L, Koza MM, Peters J, Laguri C, Lortat-Jacob H and Zaccai G
Dynamics of heparan sulfate explored by neutron scattering.
Physical Chemistry Chemical Physics (2010) 12(14) : 3360-3362

Knoll W, Natali F, Peters J, Nanekar R, Wang P and Kursula P
Dynamic properties of a reconstituted myelin sheat.
Spectroscopy (2010) 24 : 585-592

Majava V, Polverini E, Mazzini A, Nanekar R, Knoll W, Peters J, Natali F, Baumgartel P, Kursula I and Kursula P
Structural and functional characterization of human peripheral nervous system myelin protein P2.
PLoS One (2010) 5(4) : e10300

Marcos E, Field MJ and Crehuet R
Pentacoordinated phosphorus revisited by high-level QM/MM calculations.
Proteins : Structure, Function and Bioinformatics (2010) 78 (11) : 2405-2411

Roy A, Carpentier P, Bourgeois D and Field M
Diffusion pathways of oxygen species in the phototoxic fluorescent protein KillerRed.
Photochemical and Photobiological Sciences (2010) 9(10) : 1342-1350

Sans JA, Martinez-Criado G, Susini J, Sanz R, Jensen J, Minguez I, Hernandez-Velez M, Labrador A and Carpentier P
Thermal instability of implanted Mn ions in ZnO.
Journal of Applied Physics (2010) 107 (2)2.064

Trapp M, Juranyi F, Tehei M, van Eijck L, Demé B, Gutberlet T and Peters J
Elastic scattering studies of aligned DMPC multilayers on different hydrations.
Spectroscopy (2010) 24 : 461-466

Trapp M, Gutberlet T, Juranyi F, Unruh T, Deme B, Tehei M and Peters J
Hydration dependent studies of highly aligned multilayer lipid membranes by neutron scattering.
Journal of Chemical Physics (2010) 133(16) : 164505

Vaccaro L, Artero V, Canaguier S, Fontecave M and Field MJ
Mechanism of hydrogen evolution catalyzed by NiFe hydrogenases : insights from a Ni-Ru model compound.
Dalton Transactions (2010) 39(12) : 3043-3049

Weik M and Colletier JP
Temperature-dependent macromolecular X-ray crystallography.
Acta Crystallographica Section D : Biological Crystallography (2010) 66(4) : 437-446

Wood K, Tobias DJ, Kessler B, Gabel F, Oesterhelt D, Mulder FAA, Zaccai G and Weik M
The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation : Direct evidence using isotope labeling and molecular dynamics simulations.
Journal of the American Chemical Society (2010) 132(14) : 4990-4991

Xu Y, Colletier JP, Weik M, Qin G, Jiang H, Silman I and Sussman JL
Long route or shortcut ? A molecular dynamics study of traffic of thiocholine within the active-site gorge of acetylcholinesterase.
Biophysical Journal (2010) 99 (12) : 4003-4011

Publications 2009

Adam V, Carpentier P, Violot S, Lelimousin M, Darnault C, Nienhaus GU and Bourgeois D
Structural basis of X-ray-induced transient photobleaching in a photoactivatable green fluorescent protein.
Journal of the American Chemical Society (2009) 131(50) : 18063-18065

Adam V, Nienhaus K, Bourgeois D and Nienhaus GU
Structural basis of enhanced photoconversion yield in green fluorescent protein-like protein Dendra2.
Biochemistry (2009) 48(22) : 4905-4915

Barros T, Royant A, Standfuss J, Dreuw A and Kuhlbrandt W
Crystal structure of plant light-harvesting complex shows the active, energy-transmitting state.
Embo Journal (2009) 28 : 298-306

Bourgeois D, Katona G, de Rosny E and Carpentier P
Raman-assisted X-ray crystallography for the analysis of biomolecules.
Methods in Molecular Biology (2009) 544 : 253-267

Bourgeois D and Weik M
Kinetic protein crystallography : a tool to watch proteins in action.
Crystallography Review (2009) 15(2) : 87-118

Canaguier S, Vaccaro L, Artero V, Ostermann R, Pecaut J, Field MJ and Fontecave M
Cyclopentadienyl ruthenium-nickel catalysts for biomimetic hydrogen evolution : electrocatalytic properties and mechanistic DFT studies.
Chemistry-a European Journal (2009) 15(37) : 9350-9364

Carletti E, Aurbek N, Gillon E, Loiodice M, Nicolet Y, Fontecilla-Camps JC, Masson P, Thiermann H, Nachon F and Worek F
Structure-activity analysis of aging and reactivation of human butyrylcholinesterase inhibited by analogues of tabun.
Biochemical Journal (2009) 421(1) : 97-106

Carpentier P, Violot S, Blanchoin L and Bourgeois D
Structural basis for the phototoxicity of the fluorescent protein KillerRed.
FEBS Letters (2009) 583(17) : 2839-2842

Del Vecchio P, Elias M, Merone L, Graziano G, Dupuy J, Mandrich L, Carullo P, Fournier B, Rochu D, Rossi M, Masson P, Chabriere E and Manco G
Structural determinants of the high thermal stability of SsoPox from the hyperthermophilic archaeon Sulfolobus solfataricus.
Extremophiles (2009) 13(3) : 461-470

Durin G, Delaunay A, Darnault C, Heyes DJ, Royant A, Vernede X, Hunter CN, Weik M and Bourgeois D
Simultaneous measurements of solvent dynamics and functional kinetics in a light-activated enzyme.
Biophysical Journal (2009) 96(5) : 1902-1910

Frolich A, Gabel F, Jasnin M, Lehnert U, Oesterhelt D, Stadler AM, Tehei M, Weik M, Wood K and Zaccai G
From shell to cell : neutron scattering studies of biological water dynamics and coupling to activity.
Faraday Discussions (2009) 141 : 117-130 ; discussion 175-207

Gabel F, Masson P, Froment MT, Doctor BP, Saxena A, Silman I, Zaccai G and Weik M
Direct correlation between molecular dynamics and enzymatic stability : A comparative neutron scattering study of native human butyrylcholinesterase and its "Aged" soman conjugate.
Biophysical Journal (2009) 96(4) : 1489-1494

Hansmann T, Sanson B, Stojan J, Weik M, Marty JL and Fournier D
Kinetic insight into the mechanism of cholinesterasterase inhibition by aflatoxin B1 to develop biosensors.
Biosensors and Bioelectronics (2009) 24(7) : 2119-2124

Howard-Jones A R, Adam V, Cowley A, Baldwin J E and Bourgeois D
Cryophotolysis of a caged oxygen compound for use in low temperature biological studies.
Photochemical & Photobiological Sciences (2009) 8(8) : 1150-1156

Lafaye C, Iwema T, Carpentier P, Jullian-Binard C, Kroll JS, Collet JF and Serre L
Biochemical and structural study of the homologues of the thiol-disulfide oxidoreductase DsbA in Neisseria meningitidis.
Journal of Molecular Biology (2009) 392(4) : 952-966

Lelimousin M, Adam V, Nienhaus GU, Bourgeois D and Field MJ
Photoconversion of the fluorescent protein EosFP : A hybrid potential simulation study reveals intersystem crossings.
Journal of the American Chemical Society (2009) 131(46) : 16814-16823

Lelimousin M, Noirclerc-Savoye M, Lazareno-Saez C, Paetzold B, Le Vot S, Chazal R, Macheboeuf P, Field MJ, Bourgeois D and Royant A
Intrinsic dynamics in ECFP and cerulean control fluorescence quantum yield.
Biochemistry (2009) 48(42) : 10038–10046

Macedo S, Pechlaner M, Schmid W, Weik M, Sato K, Dennison C and Djinovic-Carugo K
Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection ?
Journal of Synchrotron Radiation (2009) 16(Pt 2) : 191-204

Masson P and Rochu D
Catalytic bioscavengers against toxic esters, an alternative approach for prophylaxis and treatments of poisonings.
Acta Naturae (2009) 1 : 68-78

McGeehan J, Ravelli RB, Murray JW, Owen RL, Cipriani F, McSweeney S, Weik M and Garman EF
Colouring cryo-cooled crystals : online microspectrophotometry.
Journal of Synchrotron Radiation (2009) 16(Pt 2) : 163-172

Roy S, Goedecker S, Field MJ and Penev E
A minima-hopping study of all-atom protein folding and structure prediction.
Journal of Physical Chemistry B (2009) 113(20) : 7315-7321

Sanson B, Nachon F, Colletier JP, Froment MT, Toker L, Greenblatt HM, Sussman JL, Ashani Y, Masson P, Silman I and Weik M
Crystallographic snapshots of nonaged and aged conjugates of soman with acetylcholinesterase, and of a ternary complex of the aged conjugate with pralidoxime (dagger).
J Med Chem (2009) 52(23) : 7593-7603

Shu X, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA and Tsien RY
Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome.
Science (2009) 324(5928) : 804-807

Violot S, Carpentier P, Blanchoin L and Bourgeois D
Reverse pH-dependence of chromophore protonation explains the large stokes shift of the red fluorescent protein mKeima.
Journal of the American Chemical Society (2009) 131(30) : 10356-10357

Publications 2008

Adam V, Lelimousin M, Boehme S, Desfonds G, Nienhaus K, Field MJ, Wiedenmann J, McSweeney S, Nienhaus GU and Bourgeois D
Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations.
Proceeding of the National Academy of Sciences U S A (2008) 105(47) : 18343-18348

Bourgeois D
The structural dynamics of myoglobin investigated by sub-nanosecond crystallography.
Actualité Chimique (2008) 317 : 55-59

Brunori M, Bourgeois D and Vallone B
Structural dynamics of myoglobin.
Methods in Enzymology (2008) 437 : 397-416

Carletti E, Li H, Li B, Ekstrom F, Nicolet Y, Loiodice M, Gillon E, Froment MT, Lockridge O, Schopfer LM, Masson P and Nachon F
Aging of cholinesterases phosphylated by tabun proceeds through o-dealkylation.
Journal of the American Chemical Society (2008) 130(47) : 16011-16020

Colletier JP, Bourgeois D, Sanson B, Fournier D, Sussman JL, Silman I and Weik M
Shoot-and-Trap : use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography.
Proceedings of the National Academy of Sciences U S A (2008) 105(33) : 11742-11747

Elias M, Dupuy J, Merone L, Mandrich L, Porzio E, Moniot S, Rochu D, Lecomte C, Rossi M, Masson P, Manco G and Chabriere E
Structural basis for natural lactonase and promiscuous phosphotriesterase activities.
Journal of Molecular Biology (2008) 379(5) : 1017-1028

Fdez Galvan I, Volbeda A, Fontecilla-Camps JC and Field MJ
A QM/MM study of proton transport pathways in a [NiFe] hydrogenase.
Proteins (2008) 73(1) : 195-203

Field MJ
The pDynamo program for molecular simulations using hybrid quantum chemical and molecular mechanical potentials.
Journal of Chemical Theory and Computation (2008) 4(7) : 1151-1161

Francesca N, Peters J, Russo D, Barbieri S, Chiapponi C, Cupane A, Deriu A, Di Bari MT, Farhi E, Gerelli Y, Mariani P, Paciaroni A, Rivasseau C, Schiro G and Sonvico F
IN13 backscattering spectrometer at ILL : Looking for motions in biological macromolecules and organisms.
Neutron News (2008) 19(4) : 14 - 18

Galvan IF and Field MJ
Improving the efficiency of the NEB reaction path finding algorithm.
Journal of Computational Chemistry (2008) 29(1) : 139-143

Koza MM, Schober H, Parker SF and Peters J
Vibrational dynamics and phonon dispersion of polycrystalline ice XII and of high-density amorphous ice.
Physical Review B (2008) 77(10) : n°104306

Lefmann K, Willendrup PK, Udby L, Lebech B, Mortensen K, Birk JO, KlenØ K, Knudsen E, Christiansen P, Saroun J, Kulda J, Filges U, Konnecke M, Tregenna-Piggott P, Peters J, Lieutenant K, Zsigmond G, Bentley P and Farhi E
Virtual experiments : the ultimate aim of neutron ray-tracing simulations.
Journal of Neutron Research (2008) 16(3) : 97-111

de Rosny E, de Groot A, Jullian-Binard C, Borel F, Suarez C, Le Pape L, Fontecilla-Camps JC and Jouve HM
DHR51, the Drosophila melanogaster homologue of the human photoreceptor cell-specific nuclear receptor, is a thiolate heme-binding protein.
Biochemistry (2008) 47(50) : 13252-13260

Peters J and Tehei M
Molecular biophysics : understanding living processes.
Neutrons and Health, ESS Scandinavia report (2008) : 6-7

Teixeira SC, Ankner J, Bellissent-Funel MC, Bewley R, Blakeley MP, Coates L, Dahint R, Dalgliesh R, Dencher N, Dhont J, Fischer P, Forsyth VT, Fragneto G, Frick B, Geue T, Gilles R, Gutberlet T, Haertlein M, Hauss T, Haussler W, Heller WT, Herwig K, Holderer O, Juranyi F, Kampmann R, Knott R, Kohlbrecher J, Kreuger S, Langan P, Lechner R, Lynn G, Majkrzak C, May R, Meilleur F, Mo Y, Mortensen K, Myles DA, Natali F, Neylon C, Niimura N, Ollivier J, Ostermann A, Peters J, Pieper J, Ruhm A, Schwahn D, Shibata K, Soper AK, Straessle T, Suzuki UI, Tanaka I, Tehei M, Timmins P, Torikai N, Unruh T, Urban V, Vavrin R, Weiss K and Zaccai G
New sources and instrumentation for neutrons in biology.
Chemical Physics (2008) 345(2-3) : 133-151

Ujwal R, Cascio D, Colletier JP, Faham S, Zhang J, Toro L, Ping P and Abramson J
The crystal structure of mouse VDAC1 at 2.3 A resolution reveals mechanistic insights into metabolite gating.
Proceedings of the National Academy of Sciences U S A (2008) 105(46) : 17742-17747

Wood K, Frolich A, Paciaroni A, Moulin M, Hartlein M, Zaccai G, Tobias DJ and Weik M
Coincidence of dynamical transitions in a soluble protein and its hydration water : direct measurements by neutron scattering and MD simulations.
Journal of the American Chemical Society (2008) 130(14) : 4586-4587

Wood K, Grudinin S, Kessler B, Weik M, Johnson M, Kneller GR, Oesterhelt D and Zaccai G
Dynamical heterogeneity of specific amino acids in bacteriorhodopsin.
Journal of Molecular Biology (2008) 380(3) : 581-591

Wood K, Plazanet M, Gabel F, Kessler B, Oesterhelt D, Zaccai G and Weik M
Dynamics of hydration water in deuterated purple membranes explored by neutron scattering.
European Biophysical Journal (2008) 37(5) : 619-626

Xu Y, Colletier JP, Jiang H, Silman I, Sussman JL and Weik M
Induced-fit or preexisting equilibrium dynamics ? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design.
Protein Science (2008) 17(4) : 601-605

Xu Y, Colletier JP, Weik M, Jiang H, Moult J, Silman I and Sussman JL
Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase : X-ray versus molecular dynamics.
Biophysical Journal (2008) 95(5) : 2500-2511

Publications 2007

Amara P, Fdez Galvan I, Fontecilla-Camps JC and Field MJ
The enamine intermediate may not be universal to thiamine catalysis.
Angewandte Chemie International Edition England (2007) 46(47) : 9019-9022

Bleif HJ, Clemens D, Eads A, Fox W, Gebauer B, Geevers M, Herbach CM, Lozowoski W, Mezei F, Peters J, Sokol P, Solberg K, Vanderwerp J, Visser G, Wilpert T and Wulf F
Square single-wire detectors for neutron diffraction studies.
Nuclear Instruments and Methods in Physics Research Section A : Accelerators, Spectrometers, Detectors and Associated Equipment (2007) 580(2) : 1110-1114

Bourgeois D, De Rosny E and Katona G
La cristallographie cinétique : un outils pour filmer les protéines au travail.
Biofutur (2007) 280 : 48-51

Bourgeois D, Schotte F, Brunori M and Vallone B
Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics.
Photochemistry and Photobiology Science (2007) 6(10) : 1047-1056

Carpentier P, Royant A, Ohana J and Bourgeois D
Advances in spectroscopic methods for biological crystals. 2. Raman spectroscopy
Journal of Applied Crystallography (2007) 40(6) : 1113-1122

Colletier JP, Royant A, Sprecht A, Sanson B, Nachon F, Masson P, Zaccai G, Sussman JL, Goeldner M, Silman I, Bourgeois D and Weik M
Use of caged analogue to study the traffic of choline within acetylcholinesterase by kinetic crystallography.
Acta Crystallographica D (2007) 63 : 1115-1128

Colletier JP and Weik M
[Exploring the conformational energy landscape of acetylcholinesterase by kinetic crystallography].
Annales Pharmaceutiques Françaises (2007) 65(2) : 108-118

Coquelle N, Fioravanti E, Weik M, Vellieux FM and Madern D
Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments.
Journal of Molecular Biology (2007) 374(2) : 547-562

Crehuet R and Field MJ
A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase.
Journal of Physical Chemistry B (2007) 111(20) : 5708-5718

Elias M, Dupuy J, Merone L, Lecomte C, Rossi M, Masson P, Manco G and Chabriere E
Crystallization and preliminary X-ray diffraction analysis of the hyperthermophilic Sulfolobus solfataricus phosphotriesterase.
Acta Crystallographica Section F Structural Biology and Crystallization Communications (2007) 63(Pt 7) : 553-555

Fioravanti E, Vellieux FM, Amara P, Madern D and Weik M
Specific radiation damage to acidic residues and its relation to their chemical and structural environment.
Journal of Synchrotron Radiation (2007) 14(Pt 1) : 84-91

Frasco MF, Colletier JP, Weik M, Carvalho F, Guilhermino L, Stojan J and Fournier D
Mechanisms of cholinesterase inhibition by inorganic mercury.
FEBS Journal (2007) 274(7) : 1849-1861

Katona G, Carpentier P, Niviere V, Amara P, Adam V, Ohana J, Tsanov N and Bourgeois D
Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.
Science (2007) 316(5823) : 449-453

Lepsik M and Field MJ
Binding of calcium and other metal ions to the EF-Hand loops of calmodulin studied by quantum chemical calculations and molecular dynamics simulations.
Journal of Physical Chemistry B (2007) 111(33) : 10012-10022

McGeehan JE, Carpentier P, Royant A, Bourgeois D and Ravelli RB
X-ray radiation-induced damage in DNA monitored by online Raman.
Journal of synchrotron radiation (2007) 14(Pt 1) : 99-108

Morales R, Berna A, Carpentier P, Contreras-Martel C, Renault F, Nicodeme M, Chesne-Seck ML, Bernier F, Dupuy J, Schaeffer C, Diemer H, Van-Dorsselaer A, Fontecilla-Camps JC, Masson P, Rochu D and Chabriere E
[Discovery and crystallographic structure of human apolipoprotein].
Annales Pharmaceutiques Françaises (2007) 65(2) : 98-107

Puig E, Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM and Field MJ
New Insights into the reaction mechanism catalyzed by the glutamate racemase enzyme : pH titration curves and classical molecular dynamics simulations.
Journal of Physical Chemistry B (2007) 111(9) : 2385-2397

Royant A, Carpentier P, Ohana J, McGeehan J, Paetzold B, Noirclerc-Savoye M, Vernéde X, Adam V and Bourgeois D
Advances in spectroscopic methods for biological crystals. 1. Fluorescence lifetime measurements
Journal of Applied Crystallography (2007) 40(6) : 1105-1112

Wood K, Plazanet M, Gabel F, Kessler B, Oesterhelt D, Tobias DJ, Zaccai G and Weik M
Coupling of protein and hydration-water dynamics in biological membranes.
Proceedings of the National Academy of Sciences U S A (2007) 104(46) : 18049-18054

Publications 2006

Bourgeois D, Vallone B, Arcovito A, Sciara G, Schotte F, Anfinrud PA and Brunori M Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography. Proceedings of the National Academy of Sciences U S A (2006) 103(13) : 4924-4929

Colletier JP, Fournier D, Greenblatt HM, Stojan J, Sussman JL, Zaccai G, Silman I and Weik M
Structural insights into substrate traffic and inhibition in acetylcholinesterase.
Embo Journal (2006) 25(12) : 2746-2756

Colletier JP, Sanson B, Nachon F, Gabellieri E, Fattorusso C, Campiani G and Weik M
Conformational flexibility in the peripheral site of torpedo californica acetylcholinesterase revealed by the complex structure with a bifunctional inhibitor.
Journal of the American Chemical Society (2006) 128(14) : 4526-4527

Contreras-Martel C, Carpentier P, Morales R, Renault F, Chesne-Seck ML, Rochu D, Masson P, Fontecilla-Camps JC and Chabriere E
Crystallization and preliminary X-ray diffraction analysis of human phosphate-binding protein.
Acta Crystallographica Section F : Structural Biology and Crystallization Communications (2006) 62(Pt 1) : 67-69

de Rosny E, de Groot A, Jullian-Binard C, Gaillard J, Borel F, Pebay-Peyroula E, Fontecilla-Camps JC and Jouve HM
Drosophila Nuclear Receptor E75 Is a Thiolate Hemoprotein.
Biochemistry (2006) 45(32) : 9727-9734

Morales R, Berna A, Carpentier P, Contreras-Martel C, Renault F, Nicodeme M, Chesne-Seck ML, Bernier F, Dupuy J, Schaeffer C, Diemer H, Van-Dorsselaer A, Fontecilla-Camps JC, Masson P, Rochu D and Chabriere E
Serendipitous discovery and x-ray structure of a human phosphate binding apolipoprotein.
Structure (2006) 14(3) : 601-609

Renault F, Chabriere E, Andrieu J-P, Dublet B, Masson P and Rochu D
Tandem purification of two HDL-associated partner proteins in human plasma, paraoxonase (PON1) and phosphate binding protein (HPBP) using hydroxyapatite chromatography.
Journal of Chromatography B Analytical Technologies in the Biomedical Life Science (2006) 836(1-2) : 15-21

Suarez D, Diaz N, Fontecilla-Camps J and Field MJ
A computational study of the deacylation mechanism of human butyrylcholinesterase.
Biochemistry (2006) 45(24) : 7529-7543

Thomas A and Field MJ
A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X)PRTases.
Journal of the American Chemical Society (2006) 128(31) : 10096-10102

Vernede X, Lavault B, Ohana J, Nurizzo D, Joly J, Jacquamet L, Felisaz F, Cipriani F and Bourgeois D
UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops.
Acta Crystallographica D Biological Crystallography (2006) 62(Pt 3) : 253-261

Williams P, Coates L, Mohammed F, Gill R, Erskine P, Bourgeois D, Wood SP, Anthony C and Cooper JB
The 1.6A X-ray structure of the unusual c-type cytochrome, cytochrome cL, from the methylotrophic bacterium Methylobacterium extorquens.
Journal of Molecular Biology (2006) 357(1) : 151-162

Publications 2005

Amara P, Volbeda A, Fontecilla-Camps JC and Field MJ
A quantum chemical study of the reaction mechanism of acetyl-coenzyme a synthase
Journal of the American Chemical Society (2005) 127(8) : 2776-2784

Berntsen P, Bergman R, Jansson H, Weik M and Swenson J
Dielectric and calorimetric studies of hydrated purple membrane.
Biophysical Journal (2005) 89(5) : 3120-3128

Bourgeois D and Royant A
Advances in kinetic protein crystallography.
Current Opinion in Structural Biology (2005) 15(5) : 538-547

Bourgeois D and Weik M
New perspectives in kinetic crystallography using caged compounds. in Dynamic studies in biology : phototriggers, photoswitches and caged biomolecules édité par Goeldner M and Givens R, Wiley-vch, (2005) : 410-435

Crehuet R, Thomas A and Field MJ
An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum
Journal of Molecular Graphics and Modelling (2005) 24(2) : 102-110

De Groot A, de Rosny E, Juillan-Binard C, Ferrer JL, Laudet V, Pierce RJ, Pebay-Peyroula E, Fontecilla-Camps JC and Borel F
Crystal structure of a novel tetrameric complex of agonist-bound ligand-binding domain of Biomphalaria glabrata retinoid X receptor.
Journal of Molecular Biology (2005) 354(4) : 841-853

Fioravanti E, Adam V, Munier-Lehmann H and Bourgeois D
The crystal structure of Mycobacterium tuberculosis thymidylate kinase in complex with 3’-azidodeoxythymidine monophosphate suggests a mechanism for competitive inhibition
Biochemistry (2005) 44(1) : 130-137

Fioravanti E, Vellieux F, Madern D and Weik M
Lactate dehydrogenases from extremophile organisms : clues for radio-resistance ?
Acta Crystallographica A (2005) A61 : C267

Gabel F, Weik M, Masson P, Renault F, Fournier D, Brochier L, Doctor BP, Saxena A, Silman I and Zaccai G
Effects of soman inhibition and of structural differences on cholinesterase molecular
dynamics : A neutron scattering study.
Biophysical Journal (2005) 89(5) : 3303-3311

Lehnert U and Weik M (2005)
Relating protein dynamics ti function and structure - the purple membrane. in Neutrons in biology : Techniques and applications, édité par Fitter J, Gutberlet T and Katsaras J Springer Verlag, pp. 419-434

Nachon F, Nicolet Y and Masson P
[Butyrylcholinesterase : 3D structure, catalytic mechanisms].
Annales Pharmaceutiques Françaises (2005) 63(3) : 194-206

Suarez D and Field MJ
Molecular dynamics simulations of human butyrylcholinesterase
Proteins : structure, function and bioinformatics (2005) 59(1) : 104-117

Tormos JR, Wiley KL, Seravalli J, Nachon F, Masson P, Nicolet Y and Quinn DM
The reactant state for substrate-activated turnover of acetylthiocholine by butyrylcholinesterase is a tetrahedral intermediate.
Journal of the American Chemical Society (2005) 127(42) : 14538-14539

Weik M, Lehnert U and Zaccai G
Liquid-like water confined in stacks of biological membranes at 200 K and its relation to protein dynamics.
Biophysical Journal (2005) 89(5) : 3639-3646

Weik M, Schreurs AMM, Leiros HKS, Zaccai G, Ravelli RBG and Gros P
Supercooled liquid-like solvent in trypsin crystals : implications for crystal annealing and temperature-controlled X-ray radiation damage studies.
Journal Of Synchrotron Radiation (2005) 12(Part 3) : 310-317

Publications 2004

Adam V, Royant A, Niviere V, Molina-Heredia F P and Bourgeois D
Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion upon X-Ray-Induced Photo-Reduction
Structure (2004) 12(9) : 1729-1740

Crehuet R, Field M J and Pellegrini E
Transition events in one dimension - art. no. 012101.
Physical Review E (2004) 6901(1) Part 1) : NIL_547-NIL_550

Diaz N and Field M J
Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations.
Journal of the American Chemical Society (2004) 126(2) : 529-42

Edman K, Royant A, Larsson G, Jacobson F, Taylor T, Van der Spoel D, Landau EM, Pebay Peyroula E and Neutze R
Deformation of helix C in the low-temperature L-intermediate of bacteriorhodopsin.
Journal of Biological Chemistry (2004) 279 : 2147-2158

Gabel F, Weik M, Doctor BP, Saxena A, Fournier D, Brochier L, Renault F, Masson P, Silman I and Zaccai G
The influence of solvent composition on global dynamics of human butyrylcholinesterase powders : a neutron-scattering study.
Biophysical Journal (2004) 86(5) : 3152-3165

Rinaldo D and Field MJ
A density functional theory study of the iron-binding site of human serum transferrin
Australian Journal of Chemistry (2004) 57(12) : 1219-1222

Rinaldo D, Vita C and Field M J
Engineering strontium binding affinity in an EF-Hand motif : a quantum chemical and molecular dynamics study
Journal of Biomolecular Structure and Dynamics (2004) 22(3) : 281-298

Weik M, Vernede X, Royant A and Bourgeois D
Temperature-derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals
Biophysical Journal (2004) 86 : 3176-3185

Publications 2003

Amara P and Field M J
Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method
Theoretical Chemistry Accounts (2003) 109(1) : 43-52

Bechinger B and Weik M
Deuterium solid-state NMR investigations of exchange labeled oriented purple membranes at different hydration levels.
Biophysical Journal (2003) 85(1) : 361-369

Bourgeois D, Vallone B, Schotte F, Arcovito A, Miele a E, Sciara G, Wulff M, Anfinrud P and Brunori M
Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography
Proceedings Of The National Academy Of Sciences Of The United States Of America (2003) 100(15) : 8704-8709

Crehuet R and Field M J
Comment on "Action-derived molecular dynamics in the study of rare events" - art. no. 089801
Physical Review Letters (2003) 9008(8) : NIL_238

Crehuet R and Field M J
A temperature-dependent nudged-elastic-band algorithm
Journal of Chemical Physics (2003) 118(21) : 9563-9571

Field M J
La simulation de la structure et de la fonction des protéines et d’autres macromolécules biologiques
Clés CEA (2003) 47 : 34-38

Field M J (2003)
Simulating chemical reactions in complex systems in Handbook of Numarical Analysis, Vol X, edited by Bris L. Elsevier Science

Field M J, Rinaldo D and Thomas A
Comment fonctionnent les protéines ? La voie de la simulation
Biofutur (2003) 238 : 28-30

Kort R, Ravelli R B, Schotte F, Bourgeois D, Crielaard W, Hellingwerf K J and Wulff M
Characterization of photocycle intermediates in crystalline photoactive yellow protein
Photochemistry and Photobiology (2003) 78(2) : 131-137

Loudwig S, Nicolet Y, Masson P, Fontecilla Camps JC, Bon S, Nachon F and Goeldner M
Photoreversible inhibition of cholinesterases : Catalytic serine-labeled caged butyrylcholinesterase.
Chembiochem (2003) 4(8) : 762-767

Nicolet Y, Lockridge O, Masson P, Fontecilla-Camps JC and Nachon F
Crystal structure of human butyrylcholinesterase and of its complexes with substrate and products.
Journal of Biological Chemistry (2003) 278(42) : 41141-41147

Oliva M, Dideberg O and Field M J
Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins : A molecular dynamics simulation study
Proteins Structure Function and Genetics (2003) 53(1) : 88-100

Pellegrini E and Field M J
Development and testing of a de novo drug-design algorithm
Journal of Computer Aided Molecular Design (2003) 17(10) : 621-41

Rinaldo D and Field M J
A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein
Biophysical Journal (2003) 85(6) : 3485-501

Weik M
Low-temperature behavior of water confined by biological macromolecules and its relation to protein dynamics.
European Physical Journal E (2003) 12 : 153-158

Wymore T, Deerfield D W, Field M J, Hempel J and Nicholas H B
Initial catalytic events in class 3 aldehyde deshydrogenase : MM and QM/MM simulations
Chemico-Biological Interactions (2003) 143/144 : 75-84

Publications 2002

Bourgeois D, Vernede X, Adam V, Fioravanti E and Ursby T
A microspectrophotometer for UV-visible absorption and fluorescence studies of protein crystals.
Journal of Applied Crystallography (2002) 35 : 319-326

Bret C, Roth M, Norager S, Hatchikian EC and Field MJ
Molecular dynamics study of Desulfovibrio africanus cytochrome c(3) in oxidized and reduced forms
Biophysical Journal (2002) 83(6) : 3049-65

David L, Amara P, Field M J and Major F
Parametrization of a force field for metals complexed to Biomacromolecules : applications to Fe(II), Cu(II) and Pb(II)
Journal of Computer Aided Molecular Design (2002) 16 : 635-651

Edman K, Royant A, Nollert P, Maxwell CA, Pebay Peyroula E, Navarro J, Neutze R and Landau EM
Early structural rearrangements in the photocycle of an integral membrane sensory receptor.
Structure (2002) 10(4) : 473-482

Field MJ
Simulating enzyme reactions : Challenges and perspectives
Journal of Computational Chemistry (2002) 23(1) : 48-58

Gabel F, Bicout D, Lehnert U, Tehei M, Weik M and Zaccai G
Protein dynamics studied by neutron scattering.
Quaterly Reviews Biophysics (2002) 35(4) : 327 - 367

Josse D, Ebel C, Stroebel D, Fontaine A, Borges F, Echalier A, Baud D, Renault F, Le Maire M, Chabrieres E and Masson P
Oligomeric States of the Detergent-solubilized Human Serum Paraoxonase (PON1).
Journal of Biological Chemistry (2002) 277(36) : 33386-33397.

Nachon F, Nicolet Y, Viguie N, Masson P, Fontecilla Camps JC and Lockridge O
Engineering of a monomeric and low-glycosylated form of human butyrylcholinesterase - Expression, purification, characterization and crystallization.
European Journal of Biochemistry (2002) 269(2) : 630-637

Neutze R, Pebay-Peyroula E, Edman K, Royant A, Navarro J and Landau EM
Bacteriorhodopsin : a high-resolution structural view of vectorial proton transport.
Biochimica and Biophysica Acta - Biomembranes (2002) 1565(2) : 144-167.

Pebay-Peyroula E, Royant A, Landau EM and Navarro J
Structural basis for sensory rhodopsin function.
Biochimica and Biophysica Acta - Biomembranes (2002) 1565(2) : 196-205.

Pellegrini E and Field MJ
A generalized-born solvation model for macromolecular hybrid-potential calculations
Journal of Physical Chemistry A (2002) 106(7) : 1316-1326

Royant A, Grizot S, Kahn R, Belrhali H, Fieschi F, Landau EM and Pebay-Peyroula E
Detection and characterization of merohedral twinning in two protein crystals : bacteriorhodopsin and p67phox.
Acta Crystallographica D Biological Crystallography (2002) 58(Pt 5) : 784-791.

Thomas A and Field MJ
Reaction mechanism of the HGXPRTase from Plasmodium falciparum : A hybrid potential quantum mechanical/molecular mechanical study
Journal of the American Chemical Society (2002) 124(42) : 12432-12438

Ursby T, Weik M, Fioravanti E, Delarue M, Goeldner M and Bourgeois D
Cryophotolysis of caged compounds : a technique for trapping intermediate states in protein crystals.
Acta Crystallographica D Biological Crystallography (2002) 58(Pt 4) : 607-614.

Weik M, Bergès J, Raves ML, Gros P, McSweeney SM, Silman I, Sussman JL, Houée-Levin and Ravelli RB
Evidence for the formation of disulfide radicals in protein crystals upon X-ray irradiation.
Journal of Synchrotron Radiation (2002) 9 : 342-346

Publications 2001

Amara, P., Andreoletti, P., Jouve, H. M. and Field, M. J.
Ligand diffusion in the catalase from Proteus mirabilis : A molecular dynamics study.
Protein Science (2001) 10(10) : 1927-1935

Dekker C, Agianian B, Weik M, Zaccai G, Kroon J, Gros P and de Kruijff B
Biophysical characterization of the influence of salt on tetrameric SecB.
Biophysical Journal (2001) 81(1) : 455-462.

Field, M. J.
Molecular dynamics simulations with the MD-Grape Special Purpose Computer in Proceedings of the workshop on new horizons in computational science held in Tokyo, September, 1997. Ebisuzaki, T and Makino, J. Terra Scientific Publishing,(2001) : 133-142

Hayashi S, Tajkhorshid E, Pebay Peyroula E, Royant A, Landau EM, Navarro J and Schulten K
Structural determinants of spectral tuning in retinal proteins-bacteriorhodopsin vs sensory rhodopsin II.
Journal of Physical Chemistry B (2001) 105(41) : 10124-10131

Marti S, Andres J, Moliner V, Silla E, Tunon I, Bertran J and Field MJ
A hybrid potential reaction path and free energy study of the chorismate mutase reaction
Journal of the American Chemical Society(2001) 123(8) : 1709-1712

Ren Z, Perman B, Srajer V, Teng TY, Pradervand C, Bourgeois D, Schotte F, Ursby T, Kort R, Wulff M and Moffat K
A molecular movie at 1.8 A resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds.
Biochemistry (2001) 40(46) : 13788-13801.

Roche O and Field M J
Theoretical study of the conformation of the lipoamide arm in a mutant H protein
Proteins (2001) 45(3) : 237-40

Royant A, Edman K, Ursby T, Pebay-Peyroula E, Landau EM and Neutze R
Spectroscopic characterization of bacteriorhodopsin’s L-intermediate in 3D crystals cooled to 170 K.
Photochemistry and Photobiology (2001) 74(6) : 794-804.

Royant A, Nollert P, Edman K, Neutze R, Landau EM, Pebay Peyroula E and Navarro J
X-ray structure of sensory rhodopsin II at 2.1-angstrom resolution.
Proceedings of the National Academy of Sciences of the United States of America (2001) 98(18) : 10131-10136

Specht A, Ursby T, Weik M, Peng L, Kroon J, Bourgeois D and Goeldner M
Cryophotolysis of ortho-Nitrobenzyl derivatives of enzyme ligands for the potentiel kinetic crystallography of macromolecules.
Chembiochem (2001) 11 : 845-848

Srajer V, Ren Z, Teng TY, Schmidt M, Ursby T, Bourgeois D, Pradervand C, Schildkamp W, Wulff M and Moffat K
Protein conformational relaxation and ligand migration in myoglobin : A nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction.
Biochemistry (2001) 40(46) : 13802-13815.

Weik M, Kryger G, Schreurs AM, Bouma B, Silman I, Sussman JL, Gros P and Kroon J
Solvent behaviour in flash-cooled protein crystals at cryogenic temperatures.
Acta Crystallographica D Biological Crystallography (2001) 57(Pt 4) : 566-573.

Weik M, Ravelli RB, Silman I, Sussman JL, Gros P and Kroon J
Specific protein dynamics near the solvent glass transition assayed by radiation-induced structural changes.
Protein Science (2001) 10(10) : 1953-1961.

Publications 2000

Amara P, Field MJ, Alhambra C and Gao JL
The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations : formulation and tests of the analytical derivatives
Theoretical Chemistry Accounts (2000) 104(5) : 336-343

Bourgeois D, Wagner U and Wulff M
Towards automated Laue data processing : application to the choice of optimal X-ray spectrum.
Acta Crystallographica D Biological Crystallography (2000) 56 : 973-985

Bret C, Field MJ and Hemmingsen L
A chemical potential equalization model for treating polarization in molecular mechanical force fields
Molecular Physics (2000) 98(11) : 751-763

Field MJ, Albe M, Bret C, Proust-De Martin F and Thomas A
The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
Journal of Computational Chemistry (2000) 21(12) : 1088-1100

Hemmingsen L, Amara P, Ansoborlo E and Field MJ
Importance of charge transfer and polarization effects for the modeling of uranyl-cation complexes
Journal of Physical Chemistry A (2000) 104(17) : 4095-4101

Proust-De Martin, F., Dumas, R. and Field, M. J.
A hybrid potential free-energy study of the isomerization step of the acetohydroxy acid isomeroreductase reaction.
Journal of the American Chemical Society (2000) 122 : 7688-7697

Royant A, Edman K, Ursby T, Pebay-Peyroula E, Landau EM and Neutze R
Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin [see comments].
Nature (2000) 406(6796) : 645-648

Srajer V, Crosson S, Schmidt M, Key J, Schotte F, Anderson S, Perman B, Ren Z, Teng TY, Bourgeois D, Wulff M and Moffat K
Extraction of accurate structure-factor amplitudes from Laue data : wavelength normalization with wiggler and undulator X-ray sources.
Journal of Synchrotron Radiation (2000) 7 : 236-244

Weik M, Ravelli RB, Kryger G, McSweeney S, Raves ML, Harel M, Gros P, Silman I, Kroon J and Sussman JL
Specific chemical and structural damage to proteins produced by synchrotron radiation.
Proceedings of the National Academy of Sciences U S A (2000) 97(2) : 623-628