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3. Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned

Author

Hadjidemetriou, K., Coquelle, N., Barends, T., De, E., Zitter, Schlichting, I., Colletiera, J., Weik, M., Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Max Planck Institute for Medical Research [Heidelberg], and Max-Planck-Gesellschaft

Subjects
photoenzymes, serial femtosecond crystallography, Crystallography, Light, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Lasers, Spectrum Analysis, structure-factor extrapolation, MESH: Crystallography, Fatty Acids, MESH: Spectrum Analysis, Crystallography, X-Ray, MESH: Crystallography, X-Ray, MESH: Light, MESH: Fatty Acids, Structural Biology, fatty-acid photodecarboxylase, time-resolved crystallography, MESH: Lasers
Abstract

Upon absorption of a blue-light photon, fatty-acid photodecarboxylase catalyzes the decarboxylation of free fatty acids to form hydrocarbons (for example alkanes or alkenes). The major components of the catalytic mechanism have recently been elucidated by combining static and time-resolved serial femtosecond crystallography (TR-SFX), time-resolved vibrational and electronic spectroscopies, quantum-chemical calculations and site-directed mutagenesis [Sorigué et al. (2021), Science, 372, eabd5687]. The TR-SFX experiments, which were carried out at four different picosecond to microsecond pump–probe delays, yielded input for the calculation of Fourier difference maps that demonstrated light-induced decarboxylation. Here, some of the difficulties encountered during the experiment as well as during data processing are highlighted, in particular regarding space-group assignment, a pump-laser power titration is described and data analysis is extended by structure-factor extrapolation of the TR-SFX data. Structure refinement against extrapolated structure factors reveals a reorientation of the generated hydrocarbon and the formation of a photoproduct close to Cys432 and Arg451. Identification of its chemical nature, CO2 or bicarbonate, was not possible because of the limited data quality, which was assigned to specificities of the crystalline system. Further TR-SFX experiments on a different crystal form are required to identify the photoproducts and their movements during the catalytic cycle.

Published
2022

26. Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps

Author

Kelpšas, V. (Vinardas), Caldararu, O. (Octav), Blakeley, M. P. (Matthew P.), Coquelle, N. (Nicolas), Wierenga, R. K. (Rikkert K.), Ryde, U. (Ulf), von Wachenfeldt, C. (Claes), Oksanen, E. (Esko), Kelpšas, V. (Vinardas), Caldararu, O. (Octav), Blakeley, M. P. (Matthew P.), Coquelle, N. (Nicolas), Wierenga, R. K. (Rikkert K.), Ryde, U. (Ulf), von Wachenfeldt, C. (Claes), and Oksanen, E. (Esko)

Abstract

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy­acetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of Leishmania mexicana TIM have been determined with both inhibitors, and joint neutron/X-ray refinement followed by quantum refinement has been performed. The structures show that in the PGA complex the postulated general base Glu167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu167 in the PGA–TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of the active-site protonation states allowed an investigation of the reaction mechanism using density-functional theory calculations.

Published
2021

28. Mechanism and dynamics of fatty acid photodecarboxylase

Author

Sorigué, D., primary, Hadjidemetriou, K., additional, Blangy, S., additional, Gotthard, G., additional, Bonvalet, A., additional, Coquelle, N., additional, Samire, P., additional, Aleksandrov, A., additional, Antonucci, L., additional, Benachir, A., additional, Boutet, S., additional, Byrdin, M., additional, Cammarata, M., additional, Carbajo, S., additional, Cuiné, S., additional, Doak, R. B., additional, Foucar, L., additional, Gorel, A., additional, Grünbein, M., additional, Hartmann, E., additional, Hienerwadel, R., additional, Hilpert, M., additional, Kloos, M., additional, Lane, T. J., additional, Légeret, B., additional, Legrand, P., additional, Li-Beisson, Y., additional, Moulin, S. L. Y., additional, Nurizzo, D., additional, Peltier, G., additional, Schirò, G., additional, Shoeman, R. L., additional, Sliwa, M., additional, Solinas, X., additional, Zhuang, B., additional, Barends, T. R. M., additional, Colletier, J.-P., additional, Joffre, M., additional, Royant, A., additional, Berthomieu, C., additional, Weik, M., additional, Domratcheva, T., additional, Brettel, K., additional, Vos, M. H., additional, Schlichting, I., additional, Arnoux, P., additional, Müller, P., additional, and Beisson, F., additional

Published
2021
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29. Structure of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals soaked with DTT at pH 7

Author

Tetreau, G., primary, Banneville, A.S., additional, Andreeva, E., additional, Brewster, A.S., additional, Hunter, M.S., additional, Sierra, R.G., additional, Young, I.D., additional, Boutet, S., additional, Coquelle, N., additional, Cascio, D., additional, Sawaya, M.R., additional, Sauter, N.K., additional, and Colletier, J.P., additional

Published
2020
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30. Structure of the C7S mutant of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 7

Author

Tetreau, G., primary, Banneville, A.S., additional, Andreeva, E., additional, Brewster, A.S., additional, Hunter, M.S., additional, Sierra, R.G., additional, Young, I.D., additional, Boutet, S., additional, Coquelle, N., additional, Cascio, D., additional, Sawaya, M.R., additional, Sauter, N.K., additional, and Colletier, J.P., additional

Published
2020
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31. Structure of mosquitocidal Cyt1Aa protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 10

Author

Tetreau, G., primary, Banneville, A.S., additional, Andreeva, E., additional, Brewster, A.S., additional, Hunter, M.S., additional, Sierra, R.G., additional, Young, I.D., additional, Boutet, S., additional, Coquelle, N., additional, Cascio, D., additional, Sawaya, M.R., additional, Sauter, N.K., additional, and Colletier, J.P., additional

Published
2020
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32. Native structure of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 7

Author

Tetreau, G., primary, Banneville, A.S., additional, Andreeva, E., additional, Brewster, A.S., additional, Hunter, M.S., additional, Sierra, R.G., additional, Young, I.D., additional, Boutet, S., additional, Coquelle, N., additional, Cascio, D., additional, Sawaya, M.R., additional, Sauter, N.K., additional, and Colletier, J.P., additional

Published
2020
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36. RT structure of HEWL at 5 kGy

Author

de la Mora, E., primary, Coquelle, N., additional, Bury, C.S., additional, Rosenthal, M., additional, Garman, E.F., additional, Burghammer, M., additional, Colletier, J.P., additional, and Weik, M., additional

Published
2020
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37. Cryo structure of HEWL at 81 kGy

Author

de la Mora, E., primary, Coquelle, N., additional, Bury, C.S., additional, Rosenthal, M., additional, Garman, E.F., additional, Burghammer, M., additional, Colletier, J.P., additional, and Weik, M., additional

Published
2020
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38. Interactive GUI for the calculation of F obs–F obs electron-density difference maps and extrapolated structure factors based on the cctbx toolbox

Author

De Zitter, E., Coquelle, N., Barends, T., and Colletier, J.

Subjects
Inorganic Chemistry, Structural Biology, General Materials Science, Physical and Theoretical Chemistry, Condensed Matter Physics, Biochemistry
Abstract

Since resolution of the first macromolecular structure, the goal of structural biology has been to link structure to function. It is now widely accepted that the latter emerges from the structural dynamics animating the macromolecule, making characterization of intermediate (and sometime excited) states of high interest to further understand molecular processes and possibly control them. With the advent of serial crystallography at X-ray free electron lasers and synchrotrons, time-resolved crystallography, performed following a specific perturbation of the crystalline system (laser excitation, substrate soak, etc), is on the verge of becoming feasible on virtually all systems opening avenues to characterize such excited and/or intermediates states. Because crystallography is an ensemble-averaged method, however, an inherent limitation is that the occupancy of intermediate states must be high enough for the “probed state” under investigation to become visible in the electron density. This is generally not the case, with “perturbed” crystals rather existing as mixtures of initial and/or final state(s) with the “probed” state. Differences in structure factor amplitudes between the reference and “perturbed” dataset can allow calculation of Fourier difference maps (Fobs,perturbed-Fobs,unperturbed), in which only the differences between the states are depicted. An even more powerful approach is to generate extrapolated structure factor amplitudes (Fextr,perturbed) solely describing the intermediate state and and to use these to refine its structure using conventional refinement tools. Such data processing has in the past been performed by a handful of well-experienced crystallographers with strong knowledge of existing software but remains out of reach for a wide audience. Here, we will present a user-friendly program, Xtrapol8, written in python and exploiting the cctbx toolbox modules, that allows the calculation of high-quality Fourier difference maps, estimation of the occupancy of the intermediate state(s) in the crystals, and generation of extrapolated structure factor amplitudes. Briefly, the program uses Bayesian statistics to weight structure factor amplitude differences [1] which are then used to generate extrapolated structure factor amplitudes for a range of possible intermediate state occupancies, with distinct weighting schemes [2, 3] (Figure 1). Based on the comparison between experimental and calculated differences, i.e. solely on experimental observations, the correct occupancy of the intermediate state is determined and its structure refined, shedding light on conformational changes not visible before. With various user-controllable parameters of which defaults are carefully chosen, the program is adapted to be used by a wide audience of structural biologists, ranging from well-experienced crystallographers to newcomers in the field. We anticipate that this program will ease and accelerate the handling of time resolved structural data, and thereby the understanding of molecular processes underlying function in a variety of proteins.

Published
2021

41. BRCA1 Circos: a visualisation resource for functional analysis of missense variants

Author

Jhuraney, A., Velkova, A., Johnson, R.C., Kessing, B., Carvalho, R.S., Whiley, P., Spurdle, A.B., Vreeswijk, M.P.G., Caputo, S.M., Millot, G.A., Vega, A., Coquelle, N., Galli, A., Eccles, D., Blok, M.J., Pal, T., Luijt, R.B. van der, Pena, M.S., Neuhausen, S.L., Donenberg, T., Machackova, E., Thomas, S., Vallee, M., Couch, F.J., Tavtigian, S.V., Glover, J.N.M., Carvalho, M.A., Brody, L.C., Sharan, S.K., Monteiro, A.N., ENIGMA Evidence-Based Network, University of South Florida [Tampa] (USF), H. Lee Moffitt Cancer Center and Research Institute, National Human Genome Research Institute (NHGRI), Frederick National Laboratory for Cancer Research (FNLCR), Instituto Nacional de Câncer [Rio de Janeiro, Brésil], Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), QIMR Berghofer Medical Research Institute, Leiden University Medical Center (LUMC), Institut Curie [Paris], Fundación Pública Galega Medicina Xenómica - SERGAS [Santiago de Compostela, Spain] (Grupo de Medicina Xenómica), CIBER de Enfermedades Raras (CIBERER)-Universidade de Santiago de Compostela [Spain] (USC ), University of Alberta, Instituto di fisiologia clinica, University of Southampton, Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], University Medical Center [Utrecht], CIBER de Enfermedades Raras (CIBERER), Beckman Research Institute of the City of Hope, University of Miami Leonard M. Miller School of Medicine (UMMSM), Masaryk Memorial Cancer Institute (RECAMO), Salisbury District Hospital, International Agency for Cancer Research (IACR), Mayo Clinic [Rochester], University of Utah School of Medicine [Salt Lake City], National Cancer Institute Frederick, This work was funded by H. Lee Moffitt Cancer Center Foundation (Milesfor Moffitt), and the US National Cancer Institute. The ENIGMA consortium is funded by a supplement to NIH RO1 award CA116167, The authors would like to sincerely thank Tyra Wolfsberg and Suiyuan Zhang for helping with webpage development and all individuals and families who have generously donated their time, samples and information to facilitate research on the predisposition factors of breast and ovarian cancer, MUMC+: DA KG Lab Centraal Lab (9), RS: GROW - Oncology, RS: GROW - R4 - Reproductive and Perinatal Medicine, Klinische Genetica, Damage and Repair in Cancer Development and Cancer Treatment (DARE), and Targeted Gynaecologic Oncology (TARGON)

Subjects
[SDV]Life Sciences [q-bio], DNA Mutational Analysis, Datasets as Topic, LIGASE ACTIVITY, MUTATION-POSITIVE FAMILIES, Databases, Genetic, SEQUENCE VARIANTS, Missense mutation, Genetics(clinical), MESH: Datasets as Topic, Molecular genetics, MESH: DNA Mutational Analysis, Non-U.S. Gov't, skin and connective tissue diseases, Genetics (clinical), MESH: Databases, Genetic, Ovarian Neoplasms, Genetics, education.field_of_study, medicine.diagnostic_test, MESH: Genetic Testing, BRCA1 Protein, Research Support, Non-U.S. Gov't, UNKNOWN CLINICAL-SIGNIFICANCE, MESH: Genetic Predisposition to Disease, BREAST-CANCER RISK, RING-DOMAIN, 3. Good health, MESH: Ovarian Neoplasms, MESH: Internet, UNCERTAIN SIGNIFICANCE, Medical genetics, Female, MESH: Computer Graphics, MESH: Computational Biology, medicine.medical_specialty, Population, Mutation, Missense, Breast Neoplasms, Biology, Research Support, OVARIAN-CANCER, N.I.H, MESH: Software, Germline mutation, Research Support, N.I.H., Extramural, GENETIC-ANALYSIS, Journal Article, Cancer Genetics, Computer Graphics, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Ligase activity, Clinical genetics, NEGATIVE WOMEN, education, Genetic testing, MESH: BRCA1 Protein, Internet, MESH: Mutation, Missense, MESH: Humans, Cancer: breast, Extramural, Computational Biology, BRCA1, Database Management Systems, MESH: Female, Software, MESH: Breast Neoplasms, MESH: Database Management Systems
Abstract

BACKGROUND: Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes.METHODS AND RESULTS: To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant.CONCLUSIONS: This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.

Published
2015

42. Toward an innovative treatment of Alzheimer's disease: Synthesis and evaluation of multi-target directed ligands (MTDLs) targeting acetylcholinesterase (AChE) and alpha7 nicotinic acetylchloline receptors (alpha7 nAChRs)

Author

Cieslikiewicz-Bouet, Monika, Chao, Sovy, Jean, Ludovic, Araoz, R., Servent, D., Coquelle, N., Colletier, J.-P., Renard, Pierre-Yves, ROUX-MERLIN, Madeleine, Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[CHIM] Chemical Sciences, [CHIM]Chemical Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

48. Difference-refined excited-state structure of rsEGFP2 1ps following 400nm-laser irradiation of the off-state.

Author

Coquelle, N., primary, Sliwa, M., additional, Woodhouse, J., additional, Schiro, G., additional, Adam, V., additional, Aquila, A., additional, Barends, T.R.M., additional, Boutet, S., additional, Byrdin, M., additional, Carbajo, S., additional, De la Mora, E., additional, Doak, R.B., additional, Feliks, M., additional, Fieschi, F., additional, Foucar, L., additional, Guillon, V., additional, Hilpert, M., additional, Hunter, M., additional, Jakobs, S., additional, Koglin, J.E., additional, Kovacsova, G., additional, Lane, T.J., additional, Levy, B., additional, Liang, M., additional, Nass, K., additional, Ridard, J., additional, Robinson, J.S., additional, Roome, C.M., additional, Ruckebusch, C., additional, Seaberg, M., additional, Thepaut, M., additional, Cammarata, M., additional, Demachy, I., additional, Field, M., additional, Shoeman, R.L., additional, Bourgeois, D., additional, Colletier, J.P., additional, Schlichting, I., additional, and Weik, M., additional

Published
2018
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49. Crystal Structure of rsEGFP2 in the fluorescent on-state determined by SFX

Author

Coquelle, N., primary, Sliwa, M., additional, Woodhouse, J., additional, Schiro, G., additional, Adam, V., additional, Aquila, A., additional, Barends, T.R.M., additional, Boutet, S., additional, Byrdin, M., additional, Carbajo, S., additional, De la Mora, E., additional, Doak, R.B., additional, Feliks, M., additional, Fieschi, F., additional, Foucar, L., additional, Guillon, V., additional, Hilpert, M., additional, Hunter, M., additional, Jakobs, S., additional, Koglin, J.E., additional, Kovacsova, G., additional, Lane, T.J., additional, Levy, B., additional, Liang, M., additional, Nass, K., additional, Ridard, J., additional, Robinson, J.S., additional, Roome, C.M., additional, Ruckebusch, C., additional, Seaberg, M., additional, Thepaut, M., additional, Cammarata, M., additional, Demachy, I., additional, Field, M., additional, Shoeman, R.L., additional, Bourgeois, D., additional, Colletier, J.P., additional, Schlichting, I., additional, and Weik, M., additional

Published
2017
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50. Composite structure of rsEGFP2 1ps following 400nm-laser irradiation of the off-state.

Author

Coquelle, N., primary, Sliwa, M., additional, Woodhouse, J., additional, Schiro, G., additional, Adam, V., additional, Aquila, A., additional, Barends, T.R.M., additional, Boutet, S., additional, Byrdin, M., additional, Carbajo, S., additional, De la Mora, E., additional, Doak, R.B., additional, Feliks, M., additional, Fieschi, F., additional, Foucar, L., additional, Guillon, V., additional, Hilpert, M., additional, Hunter, M., additional, Jakobs, S., additional, Koglin, J.E., additional, Kovacsova, G., additional, Lane, T.J., additional, Levy, B., additional, Liang, M., additional, Nass, K., additional, Ridard, J., additional, Robinson, J.S., additional, Roome, C.M., additional, Ruckebusch, C., additional, Seaberg, M., additional, Thepaut, M., additional, Cammarata, M., additional, Demachy, I., additional, Field, M., additional, Shoeman, R.L., additional, Bourgeois, D., additional, Colletier, J.P., additional, Schlichting, I., additional, and Weik, M., additional

Published
2017
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