1
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Faure C, Min Ng Y, Belle C, Soler-Lopez M, Khettabi L, Saïdi M, Berthet N, Maresca M, Philouze C, Rachidi W, Réglier M, du Moulinet d'Hardemare A, Jamet H. Interactions of Phenylalanine Derivatives with Human Tyrosinase: Lessons from Experimental and Theoretical tudies. Chembiochem 2024; 25:e202400235. [PMID: 38642076 DOI: 10.1002/cbic.202400235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/22/2024]
Abstract
The pigmentation of the skin, modulated by different actors in melanogenesis, is mainly due to the melanins (protective pigments). In humans, these pigments' precursors are synthetized by an enzyme known as tyrosinase (TyH). The regulation of the enzyme activity by specific modulators (inhibitors or activators) can offer a means to fight hypo- and hyper-pigmentations responsible for medical, psychological and societal handicaps. Herein, we report the investigation of phenylalanine derivatives as TyH modulators. Interacting with the binuclear copper active site of the enzyme, phenylalanine derivatives combine effects induced by combination with known resorcinol inhibitors and natural substrate/intermediate (amino acid part). Computational studies including docking, molecular dynamics and free energy calculations combined with biological activity assays on isolated TyH and in human melanoma MNT-1 cells, and X-ray crystallography analyses with the TyH analogue Tyrp1, provide conclusive evidence of the interactions of phenylalanine derivatives with human tyrosinase. In particular, our findings indicate that an analogue of L-DOPA, namely (S)-3-amino-tyrosine, stands out as an amino phenol derivative with inhibitory properties against TyH.
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Affiliation(s)
- Clarisse Faure
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Yi Min Ng
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Catherine Belle
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Lyna Khettabi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Mélissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Nathalie Berthet
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Marc Maresca
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France)
| | - Christian Philouze
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Walid Rachidi
- IRIG-BGE U1038, INSERM, Univ. Grenoble Alpes, Biomics, 38054, Grenoble, France
| | - Marius Réglier
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France)
| | | | - Hélène Jamet
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
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2
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Kind L, Molnes J, Tjora E, Raasakka A, Myllykoski M, Colclough K, Saint-Martin C, Adelfalk C, Dusatkova P, Pruhova S, Valtonen-André C, Bellanné-Chantelot C, Arnesen T, Kursula P, Njølstad PR. Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes. JCI Insight 2024; 9:e175278. [PMID: 38855865 DOI: 10.1172/jci.insight.175278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/25/2024] [Indexed: 06/11/2024] Open
Abstract
Monogenic diabetes is a gateway to precision medicine through molecular mechanistic insight. Hepatocyte nuclear factor 1A (HNF-1A) and HNF-4A are transcription factors that engage in crossregulatory gene transcription networks to maintain glucose-stimulated insulin secretion in pancreatic β cells. Variants in the HNF1A and HNF4A genes are associated with maturity-onset diabetes of the young (MODY). Here, we explored 4 variants in the P2-HNF4A promoter region: 3 in the HNF-1A binding site and 1 close to the site, which were identified in 63 individuals from 21 families of different MODY disease registries across Europe. Our goal was to study the disease causality for these variants and to investigate diabetes mechanisms on the molecular level. We solved a crystal structure of HNF-1A bound to the P2-HNF4A promoter and established a set of techniques to probe HNF-1A binding and transcriptional activity toward different promoter variants. We used isothermal titration calorimetry, biolayer interferometry, x-ray crystallography, and transactivation assays, which revealed changes in HNF-1A binding or transcriptional activities for all 4 P2-HNF4A variants. Our results suggest distinct disease mechanisms of the promoter variants, which can be correlated with clinical phenotype, such as age of diagnosis of diabetes, and be important tools for clinical utility in precision medicine.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine and
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics and
| | - Erling Tjora
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics and Adolescent Medicine, Haukeland University Hospital, Bergen, Norway
| | | | | | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Cécile Saint-Martin
- Department of Medical Genetics, Sorbonne Université, AP-HP, Pitié-Salpêtrière Hospital, DMU BioGeM, Paris, France
- Monogenic Diabetes Study Group of the Société Francophone du Diabète, Paris, France
| | - Caroline Adelfalk
- Clinical Genetics, Pathology and Molecular Diagnostics, University Hospital Skåne, Lund, Sweden
| | - Petra Dusatkova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Stepanka Pruhova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | - Christine Bellanné-Chantelot
- Department of Medical Genetics, Sorbonne Université, AP-HP, Pitié-Salpêtrière Hospital, DMU BioGeM, Paris, France
- Monogenic Diabetes Study Group of the Société Francophone du Diabète, Paris, France
| | - Thomas Arnesen
- Department of Biomedicine and
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine and
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
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3
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Carpentier P, van der Linden P, Mueller-Dieckmann C. The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF. Acta Crystallogr D Struct Biol 2024; 80:80-92. [PMID: 38265873 PMCID: PMC10836400 DOI: 10.1107/s2059798323010707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.
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Affiliation(s)
- Philippe Carpentier
- Université Grenoble Alpes CEA CNRS, IRIG–LCBM UMR 5249, 17 Avenue des Martyrs, 38000 Grenoble, France
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Peter van der Linden
- ESRF, PSCM (Partnership for Soft Condensed Matter), 71 Avenue des Martyrs, 38000 Grenoble, France
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4
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Oliveira AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA. An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat Chem Biol 2024; 20:111-119. [PMID: 37985883 DOI: 10.1038/s41589-023-01484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vincent Fourmond
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Kateryna Klymanska
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Christophe Léger
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Bruno Guigliarelli
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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5
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Sinatra L, Vogelmann A, Friedrich F, Tararina MA, Neuwirt E, Colcerasa A, König P, Toy L, Yesiloglu TZ, Hilscher S, Gaitzsch L, Papenkordt N, Zhai S, Zhang L, Romier C, Einsle O, Sippl W, Schutkowski M, Gross O, Bendas G, Christianson DW, Hansen FK, Jung M, Schiedel M. Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J Med Chem 2023; 66:14787-14814. [PMID: 37902787 PMCID: PMC10641818 DOI: 10.1021/acs.jmedchem.3c01385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/31/2023]
Abstract
Dysregulation of both tubulin deacetylases sirtuin 2 (Sirt2) and the histone deacetylase 6 (HDAC6) has been associated with the pathogenesis of cancer and neurodegeneration, thus making these two enzymes promising targets for pharmaceutical intervention. Herein, we report the design, synthesis, and biological characterization of the first-in-class dual Sirt2/HDAC6 inhibitors as molecular tools for dual inhibition of tubulin deacetylation. Using biochemical in vitro assays and cell-based methods for target engagement, we identified Mz325 (33) as a potent and selective inhibitor of both target enzymes. Inhibition of both targets was further confirmed by X-ray crystal structures of Sirt2 and HDAC6 in complex with building blocks of 33. In ovarian cancer cells, 33 evoked enhanced effects on cell viability compared to single or combination treatment with the unconjugated Sirt2 and HDAC6 inhibitors. Thus, our dual Sirt2/HDAC6 inhibitors are important new tools to study the consequences and the therapeutic potential of dual inhibition of tubulin deacetylation.
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Affiliation(s)
- Laura Sinatra
- Institute
for Drug Discovery, Medical Faculty, Leipzig
University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Anja Vogelmann
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Florian Friedrich
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Margarita A. Tararina
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Emilia Neuwirt
- Institute
of Neuropathology, Medical Center−University of Freiburg, Faculty
of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
- CIBSS−Centre
for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
| | - Arianna Colcerasa
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Philipp König
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lara Toy
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Talha Z. Yesiloglu
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
| | - Sebastian Hilscher
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
- Department
of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry
and Biotechnology, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Lena Gaitzsch
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Niklas Papenkordt
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Shiyang Zhai
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lin Zhang
- Institute
of Biochemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Christophe Romier
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire
(IGBMC), Université de Strasbourg,
CNRS UMR 7104, Inserm UMR-S 1258, 1 rue Laurent Fries, F-67400 Illkirch, France
| | - Oliver Einsle
- Institute
of Biochemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Wolfgang Sippl
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
| | - Mike Schutkowski
- Department
of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry
and Biotechnology, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Olaf Gross
- Institute
of Neuropathology, Medical Center−University of Freiburg, Faculty
of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
- CIBSS−Centre
for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Center
for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
| | - Gerd Bendas
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Finn K. Hansen
- Institute
for Drug Discovery, Medical Faculty, Leipzig
University, Brüderstraße 34, 04103 Leipzig, Germany
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Manfred Jung
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Matthias Schiedel
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
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6
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Makita H, Simon PS, Kern J, Yano J, Yachandra VK. Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography. Curr Opin Struct Biol 2023; 80:102604. [PMID: 37148654 PMCID: PMC10793627 DOI: 10.1016/j.sbi.2023.102604] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023]
Abstract
With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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7
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Sun P, Huang Z, Banerjee S, Kadowaki MAS, Veersma RJ, Magri S, Hilgers R, Muderspach SJ, Laurent CV, Ludwig R, Cannella D, Lo Leggio L, van Berkel WJH, Kabel MA. AA16 Oxidoreductases Boost Cellulose-Active AA9 Lytic Polysaccharide Monooxygenases from Myceliophthora thermophila. ACS Catal 2023; 13:4454-4467. [PMID: 37066045 PMCID: PMC10088020 DOI: 10.1021/acscatal.3c00874] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/06/2023] [Indexed: 04/18/2023]
Abstract
Copper-dependent lytic polysaccharide monooxygenases (LPMOs) classified in Auxiliary Activity (AA) families are considered indispensable as synergistic partners for cellulolytic enzymes to saccharify recalcitrant lignocellulosic plant biomass. In this study, we characterized two fungal oxidoreductases from the new AA16 family. We found that MtAA16A from Myceliophthora thermophila and AnAA16A from Aspergillus nidulans did not catalyze the oxidative cleavage of oligo- and polysaccharides. Indeed, the MtAA16A crystal structure showed a fairly LPMO-typical histidine brace active site, but the cellulose-acting LPMO-typical flat aromatic surface parallel to the histidine brace region was lacking. Further, we showed that both AA16 proteins are able to oxidize low-molecular-weight reductants to produce H2O2. The oxidase activity of the AA16s substantially boosted cellulose degradation by four AA9 LPMOs from M. thermophila (MtLPMO9s) but not by three AA9 LPMOs from Neurospora crassa (NcLPMO9s). The interplay with MtLPMO9s is explained by the H2O2-producing capability of the AA16s, which, in the presence of cellulose, allows the MtLPMO9s to optimally drive their peroxygenase activity. Replacement of MtAA16A by glucose oxidase (AnGOX) with the same H2O2-producing activity could only achieve less than 50% of the boosting effect achieved by MtAA16A, and earlier MtLPMO9B inactivation (6 h) was observed. To explain these results, we hypothesized that the delivery of AA16-produced H2O2 to the MtLPMO9s is facilitated by protein-protein interaction. Our findings provide new insights into the functions of copper-dependent enzymes and contribute to a further understanding of the interplay of oxidative enzymes within fungal systems to degrade lignocellulose.
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Affiliation(s)
- Peicheng Sun
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Zhiyu Huang
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Sanchari Banerjee
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Marco A. S. Kadowaki
- PhotoBioCatalysis
Unit (CPBL) and Biomass Transformation Lab (BTL), École Interfacultaire
de Bioingénieurs (EIB), Université
Libre de Bruxelles, Avenue Franklin D. Roosevelt 50, 1050 Bruxelles, Belgium
| | - Romy J. Veersma
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Silvia Magri
- PhotoBioCatalysis
Unit (CPBL) and Biomass Transformation Lab (BTL), École Interfacultaire
de Bioingénieurs (EIB), Université
Libre de Bruxelles, Avenue Franklin D. Roosevelt 50, 1050 Bruxelles, Belgium
| | - Roelant Hilgers
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Sebastian J. Muderspach
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Christophe V.F.P. Laurent
- Biocatalysis
and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences
(BOKU), Muthgasse 18, 1190 Vienna, Austria
- Institute
of Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Biocatalysis
and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences
(BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - David Cannella
- PhotoBioCatalysis
Unit (CPBL) and Biomass Transformation Lab (BTL), École Interfacultaire
de Bioingénieurs (EIB), Université
Libre de Bruxelles, Avenue Franklin D. Roosevelt 50, 1050 Bruxelles, Belgium
| | - Leila Lo Leggio
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Willem J. H. van Berkel
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Mirjam A. Kabel
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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8
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Schneider DK, Soares AS, Lazo EO, Kreitler DF, Qian K, Fuchs MR, Bhogadi DK, Antonelli S, Myers SS, Martins BS, Skinner JM, Aishima J, Bernstein HJ, Langdon T, Lara J, Petkus R, Cowan M, Flaks L, Smith T, Shea-McCarthy G, Idir M, Huang L, Chubar O, Sweet RM, Berman LE, McSweeney S, Jakoncic J. AMX - the highly automated macromolecular crystallography (17-ID-1) beamline at the NSLS-II. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1480-1494. [PMID: 36345756 PMCID: PMC9641562 DOI: 10.1107/s1600577522009377] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 1012 photons s-1), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5-18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented.
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Affiliation(s)
| | | | - Edwin O. Lazo
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | | | - Kun Qian
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Martin R. Fuchs
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Dileep K. Bhogadi
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Steve Antonelli
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Stuart S. Myers
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | | | - John M. Skinner
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Jun Aishima
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Herbert J. Bernstein
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
- Ronin Institute, Montclair, New Jersey, USA
| | - Thomas Langdon
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - John Lara
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Robert Petkus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Matt Cowan
- CSI, Brookhaven National Laboratory, Upton, New York, USA
| | - Leonid Flaks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Thomas Smith
- Physics Department, Brookhaven National Laboratory, Upton, New York, USA
| | | | - Mourad Idir
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Lei Huang
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Oleg Chubar
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Robert M. Sweet
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Lonny E. Berman
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Sean McSweeney
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Jean Jakoncic
- NSLS-II, Brookhaven National Laboratory, Upton, New York, USA
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9
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Aumonier S, Engilberge S, Caramello N, von Stetten D, Gotthard G, Leonard GA, Mueller-Dieckmann C, Royant A. Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature. IUCRJ 2022; 9:756-767. [PMID: 36381146 PMCID: PMC9634615 DOI: 10.1107/s2052252522009150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/14/2022] [Indexed: 05/23/2023]
Abstract
The development of serial crystallography over the last decade at XFELs and synchrotrons has produced a renaissance in room-temperature macromolecular crystallography (RT-MX), and fostered many technical and methodological breakthroughs designed to study phenomena occurring in proteins on the picosecond-to-second timescale. However, there are components of protein dynamics that occur in much slower regimes, of which the study could readily benefit from state-of-the-art RT-MX. Here, the room-temperature structural study of the relaxation of a reaction intermediate at a synchrotron, exploiting a handful of single crystals, is described. The intermediate in question is formed in microseconds during the photoreaction of the LOV2 domain of phototropin 2 from Arabidopsis thaliana, which then decays in minutes. This work monitored its relaxation in the dark using a fast-readout EIGER X 4M detector to record several complete oscillation X-ray diffraction datasets, each of 1.2 s total exposure time, at different time points in the relaxation process. Coupled with in crystallo UV-Vis absorption spectroscopy, this RT-MX approach allowed the authors to follow the relaxation of the photoadduct, a thio-ether covalent bond between the chromophore and a cysteine residue. Unexpectedly, the return of the chromophore to its spectroscopic ground state is followed by medium-scale protein rearrangements that trigger a crystal phase transition and hinder the full recovery of the structural ground state of the protein. In addition to suggesting a hitherto unexpected role of a conserved tryptophan residue in the regulation of the photocycle of LOV2, this work provides a basis for performing routine time-resolved protein crystallography experiments at synchrotrons for phenomena occurring on the second-to-hour timescale.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Sylvain Engilberge
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Christoph Mueller-Dieckmann
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 avenue des Martyrs, Grenoble 38044, France
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10
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Chidyausiku TM, Mendes SR, Klima JC, Nadal M, Eckhard U, Roel-Touris J, Houliston S, Guevara T, Haddox HK, Moyer A, Arrowsmith CH, Gomis-Rüth FX, Baker D, Marcos E. De novo design of immunoglobulin-like domains. Nat Commun 2022; 13:5661. [PMID: 36192397 PMCID: PMC9530121 DOI: 10.1038/s41467-022-33004-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies, and antibody derivatives such as nanobodies, contain immunoglobulin-like (Ig) β-sandwich scaffolds which anchor the hypervariable antigen-binding loops and constitute the largest growing class of drugs. Current engineering strategies for this class of compounds rely on naturally existing Ig frameworks, which can be hard to modify and have limitations in manufacturability, designability and range of action. Here, we develop design rules for the central feature of the Ig fold architecture—the non-local cross-β structure connecting the two β-sheets—and use these to design highly stable Ig domains de novo, confirm their structures through X-ray crystallography, and show they can correctly scaffold functional loops. Our approach opens the door to the design of antibody-like scaffolds with tailored structures and superior biophysical properties. The immunoglobulin domain framework of antibodies has been a long standing design challenge. Here, the authors describe design rules for tailoring these domains and show they can be accurately designed, de novo, with high stability and the ability to scaffold functional loops.
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Affiliation(s)
- Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.,Novartis Institutes for BioMedical Research Inc., San Diego, CA, 92121, USA
| | - Soraia R Mendes
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jason C Klima
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Encodia, Inc., San Diego, CA, 92121, USA
| | - Marta Nadal
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Ulrich Eckhard
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jorge Roel-Touris
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Scott Houliston
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Hugh K Haddox
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Adam Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
| | - Enrique Marcos
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
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11
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Cianci M, Giacchè N, Cialabrini L, Carotti A, Liscio P, Rosatelli E, De Franco F, Gasparrini M, Robertson J, Amici A, Raffaelli N, Pellicciari R. Structural Basis of Human Dimeric α-Amino-β-Carboxymuconate-ε-Semialdehyde Decarboxylase Inhibition With TES-1025. Front Mol Biosci 2022; 9:834700. [PMID: 35463964 PMCID: PMC9021598 DOI: 10.3389/fmolb.2022.834700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) stands at a branch point of the de novo NAD+ synthesis pathway and plays an important role in maintaining NAD+ homeostasis. It has been recently identified as a novel therapeutic target for a wide range of diseases, including inflammatory, metabolic disorders, and aging. So far, in absence of potent and selective enzyme inhibitors, only a crystal structure of the complex of human dimeric ACMSD with pseudo-substrate dipicolinic acid has been resolved. In this study, we report the crystal structure of the complex of human dimeric ACMSD with TES-1025, the first nanomolar inhibitor of this target, which shows a binding conformation different from the previously published predicted binding mode obtained by docking experiments. The inhibitor has a Ki value of 0.85 ± 0.22 nM and binds in the catalytic site, interacting with the Zn2+ metal ion and with residues belonging to both chains of the dimer. The results provide new structural information about the mechanism of inhibition exerted by a novel class of compounds on the ACMSD enzyme, a novel therapeutic target for liver and kidney diseases.
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Affiliation(s)
- Michele Cianci
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- *Correspondence: Michele Cianci, ; Nicola Giacchè,
| | - Nicola Giacchè
- TES Pharma S.r.l, Perugia, Italy
- *Correspondence: Michele Cianci, ; Nicola Giacchè,
| | - Lucia Cialabrini
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | | | | | - Massimiliano Gasparrini
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Adolfo Amici
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Nadia Raffaelli
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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12
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Nanao M, Basu S, Zander U, Giraud T, Surr J, Guijarro M, Lentini M, Felisaz F, Sinoir J, Morawe C, Vivo A, Beteva A, Oscarsson M, Caserotto H, Dobias F, Flot D, Nurizzo D, Gigmes J, Foos N, Siebrecht R, Roth T, Theveneau P, Svensson O, Papp G, Lavault B, Cipriani F, Barrett R, Clavel C, Leonard G. ID23-2: an automated and high-performance microfocus beamline for macromolecular crystallography at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:581-590. [PMID: 35254323 PMCID: PMC8900849 DOI: 10.1107/s1600577522000984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/28/2022] [Indexed: 05/30/2023]
Abstract
ID23-2 is a fixed-energy (14.2 keV) microfocus beamline at the European Synchrotron Radiation Facility (ESRF) dedicated to macromolecular crystallography. The optics and sample environment have recently been redesigned and rebuilt to take full advantage of the upgrade of the ESRF to the fourth generation Extremely Brilliant Source (ESRF-EBS). The upgraded beamline now makes use of two sets of compound refractive lenses and multilayer mirrors to obtain a highly intense (>1013 photons s-1) focused microbeam (minimum size 1.5 µm × 3 µm full width at half-maximum). The sample environment now includes a FLEX-HCD sample changer/storage system, as well as a state-of-the-art MD3Up high-precision multi-axis diffractometer. Automatic data reduction and analysis are also provided for more advanced protocols such as synchrotron serial crystallographic experiments.
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Affiliation(s)
- Max Nanao
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christian Morawe
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Amparo Vivo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Marcus Oscarsson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Jonathan Gigmes
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Nicolas Foos
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Thomas Roth
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gergely Papp
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Florent Cipriani
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Carole Clavel
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gordon Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
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13
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Rodrigues CF, Borges PT, Scocozza MF, Silva D, Taborda A, Brissos V, Frazão C, Martins LO. Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis. Int J Mol Sci 2021; 22:ijms221910862. [PMID: 34639208 PMCID: PMC8509576 DOI: 10.3390/ijms221910862] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022] Open
Abstract
Bacillus subtilis BsDyP belongs to class I of the dye-decolorizing peroxidase (DyP) family of enzymes and is an interesting biocatalyst due to its high redox potential, broad substrate spectrum and thermostability. This work reports the optimization of BsDyP using directed evolution for improved oxidation of 2,6-dimethoxyphenol, a model lignin-derived phenolic. After three rounds of evolution, one variant was identified displaying 7-fold higher catalytic rates and higher production yields as compared to the wild-type enzyme. The analysis of X-ray structures of the wild type and the evolved variant showed that the heme pocket is delimited by three long conserved loop regions and a small α helix where, incidentally, the mutations were inserted in the course of evolution. One loop in the proximal side of the heme pocket becomes more flexible in the evolved variant and the size of the active site cavity is increased, as well as the width of its mouth, resulting in an enhanced exposure of the heme to solvent. These conformational changes have a positive functional role in facilitating electron transfer from the substrate to the enzyme. However, they concomitantly resulted in decreasing the enzyme’s overall stability by 2 kcal mol−1, indicating a trade-off between functionality and stability. Furthermore, the evolved variant exhibited slightly reduced thermal stability compared to the wild type. The obtained data indicate that understanding the role of loops close to the heme pocket in the catalysis and stability of DyPs is critical for the development of new and more powerful biocatalysts: loops can be modulated for tuning important DyP properties such as activity, specificity and stability.
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Affiliation(s)
- Carolina F. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Magali F. Scocozza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET—Universidad de Buenos Aires, Buenos Aires 148EHA, Argentina;
| | - Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
- Correspondence:
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14
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Lima GMA, Jagudin E, Talibov VO, Benz LS, Marullo C, Barthel T, Wollenhaupt J, Weiss MS, Mueller U. FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. Acta Crystallogr D Struct Biol 2021; 77:799-808. [PMID: 34076593 PMCID: PMC8171072 DOI: 10.1107/s2059798321003818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/08/2021] [Indexed: 01/13/2023] Open
Abstract
Crystallographic fragment screening (CFS) has become one of the major techniques for screening compounds in the early stages of drug-discovery projects. Following the advances in automation and throughput at modern macromolecular crystallography beamlines, the bottleneck for CFS has shifted from collecting data to organizing and handling the analysis of such projects. The complexity that emerges from the use of multiple methods for processing and refinement and to search for ligands requires an equally sophisticated solution to summarize the output, allowing researchers to focus on the scientific questions instead of on software technicalities. FragMAXapp is the fragment-screening project-management tool designed to handle CFS projects at MAX IV Laboratory. It benefits from the powerful computing infrastructure of large-scale facilities and, as a web application, it is accessible from everywhere.
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Affiliation(s)
| | - Elmir Jagudin
- BioMAX, MAX IV Laboratory, Fotongatan 2, 224 84 Lund, Sweden
| | | | - Laila S. Benz
- Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | | | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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15
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Sorigué D, Hadjidemetriou K, Blangy S, Gotthard G, Bonvalet A, Coquelle N, Samire P, Aleksandrov A, Antonucci L, Benachir A, Boutet S, Byrdin M, Cammarata M, Carbajo S, Cuiné S, Doak RB, Foucar L, Gorel A, Grünbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Légeret B, Legrand P, Li-Beisson Y, Moulin SLY, Nurizzo D, Peltier G, Schirò G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier JP, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Müller P, Beisson F. Mechanism and dynamics of fatty acid photodecarboxylase. Science 2021; 372:372/6538/eabd5687. [PMID: 33833098 DOI: 10.1126/science.abd5687] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/17/2021] [Indexed: 12/21/2022]
Abstract
Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.
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Affiliation(s)
- D Sorigué
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - K Hadjidemetriou
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - S Blangy
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Gotthard
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - A Bonvalet
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - N Coquelle
- Large-Scale Structures Group, Institut Laue Langevin, 38042 Grenoble Cedex 9, France
| | - P Samire
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - A Aleksandrov
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - L Antonucci
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Benachir
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - S Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M Byrdin
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, F-Rennes, France.
| | - S Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - S Cuiné
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - R B Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - L Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - A Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - E Hartmann
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R Hienerwadel
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - M Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - T J Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - B Légeret
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - P Legrand
- Synchrotron SOLEIL. L'Orme des Merisiers Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Y Li-Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - S L Y Moulin
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - D Nurizzo
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - G Peltier
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - R L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Sliwa
- Univ. Lille, CNRS, UMR 8516, LASIRE, LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, 59000 Lille, France
| | - X Solinas
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - B Zhuang
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - T R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - J-P Colletier
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Joffre
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Royant
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.,European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - C Berthomieu
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - M Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.
| | - T Domratcheva
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany. .,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - K Brettel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - M H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.
| | - I Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - P Arnoux
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - P Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - F Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
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16
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Pallesen JS, Narayanan D, Tran KT, Solbak SMØ, Marseglia G, Sørensen LME, Høj LJ, Munafò F, Carmona RMC, Garcia AD, Desu HL, Brambilla R, Johansen TN, Popowicz GM, Sattler M, Gajhede M, Bach A. Deconstructing Noncovalent Kelch-like ECH-Associated Protein 1 (Keap1) Inhibitors into Fragments to Reconstruct New Potent Compounds. J Med Chem 2021; 64:4623-4661. [PMID: 33818106 DOI: 10.1021/acs.jmedchem.0c02094] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Targeting the protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associated protein 1 (Keap1) is a potential therapeutic strategy to control diseases involving oxidative stress. Here, six classes of known small-molecule Keap1-Nrf2 PPI inhibitors were dissected into 77 fragments in a fragment-based deconstruction reconstruction (FBDR) study and tested in four orthogonal assays. This gave 17 fragment hits of which six were shown by X-ray crystallography to bind in the Keap1 Kelch binding pocket. Two hits were merged into compound 8 with a 220-380-fold stronger affinity (Ki = 16 μM) relative to the parent fragments. Systematic optimization resulted in several novel analogues with Ki values of 0.04-0.5 μM, binding modes determined by X-ray crystallography, and enhanced microsomal stability. This demonstrates how FBDR can be used to find new fragment hits, elucidate important ligand-protein interactions, and identify new potent inhibitors of the Keap1-Nrf2 PPI.
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Affiliation(s)
- Jakob S Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kim T Tran
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Giuseppe Marseglia
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,Food and Drug Department, University of Parma, Parco Area delle Scienze 27/a, 43124 Parma, Italy
| | - Louis M E Sørensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars J Høj
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Federico Munafò
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Rosa M C Carmona
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anthony D Garcia
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,École Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, CS 50837, Rennes Cedex 7 35708, France
| | - Haritha L Desu
- The Miami Project to Cure Paralysis, Dept. Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Roberta Brambilla
- The Miami Project to Cure Paralysis, Dept. Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida 33136, United States.,Department of Neurobiology Research, Institute of Molecular Medicine, and BRIDGE-Brain Research Inter Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Tommy N Johansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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17
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Schneider DK, Shi W, Andi B, Jakoncic J, Gao Y, Bhogadi DK, Myers SF, Martins B, Skinner JM, Aishima J, Qian K, Bernstein HJ, Lazo EO, Langdon T, Lara J, Shea-McCarthy G, Idir M, Huang L, Chubar O, Sweet RM, Berman LE, McSweeney S, Fuchs MR. FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:650-665. [PMID: 33650577 PMCID: PMC7941291 DOI: 10.1107/s1600577520016173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023]
Abstract
Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5-30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s-1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s-1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods - serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362-1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238-246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.
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Affiliation(s)
| | - Wuxian Shi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jean Jakoncic
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yuan Gao
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Stuart F. Myers
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Bruno Martins
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, MI 48824, USA
| | - John M. Skinner
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jun Aishima
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kun Qian
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Herbert J. Bernstein
- Ronin Institute for Independent Scholarship, c/o NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Edwin O. Lazo
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Thomas Langdon
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John Lara
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Mourad Idir
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lei Huang
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Oleg Chubar
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Robert M. Sweet
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lonny E. Berman
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sean McSweeney
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
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18
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Stohrer C, Horrell S, Meier S, Sans M, von Stetten D, Hough M, Goldman A, Monteiro DCF, Pearson AR. Homogeneous batch micro-crystallization of proteins from ammonium sulfate. Acta Crystallogr D Struct Biol 2021; 77:194-204. [PMID: 33559608 PMCID: PMC7869895 DOI: 10.1107/s2059798320015454] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/21/2020] [Indexed: 01/19/2023] Open
Abstract
The emergence of X-ray free-electron lasers has led to the development of serial macromolecular crystallography techniques, making it possible to study smaller and more challenging crystal systems and to perform time-resolved studies on fast time scales. For most of these studies the desired crystal size is limited to a few micrometres, and the generation of large amounts of nanocrystals or microcrystals of defined size has become a bottleneck for the wider implementation of these techniques. Despite this, methods to reliably generate microcrystals and fine-tune their size have been poorly explored. Working with three different enzymes, L-aspartate α-decarboxylase, copper nitrite reductase and copper amine oxidase, the precipitating properties of ammonium sulfate were exploited to quickly transition from known vapour-diffusion conditions to reproducible, large-scale batch crystallization, circumventing the tedious determination of phase diagrams. Furthermore, the specific ammonium sulfate concentration was used to fine-tune the crystal size and size distribution. Ammonium sulfate is a common precipitant in protein crystallography, making these findings applicable to many crystallization systems to facilitate the production of large amounts of microcrystals for serial macromolecular crystallography experiments.
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Affiliation(s)
- Claudia Stohrer
- Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sam Horrell
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Adrian Goldman
- Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
- Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, FIN-00014 Helsinki, Finland
| | - Diana C. F. Monteiro
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Arwen R. Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
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19
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van der Linden PJEM, Popov AM, Pontoni D. Accurate and rapid 3D printing of microfluidic devices using wavelength selection on a DLP printer. LAB ON A CHIP 2020; 20:4128-4140. [PMID: 33057528 DOI: 10.1039/d0lc00767f] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The use of microfluidics on synchrotron X-ray beamlines represents an advanced sample preparation and delivery platform for state-of-the-art X-ray characterization of micro-samples. The recent developments of 3D printing technologies have opened possibilities for rapid fabrication of complex microfluidic devices. One of the major challenges in 3D printing of microfluidic devices using a digital light processing (DLP) desktop printer is that the static liquid resin trapped in the channels, once the "ceiling" is printed, still receives small doses of light through the subsequently printed layers. This easily triggers partial polymerisation of the resin which impedes its flushing out of the channels after completion of the printing session. We show here that it is possible to gain better control over the resin polymerisation and improve the quality of the microfluidic devices by efficiently reducing the penetration depth of the UV LED light through wavelength selection combined with a careful choice of absorber and photo-initiator materials. We produced and tested several structures using a slightly modified desktop printer at 385 nm wavelength with 37 × 37 μm2 pixel resolution at a printed layer thickness of 25 μm. The structures include particle filters, mixers, droplet generators and droplet storage traps with features below 100 μm. We demonstrate crystallisation of model inorganic and organic compounds in trapped droplets and assess the feasibility of in-device X-ray diffraction experiments. This research opens the path for the use of 3D printed microfluidic devices on X-ray beamlines.
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Affiliation(s)
- Peter J E M van der Linden
- Partnership for Soft Condensed Matter (PSCM), ESRF - The European Synchrotron, 71 avenue des Martyrs, 38043 Grenoble, France.
| | - Anton M Popov
- ESRF- The European Synchrotron, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Diego Pontoni
- Partnership for Soft Condensed Matter (PSCM), ESRF - The European Synchrotron, 71 avenue des Martyrs, 38043 Grenoble, France.
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20
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Zacarias S, Temporão A, Carpentier P, van der Linden P, Pereira IAC, Matias PM. Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen. J Biol Inorg Chem 2020; 25:863-874. [PMID: 32865640 DOI: 10.1007/s00775-020-01814-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/20/2020] [Indexed: 11/25/2022]
Abstract
Hydrogenases are metalloenzymes that catalyse both H2 evolution and uptake. They are gas-processing enzymes with deeply buried active sites, so the gases diffuse through channels that connect the active site to the protein surface. The [NiFeSe] hydrogenases are a special class of hydrogenases containing a selenocysteine as a nickel ligand; they are more catalytically active and less O2-sensitive than standard [NiFe] hydrogenases. Characterisation of the channel system of hydrogenases is important to understand how the inhibitor oxygen reaches the active site to cause oxidative damage. To this end, crystals of Desulfovibrio vulgaris Hildenborough [NiFeSe] hydrogenase were pressurized with krypton and oxygen, and a method for tracking labile O2 molecules was developed, for mapping a hydrophobic channel system similar to that of the [NiFe] enzymes as the major route for gas diffusion.
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Affiliation(s)
- Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Adriana Temporão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Philippe Carpentier
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM), Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Peter van der Linden
- Partnership for Soft Condensed Matter, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043, Grenoble, France
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901, Oeiras, Portugal.
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21
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Pearson AR, Mehrabi P. Serial synchrotron crystallography for time-resolved structural biology. Curr Opin Struct Biol 2020; 65:168-174. [PMID: 32846363 DOI: 10.1016/j.sbi.2020.06.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based experiments. However, there is a large range of macromolecular systems where the biological interest is predominantly in the slower dynamics (μs-s), that produce well diffracting microcrystals, and for which synchrotron-based experiments are extremely well suited. The combination of microfocus X-ray beams and the development of a range of sample delivery platforms has now made routine millisecond time-resolved experiments at microfocus macromolecular crystallography beamlines a real possibility and is driving development of dedicated endstations for time-resolved serial synchrotron crystallography.
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Affiliation(s)
- Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany.
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany
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Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCRJ 2020; 7:728-736. [PMID: 32695419 PMCID: PMC7340269 DOI: 10.1107/s2052252520007411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/03/2020] [Indexed: 05/23/2023]
Abstract
The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
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