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Kapuścińska K, Dukała Z, Doha M, Ansari E, Wang J, Brudvig GW, Brooks B, Amin M. Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. J Chem Inf Model 2024; 64:2586-2593. [PMID: 38054243 DOI: 10.1021/acs.jcim.3c01564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Metalloproteins require metal ions as cofactors to catalyze specific reactions with remarkable efficiency and specificity. In various electron transfer reactions, metals in the active sites change their oxidation states to facilitate the biochemical reactions. Cryogenic electron microscopy, X-ray, and X-ray free electron laser (XFEL) crystallography are used to image metalloproteins to understand the reaction mechanisms. However, radiation damage in cryoEM and X-ray crystallography, and the challenge of generating homogeneous crystals and keeping the appropriate experimental conditions for all the crystals in XFEL crystallography, may alter the oxidation states. Here, we build machine learning models trained on a large data set from the Cambridge Crystallographic Data Center to evaluate the metal oxidation states. The models yield high accuracy scores (from 82% to 94%) for all metals in the small molecules. Then, they were used to predict the oxidation states of more than 30 000 metal clusters in metalloproteins with Fe, Mn, Co, and Cu in their active sites. We found that most of the metals exist in the lower oxidation states (Fe2+ 77%, Mn2+ 85%, Co2+ 65%, and Cu+ 64%), and these populations correlate with the standard reduction potentials of the metal ions. Furthermore, we found no clear correlation between these populations and the resolution of the structures, which suggests no significant dependence of these predictions on the resolution. Our models represent a valuable tool for evaluating the oxidation states of the metals in metalloproteins imaged with different techniques. The data files and the machine learning code are available in a public GitHub repository: https://github.com/mamin03/OxitationStatesMetalloprotein.git.
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Affiliation(s)
- Katarzyna Kapuścińska
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Zofia Dukała
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Mekhola Doha
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Eman Ansari
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Bernand Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Muhamed Amin
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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Amin M. Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning. PHOTOSYNTHESIS RESEARCH 2023; 156:89-100. [PMID: 35896927 PMCID: PMC10070209 DOI: 10.1007/s11120-022-00941-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/13/2022] [Indexed: 05/21/2023]
Abstract
Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn's oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S1 state. However, significant discrepancies are observed for the excited XFEL states (S2, S3, and S0) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.
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Affiliation(s)
- Muhamed Amin
- Department of Sciences, University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG, Groningen, The Netherlands.
- Rijksuniversiteit Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
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Dali A, Gabler T, Sebastiani F, Destinger A, Furtmüller PG, Pfanzagl V, Becucci M, Smulevich G, Hofbauer S. Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation. Protein Sci 2023; 32:e4534. [PMID: 36479958 PMCID: PMC9794026 DOI: 10.1002/pro.4534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin-dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII-ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in-solution data obtained by resonance Raman and UV-vis spectroscopy, for wild-type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in-depth characterization of the catalytically-relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin-enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Thomas Gabler
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Alina Destinger
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Paul Georg Furtmüller
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Vera Pfanzagl
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy,INSTM Research Unit of FirenzeSesto Fiorentino (Fi)Italy
| | - Stefan Hofbauer
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
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Smulevich G. Solution and crystal phase resonance Raman spectroscopy: Valuable tools to unveil the structure and function of heme proteins. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the present review, examples are provided illustrating the application of resonance Raman microscopy to heme protein single crystals to highlight the artifacts induced by the crystallization process or the conformational alteration induced by cooling. Moreover, the structural information determined from the RR spectra of heme proteins in solution and crystals is compared to that obtained from their X-ray structures to show how the combined spectroscopic/crystallographic approach is a powerful weapon in the structural biologist’s armamentarium.
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Affiliation(s)
- Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff,” Università di Firenze, Via Della Lastruccia 3-13, 50019 Sesto Fiorentino(Fi), Italy
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Taube M, Pietralik Z, Szymanska A, Szutkowski K, Clemens D, Grubb A, Kozak M. The domain swapping of human cystatin C induced by synchrotron radiation. Sci Rep 2019; 9:8548. [PMID: 31189973 PMCID: PMC6561922 DOI: 10.1038/s41598-019-44811-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/13/2019] [Indexed: 02/04/2023] Open
Abstract
Domain swapping is observed for many proteins with flexible conformations. This phenomenon is often associated with the development of conformational diseases. Importantly, domain swapping has been observed for human cystatin C (HCC), a protein capable of forming amyloid deposits in brain arteries. In this study, the ability of short exposure to high-intensity X-ray radiation to induce domain swapping in solutions of several HCC variants (wild-type HCC and V57G, V57D, V57N, V57P, and L68V mutants) was determined. The study was conducted using time-resolved small-angle X-ray scattering (TR-SAXS) synchrotron radiation. The protein samples were also analysed using small-angle neutron scattering and NMR diffusometry. Exposing HCC to synchrotron radiation (over 50 ms) led to a gradual increase in the dimeric fraction, and for exposures longer than 150 ms, the oligomer fraction was dominant. In contrast, the non-irradiated protein solutions, apart from the V57P variant, were predominantly monomeric (e.g., V57G) or in monomer/dimer equilibrium. This work might represent the first observation of domain swapping induced by high-intensity X-rays.
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Affiliation(s)
- Michal Taube
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
- Joint Laboratory for SAXS Studies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
| | - Zuzanna Pietralik
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
| | - Aneta Szymanska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Kosma Szutkowski
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
- NanoBioMedical Centre at Adam Mickiewicz University in Poznań, Wszechnicy Piastowskiej 3, 61-614, Poznań, Poland
| | - Daniel Clemens
- Helmholtz-Zentrum Berlin für Materialien und Energie Lise-Meitner-Campus Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Anders Grubb
- Department of Clinical Chemistry, Lund University Hospital, S-22185, Lund, Sweden
| | - Maciej Kozak
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland.
- Joint Laboratory for SAXS Studies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland.
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Crosas E, Castellvi A, Crespo I, Fulla D, Gil-Ortiz F, Fuertes G, Kamma-Lorger CS, Malfois M, Aranda MAG, Juanhuix J. Uridine as a new scavenger for synchrotron-based structural biology techniques. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:53-62. [PMID: 28009546 DOI: 10.1107/s1600577516018452] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D1/2 is increased by a factor of ∼1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.
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Affiliation(s)
- Eva Crosas
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Albert Castellvi
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Isidro Crespo
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Daniel Fulla
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Fernando Gil-Ortiz
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | | | | | - Marc Malfois
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Miguel A G Aranda
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Jordi Juanhuix
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
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7
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Schmidt M, Pande K, Basu S, Tenboer J. Room temperature structures beyond 1.5 Å by serial femtosecond crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041708. [PMID: 26798807 PMCID: PMC4711625 DOI: 10.1063/1.4919903] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/15/2015] [Accepted: 04/28/2015] [Indexed: 05/12/2023]
Abstract
About 2.5 × 10(6) snapshots on microcrystals of photoactive yellow protein (PYP) from a recent serial femtosecond crystallographic (SFX) experiment were reanalyzed to maximum resolution. The resolution is pushed to 1.46 Å, and a PYP structural model is refined at that resolution. The result is compared to other PYP models determined at atomic resolution around 1 Å and better at the synchrotron. By comparing subtleties such as individual isotropic temperature factors and hydrogen bond lengths, we were able to assess the quality of the SFX data at that resolution. We also show that the determination of anisotropic temperature factor ellipsoids starts to become feasible with the SFX data at resolutions better than 1.5 Å.
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Affiliation(s)
- Marius Schmidt
- Physics Department , University of Wisconsin Milwaukee, Milwaukee, Wisconsin 53211, USA
| | - Kanupriya Pande
- Physics Department , University of Wisconsin Milwaukee, Milwaukee, Wisconsin 53211, USA
| | - Shibom Basu
- Department of Chemistry and Biochemistry , Arizona State University, Tempe, Arizona 85287, USA
| | - Jason Tenboer
- Physics Department , University of Wisconsin Milwaukee, Milwaukee, Wisconsin 53211, USA
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8
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Waltersperger S, Olieric V, Pradervand C, Glettig W, Salathe M, Fuchs MR, Curtin A, Wang X, Ebner S, Panepucci E, Weinert T, Schulze-Briese C, Wang M. PRIGo: a new multi-axis goniometer for macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:895-900. [PMID: 26134792 PMCID: PMC4489532 DOI: 10.1107/s1600577515005354] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/15/2015] [Indexed: 05/29/2023]
Abstract
The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0-90°), followed by a ϕ stage (0-360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.
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Affiliation(s)
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claude Pradervand
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Wayne Glettig
- Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002, Switzerland
| | - Marco Salathe
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Martin R. Fuchs
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Adrian Curtin
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Xiaoqiang Wang
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Simon Ebner
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| | | | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
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Dworkowski FSN, Hough MA, Pompidor G, Fuchs MR. Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:27-35. [PMID: 25615857 PMCID: PMC4304683 DOI: 10.1107/s1399004714015107] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/26/2014] [Indexed: 11/22/2022]
Abstract
Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the present article, how to characterize and treat these sample-dependent artefacts in a reproducible manner is discussed and the SLS-APE in situ, in crystallo optical spectroscopy data-analysis toolbox is demonstrated.
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Affiliation(s)
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Guillaume Pompidor
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Mail Stop 745, Upton, NY 11973, USA
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Yano J, Yachandra V. Mn4Ca cluster in photosynthesis: where and how water is oxidized to dioxygen. Chem Rev 2014; 114:4175-205. [PMID: 24684576 PMCID: PMC4002066 DOI: 10.1021/cr4004874] [Citation(s) in RCA: 476] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Vittal Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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11
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Sanson B, Wang T, Sun J, Wang L, Kaczocha M, Ojima I, Deutsch D, Li H. Crystallographic study of FABP5 as an intracellular endocannabinoid transporter. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:290-8. [PMID: 24531463 PMCID: PMC3940194 DOI: 10.1107/s1399004713026795] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/30/2013] [Indexed: 11/10/2022]
Abstract
In addition to binding intracellular fatty acids, fatty-acid-binding proteins (FABPs) have recently been reported to also transport the endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), arachidonic acid derivatives that function as neurotransmitters and mediate a diverse set of physiological and psychological processes. To understand how the endocannabinoids bind to FABPs, the crystal structures of FABP5 in complex with AEA, 2-AG and the inhibitor BMS-309403 were determined. These ligands are shown to interact primarily with the substrate-binding pocket via hydrophobic interactions as well as a common hydrogen bond to the Tyr131 residue. This work advances our understanding of FABP5-endocannabinoid interactions and may be useful for future efforts in the development of small-molecule inhibitors to raise endocannabinoid levels.
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Affiliation(s)
- Benoît Sanson
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Tao Wang
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Jing Sun
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5213, USA
| | - Liqun Wang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5213, USA
| | - Martin Kaczocha
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5213, USA
| | - Iwao Ojima
- Department of Chemistry, Stony Brook University, Stony Brook, NY 1794-3400, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Dale Deutsch
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5213, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Huilin Li
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5213, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA
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12
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Pompidor G, Dworkowski FSN, Thominet V, Schulze-Briese C, Fuchs MR. A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:765-76. [PMID: 23955041 PMCID: PMC3747950 DOI: 10.1107/s0909049513016063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/10/2013] [Indexed: 05/08/2023]
Abstract
The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years.
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Affiliation(s)
| | | | | | | | - Martin R. Fuchs
- Paul Scherrer Institut, CH-5232 Villigen, Switzerland
- Correspondence e-mail:
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13
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Finfrock YZ, Stern EA, Alkire RW, Kas JJ, Evans-Lutterodt K, Stein A, Duke N, Lazarski K, Joachimiak A. Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1463-9. [PMID: 23897469 DOI: 10.1107/s0907444913009335] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/06/2013] [Indexed: 11/10/2022]
Abstract
Reported here are measurements of the penetration depth and spatial distribution of photoelectron (PE) damage excited by 18.6 keV X-ray photons in a lysozyme crystal with a vertical submicrometre line-focus beam of 0.7 µm full-width half-maximum (FWHM). The experimental results determined that the penetration depth of PEs is 5 ± 0.5 µm with a monotonically decreasing spatial distribution shape, resulting in mitigation of diffraction signal damage. This does not agree with previous theoretical predication that the mitigation of damage requires a peak of damage outside the focus. A new improved calculation provides some qualitative agreement with the experimental results, but significant errors still remain. The mitigation of radiation damage by line focusing was measured experimentally by comparing the damage in the X-ray-irradiated regions of the submicrometre focus with the large-beam case under conditions of equal exposure and equal volumes of the protein crystal, and a mitigation factor of 4.4 ± 0.4 was determined. The mitigation of radiation damage is caused by spatial separation of the dominant PE radiation-damage component from the crystal region of the line-focus beam that contributes the diffraction signal. The diffraction signal is generated by coherent scattering of incident X-rays (which introduces no damage), while the overwhelming proportion of damage is caused by PE emission as X-ray photons are absorbed.
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Affiliation(s)
- Y Zou Finfrock
- Physics Department, University of Washington, Seattle, WA 98195, USA
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14
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Glaeser RM. Electron microscopy of biological specimens in liquid water. Biophys J 2012; 103:163-4; author reply 165-6. [PMID: 22828343 DOI: 10.1016/j.bpj.2012.05.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/13/2012] [Accepted: 05/17/2012] [Indexed: 11/17/2022] Open
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15
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Schmidt M, Šrajer V, Purwar N, Tripathi S. The kinetic dose limit in room-temperature time-resolved macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:264-73. [PMID: 22338689 PMCID: PMC3284346 DOI: 10.1107/s090904951105549x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/23/2011] [Indexed: 05/16/2023]
Abstract
Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.
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Affiliation(s)
- M Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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