1
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Dickerson JL, McCubbin PTN, Brooks‐Bartlett JC, Garman EF. Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models. Protein Sci 2024; 33:e5005. [PMID: 38923423 PMCID: PMC11196903 DOI: 10.1002/pro.5005] [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: 01/17/2024] [Revised: 03/17/2024] [Accepted: 04/15/2024] [Indexed: 06/28/2024]
Abstract
New features in the dose estimation program RADDOSE-3D are summarised. They include the facility to enter a diffraction intensity decay model which modifies the "Diffraction Weighted Dose" output from a "Fluence Weighted Dose" to a "Diffraction-Decay Weighted Dose", a description of RADDOSE-ED for use in electron diffraction experiments, where dose is historically quoted in electrons/Å2 rather than in gray (Gy), and finally the development of a RADDOSE-3D GUI, enabling easy access to all the options available in the program.
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Affiliation(s)
- Joshua L. Dickerson
- Department of Biochemistry, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordUK
- MRC Laboratory of Molecular BiologyCambridge Biomedical CampusCambridgeUK
| | - Patrick T. N. McCubbin
- Department of Biochemistry, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordUK
- Division of Structural Biology, Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | | | - Elspeth F. Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordUK
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2
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Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [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: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
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3
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Carugo O. Location of S-nitrosylated cysteines in protein three-dimensional structures. Proteins 2024; 92:464-473. [PMID: 37941304 DOI: 10.1002/prot.26629] [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: 05/05/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Although S-nitrosylation of cysteines is a common protein posttranslational modification, little is known about its three-dimensional structural features. This paper describes a systematic survey of the data available in the Protein Data Bank. Several interesting observations could be made. (1) As a result of radiation damage, S-nitrosylated cysteines (Snc) are frequently reduced, at least partially. (2) S-nitrosylation may be a protection against irreversible thiol oxidation; because the NO group of Snc is relatively accessible to the solvent, it may act as a cork to protect the sulfur atoms of cysteines from oxidation by molecular oxygen to sulfenic, sulfinic, and sulfonic acid; moreover, Snc are frequently found at the start or end of helices and strands and this might shield secondary structural elements from unfolding.
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Affiliation(s)
- Oliviero Carugo
- Department of Chemistry, University of Pavia, Pavia, Italy
- Department of Structural and Computational Biology, Max Perutz Labs University of Vienna, Vienna, Austria
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4
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Pražnikar J. Using graphlet degree vectors to predict atomic displacement parameters in protein structures. Acta Crystallogr D Struct Biol 2023; 79:1109-1119. [PMID: 37987168 PMCID: PMC10833351 DOI: 10.1107/s2059798323009142] [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: 06/26/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
In structural biology, atomic displacement parameters, commonly used in the form of B values, describe uncertainties in atomic positions. Their distribution over the structure can provide hints on local structural reliability and mobility. A spatial macromolecular model can be represented by a graph whose nodes are atoms and whose edges correspond to all interatomic contacts within a certain distance. Small connected subgraphs, called graphlets, provide information about the wiring of a particular atom. The multiple linear regression approach based on this information aims to predict a distribution of values of isotropic atomic displacement parameters (B values) within a protein structure, given the atomic coordinates and molecular packing. By modeling the dynamic component of atomic uncertainties, this method allows the B values obtained from experimental crystallographic or cryo-electron microscopy studies to be reproduced relatively well.
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Affiliation(s)
- Jure Pražnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, Koper, Slovenia
- Department of Biochemistry, Molecular and Structural Biology, Institute Jožef Stefan, Jamova 39, Ljubljana, Slovenia
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5
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Garman EF, Weik M. Radiation damage to biological macromolecules∗. Curr Opin Struct Biol 2023; 82:102662. [PMID: 37573816 DOI: 10.1016/j.sbi.2023.102662] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.
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Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
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6
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Gul M, Ayan E, Destan E, Johnson JA, Shafiei A, Kepceoğlu A, Yilmaz M, Ertem FB, Yapici İ, Tosun B, Baldir N, Tokay N, Nergiz Z, Karakadioğlu G, Paydos SS, Kulakman C, Ferah CK, Güven Ö, Atalay N, Akcan EK, Cetinok H, Arslan NE, Şabanoğlu K, Aşci B, Tavli S, Gümüsboğa H, Altuntaş S, Otsuka M, Fujita M, Teki N Ş, Çi Ftçi H, Durdaği S, Karaca E, Kaplan Türköz B, Kabasakal BV, Kati A, DeMi Rci H. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source. Sci Rep 2023; 13:8123. [PMID: 37208392 DOI: 10.1038/s41598-023-33989-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.
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Affiliation(s)
- Mehmet Gul
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Esra Ayan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - J Austin Johnson
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Alaleh Shafiei
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Abdullah Kepceoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Surface Science and Technology Center (KUYTAM), Koç University, Istanbul, Türkiye
| | - Merve Yilmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Fatma Betül Ertem
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - İlkin Yapici
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Bilge Tosun
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nilüfer Baldir
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nurettin Tokay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Zeliş Nergiz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye
| | - Gözde Karakadioğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Seyide Seda Paydos
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cahine Kulakman
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cengiz Kaan Ferah
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ömür Güven
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Necati Atalay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical University, Kocaeli, Türkiye
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Enver Kamil Akcan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Türkiye
| | - Haluk Cetinok
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nazlı Eylül Arslan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Arel University, Istanbul, Türkiye
| | - Kardelen Şabanoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yıldız Technical University, Istanbul, Türkiye
| | - Bengisu Aşci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Serra Tavli
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Helin Gümüsboğa
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Sevde Altuntaş
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Tissue Engineering, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Şaban Teki N
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- The Scientific and Technological Research Council of Türkiye (TÜBİTAK) Marmara Research Center (MAM), Life Sciences, Kocaeli, Türkiye
- Department of Basic Medical Sciences, Division of Medical Biology, Faculty of Medicine, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Halilibrahim Çi Ftçi
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Serdar Durdaği
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Türkiye
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Burcu Kaplan Türköz
- Department of Food Engineering, Faculty of Engineering, Ege University, Izmir, Türkiye
| | - Burak Veli Kabasakal
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara University, Ankara, Türkiye
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Ahmet Kati
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Biotechnology, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Hasan DeMi Rci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye.
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye.
- SLAC National Laboratory, Stanford PULSE Institute, Menlo Park, CA, USA.
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7
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Boström HLB, Cairns AB, Chen M, Daisenberger D, Ridley CJ, Funnell NP. Radiation effects, zero thermal expansion, and pressure-induced phase transition in CsMnCo(CN) 6. Phys Chem Chem Phys 2022; 24:25072-25076. [PMID: 36227089 DOI: 10.1039/d2cp03754h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Prussian blue analogue CsMnCo(CN)6 is studied using powder X-ray and neutron diffraction under variable temperature, pressure, and X-ray exposure. It retains cubic F4̄3m symmetry in the range 85-500 K with minimal thermal expansion, whereas a phase transition to P4̄n2 occurs at ∼2 GPa, driven by octahedral tilting. A small lattice contraction occurs upon increased X-ray dose. Comparisons with related systems indicate that the CsI ions decrease the thermal expansion and suppress the likelihood of phase transformations. The results improve the understanding of the stimuli-responsive behaviour of coordination polymers.
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Affiliation(s)
- Hanna L B Boström
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569, Stuttgart, Germany.
| | - Andrew B Cairns
- Department of Materials, Imperial College London, Royal School of Mines, Exhibition Road, SW7 2AZ, London, UK
- London Centre for Nanotechnology, Imperial College London, SW7 2AZ, London, UK
| | - Muzi Chen
- Department of Materials, Imperial College London, Royal School of Mines, Exhibition Road, SW7 2AZ, London, UK
- London Centre for Nanotechnology, Imperial College London, SW7 2AZ, London, UK
| | | | - Christopher J Ridley
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Nicholas P Funnell
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
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8
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Martin-Garcia JM, Botha S, Hu H, Jernigan R, Castellví A, Lisova S, Gil F, Calisto B, Crespo I, Roy-Chowdhury S, Grieco A, Ketawala G, Weierstall U, Spence J, Fromme P, Zatsepin N, Boer DR, Carpena X. Serial macromolecular crystallography at ALBA Synchrotron Light Source. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:896-907. [PMID: 35511023 PMCID: PMC9070724 DOI: 10.1107/s1600577522002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.
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Affiliation(s)
- Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Rebecca Jernigan
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Albert Castellví
- Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Fernando Gil
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Isidro Crespo
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | - Shatabdi Roy-Chowdhury
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Gihan Ketawala
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - John Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
- ARC Centre of Excellence in Advance Molecular Physics, La Trobe Institute for Molecular ScienceImaging, Department of Chemistry and Physics, La Trobe University, Melbourne, Australia
| | | | - Xavi Carpena
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
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9
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Quantifying and comparing radiation damage in the Protein Data Bank. Nat Commun 2022; 13:1314. [PMID: 35288575 PMCID: PMC8921271 DOI: 10.1038/s41467-022-28934-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractRadiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.
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10
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Carugo O. B-factor accuracy in protein crystal structures. Acta Crystallogr D Struct Biol 2022; 78:69-74. [PMID: 34981763 PMCID: PMC8725162 DOI: 10.1107/s2059798321011736] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/04/2021] [Indexed: 11/10/2022] Open
Abstract
The accuracy of B factors in protein crystal structures has been determined by comparing the same atoms in numerous, independent crystal structures of Gallus gallus lysozyme. Both B-factor absolute differences and normal probability plots indicate that the estimated B-factor errors are quite large, close to 9 Å2 in ambient-temperature structures and to 6 Å2 in low-temperature structures, and surprisingly are comparable to values estimated two decades ago. It is well known that B factors are not due to local movements only but reflect several, additional factors from crystal defects, large-scale disorder, diffraction data quality etc. It therefore remains essential to normalize B factors when comparing different crystal structures, although it has clearly been shown that they provide useful information about protein dynamics. Improved, quantitative analyses of raw B factors require novel experimental and computational tools that are able to disaggregate local movements from other features and properties that affect B factors.
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Affiliation(s)
- Oliviero Carugo
- Department of Chemistry, University of Pavia, Viale Taramelli 12, I-27100 Pavia, Italy
- Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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11
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Carugo O. Uses and Abuses of the Atomic Displacement Parameters in Structural Biology. Methods Mol Biol 2022; 2449:281-298. [PMID: 35507268 DOI: 10.1007/978-1-0716-2095-3_12] [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] [Indexed: 06/14/2023]
Abstract
B-factors determined with X-ray crystallographic analyses are commonly used to estimate the flexibility degree of atoms, residues, and molecular moieties in biological macromolecules. In this chapter, the most recent studies and applications of B-factors in protein engineering and structural biology are briefly summarized. Particular emphasis is given to the limitations in using B-factors, in order to prevent inappropriate applications. It is eventually predicted that future applications will involve anisotropically refined B-factors, deep learning, and data produced by cryo-EM.
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12
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Gotte G, Campagnari R, Loreto D, Bettin I, Calzetti F, Menegazzi M, Merlino A. The crystal structure of the domain-swapped dimer of onconase highlights some catalytic and antitumor activity features of the enzyme. Int J Biol Macromol 2021; 191:560-571. [PMID: 34563576 DOI: 10.1016/j.ijbiomac.2021.09.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Onconase (ONC) is a monomeric amphibian "pancreatic-type" RNase endowed with remarkable anticancer activity. ONC spontaneously forms traces of a dimer (ONC-D) in solution, while larger amounts can be formed when ONC is lyophilized from mildly acidic solutions. Here, we report the crystal structure of ONC-D and analyze its catalytic and antitumor activities in comparison to ONC. ONC-D forms via the three-dimensional swapping of the N-terminal α-helix between two monomers, but it displays a significantly different quaternary structure from that previously modeled [Fagagnini A et al., 2017, Biochem J 474, 3767-81], and based on the crystal structure of the RNase A N-terminal swapped dimer. ONC-D presents a variable quaternary assembly deriving from a variable open interface, while it retains a catalytic activity that is similar to that of ONC. Notably, ONC-D displays antitumor activity against two human melanoma cell lines, although it exerts a slightly lower cytostatic effect than the monomer. The inhibition of melanoma cell proliferation by ONC or ONC-D is associated with the reduction of the expression of the anti-apoptotic B cell lymphoma 2 (Bcl2), as well as of the total expression and phosphorylation of the Signal Transducer and Activator of Transcription (STAT)-3. Phosphorylation is inhibited in both STAT3 Tyr705 and Ser727 key-residues, as well as in its upstream tyrosine-kinase Src. Consequently, both ONC species should exert their anti-cancer action by inhibiting the pro-tumor pleiotropic STAT3 effects deriving either by its phospho-tyrosine activation or by its non-canonical signaling pathways. Both ONC species, indeed, increase the portion of A375 cells undergoing apoptotic cell death. This study expands the variety of RNase domain-swapped dimeric structures, underlining the unpredictability of the open interface arrangement upon domain swapping. Structural data also offer valuable insights to analyze the differences in the measured ONC or ONC-D biological activities.
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Affiliation(s)
- Giovanni Gotte
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
| | - Rachele Campagnari
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Domenico Loreto
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy
| | - Ilaria Bettin
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Federica Calzetti
- Department of Medicine, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Marta Menegazzi
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy.
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13
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Abstract
Usutu virus (USUV) is an emerging arbovirus in Europe that has been increasingly identified in asymptomatic humans and donated blood samples and is a cause of increased incidents of neuroinvasive human disease. Treatment or prevention options for USUV disease are currently nonexistent, the result of a lack of understanding of the fundamental elements of USUV pathogenesis. Here, we report two structures of the mature USUV virus, determined at a resolution of 2.4 Å, using single-particle cryogenic electron microscopy. Mature USUV is an icosahedral shell of 180 copies of envelope (E) and membrane (M) proteins arranged in the classic herringbone pattern. However, unlike previous reports of flavivirus structures, we observe virus subpopulations and differences in the fusion loop disulfide bond. Presence of a second, unique E glycosylation site could elucidate host interactions, contributing to the broad USUV tissue tropism. The structures provide a basis for exploring USUV interactions with glycosaminoglycans and lectins, the role of the RGD motif as a receptor, and the inability of West Nile virus therapeutic antibody E16 to neutralize the mature USUV strain SAAR-1776. Finally, we identify three lipid binding sites and predict key residues that likely participate in virus stability and flexibility during membrane fusion. Our findings provide a framework for the development of USUV therapeutics and expand the current knowledge base of flavivirus biology.
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14
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Sen K, Hough MA, Strange RW, Yong C, Keal TW. QM/MM Simulations of Protein Crystal Reactivity Guided by MSOX Crystallography: A Copper Nitrite Reductase Case Study. J Phys Chem B 2021; 125:9102-9114. [PMID: 34357776 DOI: 10.1021/acs.jpcb.1c03661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recently developed multiple structures from one crystal (MSOX) serial crystallography method can be used to provide multiple snapshots of the progress of enzymatic reactions taking place within a protein crystal. Such MSOX snapshots can be used as a reference for combined quantum mechanical/molecular mechanical (QM/MM) simulations of enzyme reactivity within the crystal. QM/MM calculations are used to identify details of reference states that cannot be directly observed by X-ray diffraction experiments, such as protonation and oxidation states. These reference states are then used as known fixed endpoints for the modeling of reaction paths. We investigate the mechanism of nitrite reduction in an Achromobacter cycloclastes copper nitrite reductase crystal using MSOX-guided QM/MM calculations, identifying the change in nitrite binding orientation with a change in copper oxidation state, and determining the reaction path to the final NO-bound MSOX structure. The results are compared with QM/MM simulations performed in a solvated environment.
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Affiliation(s)
- Kakali Sen
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom.,Scientific Computing Department, STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Richard W Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Chin Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
| | - Thomas W Keal
- Scientific Computing Department, STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
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15
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Yang C, Meng Y, Xie B, Xia S. Impacts of solvation on photo-damage of polypeptides: Modulation and biological implications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 220:112214. [PMID: 34049181 DOI: 10.1016/j.jphotobiol.2021.112214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 11/30/2022]
Abstract
We investigate the photon/matter interactions between soft X-rays and three selected polypeptides, poly-glycine (poly-Gly), poly-L-arginine (poly-Arg), and poly-l-lysine (poly-Lys), where the effects of molecular packing under the influence of solvent, e.g., water, substrates (Au foil or Si wafer) and X-ray irradiation under different durations were systematically investigated. Compared with negligible photo-damage on bare polypeptide powders, significantly enhanced degradation in pre-solvated polypeptides was observed likely because of the formation photo-generated radicals. X-ray photoemission spectroscopy (XPS) were employed as the analysis means to identify and quantify the chemical changes, especially the high-resolution photoemission spectra of C 1s, O 1s, N 1s and their evolution under continuous X-ray irradiation. The photo-degradation was found to preferentially occur on the CO entity in poly-Gly and the guanidinium group in poly-Arg. In poly-Arg, deprotonation occurs via the switch from zwittterionic to a neutral configuration, whereas poly-Lys deprotonates by directly losing the corresponding amine. The critical role of the interactions between amino acids, the building blocks of protein and almost all forms of biological activities, and the free-radical-generating living environment under irradiation was critically analyzed. The present study found that the preparation history of a sample, especially its inadvertent exposure to the sources of H2O, O2 and OH, could significantly alter the outcome of a radiation-related chemical process. Implications on the non-destructive probe of biologically important systems using physical methods involving X-rays were discussed as well.
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Affiliation(s)
- Chao Yang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yue Meng
- School of Life Science, Huzhou University, 759 East Erhuan Road, Huzhou 313000, P R, China
| | - Bo Xie
- Department of Chemistry, College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, P R, China
| | - Shengjie Xia
- Department of Chemistry, College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, P R, China.
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16
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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17
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Mehr A, Henneberg F, Chari A, Görlich D, Huyton T. The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography. Acta Crystallogr D Struct Biol 2020; 76:1222-1232. [PMID: 33263328 PMCID: PMC7709198 DOI: 10.1107/s2059798320013741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
The growth of diffraction-quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high-affinity copper(II)-binding tripeptide GHK was fused to the N-terminus of a GFP variant and an MBP-FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square-pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S-atom positions could also be located in log-likelihood-gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR-SAD phasing.
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Affiliation(s)
- Alexander Mehr
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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18
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Stachowski TR, Snell ME, Snell EH. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. PLoS One 2020; 15:e0239702. [PMID: 33201877 PMCID: PMC7671560 DOI: 10.1371/journal.pone.0239702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022] Open
Abstract
A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Materials Design and Innovation, State University at New York at Buffalo, Buffalo, New York, United States of America
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19
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Fenn GD, Waller-Evans H, Atack JR, Bax BD. Crystallization and structure of ebselen bound to Cys141 of human inositol monophosphatase. Acta Crystallogr F Struct Biol Commun 2020; 76:469-476. [PMID: 33006574 PMCID: PMC7531247 DOI: 10.1107/s2053230x20011310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 11/21/2022] Open
Abstract
Inositol monophosphatase (IMPase) is inhibited by lithium, which is the most efficacious treatment for bipolar disorder. Several therapies have been approved, or are going through clinical trials, aimed at the replacement of lithium in the treatment of bipolar disorder. One candidate small molecule is ebselen, a selenium-containing antioxidant, which has been demonstrated to produce lithium-like effects both in a murine model and in clinical trials. Here, the crystallization and the first structure of human IMPase covalently complexed with ebselen, a 1.47 Å resolution crystal structure (PDB entry 6zk0), are presented. In the complex with human IMPase, ebselen in a ring-opened conformation is covalently attached to Cys141, a residue located away from the active site. IMPase is a dimeric enzyme and in the crystal structure two adjacent dimers share four ebselen molecules, creating a tetramer with approximate 222 symmetry. In the crystal structure presented in this publication, the active site in the tetramer is still accessible, suggesting that ebselen may function as an allosteric inhibitor or may block the binding of partner proteins.
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Affiliation(s)
- Gareth D. Fenn
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Helen Waller-Evans
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - John R. Atack
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Benjamin D. Bax
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
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20
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Bhattacharyya R, Dhar J, Ghosh Dastidar S, Chakrabarti P, Weiss MS. The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions. IUCRJ 2020; 7:825-834. [PMID: 32939274 PMCID: PMC7467163 DOI: 10.1107/s2052252520008520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/25/2020] [Indexed: 05/30/2023]
Abstract
Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S-S bonds which engage in a close contact with a carbonyl O atom along the extension of the S-S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S-S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.
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Affiliation(s)
- Rajasri Bhattacharyya
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Jesmita Dhar
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Manfred S. Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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21
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Plaza-Garrido M, Salinas-Garcia MC, Alba-Elena D, Martínez JC, Camara-Artigas A. Lysozyme crystals dyed with bromophenol blue: where has the dye gone? ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:845-856. [PMID: 32876060 DOI: 10.1107/s2059798320008803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/30/2020] [Indexed: 11/10/2022]
Abstract
Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein-dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme-bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices α1 (residues 4-15) and α3 (residues 88-100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 Å). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 Å). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions.
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Affiliation(s)
- Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - M Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Daniel Alba-Elena
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Jose C Martínez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
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22
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Haas DJ. The early history of cryo-cooling for macromolecular crystallography. IUCRJ 2020; 7:148-157. [PMID: 32148843 PMCID: PMC7055388 DOI: 10.1107/s2052252519016993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
This paper recounts the first successful cryo-cooling of protein crystals that demonstrated the reduction in X-ray damage to macromolecular crystals. The project was suggested by David C. Phillips in 1965 at the Royal Institution of Great Britain and continued in 1967 at the Weizmann Institute of Science, where the first cryo-cooling experiments were performed on lysozyme crystals, and was completed in 1969 at Purdue University on lactate dehydrogenase crystals. A 1970 publication in Acta Crystallographica described the cryo-procedures, the use of cryo-protectants to prevent ice formation, the importance of fast, isotropic cryo-cooling and the collection of analytical data showing more than a tenfold decrease in radiation damage in cryo-cooled lactate dehydrogenase crystals. This was the first demonstration of any method that reduced radiation damage in protein crystals, which provided crystallographers with suitable means to employ synchrotron X-ray sources for protein-crystal analysis. Today, fifty years later, more than 90% of the crystal structures deposited in the Protein Data Bank have been cryo-cooled.
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Affiliation(s)
- David J. Haas
- Tecco Corporation, 19 West Gate Road, Suffern, NY 10901, USA
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23
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Taberman H, Bury CS, van der Woerd MJ, Snell EH, Garman EF. Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:931-944. [PMID: 31274415 PMCID: PMC6613113 DOI: 10.1107/s1600577519005599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/23/2019] [Indexed: 05/29/2023]
Abstract
Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13-3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.
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Affiliation(s)
- Helena Taberman
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein Straße 15, 12489 Berlin, Germany
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Charles S. Bury
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark J. van der Woerd
- Department of Enterprise Technology Services, 2001 Capitol Avenue, Cheyenne, WY 82001, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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24
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Sánchez-Murcia PA, Mills A, Cortés-Cabrera Á, Gago F. Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule. J Comput Aided Mol Des 2019; 33:627-644. [DOI: 10.1007/s10822-019-00208-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/24/2019] [Indexed: 01/27/2023]
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25
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The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity. Proc Natl Acad Sci U S A 2019; 116:9333-9339. [PMID: 31019074 PMCID: PMC6511015 DOI: 10.1073/pnas.1814999116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
While cellular dNTPases display broad activity toward dNTPs (e.g., SAMHD1), Escherichia coli (Ec)-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. Here, we present methods for highly efficient, fixed-target X-ray free-electron laser data collection, which is broadly applicable to multiple crystal systems including RNA polymerase II complexes, and the free Ec-dGTPase enzyme. Structures of free and bound Ec-dGTPase shed light on the mechanisms of dGTP selectivity, highlighted by a dynamic active site where conformational changes are coupled to dGTP binding. Moreover, despite no sequence homology between Ec-dGTPase and SAMHD1, both enzymes share similar active-site architectures; however, dGTPase residues at the end of the substrate-binding pocket provide dGTP specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP. Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli (Ec)-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec-dGTPase, including an X-ray free-electron laser structure of the free Ec-dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec-dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec-dGTPase residues at the end of the substrate-binding pocket mimic Watson–Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally “opening” a tyrosine gate allowing enhanced substrate binding.
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26
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Lin G, Weiss SC, Vergara S, Camacho C, Calero G. Transcription with a laser: Radiation-damage-free diffraction of RNA Polymerase II crystals. Methods 2019; 159-160:23-28. [PMID: 31029767 DOI: 10.1016/j.ymeth.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
Well-diffracting crystals are essential to obtain relevant structural data that will lead to understanding of RNA Polymerase II (Pol II) transcriptional processes at a molecular level. Here we present a strategy to study Pol II crystals using negative stain transmission electron microscopy (TEM) and a methodology to optimize radiation damage free data collection using free electron laser (FEL) at the Linac Coherent Light Source (LCLS). The use of negative stain TEM allowed visualization and optimization of crystal diffraction by monitoring the lattice quality of crystallization conditions. Nano crystals bearing perfect lattices were seeded and used to grow larger crystals for FEL data collection. Moreover, the use of in house designed crystal loops together with ultra-violet (UV) microscopy for crystal detection facilitated data collection. Such strategy permitted collection of multiple crystals of radiation-free-damage data, resulting in the highest resolution of wild type (WT) Pol II crystals ever observed.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Simon C Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Carlos Camacho
- Department of Computanional and Systems Biology, University of Pittsburgh School of Medicine, United States
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States.
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27
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Fobe TL, Kazakov A, Riccardi D. Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. J Chem Inf Model 2019; 59:931-943. [PMID: 30694665 PMCID: PMC6999612 DOI: 10.1021/acs.jcim.8b00950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90°. In this study, we transform over 30 000 Protein Databank files (PDBx/mmCIFs) into a single file, the SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information on both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance. Cys.sqlite contains over 95 000 peptide chains and 500 000 cysteines (700 000 structural conformers); there are over 265 000 cysteine disulfide bond conformations from structures solved with all available experimental methods. The structural information is analyzed with respect to sequence identity cutoff, the experimental method, and energetics of the disulfide. We find that as the experimental information becomes limiting and the influence of modeling becomes more pronounced, the observed average strain increases artificially. The database and analyses presented here can be used to improve the refinement of biological structures from experiments that are known to contain one or more disulfide bonds.
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Affiliation(s)
- Theodore L Fobe
- University of Maryland , Department of Chemical and Biomolecular Engineering , College Park , Maryland 20742 , United States
- Summer Undergraduate Research Fellowship , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Andrei Kazakov
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Demian Riccardi
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
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Vergara A, Caterino M, Merlino A. Raman-markers of X-ray radiation damage of proteins. Int J Biol Macromol 2018; 111:1194-1205. [PMID: 29374529 DOI: 10.1016/j.ijbiomac.2018.01.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/25/2022]
Abstract
Despite their high relevance, the mechanisms of X-ray radiation damage on protein structure yet have to be completely established. Here, we used Raman microspectrophotometry to follow X-ray-induced chemical modifications on the structure of the model protein bovine pancreatic ribonuclease (RNase A). The combination of dose-dependent Raman spectra and ultrahigh resolution (eight structures solved using data collected between 0.85 and 1.17 Å resolution on the same single crystal) allowed direct observation of several radiation damage events, including covalent bond breakages and formation of radicals. Our results are relevant for analytical photodamage detection and provide implications for a detailed understanding of the mechanisms of photoproduct formation.
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Affiliation(s)
- Alessandro Vergara
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy; CEINGE Biotecnologie Avanzate Scarl, Via G. Salvatore, Napoli, Italy
| | - Marco Caterino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy.
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29
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Abstract
Radiation damage still remains a major limitation and challenge in macromolecular X-ray crystallography. Some of the high-intensity radiation used for diffraction data collection experiments is absorbed by the crystals, generating free radicals. These give rise to radiation damage even at cryotemperatures (~100 K), which can lead to incorrect biological conclusions being drawn from the resulting structure, or even prevent structure solution entirely. Investigation of mitigation strategies and the effects caused by radiation damage has been extensive over the past fifteen years. Here, recent understanding of the physical and chemical phenomena of radiation damage is described, along with the global effects inflicted on the collected data and the specific effects observed in the solved structure. Furthermore, this review aims to summarise the progress made in radiation damage studies in macromolecular crystallography from the experimentalist’s point of view and to give an introduction to the current literature.
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Shelley KL, Dixon TPE, Brooks-Bartlett JC, Garman EF. RABDAM: quantifying specific radiation damage in individual protein crystal structures. J Appl Crystallogr 2018; 51:552-559. [PMID: 29657569 PMCID: PMC5884390 DOI: 10.1107/s1600576718002509] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/12/2018] [Indexed: 11/10/2022] Open
Abstract
Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of the BDamage metric has helped to address this problem. BDamage is a quantitative, per-atom metric identifies potential sites of specific damage by comparing the atomic B-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program, RABDAM, to calculate the BDamage metric for all selected atoms within any standard-format PDB or mmCIF file. RABDAM provides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas P. E. Dixon
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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31
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Borek D, Bromberg R, Hattne J, Otwinowski Z. Real-space analysis of radiation-induced specific changes with independent component analysis. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:451-467. [PMID: 29488925 PMCID: PMC5829680 DOI: 10.1107/s1600577517018148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/19/2017] [Indexed: 05/06/2023]
Abstract
A method of analysis is presented that allows for the separation of specific radiation-induced changes into distinct components in real space. The method relies on independent component analysis (ICA) and can be effectively applied to electron density maps and other types of maps, provided that they can be represented as sets of numbers on a grid. Here, for glucose isomerase crystals, ICA was used in a proof-of-concept analysis to separate temperature-dependent and temperature-independent components of specific radiation-induced changes for data sets acquired from multiple crystals across multiple temperatures. ICA identified two components, with the temperature-independent component being responsible for the majority of specific radiation-induced changes at temperatures below 130 K. The patterns of specific temperature-independent radiation-induced changes suggest a contribution from the tunnelling of electron holes as a possible explanation. In the second case, where a group of 22 data sets was collected on a single thaumatin crystal, ICA was used in another type of analysis to separate specific radiation-induced effects happening on different exposure-level scales. Here, ICA identified two components of specific radiation-induced changes that likely result from radiation-induced chemical reactions progressing with different rates at different locations in the structure. In addition, ICA unexpectedly identified the radiation-damage state corresponding to reduced disulfide bridges rather than the zero-dose extrapolated state as the highest contrast structure. The application of ICA to the analysis of specific radiation-induced changes in real space and the data pre-processing for ICA that relies on singular value decomposition, which was used previously in data space to validate a two-component physical model of X-ray radiation-induced changes, are discussed in detail. This work lays a foundation for a better understanding of protein-specific radiation chemistries and provides a framework for analysing effects of specific radiation damage in crystallographic and cryo-EM experiments.
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Affiliation(s)
- Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Raquel Bromberg
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Johan Hattne
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
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32
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Morelhão SL, Remédios CMR, Calligaris GA, Nisbet G. X-ray dynamical diffraction in amino acid crystals: a step towards improving structural resolution of biological molecules via physical phase measurements. J Appl Crystallogr 2017; 50:689-700. [PMID: 28656034 PMCID: PMC5458588 DOI: 10.1107/s1600576717004757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/27/2017] [Indexed: 12/29/2022] Open
Abstract
X-ray phase measurements have been applied to study hydrogen bonds and radiation damage in amino acid crystals. In this work, experimental and data analysis procedures were developed and applied for studying amino acid crystals by means of X-ray phase measurements. The results clearly demonstrated the sensitivity of invariant triplet phases to electronic charge distribution in d-alanine crystals, providing useful information for molecular dynamics studies of intermolecular forces. The feasibility of using phase measurements to investigate radiation damage mechanisms is also discussed on experimental and theoretical grounds.
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Affiliation(s)
- Sérgio L Morelhão
- Instituto de Física, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Gareth Nisbet
- Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE, UK
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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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34
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Polsinelli I, Savko M, Rouanet-Mehouas C, Ciccone L, Nencetti S, Orlandini E, Stura EA, Shepard W. Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:42-52. [PMID: 28009545 DOI: 10.1107/s1600577516018488] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
X-ray radiation in macromolecular crystallography can chemically alter the biological material and deteriorate the integrity of the crystal lattice with concomitant loss of resolution. Typical alterations include decarboxylation of glutamic and aspartic residues, breaking of disulfide bonds and the reduction of metal centres. Helical scans add a small translation to the crystal in the rotation method, so that for every image the crystal is shifted to expose a fresh part. On beamline PROXIMA 2A at Synchrotron SOLEIL, this procedure has been tested with various parameters in an attempt to understand how to mitigate the effects of radiation damage. Here, the strategies used and the crystallographic metrics for various scenarios are reported. Among these, the loss of bromine from bromophenyl moieties appears to be a useful monitor of radiation damage as the carbon-bromine bond is very sensitive to X-ray irradiation. Two cases are focused on where helical scans are shown to be superior in obtaining meaningful data compared with conventional methods. In one case the initial resolution of the crystal is extended over time, and in the second case the anomalous signal is preserved to provide greater effective multiplicity and easier phasing.
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Affiliation(s)
- Ivan Polsinelli
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Cecile Rouanet-Mehouas
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), F-91191 Gif-sur-Yvette, France
| | - Lidia Ciccone
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Susanna Nencetti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Enrico A Stura
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
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35
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Bury CS, Carmichael I, Garman EF. OH cleavage from tyrosine: debunking a myth. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:7-18. [PMID: 28009542 PMCID: PMC5182017 DOI: 10.1107/s1600577516016775] [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: 07/15/2016] [Accepted: 10/19/2016] [Indexed: 05/09/2023]
Abstract
During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.
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Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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36
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Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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38
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Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF. RNA protects a nucleoprotein complex against radiation damage. Acta Crystallogr D Struct Biol 2016; 72:648-57. [PMID: 27139628 PMCID: PMC4854314 DOI: 10.1107/s2059798316003351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/26/2016] [Indexed: 11/10/2022] Open
Abstract
Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.
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Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry I Street, Portsmouth PO1 2DY, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Markus Gerstel
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Mikhail B. Shevtsov
- Laboratory of Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
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39
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Bernasconi L, Brandao-Neto J. Radiation damage in X-ray crystallography: a quantum-mechanical study of photoinduced defect formation in beeswax-analogue n-eicosane crystals. Theor Chem Acc 2016. [DOI: 10.1007/s00214-015-1779-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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40
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Affiliation(s)
- Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Martin Weik
- University Grenoble Alpes, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
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41
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Vergucht E, Brans T, Beunis F, Garrevoet J, Bauters S, De Rijcke M, Deruytter D, Janssen C, Riekel C, Burghammer M, Vincze L. Methodological challenges of optical tweezers-based X-ray fluorescence imaging of biological model organisms at synchrotron facilities. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1096-1105. [PMID: 26134817 DOI: 10.1107/s1600577515009534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
Recently, a radically new synchrotron radiation-based elemental imaging approach for the analysis of biological model organisms and single cells in their natural in vivo state was introduced. The methodology combines optical tweezers (OT) technology for non-contact laser-based sample manipulation with synchrotron radiation confocal X-ray fluorescence (XRF) microimaging for the first time at ESRF-ID13. The optical manipulation possibilities and limitations of biological model organisms, the OT setup developments for XRF imaging and the confocal XRF-related challenges are reported. In general, the applicability of the OT-based setup is extended with the aim of introducing the OT XRF methodology in all research fields where highly sensitive in vivo multi-elemental analysis is of relevance at the (sub)micrometre spatial resolution level.
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Affiliation(s)
- Eva Vergucht
- Department of Analytical Chemistry, Ghent University, Krijgslaan 281, Ghent 9000, Belgium
| | - Toon Brans
- Department of Electronics and Information Systems, Ghent University, Sint-Pietersnieuwstraat 41, Ghent 9000, Belgium
| | - Filip Beunis
- Department of Electronics and Information Systems, Ghent University, Sint-Pietersnieuwstraat 41, Ghent 9000, Belgium
| | - Jan Garrevoet
- Department of Analytical Chemistry, Ghent University, Krijgslaan 281, Ghent 9000, Belgium
| | - Stephen Bauters
- Department of Analytical Chemistry, Ghent University, Krijgslaan 281, Ghent 9000, Belgium
| | - Maarten De Rijcke
- Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, Jozef Plateaustraat 22, Ghent 9000, Belgium
| | - David Deruytter
- Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, Jozef Plateaustraat 22, Ghent 9000, Belgium
| | - Colin Janssen
- Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, Jozef Plateaustraat 22, Ghent 9000, Belgium
| | - Christian Riekel
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38000, France
| | - Manfred Burghammer
- Department of Analytical Chemistry, Ghent University, Krijgslaan 281, Ghent 9000, Belgium
| | - Laszlo Vincze
- Department of Analytical Chemistry, Ghent University, Krijgslaan 281, Ghent 9000, Belgium
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42
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Blakeley MP, Hasnain SS, Antonyuk SV. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential. IUCRJ 2015; 2:464-74. [PMID: 26175905 PMCID: PMC4491318 DOI: 10.1107/s2052252515011239] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/09/2015] [Indexed: 05/20/2023]
Abstract
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.
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Affiliation(s)
- Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Samar S. Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
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Garman EF, Weik M. Radiation damage to macromolecules: kill or cure? JOURNAL OF SYNCHROTRON RADIATION 2015; 22:195-200. [PMID: 25723921 DOI: 10.1107/s160057751500380x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 05/07/2023]
Abstract
Radiation damage induced by X-ray beams during macromolecular diffraction experiments remains an issue of concern in structural biology. While advances in our understanding of this phenomenon, driven in part by a series of workshops in this area, undoubtedly have been and are still being made, there are still questions to be answered. Eight papers in this volume give a flavour of ongoing investigations, addressing various issues. These range over: a proposed new metric derived from atomic B-factors for identifying potentially damaged amino acid residues, a study of the relative damage susceptibility of protein and DNA in a DNA/protein complex, a report of an indication of specific radiation damage to a protein determined from data collected using an X-ray free-electron laser (FEL), an account of the challenges in FEL raw diffraction data analysis, an exploration of the possibilities of using radiation damage induced phasing to solve structures using FELs, simulations of radiation damage as a function of FEL temporal pulse profiles, results on the influence of radiation damage during scanning X-ray diffraction measurements and, lastly, consideration of strategies for minimizing radiation damage during SAXS experiments. In this short introduction, these contributions are briefly placed in the context of other current work on radiation damage in the field.
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Affiliation(s)
- Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
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