1
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Adams MC, Schiltz C, Sun J, Hosford C, Johnson V, Pan H, Borbat P, Freed J, Thomason L, Court C, Court D, Chappie J. The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins. Nucleic Acids Res 2024; 52:4659-4675. [PMID: 38554102 PMCID: PMC11077077 DOI: 10.1093/nar/gkae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/01/2024] Open
Abstract
RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jing Sun
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Virginia M Johnson
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hao Pan
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Lynn C Thomason
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Carolyn Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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2
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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3
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Barnett MJ, Kingston RL. A note on the Hendrickson-Lattman phase probability distribution and its equivalence to the generalized von Mises distribution. J Appl Crystallogr 2024; 57:492-498. [PMID: 38596730 PMCID: PMC11001409 DOI: 10.1107/s1600576724000311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 04/11/2024] Open
Abstract
Hendrickson & Lattman [Acta Cryst. (1970), B26, 136-143] introduced a method for representing crystallographic phase probabilities defined on the unit circle. Their approach could model the bimodal phase probability distributions that can result from experimental phase determination procedures. It also provided simple and highly effective means to combine independent sources of phase information. The present work discusses the equivalence of the Hendrickson-Lattman distribution and the generalized von Mises distribution of order two, which has been studied in the statistical literature. Recognizing this connection allows the Hendrickson-Lattman distribution to be expressed in an alternative form which is easier to interpret, as it involves the location and concentration parameters of the component von Mises distributions. It also allows clarification of the conditions for bimodality and access to a simplified analytical method for evaluating the trigonometric moments of the distribution, the first of which is required for computing the best Fourier synthesis in the presence of phase, but not amplitude, uncertainty.
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Affiliation(s)
- Michael J. Barnett
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard L. Kingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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4
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El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner A. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Commun Chem 2023; 6:219. [PMID: 37828292 PMCID: PMC10570326 DOI: 10.1038/s42004-023-01014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Christian M Orr
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | | | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Vinay Grama
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Feng Qu
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hok Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosana I Reis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Lutz Vogeley
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Raymond J Owens
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David G Brown
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
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5
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Santos MFA, Pessoa JC. Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015. Molecules 2023; 28:6538. [PMID: 37764313 PMCID: PMC10536487 DOI: 10.3390/molecules28186538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structural determination and characterization of molecules, namely proteins and enzymes, is crucial to gaining a better understanding of their role in different chemical and biological processes. The continuous technical developments in the experimental and computational resources of X-ray diffraction (XRD) and, more recently, cryogenic Electron Microscopy (cryo-EM) led to an enormous growth in the number of structures deposited in the Protein Data Bank (PDB). Bioinorganic chemistry arose as a relevant discipline in biology and therapeutics, with a massive number of studies reporting the effects of metal complexes on biological systems, with vanadium complexes being one of the relevant systems addressed. In this review, we focus on the interactions of vanadium compounds (VCs) with proteins. Several types of binding are established between VCs and proteins/enzymes. Considering that the V-species that bind may differ from those initially added, the mentioned structural techniques are pivotal to clarifying the nature and variety of interactions of VCs with proteins and to proposing the mechanisms involved either in enzymatic inhibition or catalysis. As such, we provide an account of the available structural information of VCs bound to proteins obtained by both XRD and/or cryo-EM, mainly exploring the more recent structures, particularly those containing organic-based vanadium complexes.
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Affiliation(s)
- Marino F. A. Santos
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - João Costa Pessoa
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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6
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Abstract
The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. Since these patterns record only amplitudes, phases for the diffracted waves must also be evaluated for systematic structure determination. Thus, we have the phase problem as a central complication, both intellectually for the field and practically so for many analyses. Here, I discuss how we - myself, my laboratory and the diffraction community - have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. During the explosive growth of macromolecular crystallography, practice in diffraction analysis evolved from a universal reliance on isomorphous replacement to the eventual domination of anomalous diffraction for de novo structure determination. As the Protein Data Bank (PDB) grew and familial relationships among proteins became clear, molecular replacement overtook all other phasing methods; however, experimental phasing remained essential for molecules without obvious precedents, with multi- and single-wavelength anomalous diffraction (MAD and SAD) predominating. While the mathematics-based direct methods had proved to be inadequate for typical macromolecules, they returned to crack substantial selenium substructures in SAD analyses of selenomethionyl proteins. Native SAD, exploiting the intrinsic S and P atoms of biomolecules, has become routine. Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. Currently, molecular replacement with AlphaFold models often obviates the need for experimental phase evaluation. For multiple reasons, we are now unfazed by the phase problem. Cryo-EM analysis is an attractive alternative to crystallography for many applications faced by today's structural biologists. It simply finesses the phase problem; however, the principles and procedures of diffraction analysis remain pertinent and are adopted in single-particle cryo-EM studies of biomolecules.
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Affiliation(s)
- Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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7
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Fang X, Lu G, Deng Y, Yang S, Hou C, Gong P. Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding. Virol Sin 2023; 38:531-540. [PMID: 37156298 PMCID: PMC10436059 DOI: 10.1016/j.virs.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
The Dicistroviridae is a virus family that includes many insect pathogens. These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase (RdRP) also named 3Dpol. Compared with the Picornaviridae RdRPs such as poliovirus (PV) 3Dpol, the Dicistroviridae representative Israeli acute paralysis virus (IAPV) 3Dpol has an additional N-terminal extension (NE) region that is about 40-residue in length. To date, both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive. Here we reported crystal structures of two truncated forms of IAPV 3Dpol, namely Δ85 and Δ40, both missing the NE region, and the 3Dpol protein in these structures exhibited three conformational states. The palm and thumb domains of these IAPV 3Dpol structures are largely consistent with those of the PV 3Dpol structures. However, in all structures, the RdRP fingers domain is partially disordered, while different conformations of RdRP substructures and interactions between them are also present. In particular, a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of the Δ40 structure, while a previously documented alternative conformation of motif A was observed in all IAPV structures. These experimental data on one hand show intrinsic conformational variances of RdRP substructures, and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.
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Affiliation(s)
- Xiang Fang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China
| | - Yanchun Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chunsheng Hou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430207, China.
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8
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Doukov T, Herschlag D, Yabukarski F. Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures. Acta Crystallogr D Struct Biol 2023; 79:212-223. [PMID: 36876431 PMCID: PMC9986799 DOI: 10.1107/s205979832300089x] [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: 11/03/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
X-ray crystallography has been invaluable in delivering structural information about proteins. Previously, an approach has been developed that allows high-quality X-ray diffraction data to be obtained from protein crystals at and above room temperature. Here, this previous work is built on and extended by showing that high-quality anomalous signal can be obtained from single protein crystals using diffraction data collected at 220 K up to physiological temperatures. The anomalous signal can be used to directly determine the structure of a protein, i.e. to phase the data, as is routinely performed under cryoconditions. This ability is demonstrated by obtaining diffraction data from model lysozyme, thaumatin and proteinase K crystals, the anomalous signal from which allowed their structures to be solved experimentally at 7.1 keV X-ray energy and at room temperature with relatively low data redundancy. It is also demonstrated that the anomalous signal from diffraction data obtained at 310 K (37°C) can be used to solve the structure of proteinase K and to identify ordered ions. The method provides useful anomalous signal at temperatures down to 220 K, resulting in an extended crystal lifetime and increased data redundancy. Finally, we show that useful anomalous signal can be obtained at room temperature using X-rays of 12 keV energy as typically used for routine data collection, allowing this type of experiment to be carried out at widely accessible synchrotron beamline energies and enabling the simultaneous extraction of high-resolution data and anomalous signal. With the recent emphasis on obtaining conformational ensemble information for proteins, the high resolution of the data allows such ensembles to be built, while the anomalous signal allows the structure to be experimentally solved, ions to be identified, and water molecules and ions to be differentiated. Because bound metal-, phosphorus- and sulfur-containing ions all have anomalous signal, obtaining anomalous signal across temperatures and up to physiological temperatures will provide a more complete description of protein conformational ensembles, function and energetics.
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Affiliation(s)
- Tzanko Doukov
- SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Bristol-Myers Squibb, San Diego, CA 92121, USA
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9
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Karasawa A, Andi B, Fuchs MR, Shi W, McSweeney S, Hendrickson WA, Liu Q. Multi-crystal native-SAD phasing at 5 keV with a helium environment. IUCRJ 2022; 9:768-777. [PMID: 36381147 PMCID: PMC9634608 DOI: 10.1107/s205225252200971x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
De novo structure determination from single-wavelength anomalous diffraction using native sulfur or phospho-rus in biomolecules (native-SAD) is an appealing method to mitigate the labor-intensive production of heavy-atom derivatives and seleno-methio-nyl substitutions. The native-SAD method is particularly attractive for membrane proteins, which are difficult to produce and often recalcitrant to grow into decent-sized crystals. Native-SAD uses lower-energy X-rays to enhance anomalous signals from sulfur or phospho-rus. However, at lower energies, the scattering and absorption of air contribute to the background noise, reduce the signals and are thus adverse to native-SAD phasing. We have previously demonstrated native-SAD phasing at an energy of 5 keV in air at the NSLS-II FMX beamline. Here, the use of a helium path developed to reduce both the noise from background scattering and the air absorption of the diffracted X-ray beam are described. The helium path was used for collection of anomalous diffraction data at 5 keV for two proteins: thaumatin and the membrane protein TehA. Although anomalous signals from each individual crystal are very weak, robust anomalous signals are obtained from data assembled from micrometre-sized crystals. The thaumatin structure was determined from 15 microcrystals and the TehA structure from 18 microcrystals. These results demonstrate the usefulness of a helium environment in support of native-SAD phasing at 5 keV.
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Affiliation(s)
- Akira Karasawa
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
| | - Babak Andi
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sean McSweeney
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A. Hendrickson
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Qun Liu
- Photon Sciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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10
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Mertens HDT. Computational methods for the analysis of solution small-angle X-ray scattering of biomolecules: ATSAS. Methods Enzymol 2022; 678:193-236. [PMID: 36641208 DOI: 10.1016/bs.mie.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ATSAS software suite provides a comprehensive set of programs for the processing, analysis and modeling of small-angle scattering data, tailored for but not limited to data acquired on biological macromolecules. In this review the major components and developments in the ATSAS package are described, with a focus on user driven application. Data reduction, analysis and modeling approaches and strategies will be introduced and discussed. At the time of writing the latest package, ATSAS 3.1, is freely available for academic users at: https://www.embl-hamburg.de/biosaxs/software.html.
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11
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Schiltz CJ, Wilson JR, Hosford CJ, Adams MC, Preising SE, DeBlasio SL, MacLeod HJ, Van Eck J, Heck ML, Chappie JS. Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids. Nat Commun 2022; 13:6368. [PMID: 36289207 PMCID: PMC9606263 DOI: 10.1038/s41467-022-33979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/10/2022] [Indexed: 12/25/2022] Open
Abstract
Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain (NRTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the NRTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV NRTD can act as an inhibitor of virus transmission and identify NRTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus NRTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.
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Affiliation(s)
- Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jennifer R Wilson
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- USDA-Agricultural Research Service, Corn, Soybean & Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Christopher J Hosford
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA
- LifeMine Therapeutics, Cambridge, MA, 02140, USA
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Stephanie E Preising
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Stacy L DeBlasio
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY, 14853, USA
| | - Hannah J MacLeod
- USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY, 14853, USA
- Accelevir Diagnostics, Baltimore, MD, 21202, USA
| | - Joyce Van Eck
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Michelle L Heck
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA.
- USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY, 14853, USA.
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA.
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12
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Kingston RL, Millane RP. A general method for directly phasing diffraction data from high-solvent-content protein crystals. IUCRJ 2022; 9:648-665. [PMID: 36071801 PMCID: PMC9438493 DOI: 10.1107/s2052252522006996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction problem, in which an image is sought that is consistent with both the diffraction data and generic constraints on the density distribution in the crystal. The problem is solved using an iterative projection algorithm, the Difference Map algorithm, which has good global convergence properties, and can locate the correct solution without any initial phase information. Computational efficiency is improved by breaking the problem down into two stages; initial approximation of the molecular envelope at low resolution, followed by subsequent phase determination using all of the data. The molecular envelope is continually updated during the phase determination step. At both stages, the algorithm is initiated with many different and random phase sets, which are evolved subject to the constraints. A clustering procedure is used to identify consistent results across multiple runs, which are then averaged to generate consensus envelopes or phase sets. The emergence of highly consistent phase sets is diagnostic of success. The effectiveness of the procedure is demonstrated by application to 42 known structures of solvent fraction 0.60-0.85. The procedure works robustly at intermediate resolutions (1.9-3.5 Å) but is strongly dependent on crystal solvent content, only working routinely with solvent fractions greater than 0.70.
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Affiliation(s)
- Richard Lawrence Kingston
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland City, Auckland 1010, New Zealand
| | - Rick P. Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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13
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Greisman JB, Dalton KM, Sheehan CJ, Klureza MA, Kurinov I, Hekstra DR. Native SAD phasing at room temperature. Acta Crystallogr D Struct Biol 2022; 78:986-996. [PMID: 35916223 PMCID: PMC9344477 DOI: 10.1107/s2059798322006799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Single-wavelength anomalous diffraction (SAD) is a routine method for overcoming the phase problem when solving macromolecular structures. This technique requires the accurate measurement of intensities to determine differences between Bijvoet pairs. Although SAD experiments are commonly conducted at cryogenic temperatures to mitigate the effects of radiation damage, such temperatures can alter the conformational ensemble of the protein and may impede the merging of data from multiple crystals due to non-uniform freezing. Here, a strategy is presented to obtain high-quality data from room-temperature, single-crystal experiments. To illustrate the strengths of this approach, native SAD phasing at 6.55 keV was used to solve four structures of three model systems at 295 K. The resulting data sets allow automatic phasing and model building, and reveal alternate conformations that reflect the structure of proteins at room temperature.
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14
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Mou TC, Zeng B, Doukov TI, Sprang SR. Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure. Acta Crystallogr D Struct Biol 2022; 78:1021-1031. [PMID: 35916226 PMCID: PMC9344479 DOI: 10.1107/s2059798322005848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
The application of sulfur single-wavelength anomalous dispersion (S-SAD) to determine the crystal structures of macromolecules can be challenging if the asymmetric unit is large, the crystals are small, the size of the anomalously scattering sulfur structure is large and the resolution at which the anomalous signals can be accurately measured is modest. Here, as a study of such a case, approaches to the SAD phasing of orthorhombic Ric-8A crystals are described. The structure of Ric-8A was published with only a brief description of the phasing process [Zeng et al. (2019), Structure, 27, 1137-1141]. Here, alternative approaches to determining the 40-atom sulfur substructure of the 103 kDa Ric-8A dimer that composes the asymmetric unit are explored. At the data-collection wavelength of 1.77 Å measured at the Frontier micro-focusing Macromolecular Crystallography (FMX) beamline at National Synchrotron Light Source II, the sulfur anomalous signal strength, |Δano|/σΔano (d''/sig), approaches 1.4 at 3.4 Å resolution. The highly redundant, 11 000 000-reflection data set measured from 18 crystals was segmented into isomorphous clusters using BLEND in the CCP4 program suite. Data sets within clusters or sets of clusters were scaled and merged using AIMLESS from CCP4 or, alternatively, the phenix.scale_and_merge tool from the Phenix suite. The latter proved to be the more effective in extracting anomalous signals. The HySS tool in Phenix, SHELXC/D and PRASA as implemented in the CRANK2 program suite were each employed to determine the sulfur substructure. All of these approaches were effective, although HySS, as a component of the phenix.autosol tool, required data from all crystals to find the positions of the sulfur atoms. Critical contributors in this case study to successful phase determination by SAD included (i) the high-flux FMX beamline, featuring helical-mode data collection and a helium-filled beam path, (ii) as recognized by many authors, a very highly redundant, multiple-crystal data set and (iii) the inclusion within that data set of data from crystals that were scanned over large ω ranges, yielding highly isomorphous and highly redundant intensity measurements.
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Affiliation(s)
- Tung Chung Mou
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Baisen Zeng
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Tzanko I Doukov
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94309, USA
| | - Stephen R Sprang
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
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15
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Griffiths SC, Schwab RA, El Omari K, Bishop B, Iverson EJ, Malinauskas T, Dubey R, Qian M, Covey DF, Gilbert RJC, Rohatgi R, Siebold C. Hedgehog-Interacting Protein is a multimodal antagonist of Hedgehog signalling. Nat Commun 2021; 12:7171. [PMID: 34887403 PMCID: PMC8660895 DOI: 10.1038/s41467-021-27475-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/19/2021] [Indexed: 01/20/2023] Open
Abstract
Hedgehog (HH) morphogen signalling, crucial for cell growth and tissue patterning in animals, is initiated by the binding of dually lipidated HH ligands to cell surface receptors. Hedgehog-Interacting Protein (HHIP), the only reported secreted inhibitor of Sonic Hedgehog (SHH) signalling, binds directly to SHH with high nanomolar affinity, sequestering SHH. Here, we report the structure of the HHIP N-terminal domain (HHIP-N) in complex with a glycosaminoglycan (GAG). HHIP-N displays a unique bipartite fold with a GAG-binding domain alongside a Cysteine Rich Domain (CRD). We show that HHIP-N is required to convey full HHIP inhibitory function, likely by interacting with the cholesterol moiety covalently linked to HH ligands, thereby preventing this SHH-attached cholesterol from binding to the HH receptor Patched (PTCH1). We also present the structure of the HHIP C-terminal domain in complex with the GAG heparin. Heparin can bind to both HHIP-N and HHIP-C, thereby inducing clustering at the cell surface and generating a high-avidity platform for SHH sequestration and inhibition. Our data suggest a multimodal mechanism, in which HHIP can bind two specific sites on the SHH morphogen, alongside multiple GAG interactions, to inhibit SHH signalling.
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Affiliation(s)
- Samuel C Griffiths
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Evotec (UK) Ltd., Milton Park, Abingdon, UK
| | - Rebekka A Schwab
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kamel El Omari
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Benjamin Bishop
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ellen J Iverson
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ramin Dubey
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mingxing Qian
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MI, USA
| | - Douglas F Covey
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MI, USA
| | - Robert J C Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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16
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Roux A, Talon R, Alsalman Z, Engilberge S, D'Aléo A, Di Pietro S, Robin A, Bartocci A, Pilet G, Dumont E, Wagner T, Shima S, Riobé F, Girard E, Maury O. Influence of Divalent Cations in the Protein Crystallization Process Assisted by Lanthanide-Based Additives. Inorg Chem 2021; 60:15208-15214. [PMID: 34597021 DOI: 10.1021/acs.inorgchem.1c01635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of lanthanide complexes as powerful auxiliaries for biocrystallography prompted us to systematically analyze the influence of the commercial crystallization kit composition on the efficiency of two lanthanide additives: [Eu(DPA)3]3- and Tb-Xo4. This study reveals that the tris(dipicolinate) complex presents a lower chemical stability and a strong tendency toward false positives, which are detrimental for its use in a high-throughput robotized crystallization platform. In particular, the crystal structures of (Mg(H2O)6)3[Eu(DPA)3]2·7H2O (1), {(Ca(H2O)4)3[Eu(DPA)3]2}n·10nH2O (2), and {Cu(DPA)(H2O)2}n (3), resulting from spontaneous crystallization in the presence of a divalent alkaline-earth cation and transmetalation, are reported. On the other hand, Tb-Xo4 is perfectly soluble in the crystallization media, stable in the presence of alkaline-earth dications, and slowly decomposes (within days) by transmetalation with transition metals. The original structure of [Tb4L4(H2O)4]Cl4·15H2O (4) is also described, where L represents a bis(pinacolato)triazacyclononane ligand. This paper also highlights a potential synergy of interactions between Tb-Xo4 and components of the crystallization mixtures, leading to the formation of complex adducts like {AdkA/Tb-Xo4/Mg2+/glycerol} in the protein binding sites. The observation of such multicomponent adducts illustrated the complexity and versatility of the supramolecular chemistry occurring at the surface of the proteins.
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Affiliation(s)
- Amandine Roux
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France.,Polyvalan, Lyon F-69342, France
| | - Romain Talon
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Zaynab Alsalman
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | | | - Anthony D'Aléo
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Sebastiano Di Pietro
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Adeline Robin
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Alessio Bartocci
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Guillaume Pilet
- CNRS UMR 5615, Université Lyon, Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, Villeurbanne Cedex F-69622, France
| | - Elise Dumont
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France.,Institut Universitaire de France, 1 rue Descartes, Paris 75005, France
| | - Tristan Wagner
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg D-35043, Germany.,Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, 1-Celsiusstrasse, Bremen 35043, Germany
| | - Seigo Shima
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg D-35043, Germany
| | - François Riobé
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Eric Girard
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Olivier Maury
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
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17
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Affiliation(s)
- Brian A. Collins
- Physics and Astronomy Washington State University Pullman Washington USA
| | - Eliot Gann
- Material Measurement Laboratory National Institute of Standards and Technology Gaithersburg Maryland USA
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18
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Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem. Sci Rep 2021; 11:17038. [PMID: 34426585 PMCID: PMC8382735 DOI: 10.1038/s41598-021-95186-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/16/2021] [Indexed: 11/09/2022] Open
Abstract
Over the last decades the phase problem in macromolecular x-ray crystallography has become more controllable as methods and approaches have diversified and improved. However, solving the phase problem is still one of the biggest obstacles on the way of successfully determining a crystal structure. To overcome this caveat, we have utilized the anomalous scattering properties of the heavy alkali metal cesium. We investigated the introduction of cesium in form of cesium chloride during the three major steps of protein treatment in crystallography: purification, crystallization, and cryo-protection. We derived a step-wise procedure encompassing a “quick-soak”-only approach and a combined approach of CsCl supplement during purification and cryo-protection. This procedure was successfully applied on two different proteins: (i) Lysozyme and (ii) as a proof of principle, a construct consisting of the PH domain of the TFIIH subunit p62 from Chaetomium thermophilum for de novo structure determination. Usage of CsCl thus provides a versatile, general, easy to use, and low cost phasing strategy.
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19
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Guimarães BG, Golinelli-Pimpaneau B. De novo crystal structure determination of double stranded RNA binding domain using only the sulfur anomalous diffraction in SAD phasing. Curr Res Struct Biol 2021; 3:112-120. [PMID: 34235491 PMCID: PMC8244422 DOI: 10.1016/j.crstbi.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/07/2021] [Accepted: 05/31/2021] [Indexed: 10/25/2022] Open
Abstract
Single-wavelength anomalous dispersion (SAD)-phasing using sulfur as the unique anomalous scatterer is a powerful method to solve the phase problem in protein crystallography. However, it is not yet widely used by non-expert crystallographers. We report here the structure determination of the double stranded RNA binding domain of human dihydrouridine synthase using the sulfur-SAD method and highly redundant data collected at 1.8 Å ("off-edge"), at which the estimated overall anomalous signal was 1.08%. High multiplicity data were collected on a single crystal rotated along the ϕ or ω axis at different κ angles, with the primary beam intensity being attenuated from 50% to 95%, compared to data collection at 0.98 Å, to reduce radiation damage. SHELXD succeeded to locate 14 out 15 sulfur sites only using the data sets recorded with highest beam attenuation, which provided phases sufficient for structure solving. In an attempt to stimulate the use of sulfur-SAD phasing by a broader community of crystallographers, we describe our experimental strategy together with a compilation of previous successful cases, suggesting that sulfur-SAD phasing should be attempted for determining the de novo structure of any protein with average sulfur content diffracting better than 3 Å resolution.
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Affiliation(s)
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75005 Paris, France
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20
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Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing. CRYSTALS 2021; 11. [PMID: 33777416 PMCID: PMC7996396 DOI: 10.3390/cryst11030273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (K D of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (K D of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.
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21
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Qiao Z, Lampugnani ER, Yan XF, Khan GA, Saw WG, Hannah P, Qian F, Calabria J, Miao Y, Grüber G, Persson S, Gao YG. Structure of Arabidopsis CESA3 catalytic domain with its substrate UDP-glucose provides insight into the mechanism of cellulose synthesis. Proc Natl Acad Sci U S A 2021; 118:e2024015118. [PMID: 33729990 PMCID: PMC7980446 DOI: 10.1073/pnas.2024015118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Cellulose is synthesized by cellulose synthases (CESAs) from the glycosyltransferase GT-2 family. In plants, the CESAs form a six-lobed rosette-shaped CESA complex (CSC). Here we report crystal structures of the catalytic domain of Arabidopsis thaliana CESA3 (AtCESA3CatD) in both apo and uridine diphosphate (UDP)-glucose (UDP-Glc)-bound forms. AtCESA3CatD has an overall GT-A fold core domain sandwiched between a plant-conserved region (P-CR) and a class-specific region (C-SR). By superimposing the structure of AtCESA3CatD onto the bacterial cellulose synthase BcsA, we found that the coordination of the UDP-Glc differs, indicating different substrate coordination during cellulose synthesis in plants and bacteria. Moreover, structural analyses revealed that AtCESA3CatD can form a homodimer mainly via interactions between specific beta strands. We confirmed the importance of specific amino acids on these strands for homodimerization through yeast and in planta assays using point-mutated full-length AtCESA3. Our work provides molecular insights into how the substrate UDP-Glc is coordinated in the CESAs and how the CESAs might dimerize to eventually assemble into CSCs in plants.
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Affiliation(s)
- Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 639798
| | - Edwin R Lampugnani
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 639798
| | - Ghazanfar Abbas Khan
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Wuan Geok Saw
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Patrick Hannah
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Feng Qian
- Division of Molecular Biology, Shanghai Genomics, Inc., Shanghai 201202, China
| | - Jacob Calabria
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia;
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551;
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 639798
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22
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Manalastas-Cantos K, Konarev PV, Hajizadeh NR, Kikhney AG, Petoukhov MV, Molodenskiy DS, Panjkovich A, Mertens HDT, Gruzinov A, Borges C, Jeffries CM, Svergun DI, Franke D. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J Appl Crystallogr 2021; 54:343-355. [PMID: 33833657 PMCID: PMC7941305 DOI: 10.1107/s1600576720013412] [Citation(s) in RCA: 395] [Impact Index Per Article: 131.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/06/2020] [Indexed: 11/11/2022] Open
Abstract
The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- Karen Manalastas-Cantos
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Maxim V. Petoukhov
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Clemente Borges
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
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23
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McCoy AJ, Stockwell DH, Sammito MD, Oeffner RD, Hatti KS, Croll TI, Read RJ. Phasertng: directed acyclic graphs for crystallographic phasing. Acta Crystallogr D Struct Biol 2021; 77:1-10. [PMID: 33404520 PMCID: PMC7787104 DOI: 10.1107/s2059798320014746] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 11/06/2020] [Indexed: 12/01/2022] Open
Abstract
Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract phase information from the placement of very small fragments of structure, from weak experimental phasing signal or from combinations of molecular replacement and experimental phasing information. Describing phasing in terms of a directed acyclic graph allows graph-management software to track and manage the path to structure solution. The crystallographic software supporting the graph data structure must be strictly modular so that nodes in the graph are efficiently generated by the encapsulated functionality. To this end, the development of new software, Phasertng, which uses directed acyclic graphs natively for input/output, has been initiated. In Phasertng, the codebase of Phaser has been rebuilt, with an emphasis on modularity, on scripting, on speed and on continuing algorithm development. As a first application of phasertng, its advantages are demonstrated in the context of phasertng.xtricorder, a tool to analyse and triage merged data in preparation for molecular replacement or experimental phasing. The description of the phasing strategy with directed acyclic graphs is a generalization that extends beyond the functionality of Phasertng, as it can incorporate results from bioinformatics and other crystallographic tools, and will facilitate multifaceted search strategies, dynamic ranking of alternative search pathways and the exploitation of machine learning to further improve phasing strategies.
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Affiliation(s)
- Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Duncan H. Stockwell
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Kaushik S. Hatti
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Tristan I. Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
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24
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El Omari K, Mohamad N, Bountra K, Duman R, Romano M, Schlegel K, Kwong HS, Mykhaylyk V, Olesen C, Moller JV, Bublitz M, Beis K, Wagner A. Experimental phasing with vanadium and application to nucleotide-binding membrane proteins. IUCRJ 2020; 7:1092-1101. [PMID: 33209320 PMCID: PMC7642786 DOI: 10.1107/s2052252520012312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
The structure determination of soluble and membrane proteins can be hindered by the crystallographic phase problem, especially in the absence of a suitable homologous structure. Experimental phasing is the method of choice for novel structures; however, it often requires heavy-atom derivatization, which can be difficult and time-consuming. Here, a novel and rapid method to obtain experimental phases for protein structure determination by vanadium phasing is reported. Vanadate is a transition-state mimic of phosphoryl-transfer reactions and it has the advantage of binding specifically to the active site of numerous enzymes catalyzing this reaction. The applicability of vanadium phasing has been validated by determining the structures of three different protein-vanadium complexes, two of which are integral membrane proteins: the rabbit sarcoplasmic reticulum Ca2+-ATPase, the antibacterial peptide ATP-binding cassette transporter McjD from Escherichia coli and the soluble enzyme RNAse A from Bos taurus. Vanadium phasing was successful even at low resolution and despite severe anisotropy in the data. This method is principally applicable to a large number of proteins, representing six of the seven Enzyme Commission classes. It relies exclusively on the specific chemistry of the protein and it does not require any modifications, making it a very powerful addition to the phasing toolkit. In addition to the phasing power of this technique, the protein-vanadium complexes also provide detailed insights into the reaction mechanisms of the studied proteins.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Nada Mohamad
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
- Institute of Biostructures and Bioimaging, National Research Council (IBB–CNR), Via Mezzocannone 16, 80134 Napoli, Italy
| | - Katja Schlegel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Hok-Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Claus Olesen
- Department of Biomedicine, Aarhus University, Ole Worms Allé 8, DK-8000 Aarhus, Denmark
| | - Jesper Vuust Moller
- Department of Biomedicine, Aarhus University, Ole Worms Allé 8, DK-8000 Aarhus, Denmark
| | - Maike Bublitz
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
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25
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Hosford CJ, Adams MC, Niu Y, Chappie JS. The N-terminal domain of Staphylothermus marinus McrB shares structural homology with PUA-like RNA binding proteins. J Struct Biol 2020; 211:107572. [PMID: 32652237 DOI: 10.1016/j.jsb.2020.107572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022]
Abstract
McrBC is a conserved modification-dependent restriction system that in Escherichia coli specifically targets foreign DNA containing methylated cytosines. Crystallographic data show that the N-terminal domain of Escherichia coli McrB binds substrates via a base flipping mechanism. This region is poorly conserved among the plethora of McrB homologs, suggesting that other species may use alternative binding strategies and/or recognize different targets. Here we present the crystal structure of the N-terminal domain from Stayphlothermus marinus McrB (Sm3-180) at 1.92 Å, which adopts a PUA-like EVE fold that is closely related to the YTH and ASCH RNA binding domains. Unlike most PUA-like domains, Sm3-180 binds DNA and can associate with different modified substrates. We find the canonical 'aromatic cage' binding pocket that confers specificity for methylated bases in other EVE/YTH domains is degenerate and occluded in Sm3-180, which may contribute to its promiscuity in target recognition. Further structural comparison between different PUA-like domains identifies motifs and conformational variations that correlate with the preference for binding either DNA or RNA. Together these data have important implications for PUA-like domain specificity and suggest a broader biological versatility for the McrBC family than previously described.
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Affiliation(s)
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Yiming Niu
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.
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26
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Assmann GM, Wang M, Diederichs K. Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods. Acta Crystallogr D Struct Biol 2020; 76:636-652. [PMID: 32627737 PMCID: PMC7336379 DOI: 10.1107/s2059798320006348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Phasing by single-wavelength anomalous diffraction (SAD) from multiple crystallographic data sets can be particularly demanding because of the weak anomalous signal and possible non-isomorphism. The identification and exclusion of non-isomorphous data sets by suitable indicators is therefore indispensable. Here, simple and robust data-selection methods are described. A multi-dimensional scaling procedure is first used to identify data sets with large non-isomorphism relative to clusters of other data sets. Within each cluster that it identifies, further selection is based on the weighted ΔCC1/2, a quantity representing the influence of a set of reflections on the overall CC1/2 of the merged data. The anomalous signal is further improved by optimizing the scaling protocol. The success of iterating the selection and scaling steps was verified by substructure determination and subsequent structure solution. Three serial synchrotron crystallography (SSX) SAD test cases with hundreds of partial data sets and one test case with 62 complete data sets were analyzed. Structure solution was dramatically simplified with this procedure, and enabled solution of the structures after a few selection/scaling iterations. To explore the limits, the procedure was tested with much fewer data than originally required and could still solve the structure in several cases. In addition, an SSX data challenge, minimizing the number of (simulated) data sets necessary to solve the structure, was significantly underbid.
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Affiliation(s)
- Greta M. Assmann
- Department of Biology, University of Konstanz, Box 647, D-78457 Konstanz, Germany
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Box 647, D-78457 Konstanz, Germany
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27
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First Experiments in Structural Biology at the European X-ray Free-Electron Laser. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10103642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ultrabright pulses produced in X-ray free-electron lasers (XFELs) offer new possibilities for industry and research, particularly for biochemistry and pharmaceuticals. The unprecedented brilliance of these next-generation sources enables structure determination from sub-micron crystals as well as radiation-sensitive proteins. The European X-Ray Free-Electron Laser (EuXFEL), with its first light in 2017, ushered in a new era for ultrabright X-ray sources by providing an unparalleled megahertz-pulse repetition rate, with orders of magnitude more pulses per second than previous XFEL sources. This rapid pulse frequency has significant implications for structure determination; not only will data collection be faster (resulting in more structures per unit time), but experiments requiring large quantities of data, such as time-resolved structures, become feasible in a reasonable amount of experimental time. Early experiments at the SPB/SFX instrument of the EuXFEL demonstrate how such closely-spaced pulses can be successfully implemented in otherwise challenging experiments, such as time-resolved studies.
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28
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Schiltz CJ, Adams MC, Chappie JS. The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. Nucleic Acids Res 2020; 48:2762-2776. [PMID: 32009148 PMCID: PMC7049728 DOI: 10.1093/nar/gkaa059] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/28/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC-Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.
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Affiliation(s)
- Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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29
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Siritapetawee J, Teamtisong K, Limphirat W, Charoenwattanasatien R, Attarataya J, Mothong N. Identification and characterization of a protease (EuRP-61) from Euphorbia resinifera latex. Int J Biol Macromol 2020; 145:998-1007. [PMID: 31678105 DOI: 10.1016/j.ijbiomac.2019.09.190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/21/2019] [Accepted: 09/21/2019] [Indexed: 01/02/2023]
Abstract
A serine protease designated as EuRP-61 was purified from Euphorbia resinifera latex. The N-terminal sequence of 15 amino acids of EuRP-61 supported the conclusion that the enzyme was a serine protease because its amino acid sequence had homology (between 50 and 70% identities) with the subtilisin-like proteases of other plants. EuRP-61 had a molecular weight estimated at 61 kDa analyzed by MALDI-TOF MS. The enzyme could cleave human fibrinogen with optimal conditions at pH 5.0 and 45 °C. The enzyme had a broad range of pH stability from 1 to 14 and tolerance to denaturation up to a temperature of approximately 65-66 °C. EuRP-61 hydrolyzed fibrinogen with a Michaelis constant (Km) of 4.95 ± 0.1 μM; a maximal velocity (Vmax) of 578.1 ± 11.81 ng min-1; and a catalytic efficiency (Vmax/Km) of 116.8 ± 1 ng μM-1 min-1. EuRP-61was crystallized under the condition of sodium iodide (0.2 M), Bis-Tris propane (0.1 M, pH 8.5) and PEG3350 (20%) by the sitting-drop method. The crystal belonged to space group P212121, with unit cell dimension a = 109.91, b = 67.38 and c = 199.45 Å and diffracted X-ray to 2.53 Å resolution. The crystal structure of EuRP-61 will be explored further by special phase solving techniques.
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Affiliation(s)
- Jaruwan Siritapetawee
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Wanwisa Limphirat
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | | | - Jakrada Attarataya
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | - Narumol Mothong
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
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30
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Hosford CJ, Bui AQ, Chappie JS. The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49932-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Conlon PF, Eguaogie O, Wilson JJ, Sweet JST, Steinhoegl J, Englert K, Hancox OGA, Law CJ, Allman SA, Tucker JHR, Hall JP, Vyle JS. Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography. Chem Sci 2019; 10:10948-10957. [PMID: 32190252 PMCID: PMC7066676 DOI: 10.1039/c9sc04098f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/11/2019] [Indexed: 01/20/2023] Open
Abstract
Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside H-phosphonate derivatives with 5'-deoxythymidine-5'-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to -3.1 °C per phosphoroselenolate) when introduced at the 5'-termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 Å. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
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Affiliation(s)
- Patrick F Conlon
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Olga Eguaogie
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jordan J Wilson
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jamie S T Sweet
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Julian Steinhoegl
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Klaudia Englert
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - Oliver G A Hancox
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Christopher J Law
- School of Biological Sciences , Queen's University Belfast , 15 Chlorine Gardens , Belfast BT9 5AH , UK
| | - Sarah A Allman
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - James H R Tucker
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - James P Hall
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
- Diamond Light Source , Chilton , Didcot , Oxfordshire OX11 0DE , UK
| | - Joseph S Vyle
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
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32
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Hosford CJ, Bui AQ, Chappie JS. The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs. J Biol Chem 2019; 295:743-756. [PMID: 31822563 DOI: 10.1074/jbc.ra119.010188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/07/2019] [Indexed: 01/12/2023] Open
Abstract
McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA-containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The side chains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. Here we present the structures of the Thermococcus gammatolerans McrB DNA-binding domain (TgΔ185) both alone and in complex with a methylated DNA substrate at 1.68 and 2.27 Å resolution, respectively. The structures reveal that TgΔ185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA-binding domain. Structural superposition and co-crystallization further show that TgΔ185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines, whereas an extended basic surface present in TgΔ185 facilitates its preferential binding to duplex DNA rather than RNA. Together, these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.
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Affiliation(s)
| | - Anthony Q Bui
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
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33
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Rocchio S, Duman R, El Omari K, Mykhaylyk V, Orr C, Yan Z, Salmon L, Wagner A, Bardwell JCA, Horowitz S. Identifying dynamic, partially occupied residues using anomalous scattering. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1084-1095. [PMID: 31793902 PMCID: PMC6889914 DOI: 10.1107/s2059798319014475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/22/2019] [Indexed: 11/24/2022]
Abstract
Structural studies of partially occupied, heterogeneous protein systems using crystallography are difficult. Here, methods are presented for detecting these states in crystals. Although often presented as taking single ‘snapshots’ of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as ∼12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.
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Affiliation(s)
- Serena Rocchio
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ramona Duman
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Kamel El Omari
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Vitaliy Mykhaylyk
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Christian Orr
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Zhen Yan
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 69100 Villeurbanne, France
| | - Armin Wagner
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - James C A Bardwell
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Horowitz
- Department of Chemistry and Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA
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Garcia-Bonete MJ, Katona G. Bayesian machine learning improves single-wavelength anomalous diffraction phasing. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:851-860. [PMID: 31692460 PMCID: PMC6833979 DOI: 10.1107/s2053273319011446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/14/2019] [Indexed: 11/25/2022]
Abstract
The a posteriori probability densities of anomalous structure-factor amplitude differences were estimated by the Markov chain Monte Carlo machine-learning method. The model incorporated the correlation between the different Bijvoet pairs and the improved estimates were shown to be beneficial for SAD phasing. Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel’s reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(−) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet’s pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel’s pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.
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Affiliation(s)
- Maria Jose Garcia-Bonete
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, 40530, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, 40530, Sweden
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Schiltz CJ, Lee A, Partlow EA, Hosford CJ, Chappie JS. Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Nucleic Acids Res 2019; 47:9448-9463. [PMID: 31400118 PMCID: PMC6755086 DOI: 10.1093/nar/gkz703] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022] Open
Abstract
Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins. The in vivo activities of OLD proteins remain poorly understood and no definitive structural information exists. Here we identify and define two classes of OLD proteins based on differences in gene neighborhood and amino acid sequence conservation and present the crystal structures of the catalytic C-terminal regions from the Burkholderia pseudomallei and Xanthamonas campestris p.v. campestris Class 2 OLD proteins at 2.24 Å and 1.86 Å resolution respectively. The structures reveal a two-domain architecture containing a Toprim domain with altered architecture and a unique helical domain. Conserved side chains contributed by both domains coordinate two bound magnesium ions in the active site of B. pseudomallei OLD in a geometry that supports a two-metal catalysis mechanism for cleavage. The spatial organization of these domains additionally suggests a novel mode of DNA binding that is distinct from other Toprim containing proteins. Together, these findings define the fundamental structural properties of the OLD family catalytic core and the underlying mechanism controlling nuclease activity.
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Affiliation(s)
- Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - April Lee
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward A Partlow
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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36
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Slack RD, Abramyan AM, Tang H, Meena S, Davis BA, Bonifazi A, Giancola JB, Deschamps JR, Naing S, Yano H, Singh SK, Newman AH, Shi L. A Novel Bromine-Containing Paroxetine Analogue Provides Mechanistic Clues for Binding Ambiguity at the Central Primary Binding Site of the Serotonin Transporter. ACS Chem Neurosci 2019; 10:3946-3952. [PMID: 31424193 DOI: 10.1021/acschemneuro.9b00375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The serotonin transporter (SERT) is the primary target for the selective serotonin reuptake inhibitors (SSRIs). However, the structural basis for the extraordinarily high binding affinity of the widely prescribed SSRI, paroxetine, to human SERT (hSERT) has not yet been fully elucidated. Our previous findings unveiled a plausible ambiguity in paroxetine's binding orientations that may constitute an integral component of this SSRI's high affinity for hSERT. Herein, we investigate factors contributing to paroxetine's high affinity by modifying both the ligand and the protein. We generated a series of bromine (Br)-containing derivatives and found that the one in which the 4-F of paroxetine had been replaced with the chemically similar but more electron-rich Br atom (13) had the highest affinity. By comparatively characterizing the binding of paroxetine and 13 to both wild type (WT) and a construct harboring a paroxetine-sensitive mutation in the binding cavity, we identified a mechanistic determinant responsible for the pose ambiguity of paroxetine, which can guide future drug design.
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Affiliation(s)
- Rachel D. Slack
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Ara M. Abramyan
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Helen Tang
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Sitaram Meena
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Bruce A. Davis
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Alessandro Bonifazi
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - JoLynn B. Giancola
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Jeffrey R. Deschamps
- Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington D. C. 20375, United States
| | - Sett Naing
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Hideaki Yano
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Satinder K. Singh
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Amy Hauck Newman
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Lei Shi
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
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Engilberge S, Wagner T, Santoni G, Breyton C, Shima S, Franzetti B, Riobé F, Maury O, Girard E. Protein crystal structure determination with the crystallophore, a nucleating and phasing agent. J Appl Crystallogr 2019; 52:722-731. [PMID: 31396026 PMCID: PMC6662991 DOI: 10.1107/s1600576719006381] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023] Open
Abstract
Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.
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Affiliation(s)
- Sylvain Engilberge
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Tristan Wagner
- Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Cécile Breyton
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Seigo Shima
- Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Bruno Franzetti
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Francois Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Eric Girard
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
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38
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Guo G, Zhu P, Fuchs MR, Shi W, Andi B, Gao Y, Hendrickson WA, McSweeney S, Liu Q. Synchrotron microcrystal native-SAD phasing at a low energy. IUCRJ 2019; 6:532-542. [PMID: 31316798 PMCID: PMC6608635 DOI: 10.1107/s2052252519004536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/03/2019] [Indexed: 05/31/2023]
Abstract
De novo structural evaluation of native biomolecules from single-wavelength anomalous diffraction (SAD) is a challenge because of the weakness of the anomalous scattering. The anomalous scattering from relevant native elements - primarily sulfur in proteins and phospho-rus in nucleic acids - increases as the X-ray energy decreases toward their K-edge transitions. Thus, measurements at a lowered X-ray energy are promising for making native SAD routine and robust. For microcrystals with sizes less than 10 µm, native-SAD phasing at synchrotron microdiffraction beamlines is even more challenging because of difficulties in sample manipulation, diffraction data collection and data analysis. Native-SAD analysis from microcrystals by using X-ray free-electron lasers has been demonstrated but has required use of thousands of thousands of microcrystals to achieve the necessary accuracy. Here it is shown that by exploitation of anomalous microdiffraction signals obtained at 5 keV, by the use of polyimide wellmounts, and by an iterative crystal and frame-rejection method, microcrystal native-SAD phasing is possible from as few as about 1 200 crystals. Our results show the utility of low-energy native-SAD phasing with microcrystals at synchrotron microdiffraction beamlines.
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Affiliation(s)
- Gongrui Guo
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ping Zhu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yuan Gao
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sean McSweeney
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
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39
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Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M. Long-wavelength native-SAD phasing: opportunities and challenges. IUCRJ 2019; 6:373-386. [PMID: 31098019 PMCID: PMC6503925 DOI: 10.1107/s2052252519002756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/22/2019] [Indexed: 05/04/2023]
Abstract
Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Naohiro Matsugaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tomizaki Takashi
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, PSI 5232, Switzerland
| | - Jerome Basquin
- Department of Biochemistry, Max Planck Institute of Biochemistry, Munich, Germany
| | - Justyna A. Wojdyla
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Correspondence e-mail:
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40
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Guo S, Campbell R, Davies PL, Allingham JS. Phasing with calcium at home. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:377-384. [PMID: 31045567 DOI: 10.1107/s2053230x19004151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/27/2019] [Indexed: 12/16/2022]
Abstract
With better tools for data processing and with synchrotron beamlines that are capable of collecting data at longer wavelengths, sulfur-based native single-wavelength anomalous dispersion (SAD) phasing has become the `first-choice' method for de novo protein structure determination. However, for many proteins native SAD phasing can be simplified by taking advantage of their interactions with natural metal cofactors that are stronger anomalous scatterers than sulfur. This is demonstrated here for four unique domains of a 1.5 MDa calcium-dependent adhesion protein using the anomalous diffraction of the chelated calcium ions. In all cases, low anomalous multiplicity X-ray data were collected on a home-source diffractometer equipped with a chromium rotating anode (λ = 2.2909 Å). In all but one case, calcium SAD phasing alone was sufficient to allow automated model building and refinement of the protein model after the calcium substructure had been determined. Given that Ca atoms will be present in a significant percentage of proteins that remain uncharacterized, many aspects of the data-collection and processing methods described here could be broadly applied for routine de novo structure elucidation.
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Affiliation(s)
- Shuaiqi Guo
- Protein Function Discovery Group and The Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Robert Campbell
- Protein Function Discovery Group and The Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Peter L Davies
- Protein Function Discovery Group and The Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - John S Allingham
- Protein Function Discovery Group and The Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
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41
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Basu S, Finke A, Vera L, Wang M, Olieric V. Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source. Acta Crystallogr D Struct Biol 2019; 75:262-271. [PMID: 30950397 PMCID: PMC6450063 DOI: 10.1107/s2059798319003103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/01/2019] [Indexed: 01/19/2023] Open
Abstract
Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 µm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin-biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Aaron Finke
- MacCHESS, Cornell University, Ithaca, New York, USA
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
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42
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Eliseev IE, Yudenko AN, Ukrainskaya VM, Chakchir OB. Cadmium SAD phasing at CuKα wavelength. F1000Res 2019; 8:84. [PMID: 30984381 PMCID: PMC6446493 DOI: 10.12688/f1000research.17694.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 12/03/2022] Open
Abstract
Single-wavelength anomalous diffraction (SAD) is the most common method for de novo elucidation of macromolecular structures by X-ray crystallography. It requires an anomalous scatterer in a crystal to calculate phases. A recent study by Panneerselvam et al. emphasized the utility of cadmium ions for SAD phasing at the standard synchrotron wavelength of 1 Å. Here we show that cadmium is also useful for phasing of crystals collected in-house with CuKα radiation. Using a crystal of single-domain antibody as an experimental model, we demonstrate how cadmium SAD can be conveniently employed to solve a CuKα dataset. We then discuss the factors which make this method generally applicable.
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Affiliation(s)
- Igor E. Eliseev
- St. Petersburg National Research Academic University RAS, St. Petersburg, 194021, Russian Federation
| | - Anna N. Yudenko
- St. Petersburg National Research Academic University RAS, St. Petersburg, 194021, Russian Federation
| | - Valeria M. Ukrainskaya
- St. Petersburg National Research Academic University RAS, St. Petersburg, 194021, Russian Federation
| | - Oleg B. Chakchir
- St. Petersburg National Research Academic University RAS, St. Petersburg, 194021, Russian Federation
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43
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Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps. Nat Commun 2018; 9:4500. [PMID: 30374105 PMCID: PMC6206036 DOI: 10.1038/s41467-018-06955-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain and a significant source of reactive oxygen species (ROS). We hypothesized that during energy conversion by complex I, electron transfer onto ubiquinone triggers the concerted rearrangement of three protein loops of subunits ND1, ND3, and 49-kDa thereby generating the power-stoke driving proton pumping. Here we show that fixing loop TMH1-2ND3 to the nearby subunit PSST via a disulfide bridge introduced by site-directed mutagenesis reversibly disengages proton pumping without impairing ubiquinone reduction, inhibitor binding or the Active/Deactive transition. The X-ray structure of mutant complex I indicates that the disulfide bridge immobilizes but does not displace the tip of loop TMH1-2ND3. We conclude that movement of loop TMH1-2ND3 located at the ubiquinone-binding pocket is required to drive proton pumping corroborating one of the central predictions of our model for the mechanism of energy conversion by complex I proposed earlier. Proton pumping of mitochondrial complex I depends on the reduction of ubiquinone but the molecular mechanism of energy conversion is unclear. Here, the authors provide structural and biochemical evidence showing that movement of loop TMH1-2 in complex I subunit ND3 is required to drive proton pumping.
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44
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Rudek B, Toyota K, Foucar L, Erk B, Boll R, Bomme C, Correa J, Carron S, Boutet S, Williams GJ, Ferguson KR, Alonso-Mori R, Koglin JE, Gorkhover T, Bucher M, Lehmann CS, Krässig B, Southworth SH, Young L, Bostedt C, Ueda K, Marchenko T, Simon M, Jurek Z, Santra R, Rudenko A, Son SK, Rolles D. Relativistic and resonant effects in the ionization of heavy atoms by ultra-intense hard X-rays. Nat Commun 2018; 9:4200. [PMID: 30305630 PMCID: PMC6180123 DOI: 10.1038/s41467-018-06745-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022] Open
Abstract
An accurate description of the interaction of intense hard X-ray pulses with heavy atoms, which is crucial for many applications of free-electron lasers, represents a hitherto unresolved challenge for theory because of the enormous number of electronic configurations and relativistic effects, which need to be taken into account. Here we report results on multiple ionization of xenon atoms by ultra-intense (about 1019 W/cm2) femtosecond X-ray pulses at photon energies from 5.5 to 8.3 keV and present a theoretical model capable of reproducing the experimental data in the entire energy range. Our analysis shows that the interplay of resonant and relativistic effects results in strongly structured charge state distributions, which reflect resonant positions of relativistically shifted electronic levels of highly charged ions created during the X-ray pulse. The theoretical approach described here provides a basis for accurate modeling of radiation damage in hard X-ray imaging experiments on targets with high-Z constituents.
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Affiliation(s)
- Benedikt Rudek
- Physikalisch-Technische Bundesanstalt, Braunschweig, Germany
| | - Koudai Toyota
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Erk
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Rebecca Boll
- Max Planck Institute for Nuclear Physics, Heidelberg, Germany
- European XFEL GmbH, Schenefeld, Germany
| | - Cédric Bomme
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jonathan Correa
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- California Lutheran University, Thousand Oaks, CA, USA
| | | | - Garth J Williams
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- NSLS-II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ken R Ferguson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Tais Gorkhover
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Stanford PULSE Institute, SLAC, Menlo Park, CA, USA
| | - Maximilian Bucher
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Argonne National Laboratory, Lemont, IL, USA
| | - Carl Stefan Lehmann
- Argonne National Laboratory, Lemont, IL, USA
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | | | - Linda Young
- Argonne National Laboratory, Lemont, IL, USA
- Department of Physics and The James Franck Institute, University of Chicago, Chicago, IL, USA
| | - Christoph Bostedt
- Argonne National Laboratory, Lemont, IL, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Sendai, Japan
| | - Tatiana Marchenko
- Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, CNRS, Sorbonne Université, Paris, France
| | - Marc Simon
- Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, CNRS, Sorbonne Université, Paris, France
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
- Department of Physics, University of Hamburg, Hamburg, Germany
| | - Artem Rudenko
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS, USA
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Daniel Rolles
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS, USA.
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45
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Huang CY, Olieric V, Howe N, Warshamanage R, Weinert T, Panepucci E, Vogeley L, Basu S, Diederichs K, Caffrey M, Wang M. In situ serial crystallography for rapid de novo membrane protein structure determination. Commun Biol 2018; 1:124. [PMID: 30272004 PMCID: PMC6123769 DOI: 10.1038/s42003-018-0123-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022] Open
Abstract
De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crystallography with de novo phasing for fast, efficient membrane protein structure determination. The method enables systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without the need for direct crystal harvesting. The requisite data quality for experimental phasing is achieved by accumulating diffraction signals from isomorphous crystals identified post-data collection. The method works in all experimental phasing scenarios and is particularly attractive with fragile, weakly diffracting microcrystals. The automated serial data collection approach can be readily adopted at most microfocus macromolecular crystallography beamlines.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Nicole Howe
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | | | - Tobias Weinert
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Lutz Vogeley
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Shibom Basu
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, M647, D-78457, Konstanz, Germany
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland.
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46
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Hosford CJ, Chappie JS. The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding. J Biol Chem 2018; 293:11758-11771. [PMID: 29895618 PMCID: PMC6066307 DOI: 10.1074/jbc.ra118.001888] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/04/2018] [Indexed: 12/11/2022] Open
Abstract
Restriction modification systems consist of an endonuclease that cleaves foreign DNA site-specifically and an associated methyltransferase that protects the corresponding target site in the host genome. Modification-dependent restriction systems, in contrast, specifically recognize and cleave methylated and/or glucosylated DNA. The LlaJI restriction system contains two 5-methylcytosine (5mC) methyltransferases (LlaJI.M1 and LlaJI.M2) and two restriction proteins (LlaJI.R1 and LlaJI.R2). LlaJI.R1 and LlaJI.R2 are homologs of McrB and McrC, respectively, which in Escherichia coli function together as a modification-dependent restriction complex specific for 5mC-containing DNA. Lactococcus lactis LlaJI.R1 binds DNA site-specifically, suggesting that the LlaJI system uses a different mode of substrate recognition. Here we present the structure of the N-terminal DNA-binding domain of Helicobacter pylori LlaJI.R1 at 1.97-Å resolution, which adopts a B3 domain fold. Structural comparison to B3 domains in plant transcription factors and other restriction enzymes identifies key recognition motifs responsible for site-specific DNA binding. Moreover, biochemistry and structural modeling provide a rationale for how H. pylori LlaJI.R1 may bind a target site that differs from the 5-bp sequence recognized by other LlaJI homologs and identify residues critical for this recognition activity. These findings underscore the inherent structural plasticity of B3 domains, allowing recognition of a variety of substrates using the same structural core.
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Affiliation(s)
- Christopher J Hosford
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Joshua S Chappie
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
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47
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Read RJ, McCoy AJ. Maximum-likelihood determination of anomalous substructures. Acta Crystallogr D Struct Biol 2018; 74:98-105. [PMID: 29533235 PMCID: PMC5947773 DOI: 10.1107/s2059798317013468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/20/2017] [Indexed: 11/10/2022] Open
Abstract
A fast Fourier transform (FFT) method is described for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by X-ray single-wavelength anomalous diffraction (SAD). This method is based on the maximum-likelihood SAD phasing function, which accounts for measurement errors and for correlations between the observed and calculated Bijvoet mates. Proof of principle is shown that this method can improve determination of the anomalously scattering substructure in challenging cases where the anomalous scattering from the substructure is weak but the substructure also constitutes a significant fraction of the real scattering. The method is deterministic and can be fast compared with existing multi-trial dual-space methods for SAD substructure determination.
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Affiliation(s)
- Randy J. Read
- Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
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48
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Li Z, Tang Y, Wu Y, Zhao S, Bao J, Luo Y, Li D. Structural insights into the committed step of bacterial phospholipid biosynthesis. Nat Commun 2017; 8:1691. [PMID: 29167463 PMCID: PMC5700162 DOI: 10.1038/s41467-017-01821-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/18/2017] [Indexed: 11/09/2022] Open
Abstract
The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 Å resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of ‘substrate-assisted catalysis’ that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme. The first step in bacterial phospholipid biosynthesis is the acylation of glycerol 3-phosphate to form lysophosphatidic acid. Here, the authors present the high resolution crystal structure of the glycerol 3-phosphate acyltransferase PlsY, a membrane protein and give insights into its catalytical mechanism.
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Affiliation(s)
- Zhenjian Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yannan Tang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yitian Luo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.
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49
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Silver and gold in the Protein Data Bank. J Inorg Biochem 2017; 175:244-247. [DOI: 10.1016/j.jinorgbio.2017.07.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/26/2017] [Indexed: 01/15/2023]
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50
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Engilberge S, Riobé F, Di Pietro S, Lassalle L, Coquelle N, Arnaud CA, Pitrat D, Mulatier JC, Madern D, Breyton C, Maury O, Girard E. Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence. Chem Sci 2017; 8:5909-5917. [PMID: 29619195 PMCID: PMC5859728 DOI: 10.1039/c7sc00758b] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/02/2017] [Indexed: 11/21/2022] Open
Abstract
Macromolecular crystallography suffers from two major issues: getting well-diffracting crystals and solving the phase problem inherent to large macromolecules. Here, we describe the first example of a lanthanide complex family named "crystallophore" (Xo4), which contributes to tackling both bottlenecks. This terbium complex, Tb-Xo4, is an appealing agent for biocrystallography, combining the exceptional phasing power of the Tb(iii) heavy atom with powerful nucleating properties, providing ready-to-use crystals for structure determination. Furthermore, protein/Tb-Xo4 co-crystals can be easily detected and discriminated from other crystalline by-products using luminescence. We demonstrate the potential of this additive for the crystallisation and structure determination of eight proteins, two of whose structures were unknown.
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Affiliation(s)
| | - François Riobé
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Sebastiano Di Pietro
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Louise Lassalle
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | - Nicolas Coquelle
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | | | - Delphine Pitrat
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Jean-Christophe Mulatier
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Dominique Madern
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | - Cécile Breyton
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | - Olivier Maury
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Eric Girard
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
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