1
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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2
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Robinson RA, Griffiths SC, van de Haar LL, Malinauskas T, van Battum EY, Zelina P, Schwab RA, Karia D, Malinauskaite L, Brignani S, van den Munkhof MH, Düdükcü Ö, De Ruiter AA, Van den Heuvel DMA, Bishop B, Elegheert J, Aricescu AR, Pasterkamp RJ, Siebold C. Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling. Cell 2021; 184:2103-2120.e31. [PMID: 33740419 PMCID: PMC8063088 DOI: 10.1016/j.cell.2021.02.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/15/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
During cell migration or differentiation, cell surface receptors are simultaneously exposed to different ligands. However, it is often unclear how these extracellular signals are integrated. Neogenin (NEO1) acts as an attractive guidance receptor when the Netrin-1 (NET1) ligand binds, but it mediates repulsion via repulsive guidance molecule (RGM) ligands. Here, we show that signal integration occurs through the formation of a ternary NEO1-NET1-RGM complex, which triggers reciprocal silencing of downstream signaling. Our NEO1-NET1-RGM structures reveal a "trimer-of-trimers" super-assembly, which exists in the cell membrane. Super-assembly formation results in inhibition of RGMA-NEO1-mediated growth cone collapse and RGMA- or NET1-NEO1-mediated neuron migration, by preventing formation of signaling-compatible RGM-NEO1 complexes and NET1-induced NEO1 ectodomain clustering. These results illustrate how simultaneous binding of ligands with opposing functions, to a single receptor, does not lead to competition for binding, but to formation of a super-complex that diminishes their functional outputs.
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Affiliation(s)
- Ross A Robinson
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Samuel C Griffiths
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Lieke L van de Haar
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eljo Y van Battum
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Pavol Zelina
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Rebekka A Schwab
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Dimple Karia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Lina Malinauskaite
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sara Brignani
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Marleen H van den Munkhof
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Özge Düdükcü
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Anna A De Ruiter
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Dianne M A Van den Heuvel
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Benjamin Bishop
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jonathan Elegheert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - A Radu Aricescu
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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3
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Daniel E, Maksimainen MM, Smith N, Ratas V, Biterova E, Murthy SN, Rahman MT, Kiema TR, Sridhar S, Cordara G, Dalwani S, Venkatesan R, Prilusky J, Dym O, Lehtiö L, Koski MK, Ashton AW, Sussman JL, Wierenga RK. IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition. Acta Crystallogr D Struct Biol 2021; 77:151-163. [PMID: 33559605 PMCID: PMC7869904 DOI: 10.1107/s2059798320015223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/15/2020] [Indexed: 12/26/2022] Open
Abstract
The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop-viewer page and to the ISPyB data-collection page, as well as to the structure deposited in the Protein Data Bank.
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Affiliation(s)
- Ed Daniel
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Mirko M. Maksimainen
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Neil Smith
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Ville Ratas
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ekaterina Biterova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Sudarshan N. Murthy
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - M. Tanvir Rahman
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Shruthi Sridhar
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Gabriele Cordara
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jaime Prilusky
- Bioinformatics and Biological Computing Unit, Life Science Core Facility, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Life Science Core Facility, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lari Lehtiö
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Alun W. Ashton
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Joel L. Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rik K. Wierenga
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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4
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Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol 2017; 599:157-196. [PMID: 29746239 DOI: 10.1016/bs.mie.2017.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.
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Affiliation(s)
- Chi-Lin Tsai
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - John A Tainer
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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5
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Healey EG, Bishop B, Elegheert J, Bell CH, Padilla-Parra S, Siebold C. Repulsive guidance molecule is a structural bridge between neogenin and bone morphogenetic protein. Nat Struct Mol Biol 2015; 22:458-65. [PMID: 25938661 PMCID: PMC4456160 DOI: 10.1038/nsmb.3016] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/31/2015] [Indexed: 02/07/2023]
Abstract
Repulsive guidance molecules (RGMs) control crucial processes including cell motility, adhesion, immune-cell regulation and systemic iron metabolism. RGMs signal via the neogenin (NEO1) and the bone morphogenetic protein (BMP) pathways. Here, we report crystal structures of the N-terminal domains of all human RGM family members in complex with the BMP ligand BMP2, revealing a new protein fold and a conserved BMP-binding mode. Our structural and functional data suggest a pH-linked mechanism for RGM-activated BMP signaling and offer a rationale for RGM mutations causing juvenile hemochromatosis. We also determined the crystal structure of the ternary BMP2-RGM-NEO1 complex, which, along with solution scattering and live-cell super-resolution fluorescence microscopy, indicates BMP-induced clustering of the RGM-NEO1 complex. Our results show how RGM acts as the central hub that links BMP and NEO1 and physically connects these fundamental signaling pathways.
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Affiliation(s)
- Eleanor G Healey
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benjamin Bishop
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan Elegheert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian H Bell
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sergi Padilla-Parra
- 1] Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [2] Cellular Imaging Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian Siebold
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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6
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Zhao Y, Ren J, Padilla-Parra S, Fry EE, Stuart DI. Lysosome sorting of β-glucocerebrosidase by LIMP-2 is targeted by the mannose 6-phosphate receptor. Nat Commun 2014; 5:4321. [PMID: 25027712 PMCID: PMC4104448 DOI: 10.1038/ncomms5321] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/05/2014] [Indexed: 01/25/2023] Open
Abstract
The integral membrane protein LIMP-2 has been a paradigm for mannose 6-phosphate receptor (MPR) independent lysosomal targeting, binding to β-glucocerebrosidase (β-GCase) and directing it to the lysosome, before dissociating in the late-endosomal/lysosomal compartments. Here we report structural results illuminating how LIMP-2 binds and releases β-GCase according to changes in pH, via a histidine trigger, and suggesting that LIMP-2 localizes the ceramide portion of the substrate adjacent to the β-GCase catalytic site. Remarkably, we find that LIMP-2 bears P-Man9GlcNAc2 covalently attached to residue N325, and that it binds MPR, via mannose 6-phosphate, with a similar affinity to that observed between LIMP-2 and β-GCase. The binding sites for β-GCase and the MPR are functionally separate, so that a stable ternary complex can be formed. By fluorescence lifetime imaging microscopy, we also demonstrate that LIMP-2 interacts with MPR in living cells. These results revise the accepted view of LIMP-2-β-GCase lysosomal targeting.
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Affiliation(s)
- Yuguang Zhao
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- These authors contributed equally to this work
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- These authors contributed equally to this work
| | - Sergi Padilla-Parra
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
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7
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Nachtergaele S, Whalen DM, Mydock LK, Zhao Z, Malinauskas T, Krishnan K, Ingham PW, Covey DF, Siebold C, Rohatgi R. Structure and function of the Smoothened extracellular domain in vertebrate Hedgehog signaling. eLife 2013; 2:e01340. [PMID: 24171105 PMCID: PMC3809587 DOI: 10.7554/elife.01340] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/26/2013] [Indexed: 12/14/2022] Open
Abstract
The Hedgehog (Hh) signal is transduced across the membrane by the heptahelical protein Smoothened (Smo), a developmental regulator, oncoprotein and drug target in oncology. We present the 2.3 Å crystal structure of the extracellular cysteine rich domain (CRD) of vertebrate Smo and show that it binds to oxysterols, endogenous lipids that activate Hh signaling. The oxysterol-binding groove in the Smo CRD is analogous to that used by Frizzled 8 to bind to the palmitoleyl group of Wnt ligands and to similar pockets used by other Frizzled-like CRDs to bind hydrophobic ligands. The CRD is required for signaling in response to native Hh ligands, showing that it is an important regulatory module for Smo activation. Indeed, targeting of the Smo CRD by oxysterol-inspired small molecules can block signaling by all known classes of Hh activators and by clinically relevant Smo mutants. DOI:http://dx.doi.org/10.7554/eLife.01340.001.
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MESH Headings
- Animals
- Binding Sites
- Crystallography, X-Ray
- Embryo, Nonmammalian
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Developmental
- Hedgehog Proteins/chemistry
- Hedgehog Proteins/genetics
- Hedgehog Proteins/metabolism
- Ligands
- Mice
- Models, Molecular
- Protein Binding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Signal Transduction
- Smoothened Receptor
- Sterols/chemistry
- Structure-Activity Relationship
- Zebrafish/genetics
- Zebrafish/growth & development
- Zebrafish/metabolism
- Zebrafish Proteins/antagonists & inhibitors
- Zebrafish Proteins/chemistry
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Sigrid Nachtergaele
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Daniel M Whalen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Laurel K Mydock
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
| | - Zhonghua Zhao
- A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kathiresan Krishnan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
| | - Philip W Ingham
- A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
- Lee Kong Chian School of Medicine, Imperial College London/Nanyang Technological University, Singapore, Singapore
| | - Douglas F Covey
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
| | - Christian Siebold
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Rajat Rohatgi
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
- Department of Medicine, Stanford University School of Medicine, Stanford, United States
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8
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Janssen BJ, Malinauskas T, Weir GA, Cader MZ, Siebold C, Jones EY. Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex. Nat Struct Mol Biol 2012; 19:1293-9. [PMID: 23104057 PMCID: PMC3590443 DOI: 10.1038/nsmb.2416] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/18/2012] [Indexed: 12/15/2022]
Abstract
Co-receptors add complexity to cell-cell signaling systems. The secreted semaphorin 3s (Sema3s) require a co-receptor, neuropilin (Nrp), to signal through plexin As (PlxnAs) in functions ranging from axon guidance to bone homeostasis, but the role of the co-receptor is obscure. Here we present the low-resolution crystal structure of a mouse semaphorin-plexin-Nrp complex alongside unliganded component structures. Dimeric semaphorin, two copies of plexin and two copies of Nrp are arranged as a dimer of heterotrimers. In each heterotrimer subcomplex, semaphorin contacts plexin, similar to in co-receptor-independent signaling complexes. The Nrp1s cross brace the assembly, bridging between sema domains of the Sema3A and PlxnA2 subunits from the two heterotrimers. Biophysical and cellular analyses confirm that this Nrp binding mode stabilizes a canonical, but weakened, Sema3-PlxnA interaction, adding co-receptor control over the mechanism by which receptor dimerization and/or oligomerization triggers signaling.
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Affiliation(s)
- Bert J.C. Janssen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Greg A. Weir
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - M. Zameel Cader
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Christian Siebold
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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9
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Bell CH, Aricescu AR, Jones EY, Siebold C. A dual binding mode for RhoGTPases in plexin signalling. PLoS Biol 2011; 9:e1001134. [PMID: 21912513 PMCID: PMC3166162 DOI: 10.1371/journal.pbio.1001134] [Citation(s) in RCA: 52] [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: 01/26/2011] [Accepted: 07/20/2011] [Indexed: 11/19/2022] Open
Abstract
A novel binding site for RhoGTPases on the intracellular region of plexins induces a trimeric ligand—receptor arrangement that appears crucial for plexin function. Plexins are cell surface receptors for the semaphorin family of cell guidance cues. The cytoplasmic region comprises a Ras GTPase-activating protein (GAP) domain and a RhoGTPase binding domain. Concomitant binding of extracellular semaphorin and intracellular RhoGTPase triggers GAP activity and signal transduction. The mechanism of this intricate regulation remains elusive. We present two crystal structures of the human Plexin-B1 cytoplasmic region in complex with a constitutively active RhoGTPase, Rac1. The structure of truncated Plexin-B1-Rac1 complex provides no mechanism for coupling RhoGTPase and Ras binding sites. On inclusion of the juxtamembrane helix, a trimeric structure of Plexin-B1-Rac1 complexes is stabilised by a second, novel, RhoGTPase binding site adjacent to the Ras site. Site-directed mutagenesis combined with cellular and biophysical assays demonstrate that this new binding site is essential for signalling. Our findings are consistent with a model in which extracellular and intracellular plexin clustering events combine into a single signalling output. Axon guidance is fundamental to the development of the central nervous system. The growing axon is guided to its correct location by a plethora of extracellular signals. One of the most important extracellular signals is semaphorin, which binds to plexin receptors on the axon. Usually, this kind of extracellular ligand binding is sufficient to transmit the extracellular signal to the intracellular space to trigger changes in the cell, like axon growth. However, activation of plexin receptors requires a “dual” ligand binding: semaphorin on the extracellular side, and a RhoGTPase on the intracellular side. Signal transduction can only occur if both ligands are present. How this intricate regulation mechanism is organized and how concomitant ligand binding can be integrated into a single signalling output within the cell has remained largely unclear. Here, we present crystal structures of one plexin receptor, Plexin-B1, in complex with an intracellular RhoGTPase ligand (Rac1) and show that binding of Rac1 brings together three Plexin-B1 molecules. In this trimeric arrangement each plexin molecule interacts with two Rac1 ligand molecules. This leads to a previously unidentified plexin-Rac1 ligand interface that is crucial for its function. Further biophysical and cellular analysis in combination with previous findings on the extracellular plexin-semaphorin complex allow us to propose a model for how ligand-induced clustering events on the extra- as well as intracellular side are combined to trigger signal transduction.
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Affiliation(s)
- Christian H. Bell
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - A. Radu Aricescu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (EYJ); (CS)
| | - Christian Siebold
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (EYJ); (CS)
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10
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Daniel E, Lin B, Diprose JM, Griffiths SL, Morris C, Berry IM, Owens RJ, Blake R, Wilson KS, Stuart DI, Esnouf RM. xtalPiMS: a PiMS-based web application for the management and monitoring of crystallization trials. J Struct Biol 2011; 175:230-5. [PMID: 21605683 PMCID: PMC3477317 DOI: 10.1016/j.jsb.2011.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 04/29/2011] [Accepted: 05/07/2011] [Indexed: 11/29/2022]
Abstract
A major advance in protein structure determination has been the advent of nanolitre-scale crystallization and (in a high-throughput environment) the development of robotic systems for storing and imaging crystallization trials. Most of these trials are carried out in 96-well (or higher density) plates and managing them is a significant information management challenge. We describe xtalPiMS, a web-based application for the management and monitoring of crystallization trials. xtalPiMS has a user-interface layer based on the standards of the Protein Information Management System (PiMS) and a database layer which links the crystallization trial images to the meta-data associated with a particular crystallization trial. The user interface has been optimized for the efficient monitoring of high-throughput environments with three different automated imagers and work to support a fourth imager is in progress, but it can even be of use without robotics. The database can either be a PiMS database or a legacy database for which a suitable mapping layer has been developed.
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Affiliation(s)
- Ed Daniel
- CSED, STFC Daresbury Laboratory, Warrington WA4 4AD, UK
| | - Bill Lin
- CSED, STFC Daresbury Laboratory, Warrington WA4 4AD, UK
| | - Jonathan M. Diprose
- Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
- The Oxford Protein Production Facility UK, Research Complex at Harwell, Rutherford Appleton Laboratory, R92, Harwell Oxford, Didcot OX11 0FA, UK
| | - Susanne L. Griffiths
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Chris Morris
- CSED, STFC Daresbury Laboratory, Warrington WA4 4AD, UK
| | - Ian M. Berry
- Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Raymond J. Owens
- Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
- The Oxford Protein Production Facility UK, Research Complex at Harwell, Rutherford Appleton Laboratory, R92, Harwell Oxford, Didcot OX11 0FA, UK
| | - Richard Blake
- CSED, STFC Daresbury Laboratory, Warrington WA4 4AD, UK
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Robert M. Esnouf
- Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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11
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Paithankar KS, Sørensen HO, Wright JP, Schmidt S, Poulsen HF, Garman EF. Simultaneous X-ray diffraction from multiple single crystals of macromolecules. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:608-18. [DOI: 10.1107/s0907444911015617] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/25/2011] [Indexed: 11/11/2022]
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12
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Alves RM, Feliciano PR, Sampaio SV, Nonato MC. A rational protocol for the successful crystallization of L-amino-acid oxidase from Bothrops atrox. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:475-8. [PMID: 21505245 PMCID: PMC3080154 DOI: 10.1107/s1744309111003770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 01/29/2011] [Indexed: 11/10/2022]
Abstract
Despite the valuable contributions of robotics and high-throughput approaches to protein crystallization, the role of an experienced crystallographer in the evaluation and rationalization of a crystallization process is still crucial to obtaining crystals suitable for X-ray diffraction measurements. In this work, the difficult task of crystallizing the flavoenzyme L-amino-acid oxidase purified from Bothrops atrox snake venom was overcome by the development of a protocol that first required the identification of a non-amorphous precipitate as a promising crystallization condition followed by the implementation of a methodology that combined crystallization in the presence of oil and seeding techniques. Crystals were obtained and a complete data set was collected to 2.3 Å resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 73.64, b = 123.92, c = 105.08 Å, β = 96.03°. There were four protein subunits in the asymmetric unit, which gave a Matthews coefficient V(M) of 2.12 Å(3) Da(-1), corresponding to 42% solvent content. The structure has been solved by molecular-replacement techniques.
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Affiliation(s)
- Raquel Melo Alves
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirao Preto–FCFRP–USP, Avenida do Café s/n, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | - Patricia Rosa Feliciano
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–FCFRP–USP, Avenida do Café s/n, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | - Suely Vilela Sampaio
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirao Preto–FCFRP–USP, Avenida do Café s/n, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–FCFRP–USP, Avenida do Café s/n, Ribeirão Preto, 14040-903 São Paulo, Brazil
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13
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Janssen BJC, Robinson RA, Pérez-Brangulí F, Bell CH, Mitchell KJ, Siebold C, Jones EY. Structural basis of semaphorin-plexin signalling. Nature 2010; 467:1118-22. [PMID: 20877282 DOI: 10.1038/nature09468] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 09/06/2010] [Indexed: 01/25/2023]
Abstract
Cell-cell signalling of semaphorin ligands through interaction with plexin receptors is important for the homeostasis and morphogenesis of many tissues and is widely studied for its role in neural connectivity, cancer, cell migration and immune responses. SEMA4D and Sema6A exemplify two diverse vertebrate, membrane-spanning semaphorin classes (4 and 6) that are capable of direct signalling through members of the two largest plexin classes, B and A, respectively. In the absence of any structural information on the plexin ectodomain or its interaction with semaphorins the extracellular specificity and mechanism controlling plexin signalling has remained unresolved. Here we present crystal structures of cognate complexes of the semaphorin-binding regions of plexins B1 and A2 with semaphorin ectodomains (human PLXNB1(1-2)-SEMA4D(ecto) and murine PlxnA2(1-4)-Sema6A(ecto)), plus unliganded structures of PlxnA2(1-4) and Sema6A(ecto). These structures, together with biophysical and cellular assays of wild-type and mutant proteins, reveal that semaphorin dimers independently bind two plexin molecules and that signalling is critically dependent on the avidity of the resulting bivalent 2:2 complex (monomeric semaphorin binds plexin but fails to trigger signalling). In combination, our data favour a cell-cell signalling mechanism involving semaphorin-stabilized plexin dimerization, possibly followed by clustering, which is consistent with previous functional data. Furthermore, the shared generic architecture of the complexes, formed through conserved contacts of the amino-terminal seven-bladed β-propeller (sema) domains of both semaphorin and plexin, suggests that a common mode of interaction triggers all semaphorin-plexin based signalling, while distinct insertions within or between blades of the sema domains determine binding specificity.
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Affiliation(s)
- Bert J C Janssen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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14
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Walter TS, Liu C, Huang P, Zhang S, Wedderburn LR, Gao B, Owens RJ, Stuart DI, Tang P, Ren J. Crystallization and preliminary X-ray analysis of mouse RANK and its complex with RANKL. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:597-600. [PMID: 19478440 DOI: 10.1107/s1744309109015735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 04/27/2009] [Indexed: 01/01/2023]
Abstract
The interaction between the TNF-family molecule receptor activator of NF-kappaB ligand (RANKL) and its receptor RANK induces osteoclast formation, activation and survival in the process of bone remodelling. RANKL-RANK also plays critical roles in T-cell/dendritic cell communication and lymph-node formation and in a variety of pathologic conditions such as tumour-cell migration and bone metastasis. Both the ectodomain of mouse RANKL and the extracellular domain of mouse RANK have been cloned, expressed and purified. Crystals of RANK alone and of RANK in complex with RANKL have been obtained that are suitable for structure determination.
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Affiliation(s)
- Thomas S Walter
- Division of Structural Biology and Oxford Protein Production Facility, The Wellcome Trust Centre for Human Genetics, The Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
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15
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Snell EH, Luft JR, Potter SA, Lauricella AM, Gulde SM, Malkowski MG, Koszelak-Rosenblum M, Said MI, Smith JL, Veatch CK, Collins RJ, Franks G, Thayer M, Cumbaa C, Jurisica I, Detitta GT. Establishing a training set through the visual analysis of crystallization trials. Part I: approximately 150,000 images. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2008; 64:1123-30. [PMID: 19020350 PMCID: PMC2631114 DOI: 10.1107/s0907444908028047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 09/02/2008] [Indexed: 11/12/2022]
Abstract
As part of a training set for automated image analysis, ∼150 000 images of crystallization experiments from 96 diverse macromolecules have been visually classified within seven categories. Outcomes and trends are analyzed. Structural crystallography aims to provide a three-dimensional representation of macromolecules. Many parts of the multistep process to produce the three-dimensional structural model have been automated, especially through various structural genomics projects. A key step is the production of crystals for diffraction. The target macromolecule is combined with a large and chemically diverse set of cocktails with some leading ideally, but infrequently, to crystallization. A variety of outcomes will be observed during these screening experiments that typically require human interpretation for classification. Human interpretation is neither scalable nor objective, highlighting the need to develop an automatic computer-based image classification. As a first step towards automated image classification, 147 456 images representing crystallization experiments from 96 different macromolecular samples were manually classified. Each image was classified by three experts into seven predefined categories or their combinations. The resulting data where all three observers are in agreement provides one component of a truth set for the development and rigorous testing of automated image-classification systems and provides information about the chemical cocktails used for crystallization. In this paper, the details of this study are presented.
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Affiliation(s)
- Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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16
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Paired Receptor Specificity Explained by Structures of Signal Regulatory Proteins Alone and Complexed with CD47. Mol Cell 2008; 31:266-77. [DOI: 10.1016/j.molcel.2008.05.026] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 03/13/2008] [Accepted: 05/13/2008] [Indexed: 11/20/2022]
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17
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Busso D, Thierry JC, Moras D. The structural biology and genomics platform in strasbourg: an overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2008; 426:523-36. [PMID: 18542888 DOI: 10.1007/978-1-60327-058-8_35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This chapter describes the modules and facilities of the Structural Biology and Genomics Platform (SBGP), Strasbourg, France. The platform consists of three modules (cloning, mini-expression screening; optimization-large scale protein production; characterization, crystallization) with dedicated scientists, and other facilities for purifying recombinant proteins and solving three-dimensional (3D) structures. Strong collaborations have been established with the Integrative Bioinformatics and Genomics group, located in the same institition, for target selection and domains definition. To handle large numbers of samples, classical and new protocols were adapted to automation, increasing reproducibility and reducing error risks as well. Using the platform and its facilities, over 2,000 expression vectors have been constructed and more than 40 novel structures, of mostly human proteins, have been solved.
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Affiliation(s)
- Didier Busso
- Structural Biology and Genomics Platform, IGBMC, CNRS/INSERM/Université Louis Pasteur, Illkirch, France
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18
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Walter TS, Mancini EJ, Kadlec J, Graham SC, Assenberg R, Ren J, Sainsbury S, Owens RJ, Stuart DI, Grimes JM, Harlos K. Semi-automated microseeding of nanolitre crystallization experiments. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:14-8. [PMID: 18097093 PMCID: PMC2373990 DOI: 10.1107/s1744309107057260] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 11/09/2007] [Indexed: 11/10/2022]
Abstract
A simple semi-automated microseeding procedure for nanolitre crystallization experiments is described. Firstly, a microseed stock solution is made from microcrystals using a Teflon bead. A dilution series of this microseed stock is then prepared and dispensed as 100 nl droplets into 96-well crystallization plates, facilitating the incorporation of seeding into high-throughput crystallization pipelines. This basic microseeding procedure has been modified to include additive-screening and cross-seeding methods. Five examples in which these techniques have been used successfully are described.
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Affiliation(s)
- Thomas S. Walter
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Erika J. Mancini
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jan Kadlec
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Stephen C. Graham
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - René Assenberg
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jingshan Ren
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Sarah Sainsbury
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Raymond J. Owens
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - David I. Stuart
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jonathan M. Grimes
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Karl Harlos
- Oxford Protein Production Facility (OPPF) and Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
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19
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Mancini EJ, Assenberg R, Verma A, Walter TS, Tuma R, Grimes JM, Owens RJ, Stuart DI. Structure of the Murray Valley encephalitis virus RNA helicase at 1.9 Angstrom resolution. Protein Sci 2007; 16:2294-300. [PMID: 17893366 PMCID: PMC2204129 DOI: 10.1110/ps.072843107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Murray Valley encephalitis virus (MVEV), a mosquito-borne flavivirus endemic to Australia, is closely related to Japanese encephalitis virus and West Nile virus. Nonstructural protein 3 (NS3) is a multifunctional enzyme with serine protease and DEXH/D-box helicase domains, whose activity is central to flavivirus replication and is therefore a possible target for anti-flaviviral compounds. Cloning, purification, and crystal structure determination to 1.9 Angstrom resolution of the NS3 helicase of MVEV and characterization of its enzymatic activity is reported. Comparison with the structures of helicases from related viruses supports a possible mechanism of ATP hydrolysis-driven strand separation.
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Affiliation(s)
- Erika J Mancini
- Division of Structural Biology and Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Oxford, UK
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20
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Derewenda ZS. Protein crystallization in drug design: towards a rational approach. Expert Opin Drug Discov 2007; 2:1329-40. [PMID: 23484529 DOI: 10.1517/17460441.2.10.1329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
X-ray crystallography is the method of choice for the detailed characterization of stereochemistry of interactions of drug leads and potential chemotherapeutics with their protein targets. The resulting atomic models allow for rational enhancement of the lead properties and consequently for the design of high-affinity inhibitors. However, a major bottleneck of the technique is the requirement for the protein and its complexes to yield high quality single crystals. Furthermore, it is highly desirable that such crystals diffract to high resolution, preferably ≥ 1.2 Å, revealing the structures in atomic detail. Unfortunately, only a small portion of proteins readily crystallize in that fashion. New approaches are being developed to circumvent this problem. One proposed option includes rational protein surface engineering to systematically improve the crystallizability of the protein. This is accomplished by creating surface patches readily mediating weak, but specific, intermolecular interactions that take on the role of crystal contacts during nucleation and crystal growth phase.
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Affiliation(s)
- Zygmunt S Derewenda
- University of Virginia, Integrated Center for Structure and Function Innovation (PSI2), Departments of Molecular Physiology and Biological Physics, PO Box 800736, Jordan Hall, Charlottesville, VA 22908-0736, USA +1 434 243 6842 ; +1 434 982 1616 ;
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21
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Assenberg R, Ren J, Verma A, Walter TS, Alderton D, Hurrelbrink RJ, Fuller SD, Bressanelli S, Owens RJ, Stuart DI, Grimes JM. Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues. J Gen Virol 2007; 88:2228-2236. [PMID: 17622627 DOI: 10.1099/vir.0.82757-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have determined the high resolution crystal structure of the methyltransferase domain of the NS5 polypeptide from the Murray Valley encephalitis virus. This domain is unusual in having both the N7 and 2'-O methyltransferase activity required for Cap 1 synthesis. We have also determined structures for complexes of this domain with nucleotides and cap analogues providing information on cap binding, based on which we suggest a model of how the sequential methylation of the N7 and 2'-O groups of the cap may be coordinated.
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Affiliation(s)
- René Assenberg
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jingshan Ren
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Anil Verma
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Thomas S Walter
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David Alderton
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Robert J Hurrelbrink
- Department of Virology, Telethon Institute for Child Health Research, University of Western Australia, Perth, WA 6008, Australia
| | - Stephen D Fuller
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stéphane Bressanelli
- INRA, UMR1157, Virologie Moléculaire et Structurale, 91198 Gif sur Yvette, France
- CNRS, UMR2472, IFR 115, Virologie Moléculaire et Structurale, 91198 Gif sur Yvette, France
| | - Raymond J Owens
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
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22
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Meier C, Aricescu AR, Assenberg R, Aplin RT, Gilbert RJ, Grimes JM, Stuart DI. The crystal structure of ORF-9b, a lipid binding protein from the SARS coronavirus. Structure 2006; 14:1157-65. [PMID: 16843897 PMCID: PMC7126280 DOI: 10.1016/j.str.2006.05.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 04/10/2006] [Accepted: 05/01/2006] [Indexed: 11/04/2022]
Abstract
To achieve the greatest output from their limited genomes, viruses frequently make use of alternative open reading frames, in which translation is initiated from a start codon within an existing gene and, being out of frame, gives rise to a distinct protein product. These alternative protein products are, as yet, poorly characterized structurally. Here we report the crystal structure of ORF-9b, an alternative open reading frame within the nucleocapsid (N) gene from the SARS coronavirus. The protein has a novel fold, a dimeric tent-like β structure with an amphipathic surface, and a central hydrophobic cavity that binds lipid molecules. This cavity is likely to be involved in membrane attachment and, in mammalian cells, ORF-9b associates with intracellular vesicles, consistent with a role in the assembly of the virion. Analysis of ORF-9b and other overlapping genes suggests that they provide snapshots of the early evolution of novel protein folds.
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Affiliation(s)
- Christoph Meier
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - A. Radu Aricescu
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Rene Assenberg
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Robin T. Aplin
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Robert J.C. Gilbert
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Jonathan M. Grimes
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - David I. Stuart
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
- Ph: 44-1865-287567; Fax: 44-1865-287547
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23
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Amin AA, Faux NG, Fenalti G, Williams G, Bernadou A, Daglish B, Keefe K, Middleton S, Rae J, Tetis K, Law RHP, Fulton KF, Rossjohn J, Whisstock JC, Buckle AM. Managing and mining protein crystallization data. Proteins 2005; 62:4-7. [PMID: 16287081 DOI: 10.1002/prot.20776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The crystallization of macromolecules remains a major bottleneck in structural biology. The routine screening of more than one thousand crystallization conditions and subsequent optimization by fine screening presents a challenge to conventional laboratory notebook keeping. In addition, the development of high-throughput robotic crystallization and imaging systems presents a pressing need for low-cost laboratory information management system (LIMS). Here we describe CLIMS2, a crystallization LIMS that features a simple, user-friendly graphical interface, allowing the storage, management, retrieval and mining of crystallization data. The CLIMS2 executable and documentation is freely available at http://clims.med.monash.edu.au.
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Affiliation(s)
- Abdullah A Amin
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
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24
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Abrescia NGA, Kivelä HM, Grimes JM, Bamford JKH, Bamford DH, Stuart DI. Preliminary crystallographic analysis of the major capsid protein P2 of the lipid-containing bacteriophage PM2. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:762-5. [PMID: 16511151 PMCID: PMC1952355 DOI: 10.1107/s174430910502141x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 07/05/2005] [Indexed: 11/10/2022]
Abstract
PM2 (Corticoviridae) is a dsDNA bacteriophage which contains a lipid membrane beneath its icosahedral capsid. In this respect it resembles bacteriophage PRD1 (Tectiviridae), although it is not known whether the similarity extends to the detailed molecular architecture of the virus, for instance the fold of the major coat protein P2. Structural analysis of PM2 has been initiated and virus-derived P2 has been crystallized by sitting-nanodrop vapour diffusion. Crystals of P2 have been obtained in space group P2(1)2(1)2, with two trimers in the asymmetric unit and unit-cell parameters a = 171.1, b = 78.7, c = 130.1 A. The crystals diffract to 4 A resolution at the ESRF BM14 beamline (Grenoble, France) and the orientation of the non-crystallographic threefold axes, the spatial relationship between the two trimers and the packing of the trimers within the unit cell have been determined. The trimers form tightly packed layers consistent with the crystal morphology, possibly recapitulating aspects of the arrangement of subunits in the virus.
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Affiliation(s)
- Nicola G. A. Abrescia
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
| | - Hanna M. Kivelä
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56, Viikinkaari 5, 00014 University of Helsinki, Finland
| | - Jonathan M. Grimes
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
| | - Jaana K. H. Bamford
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56, Viikinkaari 5, 00014 University of Helsinki, Finland
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56, Viikinkaari 5, 00014 University of Helsinki, Finland
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
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