1
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Caballero I, Castellví A, Triviño J, Jiménez E, Soler N, Borges R, Usón I. ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins. Protein Sci 2024; 33:e5136. [PMID: 39150227 PMCID: PMC11328115 DOI: 10.1002/pro.5136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/07/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024]
Abstract
Crystallography at low resolution must determine the atomic model from less experimental observations, which is challenging in the absence of a model. In addition, model bias is more severe when independent experimental data are scarce. Our methods solve the phase problem by combining the location of accurate model fragments using Phaser with density modification and interpretation of the resulting maps using SHELXE. From a partial, correct structure, the density modification process and the stereochemical constraints draw the rest of the structure, validating the result. This same principle is now exploited at low resolution. Coiled coils are important, ubiquitous structures but notoriously difficult to phase and to predict. Both correct solutions and incorrect ones are poorly discriminated by the crystallographic figures of merit as long as helices are correctly oriented. We incorporate coiled-coil verification, designed to set up competing, incompatible structural hypotheses to probe both the results and establish the power of the data to discriminate them. Efficiency of coiled-coil phasing and validation in test cases from 3 to 4 Å is demonstrated in ARCIMBOLDO_LITE, placing single helices, and in ARCIMBOLDO_SHREDDER, with fragments derived from AlphaFold models. SHELXE tracing at low resolution has been enhanced, maintaining its local character but extending the environment assessment. For non-helical structures, verification is demonstrated in the fragment location process. Its use is exemplified with the solution of the VSR1 structure at 3.5 Å, depending on LLG optimization and the emergence of new features in the electron density. Relying on verification, we have extended the use of the ARCIMBOLDO software to low resolution.
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Affiliation(s)
- Iracema Caballero
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Albert Castellví
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Josep Triviño
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Elisabet Jiménez
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Nicolas Soler
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Rafael Borges
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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2
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Alcorlo M, Abdullah MR, Steil L, Sotomayor F, López-de Oro L, de Castro S, Velázquez S, Kohler TP, Jiménez E, Medina A, Usón I, Keller LE, Bradshaw JL, McDaniel LS, Camarasa MJ, Völker U, Hammerschmidt S, Hermoso JA. Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci. PLoS Pathog 2024; 20:e1011883. [PMID: 38838057 PMCID: PMC11192437 DOI: 10.1371/journal.ppat.1011883] [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: 12/07/2023] [Revised: 06/21/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024] Open
Abstract
ATP-binding cassette (ABC) transport systems are crucial for bacteria to ensure sufficient uptake of nutrients that are not produced de novo or improve the energy balance. The cell surface of the pathobiont Streptococcus pneumoniae (pneumococcus) is decorated with a substantial array of ABC transporters, critically influencing nasopharyngeal colonization and invasive infections. Given the auxotrophic nature of pneumococci for certain amino acids, the Ami ABC transporter system, orchestrating oligopeptide uptake, becomes indispensable in host compartments lacking amino acids. The system comprises five exposed Oligopeptide Binding Proteins (OBPs) and four proteins building the ABC transporter channel. Here, we present a structural analysis of all the OBPs in this system. Multiple crystallographic structures, capturing both open and closed conformations along with complexes involving chemically synthesized peptides, have been solved at high resolution providing insights into the molecular basis of their diverse peptide specificities. Mass spectrometry analysis of oligopeptides demonstrates the unexpected remarkable promiscuity of some of these proteins when expressed in Escherichia coli, displaying affinity for a wide range of peptides. Finally, a model is proposed for the complete Ami transport system in complex with its various OBPs. We further disclosed, through in silico modelling, some essential structural changes facilitating oligopeptide transport into the cellular cytoplasm. Thus, the structural analysis of the Ami system provides valuable insights into the mechanism and specificity of oligopeptide binding by the different OBPs, shedding light on the intricacies of the uptake mechanism and the in vivo implications for this human pathogen.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Mohammed R. Abdullah
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Leif Steil
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Francisco Sotomayor
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Laura López-de Oro
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | | | | | - Thomas P. Kohler
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona; Spain
| | - Lance E. Keller
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Jessica L. Bradshaw
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Larry S. McDaniel
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | | | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
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3
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Hernández-Rocamora VM, Molina R, Alba A, Carrasco-López C, Rojas-Altuve A, Panjikar S, Medina A, Usón I, Alfonso C, Galán B, Rivas G, Hermoso JA, Sanz JM. Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins. Int J Biol Macromol 2024; 254:127935. [PMID: 37949283 DOI: 10.1016/j.ijbiomac.2023.127935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
PaaX is a transcriptional repressor of the phenylacetic acid (PAA) catabolic pathway, a central route for bacterial aerobic degradation of aromatic compounds. Induction of the route is achieved through the release of PaaX from its promoter sequences by the first compound of the pathway, phenylacetyl-coenzyme A (PA-CoA). We report the crystal structure of PaaX from Escherichia coli W. PaaX displays a novel type of fold for transcription regulators, showing a dimeric conformation where the monomers present a three-domain structure: an N-terminal winged helix-turn-helix domain, a dimerization domain similar to the Cas2 protein and a C-terminal domain without structural homologs. The domains are separated by a crevice amenable to harbour a PA-CoA molecule. The biophysical characterization of the protein in solution confirmed several hints predicted from the structure, i.e. its dimeric conformation, a modest importance of cysteines and a high dependence of solubility and thermostability on ionic strength. At a moderately acidic pH, the protein formed a stable folding intermediate with remaining α-helical structure, a disrupted tertiary structure and exposed hydrophobic patches. Our results provide valuable information to understand the stability and mechanism of PaaX and pave the way for further analysis of other regulators with similar structural configurations.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Av. Universidad, s/n, E-03202 Elche, Alicante, Spain; Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alejandra Alba
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alzoray Rojas-Altuve
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain; ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
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4
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Usón I, Sheldrick GM. Modes and model building in SHELXE. Acta Crystallogr D Struct Biol 2024; 80:4-15. [PMID: 38088896 PMCID: PMC10833347 DOI: 10.1107/s2059798323010082] [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: 10/01/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024] Open
Abstract
Density modification is a standard step to provide a route for routine structure solution by any experimental phasing method, with single-wavelength or multi-wavelength anomalous diffraction being the most popular methods, as well as to extend fragments or incomplete models into a full solution. The effect of density modification on the starting maps from either source is illustrated in the case of SHELXE. The different modes in which the program can run are reviewed; these include less well known uses such as reading external phase values and weights or phase distributions encoded in Hendrickson-Lattman coefficients. Typically in SHELXE, initial phases are calculated from experimental data, from a partial model or map, or from a combination of both sources. The initial phase set is improved and extended by density modification and, if the resolution of the data and the type of structure permits, polyalanine tracing. As a feature to systematically eliminate model bias from phases derived from predicted models, the trace can be set to exclude the area occupied by the starting model. The trace now includes an extension into the gamma position or hydrophobic and aromatic side chains if a sequence is provided, which is performed in every tracing cycle. Once a correlation coefficient of over 30% between the structure factors calculated from such a trace and the native data indicates that the structure has been solved, the sequence is docked in all model-building cycles and side chains are fitted if the map supports it. The extensions to the tracing algorithm brought in to provide a complete model are discussed. The improvement in phasing performance is assessed using a set of tests.
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Affiliation(s)
- Isabel Usón
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, Barcelona, E-08003, Spain
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixach, 15, Barcelona, 08028, Spain
| | - George M. Sheldrick
- Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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5
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Brehm W, Triviño J, Krahn JM, Usón I, Diederichs K. XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J Appl Crystallogr 2023; 56:1585-1594. [PMID: 37791359 PMCID: PMC10543682 DOI: 10.1107/s1600576723007057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
XDSGUI is a lightweight graphical user interface (GUI) for the XDS, SHELX and ARCIMBOLDO program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X-ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user-modifiable and user-extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.
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Affiliation(s)
- Wolfgang Brehm
- Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Josep Triviño
- Instituto de Biologia Molecular de Barcelona (IBMB), Baldiri Reixach 15, Barcelona 08028, Spain
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Isabel Usón
- Instituto de Biologia Molecular de Barcelona (IBMB), Baldiri Reixach 15, Barcelona 08028, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz 78457, Germany
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6
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Simpkin AJ, Caballero I, McNicholas S, Stevenson K, Jiménez E, Sánchez Rodríguez F, Fando M, Uski V, Ballard C, Chojnowski G, Lebedev A, Krissinel E, Usón I, Rigden DJ, Keegan RM. Predicted models and CCP4. Acta Crystallogr D Struct Biol 2023; 79:806-819. [PMID: 37594303 PMCID: PMC10478639 DOI: 10.1107/s2059798323006289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Iracema Caballero
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
| | - Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Kyle Stevenson
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
| | - Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Maria Fando
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Ville Uski
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Charles Ballard
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrey Lebedev
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Eugene Krissinel
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Ronan M. Keegan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
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7
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Richards L, Flores MD, Millán C, Glynn C, Zee CT, Sawaya MR, Gallagher-Jones M, Borges RJ, Usón I, Rodriguez JA. Fragment-Based Ab Initio Phasing of Peptidic Nanocrystals by MicroED. ACS BIO & MED CHEM AU 2023; 3:201-210. [PMID: 37096030 PMCID: PMC10119933 DOI: 10.1021/acsbiomedchemau.2c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 04/26/2023]
Abstract
Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its de novo determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.
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Affiliation(s)
- Logan
S. Richards
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Maria D. Flores
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Claudia Millán
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
| | - Calina Glynn
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Chih-Te Zee
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Michael R. Sawaya
- Department
of Biological Chemistry and Department of Chemistry and Biochemistry, University of California Los Angeles (UCLA), Howard
Hughes Medical Institute (HHMI), UCLA-DOE Institute for Genomics and
Proteomics, Los Angeles, California 90095, United States
| | - Marcus Gallagher-Jones
- Correlated
Imaging, The Rosalind Franklin Institute, Harwell Science & Innovation
Campus, Rutherford Avenue, Harwell, Didcot OX11 0GD, United Kingdom
| | - Rafael J. Borges
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
- ICREA,
Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Jose A. Rodriguez
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
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8
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Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria. mBio 2023; 14:e0336322. [PMID: 36602305 PMCID: PMC9973260 DOI: 10.1128/mbio.03363-22] [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] [Indexed: 01/06/2023] Open
Abstract
Bacteria have evolved a sophisticated array of signal transduction systems that allow them to adapt their physiology and metabolism to changing environmental conditions. Typically, these systems recognize signals through dedicated ligand binding domains (LBDs) to ultimately trigger a diversity of physiological responses. Nonetheless, an increasing number of reports reveal that signal transduction receptors also bind antagonists to inhibit responses mediated by agonists. The mechanisms by which antagonists block the downstream signaling cascade remain largely unknown. To advance our knowledge in this field, we used the LysR-type transcriptional regulator AdmX as a model. AdmX activates the expression of an antibiotic biosynthetic cluster in the rhizobacterium Serratia plymuthica. AdmX specifically recognizes the auxin phytohormone indole-3-acetic acid (IAA) and its biosynthetic intermediate indole-3-pyruvic acid (IPA) as signals. However, only IAA, but not IPA, was shown to regulate antibiotic production in S. plymuthica. Here, we report the high-resolution structures of the LBD of AdmX in complex with IAA and IPA. We found that IAA and IPA compete for binding to AdmX. Although IAA and IPA binding does not alter the oligomeric state of AdmX, IPA binding causes a higher degree of compactness in the protein structure. Molecular dynamics simulations revealed significant differences in the binding modes of IAA and IPA by AdmX, and the inspection of the three-dimensional structures evidenced differential agonist- and antagonist-mediated structural changes. Key residues for auxin binding were identified and an auxin recognition motif defined. Phylogenetic clustering supports the recent evolutionary emergence of this motif specifically in plant-associated enterobacteria. IMPORTANCE Although antagonists were found to bind different bacterial signal transduction receptors, we are still at the early stages of understanding the molecular details by which these molecules exert their inhibitory effects. Here, we provide insight into the structural changes resulting from the binding of an agonist and an antagonist to a sensor protein. Our data indicate that agonist and antagonist recognition is characterized by small conformational differences in the LBDs that can be efficiently transmitted to the output domain to modulate the final response. LBDs are subject to strong selective pressures and are rapidly evolving domains. An increasing number of reports support the idea that environmental factors drive the evolution of sensor domains. Given the recent evolutionary history of AdmX homologs, as well as their narrow phyletic distribution within plant-associated bacteria, our results are in accordance with a plant-mediated evolutionary process that resulted in the emergence of receptor proteins that specifically sense auxin phytohormones.
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9
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Medina A, Jiménez E, Caballero I, Castellví A, Triviño Valls J, Alcorlo M, Molina R, Hermoso JA, Sammito MD, Borges R, Usón I. Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER. Acta Crystallogr D Struct Biol 2022; 78:1283-1293. [PMID: 36322413 PMCID: PMC9629495 DOI: 10.1107/s2059798322009706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/03/2022] [Indexed: 11/23/2022] Open
Abstract
Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios.
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Affiliation(s)
- Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Iracema Caballero
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Albert Castellví
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Josep Triviño Valls
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Martin Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, Spanish National Research Council (CSIC), Madrid, Spain
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, Spanish National Research Council (CSIC), Madrid, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, Spanish National Research Council (CSIC), Madrid, Spain
| | - Massimo D. Sammito
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Rafael Borges
- Department of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
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10
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Vance TDR, Yip P, Jiménez E, Li S, Gawol D, Byrnes J, Usón I, Ziyyat A, Lee JE. SPACA6 ectodomain structure reveals a conserved superfamily of gamete fusion-associated proteins. Commun Biol 2022; 5:984. [PMID: 36115925 PMCID: PMC9482655 DOI: 10.1038/s42003-022-03883-y] [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: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
SPACA6 is a sperm-expressed surface protein that is critical for gamete fusion during mammalian sexual reproduction. Despite this fundamental role, little is known about how SPACA6 specifically functions. We elucidated the crystal structure of the SPACA6 ectodomain at 2.2-Å resolution, revealing a two-domain protein containing a four-helix bundle and Ig-like β-sandwich connected via a quasi-flexible linker. This structure is reminiscent of IZUMO1, another gamete fusion-associated protein, making SPACA6 and IZUMO1 founding members of a superfamily of fertilization-associated proteins, herein dubbed the IST superfamily. The IST superfamily is defined structurally by its distorted four-helix bundle and a pair of disulfide-bonded CXXC motifs. A structure-based search of the AlphaFold human proteome identified more protein members to this superfamily; remarkably, many of these proteins are linked to gamete fusion. The SPACA6 structure and its connection to other IST-superfamily members provide a missing link in our knowledge of mammalian gamete fusion.
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Affiliation(s)
- Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Patrick Yip
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Elisabet Jiménez
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028, Barcelona, Spain
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Diana Gawol
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Isabel Usón
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Ahmed Ziyyat
- Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014, Paris, France
- Service d'Histologie, d'Embryologie, Biologie de la Reproduction, AP-HP, Hôpital Cochin, F-75014, Paris, France
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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11
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McCoy AJ, Sammito MD, Read RJ. Implications of AlphaFold2 for crystallographic phasing by molecular replacement. Acta Crystallogr D Struct Biol 2022; 78:1-13. [PMID: 34981757 PMCID: PMC8725160 DOI: 10.1107/s2059798321012122] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/13/2021] [Indexed: 12/11/2022] Open
Abstract
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing methods, and in particular to explore the prospects for molecular-replacement phasing using in silico models.
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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
| | - Massimo D. Sammito
- 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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12
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Zouhir S, Contreras-Martel C, Maragno Trindade D, Attrée I, Dessen A, Macheboeuf P. MagC is a NplC/P60-like member of the α-2-macroglobulin Mag complex of Pseudomonas aeruginosa that interacts with peptidoglycan. FEBS Lett 2021; 595:2034-2046. [PMID: 34115884 DOI: 10.1002/1873-3468.14148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/17/2021] [Accepted: 06/08/2021] [Indexed: 11/07/2022]
Abstract
Bacterial α-2 macroglobulins (A2Ms) structurally resemble the large spectrum protease inhibitors of the eukaryotic immune system. In Pseudomonas aeruginosa, MagD acts as an A2M and is expressed within a six-gene operon encoding the MagA-F proteins. In this work, we employ isothermal calorimetry (ITC), analytical ultracentrifugation (AUC), and X-ray crystallography to investigate the function of MagC and show that MagC associates with the macroglobulin complex and with the peptidoglycan (PG). However, the catalytic residues of MagC display an inactive conformation that could suggest that it binds to PG but does not degrade it. We hypothesize that MagC could serve as an anchor between the MagD macroglobulin and the PG and could provide stabilization and/or regulation for the entire complex.
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Affiliation(s)
- Samira Zouhir
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, Brazil
| | | | | | - Ina Attrée
- Unité de Biologie Cellulaire et Infection, CEA, INSERM, CNRS, Université Grenoble Alpes, France
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, Brazil.,CNRS, CEA, IBS, Université Grenoble Alpes, France
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13
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Self-association of MreC as a regulatory signal in bacterial cell wall elongation. Nat Commun 2021; 12:2987. [PMID: 34016967 PMCID: PMC8137920 DOI: 10.1038/s41467-021-22957-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the cytoskeletal element MreB and regulates the activity of cell wall biosynthesis enzymes, in a process that may be dependent on MreC self-association. Here, we use electron cryo-microscopy and X-ray crystallography to determine the structure of a self-associated form of MreC from Pseudomonas aeruginosa in atomic detail. MreC monomers interact in head-to-tail fashion. Longitudinal and lateral interfaces are essential for oligomerization in vitro, and a phylogenetic analysis of proteobacterial MreC sequences indicates the prevalence of the identified interfaces. Our results are consistent with a model where MreC's ability to alternate between self-association and interaction with the cell wall biosynthesis machinery plays a key role in the regulation of elongasome activity.
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14
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Turowski VR, Ruiz DM, Nascimento AFZ, Millán C, Sammito MD, Juanhuix J, Cremonesi AS, Usón I, Giuseppe PO, Murakami MT. Structure of the class XI myosin globular tail reveals evolutionary hallmarks for cargo recognition in plants. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:522-533. [PMID: 33825712 DOI: 10.1107/s2059798321001583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/09/2021] [Indexed: 11/10/2022]
Abstract
The plant-specific class XI myosins (MyoXIs) play key roles at the molecular, cellular and tissue levels, engaging diverse adaptor proteins to transport cargoes along actin filaments. To recognize their cargoes, MyoXIs have a C-terminal globular tail domain (GTD) that is evolutionarily related to those of class V myosins (MyoVs) from animals and fungi. Despite recent advances in understanding the functional roles played by MyoXI in plants, the structure of its GTD, and therefore the molecular determinants for cargo selectivity and recognition, remain elusive. In this study, the first crystal structure of a MyoXI GTD, that of MyoXI-K from Arabidopsis thaliana, was elucidated at 2.35 Å resolution using a low-identity and fragment-based phasing approach in ARCIMBOLDO_SHREDDER. The results reveal that both the composition and the length of the α5-α6 loop are distinctive features of MyoXI-K, providing evidence for a structural stabilizing role for this loop, which is otherwise carried out by a molecular zipper in MyoV GTDs. The crystal structure also shows that most of the characterized cargo-binding sites in MyoVs are not conserved in plant MyoXIs, pointing to plant-specific cargo-recognition mechanisms. Notably, the main elements involved in the self-regulation mechanism of MyoVs are conserved in plant MyoXIs, indicating this to be an ancient ancestral trait.
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Affiliation(s)
- Valeria R Turowski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Diego M Ruiz
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Andrey F Z Nascimento
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer de Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer de Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Massimo D Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Judith Juanhuix
- XALOC Beamline, Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Aline Sampaio Cremonesi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Isabel Usón
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer de Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Priscila O Giuseppe
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Mario T Murakami
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
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15
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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: 9] [Impact Index Per Article: 3.0] [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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16
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Denisov SS, Ramírez-Escudero M, Heinzmann ACA, Ippel JH, Dawson PE, Koenen RR, Hackeng TM, Janssen BJC, Dijkgraaf I. Structural characterization of anti-CCL5 activity of the tick salivary protein evasin-4. J Biol Chem 2020; 295:14367-14378. [PMID: 32817341 PMCID: PMC7573271 DOI: 10.1074/jbc.ra120.013891] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/13/2020] [Indexed: 01/30/2023] Open
Abstract
Ticks, as blood-sucking parasites, have developed a complex strategy to evade and suppress host immune responses during feeding. The crucial part of this strategy is expression of a broad family of salivary proteins, called Evasins, to neutralize chemokines responsible for cell trafficking and recruitment. However, structural information about Evasins is still scarce, and little is known about the structural determinants of their binding mechanism to chemokines. Here, we studied the structurally uncharacterized Evasin-4, which neutralizes a broad range of CC-motif chemokines, including the chemokine CC-motif ligand 5 (CCL5) involved in atherogenesis. Crystal structures of Evasin-4 and E66S CCL5, an obligatory dimeric variant of CCL5, were determined to a resolution of 1.3–1.8 Å. The Evasin-4 crystal structure revealed an L-shaped architecture formed by an N- and C-terminal subdomain consisting of eight β-strands and an α-helix that adopts a substantially different position compared with closely related Evasin-1. Further investigation into E66S CCL5–Evasin-4 complex formation with NMR spectroscopy showed that residues of the N terminus are involved in binding to CCL5. The peptide derived from the N-terminal region of Evasin-4 possessed nanomolar affinity to CCL5 and inhibited CCL5 activity in monocyte migration assays. This suggests that Evasin-4 derivatives could be used as a starting point for the development of anti-inflammatory drugs.
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Affiliation(s)
- Stepan S Denisov
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Mercedes Ramírez-Escudero
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Alexandra C A Heinzmann
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Johannes H Ippel
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Rory R Koenen
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Tilman M Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Bert J C Janssen
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ingrid Dijkgraaf
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
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17
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Richards LS, Millán C, Miao J, Martynowycz MW, Sawaya MR, Gonen T, Borges RJ, Usón I, Rodriguez JA. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER. Acta Crystallogr D Struct Biol 2020; 76:703-712. [PMID: 32744252 PMCID: PMC7397493 DOI: 10.1107/s2059798320008049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.
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Affiliation(s)
- Logan S. Richards
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Jennifer Miao
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Rafael J. Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
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18
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Millán C, Jiménez E, Schuster A, Diederichs K, Usón I. ALIXE: a phase-combination tool for fragment-based molecular replacement. Acta Crystallogr D Struct Biol 2020; 76:209-220. [PMID: 32133986 PMCID: PMC7057212 DOI: 10.1107/s205979832000056x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/15/2020] [Indexed: 11/10/2022] Open
Abstract
Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.
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Affiliation(s)
- Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Antonia Schuster
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
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19
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Medina A, Triviño J, Borges RJ, Millán C, Usón I, Sammito MD. ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation. Acta Crystallogr D Struct Biol 2020; 76:193-208. [PMID: 32133985 PMCID: PMC7057218 DOI: 10.1107/s2059798320001679] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/05/2020] [Indexed: 11/17/2022] Open
Abstract
The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.
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Grants
- 790122 H2020 Marie Skłodowska-Curie Actions
- BES-2017-080368 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BES-2015-071397 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2015-64216-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2013-49604-EXP Ministerio de Economía, Industria y Competitividad, Gobierno de España
- MDM2014-0435-01 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- 16/24191-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- 17/13485-3 Fundação de Amparo à Pesquisa do Estado de São Paulo
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Affiliation(s)
- Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Josep Triviño
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Rafael J. Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu-SP 18618-689, Brazil
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
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20
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Borges RJ, Meindl K, Triviño J, Sammito M, Medina A, Millán C, Alcorlo M, Hermoso JA, Fontes MRDM, Usón I. SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses. Acta Crystallogr D Struct Biol 2020; 76:221-237. [PMID: 32133987 PMCID: PMC7057211 DOI: 10.1107/s2059798320000339] [Citation(s) in RCA: 8] [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: 06/28/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content.
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Affiliation(s)
- Rafael Junqueira Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu-SP 18618-689, Brazil
| | - Kathrin Meindl
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Josep Triviño
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Massimo Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Martin Alcorlo
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Marcos Roberto de Mattos Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu-SP 18618-689, Brazil
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
- ICREA at IBMB–CSIC, Baldiri Reixach 13-15, 08028 Barcelona, Spain
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21
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Ding W, Zhang T, He Y, Wang J, Wu L, Han P, Zheng C, Gu Y, Zeng L, Hao Q, Fan H. IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576719015115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.
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22
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Nguyen VH, Singh N, Medina A, Usón I, Fraser ME. Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion. Protein Sci 2019; 28:1840-1849. [PMID: 31411782 DOI: 10.1002/pro.3708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 01/25/2023]
Abstract
ATP-citrate lyase (ACLY) catalyzes production of acetyl-CoA and oxaloacetate from CoA and citrate using ATP. In humans, this cytoplasmic enzyme connects energy metabolism from carbohydrates to the production of lipids. In certain bacteria, ACLY is used to fix carbon in the reductive tricarboxylic acid cycle. The carboxy(C)-terminal portion of ACLY shows sequence similarity to citrate synthase of the tricarboxylic acid cycle. To investigate the roles of residues of ACLY equivalent to active site residues of citrate synthase, these residues in ACLY from Chlorobium limicola were mutated, and the proteins were investigated using kinetics assays and biophysical techniques. To obtain the crystal structure of the C-terminal portion of ACLY, full-length C. limicola ACLY was cleaved, first non-specifically with chymotrypsin and subsequently with Tobacco Etch Virus protease. Crystals of the C-terminal portion diffracted to high resolution, providing structures that show the positions of active site residues and how ACLY tetramerizes.
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Affiliation(s)
- Vinh H Nguyen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Noreen Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Ana Medina
- Structural Biology Unit, CSIC, Barcelona, Spain
| | - Isabel Usón
- Structural Biology Unit, CSIC, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Marie E Fraser
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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23
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Bamford NC, Le Mauff F, Subramanian AS, Yip P, Millán C, Zhang Y, Zacharias C, Forman A, Nitz M, Codée JDC, Usón I, Sheppard DC, Howell PL. Ega3 from the fungal pathogen Aspergillus fumigatus is an endo-α-1,4-galactosaminidase that disrupts microbial biofilms. J Biol Chem 2019; 294:13833-13849. [PMID: 31416836 DOI: 10.1074/jbc.ra119.009910] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/01/2019] [Indexed: 11/06/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen that causes both chronic and acute invasive infections. Galactosaminogalactan (GAG) is an integral component of the A. fumigatus biofilm matrix and a key virulence factor. GAG is a heterogeneous linear α-1,4-linked exopolysaccharide of galactose and GalNAc that is partially deacetylated after secretion. A cluster of five co-expressed genes has been linked to GAG biosynthesis and modification. One gene in this cluster, ega3, is annotated as encoding a putative α-1,4-galactosaminidase belonging to glycoside hydrolase family 114 (GH114). Herein, we show that recombinant Ega3 is an active glycoside hydrolase that disrupts GAG-dependent A. fumigatus and Pel polysaccharide-dependent Pseudomonas aeruginosa biofilms at nanomolar concentrations. Using MS and functional assays, we demonstrate that Ega3 is an endo-acting α-1,4-galactosaminidase whose activity depends on the conserved acidic residues, Asp-189 and Glu-247. X-ray crystallographic structural analysis of the apo Ega3 and an Ega3-galactosamine complex, at 1.76 and 2.09 Å resolutions, revealed a modified (β/α)8-fold with a deep electronegative cleft, which upon ligand binding is capped to form a tunnel. Our structural analysis coupled with in silico docking studies also uncovered the molecular determinants for galactosamine specificity and substrate binding at the -2 to +1 binding subsites. The findings in this study increase the structural and mechanistic understanding of the GH114 family, which has >600 members encoded by plant and opportunistic human pathogens, as well as in industrially used bacteria and fungi.
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Affiliation(s)
- Natalie C Bamford
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - François Le Mauff
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada.,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - Adithya S Subramanian
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Patrick Yip
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Claudia Millán
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer Baldiri Reixac 15, 3 A17, Barcelona 08028, Spain
| | - Yongzhen Zhang
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands
| | - Caitlin Zacharias
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada.,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - Adam Forman
- Department of Chemistry, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands
| | - Isabel Usón
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer Baldiri Reixac 15, 3 A17, Barcelona 08028, Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, E-08003 Barcelona, Spain
| | - Donald C Sheppard
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada .,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada .,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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24
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Howard SP, Estrozi LF, Bertrand Q, Contreras-Martel C, Strozen T, Job V, Martins A, Fenel D, Schoehn G, Dessen A. Structure and assembly of pilotin-dependent and -independent secretins of the type II secretion system. PLoS Pathog 2019; 15:e1007731. [PMID: 31083688 PMCID: PMC6532946 DOI: 10.1371/journal.ppat.1007731] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/23/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023] Open
Abstract
The type II secretion system (T2SS) is a cell envelope-spanning macromolecular complex that is prevalent in Gram-negative bacterial species. It serves as the predominant virulence mechanism of many bacteria including those of the emerging human pathogens Vibrio vulnificus and Aeromonas hydrophila. The system is composed of a core set of highly conserved proteins that assemble an inner membrane platform, a periplasmic pseudopilus and an outer membrane complex termed the secretin. Localization and assembly of secretins in the outer membrane requires recognition of secretin monomers by two different partner systems: an inner membrane accessory complex or a highly sequence-diverse outer membrane lipoprotein, termed the pilotin. In this study, we addressed the question of differential secretin assembly mechanisms by using cryo-electron microscopy to determine the structures of the secretins from A. hydrophila (pilotin-independent ExeD) and V. vulnificus (pilotin-dependent EpsD). These structures, at approximately 3.5 Å resolution, reveal pentadecameric stoichiometries and C-terminal regions that carry a signature motif in the case of a pilotin-dependent assembly mechanism. We solved the crystal structure of the V. vulnificus EpsS pilotin and confirmed the importance of the signature motif for pilotin-dependent secretin assembly by performing modelling with the C-terminus of EpsD. We also show that secretin assembly is essential for membrane integrity and toxin secretion in V. vulnificus and establish that EpsD requires the coordinated activity of both the accessory complex EpsAB and the pilotin EpsS for full assembly and T2SS function. In contrast, mutation of the region of the S-domain that is normally the site of pilotin interactions has little effect on assembly or function of the ExeD secretin. Since secretins are essential outer membrane channels present in a variety of secretion systems, these results provide a structural and functional basis for understanding the key assembly steps for different members of this vast pore-forming family of proteins.
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Affiliation(s)
- S. Peter Howard
- Dept. Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Leandro F. Estrozi
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Quentin Bertrand
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | | | - Timothy Strozen
- Dept. Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Viviana Job
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Alexandre Martins
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Daphna Fenel
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Guy Schoehn
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Andréa Dessen
- Univ Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, São Paulo, Brazil
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25
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Dunce JM, Dunne OM, Ratcliff M, Millán C, Madgwick S, Usón I, Davies OR. Structural basis of meiotic chromosome synapsis through SYCP1 self-assembly. Nat Struct Mol Biol 2018; 25:557-569. [PMID: 29915389 DOI: 10.1038/s41594-018-0078-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/25/2018] [Indexed: 11/10/2022]
Abstract
Meiotic chromosomes adopt unique structures in which linear arrays of chromatin loops are bound together in homologous chromosome pairs by a supramolecular protein assembly, the synaptonemal complex. This three-dimensional scaffold provides the essential structural framework for genetic exchange by crossing over and subsequent homolog segregation. The core architecture of the synaptonemal complex is provided by SYCP1. Here we report the structure and self-assembly mechanism of human SYCP1 through X-ray crystallographic and biophysical studies. SYCP1 has an obligate tetrameric structure in which an N-terminal four-helical bundle bifurcates into two elongated C-terminal dimeric coiled-coils. This building block assembles into a zipper-like lattice through two self-assembly sites. N-terminal sites undergo cooperative head-to-head assembly in the midline, while C-terminal sites interact back to back on the chromosome axis. Our work reveals the underlying molecular structure of the synaptonemal complex in which SYCP1 self-assembly generates a supramolecular lattice that mediates meiotic chromosome synapsis.
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Affiliation(s)
- James M Dunce
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Orla M Dunne
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew Ratcliff
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Suzanne Madgwick
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.
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26
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Oeffner RD, Afonine PV, Millán C, Sammito M, Usón I, Read RJ, McCoy AJ. On the application of the expected log-likelihood gain to decision making in molecular replacement. Acta Crystallogr D Struct Biol 2018; 74:245-255. [PMID: 29652252 PMCID: PMC5892874 DOI: 10.1107/s2059798318004357] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/14/2018] [Indexed: 11/18/2022] Open
Abstract
Molecular-replacement phasing of macromolecular crystal structures is often fast, but if a molecular-replacement solution is not immediately obtained the crystallographer must judge whether to pursue molecular replacement or to attempt experimental phasing as the quickest path to structure solution. The introduction of the expected log-likelihood gain [eLLG; McCoy et al. (2017), Proc. Natl Acad. Sci. USA, 114, 3637-3641] has given the crystallographer a powerful new tool to aid in making this decision. The eLLG is the log-likelihood gain on intensity [LLGI; Read & McCoy (2016), Acta Cryst. D72, 375-387] expected from a correctly placed model. It is calculated as a sum over the reflections of a function dependent on the fraction of the scattering for which the model accounts, the estimated model coordinate error and the measurement errors in the data. It is shown how the eLLG may be used to answer the question `can I solve my structure by molecular replacement?'. However, this is only the most obvious of the applications of the eLLG. It is also discussed how the eLLG may be used to determine the search order and minimal data requirements for obtaining a molecular-replacement solution using a given model, and for decision making in fragment-based molecular replacement, single-atom molecular replacement and likelihood-guided model pruning.
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Affiliation(s)
- Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Pavel V. Afonine
- Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People’s Republic of China
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Massimo Sammito
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
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27
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McCoy AJ, Oeffner RD, Millán C, Sammito M, Usón I, Read RJ. Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement. Acta Crystallogr D Struct Biol 2018; 74:279-289. [PMID: 29652255 PMCID: PMC5892877 DOI: 10.1107/s2059798318001353] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 01/22/2018] [Indexed: 11/22/2022] Open
Abstract
Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.
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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, England
| | - Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Massimo Sammito
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
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