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Agirre J, Atanasova M, Bagdonas H, Ballard CB, Baslé A, Beilsten-Edmands J, Borges RJ, Brown DG, Burgos-Mármol JJ, Berrisford JM, Bond PS, Caballero I, Catapano L, Chojnowski G, Cook AG, Cowtan KD, Croll TI, Debreczeni JÉ, Devenish NE, Dodson EJ, Drevon TR, Emsley P, Evans G, Evans PR, Fando M, Foadi J, Fuentes-Montero L, Garman EF, Gerstel M, Gildea RJ, Hatti K, Hekkelman ML, Heuser P, Hoh SW, Hough MA, Jenkins HT, Jiménez E, Joosten RP, Keegan RM, Keep N, Krissinel EB, Kolenko P, Kovalevskiy O, Lamzin VS, Lawson DM, Lebedev AA, Leslie AGW, Lohkamp B, Long F, Malý M, McCoy AJ, McNicholas SJ, Medina A, Millán C, Murray JW, Murshudov GN, Nicholls RA, Noble MEM, Oeffner R, Pannu NS, Parkhurst JM, Pearce N, Pereira J, Perrakis A, Powell HR, Read RJ, Rigden DJ, Rochira W, Sammito M, Sánchez Rodríguez F, Sheldrick GM, Shelley KL, Simkovic F, Simpkin AJ, Skubak P, Sobolev E, Steiner RA, Stevenson K, Tews I, Thomas JMH, Thorn A, Valls JT, Uski V, Usón I, Vagin A, Velankar S, Vollmar M, Walden H, Waterman D, Wilson KS, Winn MD, Winter G, Wojdyr M, Yamashita K. The CCP4 suite: integrative software for macromolecular crystallography. Acta Crystallogr D Struct Biol 2023; 79:449-461. [PMID: 37259835 PMCID: PMC10233625 DOI: 10.1107/s2059798323003595] [Citation(s) in RCA: 84] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/19/2023] [Indexed: 06/02/2023] Open
Abstract
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Mihaela Atanasova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Haroldas Bagdonas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Charles B. Ballard
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - James Beilsten-Edmands
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Rafael J. Borges
- The Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - David G. Brown
- Laboratoires Servier SAS Institut de Recherches, Croissy-sur-Seine, France
| | - J. Javier Burgos-Mármol
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - John M. Berrisford
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Paul S. Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Iracema Caballero
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Lucrezia Catapano
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Atlanta G. Cook
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King’s Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Tristan I. Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
- Altos Labs, Portway Building, Granta Park, Great Abington, Cambridge CB21 6GP, United Kingdom
| | - Judit É. Debreczeni
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Nicholas E. Devenish
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Eleanor J. Dodson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Tarik R. Drevon
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0QS, United Kingdom
| | - Phil R. Evans
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Maria Fando
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Bath, United Kingdom
| | - Luis Fuentes-Montero
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, United Kingdom
| | - Markus Gerstel
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Richard J. Gildea
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Kaushik Hatti
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Maarten L. Hekkelman
- Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philipp Heuser
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Michael A. Hough
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Robbie P. Joosten
- Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ronan M. Keegan
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Nicholas Keep
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Eugene B. Krissinel
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Petr Kolenko
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague 1, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 55, 252 50 Vestec, Czech Republic
| | - Oleg Kovalevskiy
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - David M. Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andrey A. Lebedev
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Andrew G. W. Leslie
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Fei Long
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin Malý
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague 1, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 55, 252 50 Vestec, Czech Republic
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Stuart J. McNicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - James W. Murray
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert A. Nicholls
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin E. M. Noble
- Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Robert Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Navraj S. Pannu
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - James M. Parkhurst
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0QS, United Kingdom
| | - Nicholas Pearce
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
| | - Joana Pereira
- Biozentrum and SIB Swiss Institute of Bioinformatics, University of Basel, 4056 Basel, Switzerland
| | - Anastassis Perrakis
- Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Harold R. Powell
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - William Rochira
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Massimo Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
- Discovery Centre, Biologics Engineering, AstraZeneca, Biomedical Campus, 1 Francis Crick Avenue, Trumpington, Cambridge CB2 0AA, United Kingdom
| | - Filomeno Sánchez Rodríguez
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - George M. Sheldrick
- Department of Structural Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Kathryn L. Shelley
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Felix Simkovic
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Adam J. Simpkin
- Laboratoires Servier SAS Institut de Recherches, Croissy-sur-Seine, France
| | - Pavol Skubak
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Egor Sobolev
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Department of Biomedical Sciences, University of Padova, Italy
| | - Kyle Stevenson
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Ivo Tews
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jens M. H. Thomas
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Andrea Thorn
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, 22761 Hamburg, Germany
| | - Josep Triviño Valls
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Ville Uski
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - 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
| | - Alexei Vagin
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Melanie Vollmar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Helen Walden
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David Waterman
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Martyn D. Winn
- Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, United Kingdom
| | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Marcin Wojdyr
- Global Phasing Limited (United Kingdom), Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Millán C, McCoy AJ, Terwilliger TC, Read RJ. Likelihood-based docking of models into cryo-EM maps. Acta Crystallogr D Struct Biol 2023; 79:281-289. [PMID: 36920336 PMCID: PMC10071562 DOI: 10.1107/s2059798323001602] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023] Open
Abstract
Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimized strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.
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Affiliation(s)
- Claudia Millán
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Thomas C. Terwilliger
- New Mexico Consortium, Los Alamos National Laboratory, 100 Entrada Drive, Los Alamos, NM 87544, USA
| | - 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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Read RJ, Millán C, McCoy AJ, Terwilliger TC. Likelihood-based signal and noise analysis for docking of models into cryo-EM maps. Acta Crystallogr D Struct Biol 2023; 79:271-280. [PMID: 36920335 PMCID: PMC10071565 DOI: 10.1107/s2059798323001596] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023] Open
Abstract
Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural biology, finding applications in both crystallography and cryo-EM. Indeed, previous crystallographic work on the errors in structural models is directly applicable to likelihood targets in cryo-EM. Likelihood targets in Fourier space are derived here to characterize, based on the comparison of half-maps, the direction- and resolution-dependent variation in the strength of both signal and noise in the data. Because the signal depends on local features, the signal and noise are analysed in local regions of the cryo-EM reconstruction. The likelihood analysis extends to prediction of the signal that will be achieved in any docking calculation for a model of specified quality and completeness. A related calculation generalizes a previous measure of the information gained by making the cryo-EM reconstruction.
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Affiliation(s)
- Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Claudia Millán
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Thomas C. Terwilliger
- New Mexico Consortium, Los Alamos National Laboratory, 100 Entrada Drive, Los Alamos, NM 87544, USA
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Terwilliger TC, Poon BK, Afonine PV, Schlicksup CJ, Croll TI, Millán C, Richardson JS, Read RJ, Adams PD. Improved AlphaFold modeling with implicit experimental information. Nat Methods 2022; 19:1376-1382. [PMID: 36266465 PMCID: PMC9636017 DOI: 10.1038/s41592-022-01645-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022]
Abstract
Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.
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Affiliation(s)
- Thomas C Terwilliger
- New Mexico Consortium, Los Alamos, NM, USA.
- Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Billy K Poon
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pavel V Afonine
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher J Schlicksup
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tristan I Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Claudia Millán
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
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Oeffner RD, Croll TI, Millán C, Poon BK, Schlicksup CJ, Read RJ, Terwilliger TC. Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE. Acta Crystallogr D Struct Biol 2022; 78:1303-1314. [PMID: 36322415 PMCID: PMC9629492 DOI: 10.1107/s2059798322010026] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/13/2022] [Indexed: 11/23/2022] Open
Abstract
AlphaFold has recently become an important tool in providing models for experimental structure determination by X-ray crystallography and cryo-EM. Large parts of the predicted models typically approach the accuracy of experimentally determined structures, although there are frequently local errors and errors in the relative orientations of domains. Importantly, residues in the model of a protein predicted by AlphaFold are tagged with a predicted local distance difference test score, informing users about which regions of the structure are predicted with less confidence. AlphaFold also produces a predicted aligned error matrix indicating its confidence in the relative positions of each pair of residues in the predicted model. The phenix.process_predicted_model tool downweights or removes low-confidence residues and can break a model into confidently predicted domains in preparation for molecular replacement or cryo-EM docking. These confidence metrics are further used in ISOLDE to weight torsion and atom-atom distance restraints, allowing the complete AlphaFold model to be interactively rearranged to match the docked fragments and reducing the need for the rebuilding of connecting regions.
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Affiliation(s)
- Robert D. Oeffner
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Tristan I. Croll
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Claudia Millán
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory (LBNL), Building 33R0349, Berkeley, CA 94720-8235, USA
| | - Christopher J. Schlicksup
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory (LBNL), Building 33R0349, Berkeley, CA 94720-8235, USA
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom,Correspondence e-mail: ,
| | - Tom C. Terwilliger
- New Mexico Consortium, Los Alamos National Laboratory, 100 Entrada Drive, Los Alamos, NM 87544, USA,Correspondence e-mail: ,
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7
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Oeffner R, McCoy A, Millán C, Croll T, Read R. Peering at the data inside the black box. Acta Cryst Sect A 2022. [DOI: 10.1107/s205327332209430x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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8
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Sagmeister T, Buhlheller C, Gubensaek N, Eder M, Grininger C, Petrowitsch L, Medina A, Millán C, Usón I, Vejzović Đ, Damisch E, Keller W, Pavkov-Keller T. A novel self-assembly mechanism for the S-layer in Lactobacillus acidophilus. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322096000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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9
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Bento MHL, Lewis EA, Ramírez de Arellano I, Millán C, King E, Scott-Baird E, McGuire P, Richardson K. Establishing the tolerability to broiler chickens and laying hens of nonanoic acid at practical levels of use as a feed flavouring. Br Poult Sci 2021; 63:218-225. [PMID: 34404304 DOI: 10.1080/00071668.2021.1966752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
1. The following experiments were conducted to evaluate the effects of nonanoic acid (NA) in broilers and laying hens, at practical levels as a flavouring in complete feed.2. In the first experiment, 1100, one-day-old Ross 308 chicks, half male and female, were randomly assigned to 50 floor pens containing 22 chicks each. Chicks were fed one of five treatment diets containing either 0 (control), 100, 300, 500 or 1,000 mg NA/kg complete feed for 42 days.3. The NA treatment had no effect on ADFI, but there was a linear relationship with ADG and FCR. No differences were observed in blood parameters or tissue pathology among treatment groups.4. In a second study, 150 Hyline hens aged 24 weeks old were randomly assigned to 50 pens containing three birds each. Laying hens were fed one of five treatment diets containing 0 (control), 100, 300, 500 or 1,000 mg NA/kg complete feed for 56 days.5. Treatment with NA has no effect on live weight, ADFI or egg production in laying hens, and there were no observed changes in tissue pathology.6. The results supported the toleration of NA in broilers or layers at dietary levels of up to 1,000 mg/kg.
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Affiliation(s)
- M H L Bento
- NutraSteward, Bridge Innovation Center, Pembroke Dock, UK
| | - E A Lewis
- NutraSteward, Bridge Innovation Center, Pembroke Dock, UK
| | | | - C Millán
- IMASDE Agroalimentaria, Madrid, Spain
| | - E King
- Drayton Animal Health, Stratford-upon-Avon, UK
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10
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Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, Pereira JH, Rodrigues AV, van Dijk AA, Ebrecht AC, Opperman DJ, Sagmeister T, Buhlheller C, Pavkov-Keller T, Rathinaswamy MK, Dalwadi U, Yip CK, Burke JE, Garcia KC, Grishin NV, Adams PD, Read RJ, Baker D. Accurate prediction of protein structures and interactions using a three-track neural network. Science 2021; 373:871-876. [PMID: 34282049 PMCID: PMC7612213 DOI: 10.1126/science.abj8754] [Citation(s) in RCA: 2062] [Impact Index Per Article: 687.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 01/17/2023]
Abstract
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.
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Affiliation(s)
- Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sergey Ovchinnikov
- Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA 02138, USA
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jue Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Claudia Millán
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Carson Adams
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Caleb R Glassman
- Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andy DeGiovanni
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jose H Pereira
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andria V Rodrigues
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alberdina A van Dijk
- Department of Biochemistry, Focus Area Human Metabolomics, North-West University, 2531 Potchefstroom, South Africa
| | - Ana C Ebrecht
- Department of Biochemistry, Focus Area Human Metabolomics, North-West University, 2531 Potchefstroom, South Africa
| | - Diederik J Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Theo Sagmeister
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Christoph Buhlheller
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- Medical University of Graz, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Udit Dalwadi
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - K Christopher Garcia
- Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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11
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Sagmeister T, Eder M, Grininger C, Buhlheller C, Vejzović Đ, Đordić A, Damisch E, Millán C, Usón I, Pavkov-Keller T. Surface layer proteins of Lactobacillus acidophilus – a story of SlpA and SlpX. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321088449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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12
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Gilani S, Gracia M, Barnard L, Dersjant-Li Y, Millán C, Gibbs K. Effects of a xylanase and beta-glucanase enzyme combination on growth performance of broilers fed maize-soybean meal-based diets. Journal of Applied Animal Nutrition 2021. [DOI: 10.3920/jaan2021.0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The following study evaluated effects of a xylanase and beta-glucanase combination on growth performance of broilers fed energy reduced versus nutritionally adequate maize-soybean meal-based diets. A total of 648, one-day-old male broilers (Ross 308) were assigned to floor-pens (24 birds/pen, nine pens/treatment, three treatments) in a randomised block design. Treatments included: (1) a nutritionally adequate positive control diet (PC); (2) a negative control (NC) diet in which energy, crude protein and digestible amino acids were reduced by 3.4% (-105 kcal apparent metabolisable energy), 2.3% and 1.2 to 3.0% vs PC, respectively; and (3) NC plus a xylanase and beta-glucanase combination that supplied 1,220 U xylanase and 152 U beta-glucanase per kilogram of final feed. All diets contained a background of 500 FTU/kg phytase and were offered to birds ad libitum. Birds fed NC showed reduced average daily gain (ADG) by -6.1% (P<0.05); increased feed conversion ratio (FCR) by 9.2 points (P<0.05), and overall (d 1-35) body weight corrected FCR which was increased by 9.4 points (P<0.05) vs the PC group. Enzyme supplementation increased final BW (+4.2%, P<0.05), ADG (+5.4%, P<0.05) and tended to reduce FCR (+7.5 points, P=0.054) from d 22-35 vs NC, without affecting average daily feed intake. Improvements in performance due to the enzyme combination were equivalent to performance on the PC diet in all cases. The results suggested that significant improvements in growth performance of broilers fed maize-soybean meal-based diets which had been reduced in energy and nutrients can be realised by supplementation with xylanase in combination with beta-glucanase.
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Affiliation(s)
- S. Gilani
- Danisco Animal Nutrition (IFF), Willem Einthovenstraat 4, 2342 BH Oegstgeest, the Netherlands
| | - M.I. Gracia
- IMASDE Agroalimentaria, S.L. C/ Nápoles 3, 28224 Pozuelo de Alarcón, Madrid, Spain
| | - L. Barnard
- Danisco Animal Nutrition (IFF), Willem Einthovenstraat 4, 2342 BH Oegstgeest, the Netherlands
| | - Y. Dersjant-Li
- Danisco Animal Nutrition (IFF), Willem Einthovenstraat 4, 2342 BH Oegstgeest, the Netherlands
| | - C. Millán
- IMASDE Agroalimentaria, S.L. C/ Nápoles 3, 28224 Pozuelo de Alarcón, Madrid, Spain
| | - K. Gibbs
- Danisco Animal Nutrition (IFF), Willem Einthovenstraat 4, 2342 BH Oegstgeest, the Netherlands
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13
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Millán C, Keegan RM, Pereira J, Sammito MD, Simpkin AJ, McCoy AJ, Lupas AN, Hartmann MD, Rigden DJ, Read RJ. Assessing the utility of CASP14 models for molecular replacement. Proteins 2021; 89:1752-1769. [PMID: 34387010 PMCID: PMC8881082 DOI: 10.1002/prot.26214] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022]
Abstract
The assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real‐world application. In CASP7, the metric for molecular replacement assessment involved full likelihood‐based molecular replacement searches; however, this restricted the assessable targets to crystal structures with only one copy of the target in the asymmetric unit, and to those where the search found the correct pose. In CASP10, full molecular replacement searches were replaced by likelihood‐based rigid‐body refinement of models superimposed on the target using the LGA algorithm, with the metric being the refined log‐likelihood‐gain (LLG) score. This enabled multi‐copy targets and very poor models to be evaluated, but a significant further issue remained: the requirement of diffraction data for assessment. We introduce here the relative‐expected‐LLG (reLLG), which is independent of diffraction data. This reLLG is also independent of any crystal form, and can be calculated regardless of the source of the target, be it X‐ray, NMR or cryo‐EM. We calibrate the reLLG against the LLG for targets in CASP14, showing that it is a robust measure of both model and group ranking. Like the LLG, the reLLG shows that accurate coordinate error estimates add substantial value to predicted models. We find that refinement by CASP groups can often convert an inadequate initial model into a successful MR search model. Consistent with findings from others, we show that the AlphaFold2 models are sufficiently good, and reliably so, to surpass other current model generation strategies for attempting molecular replacement phasing.
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Affiliation(s)
- Claudia Millán
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Ronan M Keegan
- Scientific Computing Dept., Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire, United Kingdom
| | - Joana Pereira
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Massimo D Sammito
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Adam J Simpkin
- Institute of Systems, Molecular and Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7BE, United Kingdom
| | - Airlie J McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Andrei N Lupas
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Marcus D Hartmann
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7BE, United Kingdom
| | - Randy J Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
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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 Crystallogr D Struct Biol 2021; 77:522-533. [PMID: 33825712 DOI: 10.1107/s2059798321001583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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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: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Caballero Muñoz I, Sammito M, Millán C, Soler N, Lebedev A, Usón I. Overcoming phasing difficulties in coiled coils with ARCIMBOLDO_LITE: verifying solutions. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318091714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Borges R, Sammito M, Millán C, Soler N, Medin A, Caballero I, Fontes MRM, Usón I. Expanding partial structures by assembling most probable side-chain composition. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318089039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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22
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Oeffner RD, Afonine PV, Millán C, Sammito M, Usón I, Read RJ, McCoy AJ. The expected log-likelihood gain for decision making in molecular replacement. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318089027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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23
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Sammito MD, Medina A, Millán C, Borges RJ, Usón I. ALEPH: a network-oriented approach to structure mapping and comparisons. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Usón I, Millán C, Sammito M, Borges RJ, Soler N, Caballero I, Medina A. All is fair in phasing: the combined artillery in ARCIMBOLDO. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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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: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Lee M, Batuecas MT, Tomoshige S, Domínguez-Gil T, Mahasenan KV, Dik DA, Hesek D, Millán C, Usón I, Lastochkin E, Hermoso JA, Mobashery S. Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2018; 115:4393-4398. [PMID: 29632171 PMCID: PMC5924928 DOI: 10.1073/pnas.1801298115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
β-Lactam antibiotics inhibit cell-wall transpeptidases, preventing the peptidoglycan, the major constituent of the bacterial cell wall, from cross-linking. This causes accumulation of long non-cross-linked strands of peptidoglycan, which leads to bacterial death. Pseudomonas aeruginosa, a nefarious bacterial pathogen, attempts to repair this aberrantly formed peptidoglycan by the function of the lytic transglycosylase Slt. We document in this report that Slt turns over the peptidoglycan by both exolytic and endolytic reactions, which cause glycosidic bond scission from a terminus or in the middle of the peptidoglycan, respectively. These reactions were characterized with complex synthetic peptidoglycan fragments that ranged in size from tetrasaccharides to octasaccharides. The X-ray structure of the wild-type apo Slt revealed it to be a doughnut-shaped protein. In a series of six additional X-ray crystal structures, we provide insights with authentic substrates into how Slt is enabled for catalysis for both the endolytic and exolytic reactions. The substrate for the exolytic reaction binds Slt in a canonical arrangement and reveals how both the glycan chain and the peptide stems are recognized by the Slt. We document that the apo enzyme does not have a fully formed active site for the endolytic reaction. However, binding of the peptidoglycan at the existing subsites within the catalytic domain causes a conformational change in the protein that assembles the surface for binding of a more expansive peptidoglycan between the catalytic domain and an adjacent domain. The complexes of Slt with synthetic peptidoglycan substrates provide an unprecedented snapshot of the endolytic reaction.
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Affiliation(s)
- Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain
| | - Shusuke Tomoshige
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Teresa Domínguez-Gil
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - David A Dik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Claudia Millán
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas, E-08028 Barcelona, Spain
| | - Isabel Usón
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas, E-08028 Barcelona, Spain
- Structural Biology Unit, Institució Catalana de Recerca i Estudis Avançats, E-08003 Barcelona, Spain
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain;
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;
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Millán C, Sammito MD, McCoy AJ, Nascimento AFZ, Petrillo G, Oeffner RD, Domínguez-Gil T, Hermoso JA, Read RJ, Usón I. Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination. Acta Crystallogr D Struct Biol 2018; 74:290-304. [PMID: 29652256 PMCID: PMC5892878 DOI: 10.1107/s2059798318001365] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/22/2018] [Indexed: 01/13/2023] Open
Abstract
Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an overall similar fold or even their featuring areas of very close geometry. Successful methods to make the most of such templates usually rely on the degree of conservation to select and improve search models. ARCIMBOLDO_SHREDDER uses fragments derived from distant homologues in a brute-force approach driven by the experimental data, instead of by sequence similarity. The new algorithms implemented in ARCIMBOLDO_SHREDDER are described in detail, illustrating its characteristic aspects in the solution of new and test structures. In an advance from the previously published algorithm, which was based on omitting or extracting contiguous polypeptide spans, model generation now uses three-dimensional volumes respecting structural units. The optimal fragment size is estimated from the expected log-likelihood gain (LLG) values computed assuming that a substructure can be found with a level of accuracy near that required for successful extension of the structure, typically below 0.6 Å root-mean-square deviation (r.m.s.d.) from the target. Better sampling is attempted through model trimming or decomposition into rigid groups and optimization through Phaser's gyre refinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimble refinement) or Phaser's LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. Phase combination among consistent partial solutions is performed in reciprocal space with ALIXE. Finally, density modification and main-chain autotracing in SHELXE serve to expand to the full structure and identify successful solutions. The performance on test data and the solution of new structures are described.
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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
| | - Massimo Domenico Sammito
- Department of Structural Chemistry, Georg August University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Airlie J. McCoy
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 OXY, England
| | - Andrey F. Ziem Nascimento
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- XALOC Beamline, Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Caixa Postal 6192, 13083-970 Campinas-SP, Brazil
| | - Giovanna Petrillo
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- Biochemize S.L, Barcelona Advanced Industry, C/Marie Curie 8-14, 08042 Barcelona, Spain
| | - Robert D. Oeffner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 OXY, England
| | - Teresa Domínguez-Gil
- Department of Crystallography and Structural Biology, Instituto Química-Física ‘Rocasolano’ CSIC (Spanish National Research Council), Serrano 119, 28006 Madrid, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Instituto Química-Física ‘Rocasolano’ CSIC (Spanish National Research Council), Serrano 119, 28006 Madrid, Spain
| | - Randy J. Read
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 OXY, England
| | - 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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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: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled-coil structures with 15-635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i.
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Affiliation(s)
- Iracema Caballero
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Massimo Sammito
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Andrey Lebedev
- CCP4, STFC Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, England
| | - Nicolas Soler
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Borges RJ, Lemke N, Sammito M, Millán C, Usón I, Fontes MMR. PLA2s-like membrane perturbation mechanism: extracting the most of crystallography data. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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García Pisón J, Fleitas F, Garbarino B, Millán C, Cerchiari E, Olivera E. TOPOGRAFÍA INTRANEURAL DE LA RAMA PROFUNDA DEL NERVIO ULNAR EN EL ANTEBRAZO DISTAL: ESTUDIO CADAVÉRICO. Intraneural topography of the deep branch of the ulnar nerve in the distal forearm: cadaveric study. Rev Arg de Anat Clin 2016. [DOI: 10.31051/1852.8023.v8.n2.14634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Objetivo: estudiar la topografía intraneural de la rama profunda del nervio ulnar (RPNU) en el antebrazo distal en vistas a su identificación mediante disección intraneural mínima durante la transferencia del nervio del pronador cuadrado (NPC) a la RPNU. Materiales y métodos: En 15 antebrazos cadavéricos se fijó el paquete vasculonervioso ulnar a los planos musculares profundos cada un centímetro tomando como referencia el hueso pisiforme. Se disecó en sentido proximal la RPNU bajo microscopio quirúrgico (Olympus OME, 4-20x) y se registró su posición intraneural en base a una división en cuadrantes. Se midió la distancia desde el origen de la rama cutánea dorsal (RCD) del nervio ulnar al pisiforme y se registró su relación intraneural con la RPNU. Resultados: La RPNU se individualizó hasta 69mm (41-94) proximal al hueso pisiforme, ubicándose en el cuadrante posteromedial del nervio ulnar en el 78% (67-87), el 93% (92-93) y el 100% de los casos entre los 0-2, 3-6 y 7-9 centímetros, respectivamente. La distancia pisiforme-RCD fue de 63mm (52-83). En 11 miembros la disección de la RPNU se extendió proximalmente al origen de la RCD, ubicándose siempre entre esta última y la rama superficial del nervio ulnar. Conclusiones: La topografía intraneural de la RPNU en el sitio óptimo para su sección en vistas a su anastomosis con el NPC es predecible en la mayoría de los casos, lo que confirma la viabilidad de su identificación precisa mediante disección intraneural mínima. Objective: to assess the intraneural anatomy of the deep branch of the ulnar nerve (DBUN) in the distal forearm in reference to its identification by means of minimal intraneural dissection during pronator quadratus nerve to DBUN transfers. Materials and methods: In 15 cadaveric forearms the ulnar neurovascular bundle was identified and attached to the subjacent muscles every one centimeter. Pisiform bone was used as reference. Intraneural proximal dissection of the deep branch of the ulnar nerve was performed under magnification (Olympus OME, 4-20x) and its intraneural position was registered using a quadrants scheme. Distance from pisiform to the origin of the dorsal cutaneous branch of the ulnar nerve (DCB) was measured and its intraneural position relative to DBUN was identified. Results: The DBUN could be identified up to 69mm (41-94) proximal to the pisiform and occupied the posteromedial quadrant of the ulnar nerve in 78% (67-87), 93% (92-93) and 100% of the cases in the 0-2, 3-6 and 7-9cm ranges, respectively. Distance from pisiform to the origin of the DCB was 63mm (52-83). The DBUN could be identified proximal to the origin of the DCB in 11 forearms, being located between the latter and the superficial branch of the ulnar nerve in all this cases. Conclusions: Intraneural topography of the DBUN in the most appropriate site for its identification during its anastomosis to the PQN is predictable in the majority of cases, which supports the viability of safe identification of the de DBUN by means of minimal intraneural dissection.
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Gracia M, Millán C, Sánchez J, Guyard-Nicodème M, Mayot J, Carre Y, Csorbai A, Chemaly M, Medel P. Efficacy of feed additives against Campylobacter in live broilers during the entire rearing period: Part B. Poult Sci 2016; 95:886-92. [DOI: 10.3382/ps/pev346] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/28/2015] [Indexed: 11/20/2022] Open
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Millán C, Sammito M, Garcia-Ferrer I, Goulas T, Sheldrick GM, Usón I. Combining phase information in reciprocal space for molecular replacement with partial models. ACTA ACUST UNITED AC 2015; 71:1931-45. [PMID: 26327383 DOI: 10.1107/s1399004715013127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/08/2015] [Indexed: 11/10/2022]
Abstract
ARCIMBOLDO allows ab initio phasing of macromolecular structures below atomic resolution by exploiting the location of small model fragments combined with density modification in a multisolution frame. The model fragments can be either secondary-structure elements predicted from the sequence or tertiary-structure fragments. The latter can be derived from libraries of typical local folds or from related structures, such as a low-homology model that is unsuccessful in molecular replacement. In all ARCIMBOLDO applications, fragments are searched for sequentially. Correct partial solutions obtained after each fragment-search stage but lacking the necessary phasing power can, if combined, succeed. Here, an analysis is presented of the clustering of partial solutions in reciprocal space and of its application to a set of different cases. In practice, the task of combining model fragments from an ARCIMBOLDO run requires their referral to a common origin and is complicated by the presence of correct and incorrect solutions as well as by their not being independent. The F-weighted mean phase difference has been used as a figure of merit. Clustering perfect, non-overlapping fragments dismembered from test structures in polar and nonpolar space groups shows that density modification before determining the relative origin shift enhances its discrimination. In the case of nonpolar space groups, clustering of ARCIMBOLDO solutions from secondary-structure models is feasible. The use of partially overlapping search fragments provides a more favourable circumstance and was assessed on a test case. Applying the devised strategy, a previously unknown structure was solved from clustered correct partial solutions.
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Affiliation(s)
- Claudia Millán
- Structural Biology, Instituto de Biologia Molecular de Barcelona, Carrer Baldiri Reixac 15, 3 A17, 08028 Barcelona, Spain
| | - Massimo Sammito
- Structural Biology, Instituto de Biologia Molecular de Barcelona, Carrer Baldiri Reixac 15, 3 A17, 08028 Barcelona, Spain
| | - Irene Garcia-Ferrer
- Structural Biology, Instituto de Biologia Molecular de Barcelona, Carrer Baldiri Reixac 15, 3 A17, 08028 Barcelona, Spain
| | - Theodoros Goulas
- Structural Biology, Instituto de Biologia Molecular de Barcelona, Carrer Baldiri Reixac 15, 3 A17, 08028 Barcelona, Spain
| | - George M Sheldrick
- Structural Chemistry, Institut für Anorganische Chemie, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Isabel Usón
- Structural Biology, ICREA at IBMB-CSIC, Carrer Baldiri Reixac 13-15, 08028 Barcelona, Spain
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Sammito M, Millán C, Frieske D, Rodríguez-Freire E, Borges RJ, Usón I. ARCIMBOLDO_LITE: single-workstation implementation and use. ACTA ACUST UNITED AC 2015; 71:1921-30. [PMID: 26327382 DOI: 10.1107/s1399004715010846] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/04/2015] [Indexed: 11/10/2022]
Abstract
ARCIMBOLDO solves the phase problem at resolutions of around 2 Å or better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation, ARCIMBOLDO_LITE, on a pool of test structures with 40-120 amino acids and resolutions between 0.54 and 2.2 Å is described. Inbuilt polyalanine helices and iron cofactors are used as search fragments. ARCIMBOLDO_BORGES can also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE.
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Affiliation(s)
- Massimo Sammito
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Dawid Frieske
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Eloy Rodríguez-Freire
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Rafael J Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Structural Biology, ICREA at IBMB-CSIC, Baldiri Reixach 13-15, 08028 Barcelona, Spain
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Sammito M, Millán C, Borges RJ, Eyck LT, Usón I. BORGESlibraries: from phasing to structural bioinformatics. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315095856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Millán C, Sammito M, Borges RJ, Usón I. Use of clustering algorithms to combine partial solutions in reciprocal space. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315097612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Uson I, Sammito M, Millán C, Borges RJ. ARCIMBOLDO, an ab initioapproach to MR phasing. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315099659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Borges RJ, Sammito M, Millán C, Fontes MRM, Usón I. SEQUENCE SLIDER: a multi sequence evaluator and its application in venomics. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315097582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Schoch GA, Sammito M, Millán C, Usón I, Rudolph MG. Structure of a 13-fold superhelix (almost) determined from first principles. IUCrJ 2015; 2:177-87. [PMID: 25866655 PMCID: PMC4392412 DOI: 10.1107/s2052252515000238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2). For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.
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Affiliation(s)
- Guillaume A. Schoch
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Massimo Sammito
- Instituto de Biología Molecular de Barcelona (IBMB), CSIC, Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Instituto de Biología Molecular de Barcelona (IBMB), CSIC, Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB), CSIC, Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys, 23, 08010 Barcelona, Spain
| | - Markus G. Rudolph
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
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Millán C, Sammito M, Usón I. Macromolecular ab initio phasing enforcing secondary and tertiary structure. IUCrJ 2015; 2:95-105. [PMID: 25610631 PMCID: PMC4285884 DOI: 10.1107/s2052252514024117] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/31/2014] [Indexed: 06/04/2023]
Abstract
Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.
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Affiliation(s)
- Claudia Millán
- Structural Biology, Molecular Biology Institute of Barcelona, Baldiri Reixac 15, Barcelona, 08028, Spain
| | - Massimo Sammito
- Structural Biology, Molecular Biology Institute of Barcelona, Baldiri Reixac 15, Barcelona, 08028, Spain
| | - Isabel Usón
- Structural Biology, ICREA at IBMB-CSIC, Baldiri Reixac 13-15, Barcelona, 08028, Spain
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Sammito M, Meindl K, de Ilarduya IM, Millán C, Artola-Recolons C, Hermoso JA, Usón I. Structure solution with ARCIMBOLDO using fragments derived from distant homology models. FEBS J 2014; 281:4029-45. [PMID: 24976038 DOI: 10.1111/febs.12897] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 11/30/2022]
Abstract
Molecular replacement, one of the general methods used to solve the crystallographic phase problem, relies on the availability of suitable models for placement in the unit cell of the unknown structure in order to provide initial phases. ARCIMBOLDO, originally conceived for ab initio phasing, operates at the limit of this approach, using small, very accurate fragments such as polyalanine α-helices. A distant homolog may contain accurate building blocks, but it may not be evident which sub-structure is the most suitable purely from the degree of conservation. Trying out all alternative possibilities in a systematic way is computationally expensive, even if effective. In the present study, the solution of the previously unknown structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli, is described. The asymmetric unit contains a dimer of this 194 amino acid protein. The closest available homolog was the catalytic domain of Slt70 (PDB code 1QTE). Originally, this template was used omitting contiguous spans of aminoacids and setting as many ARCIMBOLDO runs as models, each aiming to locate two copies sequentially with PHASER. Fragment trimming against the correlation coefficient prior to expansion through density modification and autotracing in SHELXE was essential. Analysis of the figures of merit led to the strategy to optimize the search model against the experimental data now implemented within ARCIMBOLDO-SHREDDER (http://chango.ibmb.csic.es/SHREDDER). In this strategy, the initial template is systematically shredded, and fragments are scored against each unique solution of the rotation function. Results are combined into a score per residue and the template is trimmed accordingly.
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Affiliation(s)
- Massimo Sammito
- Instituto de Biología Molecular de Barcelona, Barcelona Science Park, Barcelona, Spain
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Sammito M, Millán C, Rodríguez DD, de Ilarduya IM, Meindl K, De Marino I, Petrillo G, Buey RM, de Pereda JM, Zeth K, Sheldrick GM, Usón I. Erratum: Corrigendum: Exploiting tertiary structure through local folds for crystallographic phasing. Nat Methods 2014. [DOI: 10.1038/nmeth0714-773b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Millán C, Sammito M, Meindl K, de Ilarduya IM, Marino ID, Usón I. Reciprocal space clustering of BORGES- ARCIMBOLDOpartial solutions: practical cases. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313097468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Sammito M, Millán C, de Ilarduya IM, De Marino I, Meindl K, Usón I. BORGES- ARCIMBOLDOexploiting tertiary folds as fragments libraries for phasing. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313097675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Sammito M, Millán C, Ilarduya IMD, Marino ID, Meindl K, Usón I. BORGES-ARCIMBOLDOexploiting tertiary folds as fragments libraries for phasing. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313094105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Lasso Betancor CE, Domínguez G, Millán C, Bignon H, Buela E, Bellia G, Albertal M, Martínez Ferro M. [Transumbilical cholecystectomy using hybrid technique: a new promising approach]. Cir Pediatr 2012; 25:193-196. [PMID: 23659020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVES The use of magnets in transumbilical cholecystectomy improves triangulation and achieves optimal critical view. However, the attraction between magnets can cause collisions and their management complicates the procedure, and this will become more important in children. In order to simplify the technique, we have developed a hybrid model with a single magnet. MATERIAL AND METHODS Retrospective review of cholecystectomies performed in our department between June 2011 and July 2012. The technique combines the use of a magnet and a curved grasper. Through transumbilical incision, a 12 mm trocar and another flexible 5 mm are placed. Laparoscope with working channel uses the 12 mm trocar. The magnet is introduced to the abdominal cavity using the working channel to provide cephalad retraction of gallbladder fundus. Curved grasper is run by the assistant to mobilize the infundibulum across flexible trocar. The surgeon operates through the working channel of the laparoscope. RESULTS Twenty-six patients were operated on with this technique. Mean age was 14 years (4-17) and weight 50 kg (18-90). 65% were girls. The mean operative time was 62 minutes (50-70) and the critical view of safety was achieved in all cases. Instrumental collision or hands crossing were not seen. There were no intraoperative or postoperative complications. The hospital stay was 1.4 +/- 0.6 days and the median follow-up 201 days (42-429). CONCLUSIONS The hybrid technique, combining magnet and a curved grasper, simplifies transumbilical surgery. It seems a feasible and safe for transumbilical cholecystectomy and potentially reproducible.
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Affiliation(s)
- C E Lasso Betancor
- Fundación Hospitalaria, Hospital Privado de Niños, Buenos Aires, Argentina.
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Millán C, Quintana B, Rodríguez A, Iglesias M, Barranco M, Navia J. [Efficacy of recombinant activated factor VII for massive bleeding after cardiac surgery: experience with 32 patients]. ACTA ACUST UNITED AC 2010; 56:485-92. [PMID: 19994617 DOI: 10.1016/s0034-9356(09)70439-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To determine the efficacy of recombinant activated factor VII (rFVIIa) to treat massive bleeding refractory to conventional treatment following cardiac surgery. PATIENTS AND METHODS Retrospective study of 32 adults who underwent cardiac surgery and received rFVIIa to treat life-threatening postoperative bleeding after conventional means of correcting coagulopathy had failed. RESULTS After administration of rFVIIa (90 microg x kg(-1), coagulation parameters soon became normal and blood loss decreased, with drainage going from a mean (SD) of 463 (321) mL in the hour when rFVIIa was infused to 155 (101) mL in the next hour (P < .001). Blood loss decreased by between 22% and 90% (mean, 66%), and the reduction was over 75% in 45% of the patients. Decreases in the transfusion of packed red blood cells (from 7A.4 [4.1] units to 2.7 [ 2.9] units; P < .001), plasma (from 4.7 [2.9] units to 1.6 [2.0] units; P < .001), and platelets were also noted. Mortality was 25%, although only 1 patient died from hemorrhagic shock. One patient developed thromboembolic complications (ischemic stroke). CONCLUSION rFVIIa was effective in treating refractory bleeding after cardiac surgery, reducing blood loss and transfusion requirements and restoring blood parameters to normal.
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Affiliation(s)
- C Millán
- Departamento de Anestesiología y Reanimación, Hospital General Universitario "Gregorio Marañńon", Madrid.
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García MA, Montecinos H, Balmaceda-Aguilera C, Millán C, Nualart F. Poster Sessions CP10: Blood-Brain Barrier. J Neurochem 2008. [DOI: 10.1046/j.1471-4159.81.s1.39_1.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ruiz Domínguez J, Millán C, Menéndez J, Sancho A, Muñoz R, Gómez A, Lodoso B, Ruza F. O.78. Perfusión tisular y disfunción renal en el postoperatorio inmediato de cirugía cardíaca. An Pediatr (Barc) 2007. [DOI: 10.1016/s1695-4033(07)70519-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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