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El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner A. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Commun Chem 2023; 6:219. [PMID: 37828292 PMCID: PMC10570326 DOI: 10.1038/s42004-023-01014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Christian M Orr
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | | | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Vinay Grama
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Feng Qu
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hok Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosana I Reis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Lutz Vogeley
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Raymond J Owens
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David G Brown
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
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2
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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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Krissinel E, Lebedev AA, Uski V, Ballard CB, Keegan RM, Kovalevskiy O, Nicholls RA, Pannu NS, Skubák P, Berrisford J, Fando M, Lohkamp B, Wojdyr M, Simpkin AJ, Thomas JMH, Oliver C, Vonrhein C, Chojnowski G, Basle A, Purkiss A, Isupov MN, McNicholas S, Lowe E, Triviño J, Cowtan K, Agirre J, Rigden DJ, Uson I, Lamzin V, Tews I, Bricogne G, Leslie AGW, Brown DG. CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:1079-1089. [PMID: 36048148 PMCID: PMC9435598 DOI: 10.1107/s2059798322007987] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.
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Cowell AR, Jacquemet G, Singh AK, Varela L, Nylund AS, Ammon YC, Brown DG, Akhmanova A, Ivaska J, Goult BT. Talin rod domain-containing protein 1 (TLNRD1) is a novel actin-bundling protein which promotes filopodia formation. J Cell Biol 2021; 220:e202005214. [PMID: 34264272 PMCID: PMC8287531 DOI: 10.1083/jcb.202005214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/29/2020] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 02/01/2023] Open
Abstract
Talin is a mechanosensitive adapter protein that couples integrins to the cytoskeleton. Talin rod domain-containing protein 1 (TLNRD1) shares 22% homology with the talin R7R8 rod domains, and is highly conserved throughout vertebrate evolution, although little is known about its function. Here we show that TLNRD1 is an α-helical protein structurally homologous to talin R7R8. Like talin R7R8, TLNRD1 binds F-actin, but because it forms a novel antiparallel dimer, it also bundles F-actin. In addition, it binds the same LD motif-containing proteins, RIAM and KANK, as talin R7R8. In cells, TLNRD1 localizes to actin bundles as well as to filopodia. Increasing TLNRD1 expression enhances filopodia formation and cell migration on 2D substrates, while TLNRD1 down-regulation has the opposite effect. Together, our results suggest that TLNRD1 has retained the diverse interactions of talin R7R8, but has developed distinct functionality as an actin-bundling protein that promotes filopodia assembly.
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Affiliation(s)
| | - Guillaume Jacquemet
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | | | - Lorena Varela
- School of Biosciences, University of Kent, Canterbury, UK
| | - Anna S. Nylund
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - York-Christoph Ammon
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - David G. Brown
- School of Biosciences, University of Kent, Canterbury, UK
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Biochemistry, University of Turku, Turku, Finland
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5
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Munday JC, Kunz S, Kalejaiye TD, Siderius M, Schroeder S, Paape D, Alghamdi AH, Abbasi Z, Huang SX, Donachie AM, William S, Sabra AN, Sterk GJ, Botros SS, Brown DG, Hoffman CS, Leurs R, de Koning HP. Cloning and functional complementation of ten Schistosoma mansoni phosphodiesterases expressed in the mammalian host stages. PLoS Negl Trop Dis 2020; 14:e0008447. [PMID: 32730343 PMCID: PMC7430754 DOI: 10.1371/journal.pntd.0008447] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/17/2020] [Accepted: 06/02/2020] [Indexed: 01/29/2023] Open
Abstract
Only a single drug against schistosomiasis is currently available and new drug development is urgently required but very few drug targets have been validated and characterised. However, regulatory systems including cyclic nucleotide metabolism are emerging as primary candidates for drug discovery. Here, we report the cloning of ten cyclic nucleotide phosphodiesterase (PDE) genes of S. mansoni, out of a total of 11 identified in its genome. We classify these PDEs by homology to human PDEs. Male worms displayed higher expression levels for all PDEs, in mature and juvenile worms, and schistosomula. Several functional complementation approaches were used to characterise these genes. We constructed a Trypanosoma brucei cell line in which expression of a cAMP-degrading PDE complements the deletion of TbrPDEB1/B2. Inhibitor screens of these cells expressing only either SmPDE4A, TbrPDEB1 or TbrPDEB2, identified highly potent inhibitors of the S. mansoni enzyme that elevated the cellular cAMP concentration. We further expressed most of the cloned SmPDEs in two pde1Δ/pde2Δ strains of Saccharomyces cerevisiae and some also in a specialised strain of Schizosacharomyces pombe. Five PDEs, SmPDE1, SmPDE4A, SmPDE8, SmPDE9A and SmPDE11 successfully complemented the S. cerevisiae strains, and SmPDE7var also complemented to a lesser degree, in liquid culture. SmPDE4A, SmPDE8 and SmPDE11 were further assessed in S. pombe for hydrolysis of cAMP and cGMP; SmPDE11 displayed considerable preferrence for cGMP over cAMP. These results and tools enable the pursuit of a rigorous drug discovery program based on inhibitors of S. mansoni PDEs.
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Affiliation(s)
- Jane C. Munday
- Institute of Infection, Immunity and inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Stefan Kunz
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, The Netherlands
| | - Titilola D. Kalejaiye
- Institute of Infection, Immunity and inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Marco Siderius
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, The Netherlands
| | | | - Daniel Paape
- Institute of Infection, Immunity and inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Ali H. Alghamdi
- Institute of Infection, Immunity and inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Zainab Abbasi
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Sheng Xiang Huang
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Anne-Marie Donachie
- Institute of Infection, Immunity and inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Samia William
- Department of Pharmacology, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Egypt
| | - Abdel Nasser Sabra
- Department of Pharmacology, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Egypt
| | - Geert Jan Sterk
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, The Netherlands
| | - Sanaa S. Botros
- Department of Pharmacology, Theodor Bilharz Research Institute, Warrak El-Hadar, Imbaba, Egypt
| | - David G. Brown
- School of Biosciences, University of Kent, United Kingdom
| | - Charles S. Hoffman
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, The Netherlands
| | - Harry P. de Koning
- Institute of Infection, Immunity and inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
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6
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de Heuvel E, Singh AK, Boronat P, Kooistra AJ, van der Meer T, Sadek P, Blaazer AR, Shaner NC, Bindels DS, Caljon G, Maes L, Sterk GJ, Siderius M, Oberholzer M, de Esch IJ, Brown DG, Leurs R. Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2). Bioorg Med Chem 2019; 27:4013-4029. [DOI: 10.1016/j.bmc.2019.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 01/27/2023]
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7
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Zak M, Hanan EJ, Lupardus P, Brown DG, Robinson C, Siu M, Lyssikatos JP, Romero FA, Zhao G, Kellar T, Mendonca R, Ray NC, Goodacre SC, Crackett PH, McLean N, Hurley CA, Yuen PW, Cheng YX, Liu X, Liimatta M, Kohli PB, Nonomiya J, Salmon G, Buckley G, Lloyd J, Gibbons P, Ghilardi N, Kenny JR, Johnson A. Discovery of a class of highly potent Janus Kinase 1/2 (JAK1/2) inhibitors demonstrating effective cell-based blockade of IL-13 signaling. Bioorg Med Chem Lett 2019; 29:1522-1531. [PMID: 30981576 DOI: 10.1016/j.bmcl.2019.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 01/22/2023]
Abstract
Disruption of interleukin-13 (IL-13) signaling with large molecule antibody therapies has shown promise in diseases of allergic inflammation. Given that IL-13 recruits several members of the Janus Kinase family (JAK1, JAK2, and TYK2) to its receptor complex, JAK inhibition may offer an alternate small molecule approach to disrupting IL-13 signaling. Herein we demonstrate that JAK1 is likely the isoform most important to IL-13 signaling. Structure-based design was then used to improve the JAK1 potency of a series of previously reported JAK2 inhibitors. The ability to impede IL-13 signaling was thereby significantly improved, with the best compounds exhibiting single digit nM IC50's in cell-based assays dependent upon IL-13 signaling. Appropriate substitution was further found to influence inhibition of a key off-target, LRRK2. Finally, the most potent compounds were found to be metabolically labile, which makes them ideal scaffolds for further development as topical agents for IL-13 mediated diseases of the lungs and skin (for example asthma and atopic dermatitis, respectively).
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Affiliation(s)
- Mark Zak
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Emily J Hanan
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - David G Brown
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Colin Robinson
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Michael Siu
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | | | - Guiling Zhao
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Terry Kellar
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohan Mendonca
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nicholas C Ray
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Simon C Goodacre
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Peter H Crackett
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Neville McLean
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Christopher A Hurley
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Po-Wai Yuen
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, PR China
| | - Yun-Xing Cheng
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, PR China
| | - Xiongcai Liu
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, PR China
| | - Marya Liimatta
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Pawan Bir Kohli
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jim Nonomiya
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gary Salmon
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Gerry Buckley
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Julia Lloyd
- Charles River Laboratories, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Paul Gibbons
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nico Ghilardi
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jane R Kenny
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Adam Johnson
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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8
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Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol 2019; 75:451-454. [PMID: 30988261 PMCID: PMC6465986 DOI: 10.1107/s2059798319004522] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 02/21/2019] [Accepted: 04/03/2019] [Indexed: 11/10/2022] Open
Abstract
This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).
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Affiliation(s)
- Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kumaran Baskaran
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gerard Bricogne
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - David G. Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Minyu Chen
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Claus Flensburg
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeffrey C. Hoch
- BioMagResBank (BMRB), UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Yasuyo Ikegawa
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yumiko Kengaku
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Eugene Krissinel
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John L. Markley
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Martin Noble
- Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eldon L. Ulrich
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Clemens Vonrhein
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Masashi Yokochi
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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9
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Mugayar LRF, Perez E, Nagasawa PR, Brown DG, Tolentino LA, Kuang HS, Behar-Horenstein LS. A Multi-Institutional Study of Dental Student Readiness to Address Adolescent Risk Behaviors. J Dent Educ 2019; 83:296-302. [PMID: 30692192 DOI: 10.21815/jde.019.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/08/2018] [Accepted: 09/10/2018] [Indexed: 11/20/2022]
Abstract
The aim of this replication study was to determine if prior findings at one U.S. dental school about dental students' comfort discussing and perceptions of the relevance of 15 risk behaviors to adolescent patient oral health care would be observed at other institutions. All first- and fourth-year dental students (n=414) at three U.S. dental schools in fall 2017 were invited to participate, and 218 completed the survey (52.7% response rate). These students reported feeling comfortable to uncomfortable discussing risk behaviors with adolescent patients, yet perceived those risk behaviors as relevant to their oral health. There were significant differences in student comfort discussing risk behaviors with adolescents and their perceptions of relevance by gender, age, class status, and school location. Males were more comfortable than females discussing oral health risk behaviors. There were no significant differences by race/ethnicity. Fourth-year students had higher levels of comfort discussing risk behaviors than first-year students. Compared to students in the South and Midwest schools, students at the West school were more comfortable discussing selected topics and had higher perceptions of their relevance to adolescent oral health care. These results suggest there is room for improvement in this area of dental education. Dental schools should aim to strengthen students' knowledge of and comfort in discussing oral health risk behaviors with adolescent patients with the use of educational activities and clinical experiences.
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Affiliation(s)
- Leda Regina Fernandes Mugayar
- Leda Regina Fernandes Mugayar is Associate Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Edna Perez is Assistant Clinical Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Pamela R. Nagasawa is Assistant Professor, Biomedical Informatics and Medical Education, School of Medicine, University of Washington; David G. Brown is Professor, College of Dentistry, University of Nebraska Medical Center; Lissette A. Tolentino is at the CTSI Clinical Translational Science Institute, University of Florida; Huan S. Kuang is at the CTSI Clinical Translational Science Institute, University of Florida; and Linda S. Behar-Horenstein, PhD, is Professor Emeritus, University of Florida
| | - Edna Perez
- Leda Regina Fernandes Mugayar is Associate Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Edna Perez is Assistant Clinical Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Pamela R. Nagasawa is Assistant Professor, Biomedical Informatics and Medical Education, School of Medicine, University of Washington; David G. Brown is Professor, College of Dentistry, University of Nebraska Medical Center; Lissette A. Tolentino is at the CTSI Clinical Translational Science Institute, University of Florida; Huan S. Kuang is at the CTSI Clinical Translational Science Institute, University of Florida; and Linda S. Behar-Horenstein, PhD, is Professor Emeritus, University of Florida
| | - Pamela R Nagasawa
- Leda Regina Fernandes Mugayar is Associate Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Edna Perez is Assistant Clinical Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Pamela R. Nagasawa is Assistant Professor, Biomedical Informatics and Medical Education, School of Medicine, University of Washington; David G. Brown is Professor, College of Dentistry, University of Nebraska Medical Center; Lissette A. Tolentino is at the CTSI Clinical Translational Science Institute, University of Florida; Huan S. Kuang is at the CTSI Clinical Translational Science Institute, University of Florida; and Linda S. Behar-Horenstein, PhD, is Professor Emeritus, University of Florida
| | - David G Brown
- Leda Regina Fernandes Mugayar is Associate Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Edna Perez is Assistant Clinical Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Pamela R. Nagasawa is Assistant Professor, Biomedical Informatics and Medical Education, School of Medicine, University of Washington; David G. Brown is Professor, College of Dentistry, University of Nebraska Medical Center; Lissette A. Tolentino is at the CTSI Clinical Translational Science Institute, University of Florida; Huan S. Kuang is at the CTSI Clinical Translational Science Institute, University of Florida; and Linda S. Behar-Horenstein, PhD, is Professor Emeritus, University of Florida
| | - Lissette A Tolentino
- Leda Regina Fernandes Mugayar is Associate Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Edna Perez is Assistant Clinical Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Pamela R. Nagasawa is Assistant Professor, Biomedical Informatics and Medical Education, School of Medicine, University of Washington; David G. Brown is Professor, College of Dentistry, University of Nebraska Medical Center; Lissette A. Tolentino is at the CTSI Clinical Translational Science Institute, University of Florida; Huan S. Kuang is at the CTSI Clinical Translational Science Institute, University of Florida; and Linda S. Behar-Horenstein, PhD, is Professor Emeritus, University of Florida
| | - Huan S Kuang
- Leda Regina Fernandes Mugayar is Associate Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Edna Perez is Assistant Clinical Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Pamela R. Nagasawa is Assistant Professor, Biomedical Informatics and Medical Education, School of Medicine, University of Washington; David G. Brown is Professor, College of Dentistry, University of Nebraska Medical Center; Lissette A. Tolentino is at the CTSI Clinical Translational Science Institute, University of Florida; Huan S. Kuang is at the CTSI Clinical Translational Science Institute, University of Florida; and Linda S. Behar-Horenstein, PhD, is Professor Emeritus, University of Florida
| | - Linda S Behar-Horenstein
- Leda Regina Fernandes Mugayar is Associate Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Edna Perez is Assistant Clinical Professor of Pediatric Dentistry, College of Dentistry, University of Florida; Pamela R. Nagasawa is Assistant Professor, Biomedical Informatics and Medical Education, School of Medicine, University of Washington; David G. Brown is Professor, College of Dentistry, University of Nebraska Medical Center; Lissette A. Tolentino is at the CTSI Clinical Translational Science Institute, University of Florida; Huan S. Kuang is at the CTSI Clinical Translational Science Institute, University of Florida; and Linda S. Behar-Horenstein, PhD, is Professor Emeritus, University of Florida.
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10
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Lawrence AD, Nemoto-Smith E, Deery E, Baker JA, Schroeder S, Brown DG, Tullet JMA, Howard MJ, Brown IR, Smith AG, Boshoff HI, Barry CE, Warren MJ. Construction of Fluorescent Analogs to Follow the Uptake and Distribution of Cobalamin (Vitamin B 12) in Bacteria, Worms, and Plants. Cell Chem Biol 2018; 25:941-951.e6. [PMID: 29779954 DOI: 10.1016/j.chembiol.2018.04.012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/18/2018] [Accepted: 04/11/2018] [Indexed: 12/25/2022]
Abstract
Vitamin B12 is made by only certain prokaryotes yet is required by a number of eukaryotes such as mammals, fish, birds, worms, and Protista, including algae. There is still much to learn about how this nutrient is trafficked across the domains of life. Herein, we describe ways to make a number of different corrin analogs with fluorescent groups attached to the main tetrapyrrole-derived ring. A further range of analogs were also constructed by attaching similar fluorescent groups to the ribose ring of cobalamin, thereby generating a range of complete and incomplete corrinoids to follow uptake in bacteria, worms, and plants. By using these fluorescent derivatives we were able to demonstrate that Mycobacterium tuberculosis is able to acquire both cobyric acid and cobalamin analogs, that Caenorhabditis elegans takes up only the complete corrinoid, and that seedlings of higher plants such as Lepidium sativum are also able to transport B12.
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Affiliation(s)
- Andrew D Lawrence
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Emi Nemoto-Smith
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20850, USA
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Joseph A Baker
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Susanne Schroeder
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - David G Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | | | - Mark J Howard
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Ian R Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Helena I Boshoff
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20850, USA
| | - Clifton E Barry
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20850, USA
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
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11
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Whitewood AJ, Singh AK, Brown DG, Goult BT. Chlamydial virulence factor TarP mimics talin to disrupt the talin-vinculin complex. FEBS Lett 2018; 592:1751-1760. [PMID: 29710402 PMCID: PMC6001692 DOI: 10.1002/1873-3468.13074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/12/2018] [Accepted: 04/21/2018] [Indexed: 11/12/2022]
Abstract
Vinculin is a central component of mechanosensitive adhesive complexes that form between cells and the extracellular matrix. A myriad of infectious agents mimic vinculin binding sites (VBS), enabling them to hijack the adhesion machinery and facilitate cellular entry. Here, we report the structural and biochemical characterisation of VBS from the chlamydial virulence factor TarP. Whilst the affinities of isolated VBS peptides from TarP and talin for vinculin are similar, their behaviour in larger fragments is markedly different. In talin, VBS are cryptic and require mechanical activation to bind vinculin, whereas the TarP VBS are located in disordered regions, and so are constitutively active. We demonstrate that the TarP VBS can uncouple talin:vinculin complexes, which may lead to adhesion destabilisation.
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Affiliation(s)
| | | | - David G Brown
- School of Biosciences, University of Kent, Canterbury, UK
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12
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Blaazer AR, Singh AK, de Heuvel E, Edink E, Orrling KM, Veerman JJN, van den Bergh T, Jansen C, Balasubramaniam E, Mooij WJ, Custers H, Sijm M, Tagoe DNA, Kalejaiye TD, Munday JC, Tenor H, Matheeussen A, Wijtmans M, Siderius M, de Graaf C, Maes L, de Koning HP, Bailey DS, Sterk GJ, de Esch IJP, Brown DG, Leurs R. Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J Med Chem 2018; 61:3870-3888. [PMID: 29672041 PMCID: PMC5949723 DOI: 10.1021/acs.jmedchem.7b01670] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Several trypanosomatid
cyclic nucleotide phosphodiesterases (PDEs)
possess a unique, parasite-specific cavity near the ligand-binding
region that is referred to as the P-pocket. One of these enzymes, Trypanosoma brucei PDE B1 (TbrPDEB1), is considered a drug
target for the treatment of African sleeping sickness. Here, we elucidate
the molecular determinants of inhibitor binding and reveal that the
P-pocket is amenable to directed design. By iterative cycles of design,
synthesis, and pharmacological evaluation and by elucidating the structures
of inhibitor-bound TbrPDEB1, hPDE4B, and hPDE4D complexes, we have
developed 4a,5,8,8a-tetrahydrophthalazinones as the first selective
TbrPDEB1 inhibitor series. Two of these, 8 (NPD-008)
and 9 (NPD-039), were potent (Ki = 100 nM) TbrPDEB1 inhibitors with antitrypanosomal effects
(IC50 = 5.5 and 6.7 μM, respectively). Treatment
of parasites with 8 caused an increase in intracellular
cyclic adenosine monophosphate (cAMP) levels and severe disruption
of T. brucei cellular organization, chemically validating
trypanosomal PDEs as therapeutic targets in trypanosomiasis.
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Affiliation(s)
- Antoni R Blaazer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Abhimanyu K Singh
- School of Biosciences , University of Kent , Canterbury CT2 7NJ , U.K
| | - Erik de Heuvel
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Ewald Edink
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Kristina M Orrling
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | | | | | - Chimed Jansen
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | | | - Wouter J Mooij
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Hans Custers
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Maarten Sijm
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Daniel N A Tagoe
- Institute of Infection, Immunity and Inflammation , University of Glasgow , Glasgow G12 8TA , U.K
| | - Titilola D Kalejaiye
- Institute of Infection, Immunity and Inflammation , University of Glasgow , Glasgow G12 8TA , U.K
| | - Jane C Munday
- Institute of Infection, Immunity and Inflammation , University of Glasgow , Glasgow G12 8TA , U.K
| | | | - An Matheeussen
- Laboratory for Microbiology, Parasitology and Hygiene , University of Antwerp , 2610 Wilrijk , Belgium
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Marco Siderius
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene , University of Antwerp , 2610 Wilrijk , Belgium
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation , University of Glasgow , Glasgow G12 8TA , U.K
| | | | - Geert Jan Sterk
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
| | - David G Brown
- School of Biosciences , University of Kent , Canterbury CT2 7NJ , U.K
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands
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13
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Barton KR, Yazdani A, Ayer N, Kalvapalle S, Brown S, Stapleton J, Brown DG, Harrigan KA. Erratum to: The Effect of Losses Disguised as Wins and Near Misses in Electronic Gaming Machines: A Systematic Review. J Gambl Stud 2017; 33:1261. [PMID: 28577047 DOI: 10.1007/s10899-017-9696-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- K R Barton
- Department of Psychology, University of Waterloo, Waterloo, Canada.
| | - A Yazdani
- Department of Kinesiology, University of Waterloo, Waterloo, Canada
| | - N Ayer
- Department of Recreation and Leisure Studies, University of Waterloo, Waterloo, Canada
| | - S Kalvapalle
- Department of Psychology, University of Waterloo, Waterloo, Canada.,Gambling Research Lab, University of Waterloo, Waterloo, Canada
| | - S Brown
- University of Waterloo Library, Waterloo, Canada
| | - J Stapleton
- University of Waterloo Library, Waterloo, Canada
| | - D G Brown
- Gambling Research Lab, University of Waterloo, Waterloo, Canada.,David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Canada
| | - K A Harrigan
- Gambling Research Lab, University of Waterloo, Waterloo, Canada.
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14
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Jones P, Storer RI, Sabnis YA, Wakenhut FM, Whitlock GA, England KS, Mukaiyama T, Dehnhardt CM, Coe JW, Kortum SW, Chrencik JE, Brown DG, Jones RM, Murphy JR, Yeoh T, Morgan P, Kilty I. Design and Synthesis of a Pan-Janus Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery for the Treatment of Inflammatory Diseases of the Lungs and Skin. J Med Chem 2017; 60:767-786. [DOI: 10.1021/acs.jmedchem.6b01634] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Peter Jones
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - R. Ian Storer
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Yogesh A. Sabnis
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Florian M. Wakenhut
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Gavin A. Whitlock
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Katherine S. England
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Takasuke Mukaiyama
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Christoph M. Dehnhardt
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Jotham W. Coe
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Steve W. Kortum
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Jill E. Chrencik
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - David G. Brown
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Rhys M. Jones
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - John R. Murphy
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Thean Yeoh
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Paul Morgan
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
| | - Iain Kilty
- Medicine Design, ‡Pharmacokinetics, Dynamics and Metabolism, and §Inflammation and
Immunology Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Medicine Design, and ⊥Medicinal Sciences, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
- Worldwide Medicinal Chemistry, ∇Structural Biology
and Biophysics, and ○Pharmaceutical
Sciences, Pfizer Ltd., Ramsgate Road, Sandwich, CT13 9NJ, U.K
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15
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Feng X, Mugayar L, Perez E, Nagasawa PR, Brown DG, Behar-Horenstein LS. Dental Students' Knowledge of Resources for LGBT Persons: Findings from Three Dental Schools. J Dent Educ 2017; 81:22-28. [PMID: 28049674] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/28/2016] [Indexed: 06/06/2023]
Abstract
Recently, there has been increased attention to including cultural diversity in the education of health professionals, including concern for lesbian, gay, bisexual, and transgender (LGBT) inclusion and visibility. Studies regarding cultural exposure and acceptance of LGBT populations have been concentrated in medicine, with findings showing that medical providers often graduate having missed the preparation required to care for LGBT persons. A visible, comprehensive, culturally competent environment in dental schools would help ensure that all oral health professionals and students are aware of services available to address the particular needs of LGBT students. The aims of this survey-based study conducted in 2015-16 were to determine dental students' perceptions regarding LGBT students' needs and to assess dental students' knowledge of resources for LGBT persons at three U.S. dental schools, one each in the Midwest, West, and South. Of the 849 students invited to participate, 364 completed the survey (338 dental, 26 dental hygiene), for an overall response rate of 43%. The response rate at individual schools ranged from 30% to 55%. The results showed perceptions of insufficient LGBT information, resources, and support at these institutions, especially at the Western school. There were significant differences among the three schools, with students at the Western school more than the other two schools perceiving that their institution was less aware of whether it met the academic, social support, and spiritual needs of LGBT students. There were no significant differences between LGBT and non-LGBT students' perceptions. The authors urge dental school administrators to explore the degree to which their programs teach respectful and caring behavior towards LGBT students and, by extension, LGBT patient populations.
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Affiliation(s)
- Xiaoying Feng
- Ms. Feng is a doctoral candidate, College of Education, University of Florida; Dr. Mugayar is Clinical Associate Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Perez is Clinical Assistant Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Nagasawa is on the faculty, Department of Biomedical Informatics and Medical Education, School of Medicine and a team member, Regional Initiatives in Dental Education (RIDE), School of Dental Medicine, University of Washington; Dr. Brown is Executive Associate Dean for Academic Affairs and Professor of Oral Biology, University of Nebraska Medical Center; and Dr. Behar-Horenstein is Distinguished Teaching Scholar and Professor, Colleges of Dentistry, Education, Veterinary Medicine, and Pharmacy, as well as being Director, CTSI Educational Development and Evaluation and Co-Director, HRSA Faculty Development in Dentistry, University of Florida
| | - Leda Mugayar
- Ms. Feng is a doctoral candidate, College of Education, University of Florida; Dr. Mugayar is Clinical Associate Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Perez is Clinical Assistant Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Nagasawa is on the faculty, Department of Biomedical Informatics and Medical Education, School of Medicine and a team member, Regional Initiatives in Dental Education (RIDE), School of Dental Medicine, University of Washington; Dr. Brown is Executive Associate Dean for Academic Affairs and Professor of Oral Biology, University of Nebraska Medical Center; and Dr. Behar-Horenstein is Distinguished Teaching Scholar and Professor, Colleges of Dentistry, Education, Veterinary Medicine, and Pharmacy, as well as being Director, CTSI Educational Development and Evaluation and Co-Director, HRSA Faculty Development in Dentistry, University of Florida
| | - Edna Perez
- Ms. Feng is a doctoral candidate, College of Education, University of Florida; Dr. Mugayar is Clinical Associate Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Perez is Clinical Assistant Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Nagasawa is on the faculty, Department of Biomedical Informatics and Medical Education, School of Medicine and a team member, Regional Initiatives in Dental Education (RIDE), School of Dental Medicine, University of Washington; Dr. Brown is Executive Associate Dean for Academic Affairs and Professor of Oral Biology, University of Nebraska Medical Center; and Dr. Behar-Horenstein is Distinguished Teaching Scholar and Professor, Colleges of Dentistry, Education, Veterinary Medicine, and Pharmacy, as well as being Director, CTSI Educational Development and Evaluation and Co-Director, HRSA Faculty Development in Dentistry, University of Florida
| | - Pamela R Nagasawa
- Ms. Feng is a doctoral candidate, College of Education, University of Florida; Dr. Mugayar is Clinical Associate Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Perez is Clinical Assistant Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Nagasawa is on the faculty, Department of Biomedical Informatics and Medical Education, School of Medicine and a team member, Regional Initiatives in Dental Education (RIDE), School of Dental Medicine, University of Washington; Dr. Brown is Executive Associate Dean for Academic Affairs and Professor of Oral Biology, University of Nebraska Medical Center; and Dr. Behar-Horenstein is Distinguished Teaching Scholar and Professor, Colleges of Dentistry, Education, Veterinary Medicine, and Pharmacy, as well as being Director, CTSI Educational Development and Evaluation and Co-Director, HRSA Faculty Development in Dentistry, University of Florida
| | - David G Brown
- Ms. Feng is a doctoral candidate, College of Education, University of Florida; Dr. Mugayar is Clinical Associate Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Perez is Clinical Assistant Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Nagasawa is on the faculty, Department of Biomedical Informatics and Medical Education, School of Medicine and a team member, Regional Initiatives in Dental Education (RIDE), School of Dental Medicine, University of Washington; Dr. Brown is Executive Associate Dean for Academic Affairs and Professor of Oral Biology, University of Nebraska Medical Center; and Dr. Behar-Horenstein is Distinguished Teaching Scholar and Professor, Colleges of Dentistry, Education, Veterinary Medicine, and Pharmacy, as well as being Director, CTSI Educational Development and Evaluation and Co-Director, HRSA Faculty Development in Dentistry, University of Florida
| | - Linda S Behar-Horenstein
- Ms. Feng is a doctoral candidate, College of Education, University of Florida; Dr. Mugayar is Clinical Associate Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Perez is Clinical Assistant Professor, Department of Pediatric Dentistry, College of Dentistry, University of Florida; Dr. Nagasawa is on the faculty, Department of Biomedical Informatics and Medical Education, School of Medicine and a team member, Regional Initiatives in Dental Education (RIDE), School of Dental Medicine, University of Washington; Dr. Brown is Executive Associate Dean for Academic Affairs and Professor of Oral Biology, University of Nebraska Medical Center; and Dr. Behar-Horenstein is Distinguished Teaching Scholar and Professor, Colleges of Dentistry, Education, Veterinary Medicine, and Pharmacy, as well as being Director, CTSI Educational Development and Evaluation and Co-Director, HRSA Faculty Development in Dentistry, University of Florida.
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16
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Feng X, Mugayar L, Perez E, Nagasawa PR, Brown DG, Behar-Horenstein LS. Dental Students’ Knowledge of Resources for LGBT Persons: Findings from Three Dental Schools. J Dent Educ 2017. [DOI: 10.1002/j.0022-0337.2017.81.1.tb06243.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Leda Mugayar
- Department of Pediatric Dentistry; College of Dentistry; University of Florida
| | - Edna Perez
- Department of Pediatric Dentistry; College of Dentistry; University of Florida
| | - Pamela R. Nagasawa
- Department of Biomedical Informatics and Medical Education; School of Medicine; Regional Initiatives in Dental Education (RIDE); School of Dental Medicine; University of Washington
| | | | - Linda S. Behar-Horenstein
- Colleges of Dentistry, Education, Veterinary Medicine, and Pharmacy; CTSI Educational Development and Evaluation; HRSA Faculty Development in Dentistry; University of Florida
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17
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18
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Abstract
Structure-based drug design has become a key tool for the development of novel drugs. The process involves elucidating the three-dimensional structure of the potential drug molecule bound to the target protein that has been identified as playing a key role in the disease state. Using this three-dimensional information facilitates the process of making improvements to the potential drug molecule by highlighting existing and possible new interactions within the binding site. This knowledge is used to inform increases in potency and selectivity of the molecules as well as to help improve other drug-like properties. The speed and numbers of samples that can be studied, combined with the improved resolution of the structures that can be obtained using synchrotron radiation, have had a significant impact on the utilization of crystallography in the drug discovery process.
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Affiliation(s)
- David G Brown
- School of Biosciences, Stacey Building, and Argenta Structural Biology, Ingram Building, University of Kent, Canterbury CT2 7NJ, UK
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19
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Abstract
Structure-based drug design has become a key tool for the development of novel drugs. The process involves elucidating the three-dimensional structure of the potential drug molecule bound to the target protein that has been identified as playing a key role in the disease state. Using this three-dimensional information facilitates the process of making improvements to the potential drug molecule by highlighting existing and possible new interactions within the binding site. This knowledge is used to inform increases in potency and selectivity of the molecules as well as to help improve other drug-like properties. The speed and numbers of samples that can be studied, combined with the improved resolution of the structures that can be obtained using synchrotron radiation, have had a significant impact on the utilization of crystallography in the drug discovery process.
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Affiliation(s)
- David G Brown
- School of Biosciences, Stacey Building, and Argenta Structural Biology, Ingram Building, University of Kent, Canterbury CT2 7NJ, UK
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20
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Palmer DJ, Schroeder S, Lawrence AD, Deery E, Lobo SA, Saraiva LM, McLean KJ, Munro AW, Ferguson SJ, Pickersgill RW, Brown DG, Warren MJ. The structure, function and properties of sirohaem decarboxylase--an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway. Mol Microbiol 2014; 93:247-61. [PMID: 24865947 PMCID: PMC4145669 DOI: 10.1111/mmi.12656] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2014] [Indexed: 11/28/2022]
Abstract
Some bacteria and archaea synthesize haem by an alternative pathway, which involves the sequestration of sirohaem as a metabolic intermediate rather than as a prosthetic group. Along this pathway the two acetic acid side-chains attached to C12 and C18 are decarboxylated by sirohaem decarboxylase, a heterodimeric enzyme composed of AhbA and AhbB, to give didecarboxysirohaem. Further modifications catalysed by two related radical SAM enzymes, AhbC and AhbD, transform didecarboxysirohaem into Fe-coproporphyrin III and haem respectively. The characterization of sirohaem decarboxylase is reported in molecular detail. Recombinant versions of Desulfovibrio desulfuricans, Desulfovibrio vulgaris and Methanosarcina barkeri AhbA/B have been produced and their physical properties compared. The D. vulgaris and M. barkeri enzyme complexes both copurify with haem, whose redox state influences the activity of the latter. The kinetic parameters of the D. desulfuricans enzyme have been determined, the enzyme crystallized and its structure has been elucidated. The topology of the enzyme reveals that it shares a structural similarity to the AsnC/Lrp family of transcription factors. The active site is formed in the cavity between the two subunits and a AhbA/B-product complex with didecarboxysirohaem has been obtained. A mechanism for the decarboxylation of the kinetically stable carboxyl groups is proposed.
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Affiliation(s)
- David J Palmer
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
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21
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Kilty I, Green MP, Bell AS, Brown DG, Dodd PG, Hewson C, Hughes SJ, Phillips C, Ryckmans T, Smith RT, van Hoorn WP, Cohen P, Jones LH. TAK1 inhibition in the DFG-out conformation. Chem Biol Drug Des 2014; 82:500-5. [PMID: 23745990 DOI: 10.1111/cbdd.12169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 03/14/2013] [Revised: 05/28/2013] [Accepted: 06/03/2013] [Indexed: 12/20/2022]
Abstract
The first example of an inhibitor of the kinase TAK1 that binds in the DFG-out conformation is disclosed. These preliminary studies used kinase-targeted screening and structure-based drug design to create a molecule with dual pharmacological inhibition of p38 and TAK1 that demonstrated significant activity in a cell-based, anti-inflammatory assay.
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Affiliation(s)
- Iain Kilty
- Pfizer World Wide Research and Development, Ramsgate Road, Sandwich, CT13 9NJ, UK; BioTherapeutics Research and Development, Pfizer, Cambridge, MA, 02140, USA
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22
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Hughes SJ, Millan DS, Kilty IC, Lewthwaite RA, Mathias JP, O'Reilly MA, Pannifer A, Phelan A, Stühmeier F, Baldock DA, Brown DG. Fragment based discovery of a novel and selective PI3 kinase inhibitor. Bioorg Med Chem Lett 2011; 21:6586-90. [PMID: 21925880 DOI: 10.1016/j.bmcl.2011.07.117] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 07/29/2011] [Accepted: 07/31/2011] [Indexed: 11/16/2022]
Abstract
We report the use of fragment screening and fragment based drug design to develop a PI3γ kinase fragment hit into a lead. Initial fragment hits were discovered by high concentration biochemical screening, followed by a round of virtual screening to identify additional ligand efficient fragments. These were developed into potent and ligand efficient lead compounds using structure guided fragment growing and merging strategies. This led to a potent, selective, and cell permeable PI3γ kinase inhibitor with good metabolic stability that was useful as a preclinical tool compound.
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Affiliation(s)
- Samantha J Hughes
- Worldwide Medicinal Chemistry, Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK.
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23
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Phillips C, Roberts LR, Schade M, Bazin R, Bent A, Davies NL, Moore R, Pannifer AD, Pickford AR, Prior SH, Read CM, Scott A, Brown DG, Xu B, Irving SL. Design and structure of stapled peptides binding to estrogen receptors. J Am Chem Soc 2011; 133:9696-9. [PMID: 21612236 DOI: 10.1021/ja202946k] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Synthetic peptides that specifically bind nuclear hormone receptors offer an alternative approach to small molecules for the modulation of receptor signaling and subsequent gene expression. Here we describe the design of a series of novel stapled peptides that bind the coactivator peptide site of estrogen receptors. Using a number of biophysical techniques, including crystal structure analysis of receptor-stapled peptide complexes, we describe in detail the molecular interactions and demonstrate that all-hydrocarbon staples modulate molecular recognition events. The findings have implications for the design of stapled peptides in general.
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24
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Brown DG, Si J, Sun R. Special issue on advances in neural networks research: IJCNN'07. Neural Netw 2008; 21:113. [PMID: 18262753 DOI: 10.1016/j.neunet.2008.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Abstract
Evaluation of computational intelligence (CI) systems designed to improve the performance of a human operator is complicated by the need to include the effect of human variability. In this paper we consider human (reader) variability in the context of medical imaging computer-assisted diagnosis (CAD) systems, and we outline how to compare the detection performance of readers with and without the CAD. An effective and statistically powerful comparison can be accomplished with a receiver operating characteristic (ROC) experiment, summarized by the reader-averaged area under the ROC curve (AUC). The comparison requires sophisticated yet well-developed methods for multi-reader multi-case (MRMC) variance analysis. MRMC variance analysis accounts for random readers, random cases, and correlations in the experiment. In this paper, we extend the methods available for estimating this variability. Specifically, we present a method that can treat arbitrary study designs. Most methods treat only the fully-crossed study design, where every reader reads every case in two experimental conditions. We demonstrate our method with a computer simulation, and we assess the statistical power of a variety of study designs.
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Affiliation(s)
- Brandon D Gallas
- NIBIB/CDRH Laboratory for the Assessment of Medical Imaging Systems, FDA, Silver Spring, MD 20993-0002, United States.
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26
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Bunnage ME, Blagg J, Steele J, Owen DR, Allerton C, McElroy AB, Miller D, Ringer T, Butcher K, Beaumont K, Evans K, Gray AJ, Holland SJ, Feeder N, Moore RS, Brown DG. Discovery of potent & selective inhibitors of activated thrombin-activatable fibrinolysis inhibitor for the treatment of thrombosis. J Med Chem 2007; 50:6095-103. [PMID: 17990866 DOI: 10.1021/jm0702433] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombin-activatable fibrinolysis inhibitor (TAFI) has emerged as a key link between the coagulation and fibrinolysis cascades and represents a promising new target for the treatment of thrombosis. A novel series of imidazolepropionic acids has been designed that exhibit high potency against activated TAFI (TAFIa) and excellent selectivity over plasma carboxypeptidase N (CPN). Structure activity relationships suggest that the imidazole moiety plays a key role in binding to the catalytic zinc of TAFIa, and this has been supported by crystallographic studies using porcine pancreatic carboxypeptidase B as a surrogate for TAFIa. The SAR program led to the identification of 21 (TAFIa Ki = 10 nM, selectivity TAFIa/CPN > 1000) as a candidate for clinical development. Compound 21 exhibited antithrombotic efficacy in a rabbit model of venous thrombosis, yet had no effect on surgical bleeding in the rabbit. In addition, 21 exhibited an excellent preclinical and clinical pharmacokinetic profile, characterized by paracellular absorption, low clearance, and a low volume of distribution, fully consistent with its physicochemical properties of low molecular weight (MW = 239) and high hydrophilicity (log D = -2.8). These data indicate 21 (UK-396,082) has potential as a novel TAFIa inhibitor for the treatment of thrombosis and other fibrin-dependent diseases in humans.
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Affiliation(s)
- Mark E Bunnage
- Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Kent, U.K.
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27
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Fish PV, Barber CG, Brown DG, Butt R, Collis MG, Dickinson RP, Henry BT, Horne VA, Huggins JP, King E, O'Gara M, McCleverty D, McIntosh F, Phillips C, Webster R. Selective Urokinase-Type Plasminogen Activator Inhibitors. 4. 1-(7-Sulfonamidoisoquinolinyl)guanidines†. J Med Chem 2007; 50:2341-51. [PMID: 17447747 DOI: 10.1021/jm061066t] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
1-isoquinolinylguanidines were previously disclosed as potent and selective inhibitors of urokinase-type plasminogen activator (uPA). Further investigation of this template has revealed that incorporation of a 7-sulfonamide group furnishes a new series of potent and highly selective uPA inhibitors. Potency and selectivity can be achieved with sulfonamides derived from a variety of amines and is further enhanced by the incorporation of sulfonamides derived from amino acids. The binding mode of these 1-isoquinolinylguanidines has been investigated by X-ray cocrystallization studies. uPA inhibitor 26 was selected for further evaluation based on its excellent enzyme potency (Ki 10 nM) and selectivity profile (4000-fold versus tPA and 2700-fold versus plasmin). In vitro, compound 26 is able to inhibit exogenous uPA in human chronic wound fluid (IC50=0.89 microM). In vivo, in a porcine acute excisional wound model, following topical delivery, compound 26 is able to penetrate into pig wounds and inhibit exogenous uPA activity with no adverse effect on wound healing parameters. On the basis of this profile, compound 26 (UK-371,804) was selected as a candidate for further preclinical evaluation for the treatment of chronic dermal ulcers.
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Affiliation(s)
- Paul V Fish
- Department of Discovery Chemistry, Pfizer Global Research and Development, Sandwich, Kent, CT13 9NJ, UK.
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28
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Abstract
The clinical significance of phosphodiesterase 5 (PDE5) inhibition is increasingly understood following the pioneering work with sildenafil, and the continuing development programmes for both sildenafil and other marketed inhibitors. Since the initial launch of sildenafil for male erectile dysfunction (MED), approval has now been granted for treatment of pulmonary hypertension, whilst ongoing studies have indicated the potential of PDE5 inhibition for the treatment of a range of additional indications including cardioprotection, memory retention and diabetes. Many of these additional indications are best suited to chronic oral dosing and emphasise the need for highly selective inhibitors with extended duration of action. This article will focus on a research programme aimed at the discovery of improved second-generation PDE5 inhibitors. Essential features of these new PDE5 inhibitors would be enhanced selectivity across the whole PDE family and pharmacokinetics compatible with once daily dosing. Key elements used in this programme are high throughput screening (HTS), exploitation of co-crystal structural information for bound inhibitor in the PDE5 active site, and employment of parallel chemistry to speed progress. Under the guidance of co-crystal structural information, a non-selective HTS hit with poor physicochemistry was initially modified using parallel chemistry to give a lead compound (3) that established a new PDE5 inhibitor series. Notably, (3) displayed physicochemistry compatible with a long plasma half-life, and wide chemical scope. Subsequent optimisation of (3) using crystal structure information to guide design, led rapidly to highly potent and selective PDE5 inhibitors (47, 50). Continued focus on physical properties through ligand efficiency evaluation and lipophilicity (cLogP), maintained the inherently desirable physicochemistry of the initial lead.
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Affiliation(s)
- Michael J Palmer
- Sandwich Discovery Chemistry, Pfizer Global Research and Development, Sandwich, Kent, CT13 9NJ, United Kingdom.
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29
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Akasaka T, Balasas T, Russell LJ, Sugimoto KJ, Majid A, Walewska R, Karran EL, Brown DG, Cain K, Harder L, Gesk S, Martin-Subero JI, Atherton MG, Brüggemann M, Calasanz MJ, Davies T, Haas OA, Hagemeijer A, Kempski H, Lessard M, Lillington DM, Moore S, Nguyen-Khac F, Radford-Weiss I, Schoch C, Struski S, Talley P, Welham MJ, Worley H, Strefford JC, Harrison CJ, Siebert R, Dyer MJS. Five members of the CEBP transcription factor family are targeted by recurrent IGH translocations in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Blood 2006; 109:3451-61. [PMID: 17170124 DOI: 10.1182/blood-2006-08-041012] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
CCAAT enhancer-binding protein (CEBP) transcription factors play pivotal roles in proliferation and differentiation, including suppression of myeloid leukemogenesis. Mutations of CEBPA are found in a subset of acute myeloid leukemia (AML) and in some cases of familial AML. Here, using cytogenetics, fluorescence in situ hybridization (FISH), and molecular cloning, we show that 5 CEBP gene family members are targeted by recurrent IGH chromosomal translocations in BCP-ALL. Ten patients with t(8;14)(q11;q32) involved CEBPD on chromosome 8, and 9 patients with t(14;19)(q32;q13) involved CEBPA, while a further patient involved CEBPG, located 71 kb telomeric of CEBPA in chromosome band 19q13; 4 patients with inv(14)(q11q32)/t(14;14)(q11;q32) involved CEBPE and 3 patients with t(14;20)(q32;q13) involved CEBPB. In 16 patients the translocation breakpoints were cloned using long-distance inverse–polymerase chain reaction (LDI-PCR). With the exception of CEBPD breakpoints, which were scattered within a 43-kb region centromeric of CEBPD, translocation breakpoints were clustered immediately 5′ or 3′ of the involved CEBP gene. Except in 1 patient with t(14;14)(q11;q32), the involved CEBP genes retained germ-line sequences. Quantitative reverse transcription (RT)–PCR showed overexpression of the translocated CEBP gene. Our findings implicate the CEBP gene family as novel oncogenes in BCP-ALL, and suggest opposing functions of CEBP dysregulation in myeloid and lymphoid leukemogenesis.
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Affiliation(s)
- Takashi Akasaka
- Toxicology Unit, Medical Research Council, University of Leicester, Lancaster Road, Leicester, UK
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30
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Knoechel TR, Tucker AD, Robinson CM, Phillips C, Taylor W, Bungay PJ, Kasten SA, Roche TE, Brown DG. Regulatory Roles of the N-Terminal Domain Based on Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands. Biochemistry 2006. [DOI: 10.1021/bi068014q] [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: 11/28/2022]
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31
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Allerton CMN, Barber CG, Beaumont KC, Brown DG, Cole SM, Ellis D, Lane CAL, Maw GN, Mount NM, Rawson DJ, Robinson CM, Street SDA, Summerhill NW. A Novel Series of Potent and Selective PDE5 Inhibitors with Potential for High and Dose-Independent Oral Bioavailability. J Med Chem 2006; 49:3581-94. [PMID: 16759100 DOI: 10.1021/jm060113e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sildenafil (5-[2-ethoxy-5-(4-methyl-1-piperazinylsulfonyl)phenyl]-1-methyl-3-n-propyl-1,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one), a potent and selective phosphodiesterase type 5 (PDE5) inhibitor, provided the first oral treatment for male erectile dysfunction. The objective of the work reported in this paper was to combine high levels of PDE5 potency and selectivity with high and dose-independent oral bioavailability, to minimize the impact on the C(max) of any interactions with coadministered drugs in the clinic. This goal was achieved through identification of a lower clearance series with a high absorption profile, by replacing the 5'-piperazine sulfonamide in the sildenafil template with a 5'-methyl ketone. This novel series provided compounds with low metabolism in human hepatocytes, excellent caco-2 flux, and the potential for good aqueous solubility. The in vivo oral and iv pharmacokinetic profiles of example compounds confirmed the high oral bioavailability predicted from these in vitro screens. 5-(5-Acetyl-2-butoxy-3-pyridinyl)-3-ethyl-2-(1-ethyl-3-azetidinyl)-2,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one (2) was selected for progression into the clinic.
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Affiliation(s)
- Charlotte M N Allerton
- Discovery Chemistry, Lead Discovery, and Discovery Biology, Pfizer Global Research & Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom.
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32
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Staudenmeier JJ, Brown DG. Regarding dissociative amnesia and cluster C personality traits. Psychiatry (Edgmont) 2006; 3:8. [PMID: 21103166 PMCID: PMC2990570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- James J Staudenmeier
- University of Hawaii and Hawaii Pacific University Uniformed Services University of the Health Sciences
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33
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Knoechel TR, Tucker AD, Robinson CM, Phillips C, Taylor W, Bungay PJ, Kasten SA, Roche TE, Brown DG. Regulatory roles of the N-terminal domain based on crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands. Biochemistry 2006; 45:402-15. [PMID: 16401071 DOI: 10.1021/bi051402s] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyruvate dehydrogenase kinase (PDHK) regulates the activity of the pyruvate dehydrogenase multienzyme complex. PDHK inhibition provides a route for therapeutic intervention in diabetes and cardiovascular disorders. We report crystal structures of human PDHK isozyme 2 complexed with physiological and synthetic ligands. Several of the PDHK2 structures disclosed have C-terminal cross arms that span a large trough region between the N-terminal regulatory (R) domains of the PDHK2 dimers. The structures containing bound ATP and ADP demonstrate variation in the conformation of the active site lid, residues 316-321, which enclose the nucleotide beta and gamma phosphates at the active site in the C-terminal catalytic domain. We have identified three novel ligand binding sites located in the R domain of PDHK2. Dichloroacetate (DCA) binds at the pyruvate binding site in the center of the R domain, which together with ADP, induces significant changes at the active site. Nov3r and AZ12 inhibitors bind at the lipoamide binding site that is located at one end of the R domain. Pfz3 (an allosteric inhibitor) binds in an extended site at the other end of the R domain. We conclude that the N-terminal domain of PDHK has a key regulatory function and propose that the different inhibitor classes act by discrete mechanisms. The structures we describe provide insights that can be used for structure-based design of PDHK inhibitors.
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34
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McGahon AJ, Brown DG, Martin SJ, Amarante-Mendes GP, Cotter TG, Cohen GM, Green DR. Downregulation of Bcr-Abl in K562 cells restores susceptibility to apoptosis: characterization of the apoptotic death. Cell Death Differ 2006; 4:95-104. [PMID: 16465215 DOI: 10.1038/sj.cdd.4400213] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/1999] [Revised: 08/06/1999] [Accepted: 08/28/1999] [Indexed: 11/09/2022] Open
Abstract
We examined the susceptibility of a variety of human leukemic cell lines to the induction of apoptosis. K562, a chronic myelogenous leukemic cell line which expresses the bcr-abl fusion gene, was found to be extremely resistant to apoptosis, irrespective of the inducing agent. This resistance can be attributed to the deregulated Abl kinase activity of bcr-abl, as downregulation of its expression using antisense oligodeoxynucleotides targeted to the beginning of the abl sequence in this chimeric gene rendered these cells susceptible to cytotoxic drug-induced apoptosis. Examination of the morphological and biochemical features of apoptosis in K562 cells revealed the typical membrane blebbing and chromatin condensation associated with this form of cell death. In situ TdT-mediated end labeling of the DNA revealed the presence of strand breaks in the treated cells and field inversion gel electrophoresis revealed the presence of large 10-50 kb fragments. However there was an absence of oligonucleosomal DNA fragmentation, whether or not Bcr-Abl was expressed. Thus, while inhibition of expression of Bcr-Abl renders K562 cells susceptible to apoptosis, the absence of oligonucleosomal DNA fragmentation in these cells is independent of the function of this molecule.
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Affiliation(s)
- A J McGahon
- Division of Cellular Immunology, La Jolla Institute for Allergy and Immunology, 11149 N. Torrey Pines Rd., La Jolla, CA 92014, USA
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35
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O'Brien SE, Brown DG, Mills JE, Phillips C, Morris G. Computational tools for the analysis and visualization of multiple protein-ligand complexes. J Mol Graph Model 2005; 24:186-94. [PMID: 16169759 DOI: 10.1016/j.jmgm.2005.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 07/05/2005] [Accepted: 08/10/2005] [Indexed: 11/16/2022]
Abstract
Modern methods in genomics and high-throughput crystallography have ensured that we have access to a large and rapidly increasing, number of X-ray structures of protein-ligand complexes. A structure-based approach to drug design aims to exploit this information, but current methods are not suited to the examination of the large numbers of complexes available. We present computational tools that analyse and display multiple protein-ligand interactions and their properties in a simplified way. We illustrate how a novel binding-mode similarity metric is able to cluster 20 ligands complexed to HIV-1 reverse transcriptase into distinct groups. The properties of each cluster are then projected onto a group surface as a series of color gradients. Analysis of these surfaces reveals fundamental similarities and differences in the binding modes of these diverse compounds. In addition, the simplicity of the surface representations facilitates the transfer of information between the crystallographer, computational chemist and the chemist. We also show how two- and three-dimensional (2- and 3-D) similarities can be combined to provide enhanced understanding of 33 factor Xa inhibitor complexes. This methodology has enabled us to identify pharmaceutically relevant relationships between ligands and their binding modes that had previously been hidden in a wealth of data.
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Affiliation(s)
- Sean E O'Brien
- Department of Medicinal Informatics Structure and Design, Pfizer Global Research and Development, Sandwich, Kent, UK.
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36
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Twiddy D, Brown DG, Adrain C, Jukes R, Martin SJ, Cohen GM, MacFarlane M, Cain K. Pro-apoptotic proteins released from the mitochondria regulate the protein composition and caspase-processing activity of the native Apaf-1/caspase-9 apoptosome complex. J Biol Chem 2004; 279:19665-82. [PMID: 14993223 DOI: 10.1074/jbc.m311388200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The apoptosome is a large caspase-activating ( approximately 700-1400 kDa) complex, which is assembled from Apaf-1 and caspase-9 when cytochrome c is released during mitochondrial-dependent apoptotic cell death. Apaf-1 the core scaffold protein is approximately 135 kDa and contains CARD (caspase recruitment domain), CED-4, and multiple (13) WD40 repeat domains, which can potentially interact with a variety of unknown regulatory proteins. To identify such proteins we activated THP.1 lysates with dATP/cytochrome c and used sucrose density centrifugation and affinity-based methods to purify the apoptosome for analysis by MALDI-TOF mass spectrometry. First, we used a glutathione S-transferase (GST) fusion protein (GST-casp9(1-130)) containing the CARD domain of caspase-9-(1-130), which binds to the CARD domain of Apaf-1 when it is in the apoptosome and blocks recruitment/activation of caspase-9. This affinity-purified apoptosome complex contained only Apaf-1XL and GST-casp9(1-130), demonstrating that the WD40 and CED-4 domains of Apaf-1 do not stably bind other cytosolic proteins. Next we used a monoclonal antibody to caspase-9 to immunopurify the native active apoptosome complex from cell lysates, containing negligible levels of cytochrome c, second mitochondria-derived activator of caspase (Smac), or Omi/HtrA2. This apoptosome complex exhibited low caspase-processing activity and contained four stably associated proteins, namely Apaf-1, pro-p35/34 forms of caspase-9, pro-p20 forms of caspase-3, X-linked inhibitor of apoptosis (XIAP), and cytochrome c, which was only bound transiently to the complex. However, in lysates containing Smac and Omi/HtrA2, the caspase-processing activity of the purified apoptosome complex increased 6-8-fold and contained only Apaf-1 and the p35/p34-processed subunits of caspase-9. During apoptosis, Smac, Omi/HtrA2, and cytochrome c are released simultaneously from mitochondria, and thus it is likely that the functional apoptosome complex in apoptotic cells consists primarily of Apaf-1 and processed caspase-9.
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Affiliation(s)
- Davina Twiddy
- Medical Research Council Toxicology Unit, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
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37
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Affiliation(s)
- D G Brown
- Randall Institute, King's College, University of London, UK
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38
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Staudenmeier JJ, Brown DG. Mental disorders among military personnel. Am J Psychiatry 2003; 160:1190; author reply 1191, 2. [PMID: 12777290 DOI: 10.1176/appi.ajp.160.6.1190-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Abstract
Modern magnetic resonance imaging (MRI) systems consist of several complex, high cost subsystems. The cost and complexity of these systems often makes them impractical for use as routine laboratory instruments, limiting their use to hospitals and dedicated laboratories. However, advances in the consumer electronics industry have led to the widespread availability of inexpensive radio-frequency integrated circuits with exceptional abilities. We have developed a small, low-cost MR system derived from these new components. When combined with inexpensive desktop magnets, this type of MR scanner has the promise of becoming standard laboratory equipment for both research and education. This paper describes the development of a prototype desktop MR scanner utilizing a 0.21 T permanent magnet with an imaging region of approximately 2 cm diameter. The system uses commercially available components where possible and is programmed in LabVIEW software. Results from 3D data sets of resolution phantoms and fixed, newborn mice demonstrate the capability of this system to obtain useful images from a system constructed for approximately $13,500.
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Affiliation(s)
- Steven M Wright
- Department of Electrical Engineering, Zachry Engineering Center, Texas A & M University, TAMU 3128, College Station, TX 77843, USA.
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40
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Cain K, Langlais C, Sun XM, Brown DG, Cohen GM. Physiological concentrations of K+ inhibit cytochrome c-dependent formation of the apoptosome. J Biol Chem 2001; 276:41985-90. [PMID: 11553634 DOI: 10.1074/jbc.m107419200] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In many forms of apoptosis, cytochrome c released from mitochondria induces the oligomerization of Apaf-1 to form a caspase-activating apoptosome complex. Activation of lysates in vitro with dATP and cytochrome c results in the formation of an active caspase-processing approximately 700-kDa apoptosome complex, which predominates in apoptotic cells, and a relatively inactive approximately 1.4-MDa complex. We now demonstrate that assembly of the active complex is suppressed by normal intracellular concentrations of K(+). Using a defined apoptosome reconstitution system with recombinant Apaf-1 and cytochrome c, K(+) also inhibits caspase activation by abrogating Apaf-1 oligomerization and apoptosome assembly. Once assembled, the apoptosome is relatively insensitive to the effects of ionic strength and processes/activates effector caspases. The inhibitory effects of K(+) on apoptosome formation are antagonized in a concentration-dependent manner by cytochrome c. These studies support the hypothesis that the normal intracellular concentrations of K(+) act to safeguard the cell against inappropriate formation of the apoptosome complex, caused by the inadvertent release of small amounts of cytochrome c. Thus, the assembly and activation of the apoptosome complex in the cell requires the rapid and extensive release of cytochrome c to overcome the inhibitory effects of normal intracellular concentrations of K(+).
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Affiliation(s)
- K Cain
- MRC Toxicology Unit, Hodgkin Bldg., University of Leicester, P.O. Box 138, Lancaster Rd., Leicester LE1 9HN, United Kingdom.
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41
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Abstract
Nonionic surfactants of the form CxEy, where x is the number of carbons in the alkyl chain and y is the number of ethylene oxide units in the polyoxyethylene (POE) chain, were studied for their ability to alter the transport of Sphingomonas pacilimobilis through an aquifer sand. The surfactants C12E4 (Brij 30) and C12E23 (Brij 35) were the focus of this study. Through a systematic study, it was shown that these nonionic surfactants were able to enhance the transport of this bacterial culture through porous media. The magnitude of the enhancement increased with decreasing solution ionic strength and increasing POE chain length. The mechanism of this enhanced transport appears to be due to expansion of the electric double layer about the bacteria and aquifer sand through displacement of the counterions by the sorbed surfactant. This expanded electric double layer increases the electrostatic repulsion, with a resultant reduction in the collision efficiency and an increase in the Langmuirian blocking parameter. Application of the colloid filtration theory with the experimental parameters of this study shows that nonionic surfactants have the potential to significantly enhance the bacterial travel distance, especially for low ionic strength systems.
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Affiliation(s)
- D G Brown
- Department of Civil and Environmental Engineering, Princeton University, New Jersey 08544, USA
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42
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Abstract
Nonionic surfactants are used in a number of different microbiological applications, including solubilization of cell membranes, washing bacterial cultures prior to experimentation, and enhancing biodegradation of low-solubility compounds. An important consideration in these applications is the potential for the surfactant to alter the cell membrane. One potential means to monitor the impact of surfactants on the bacterial cell membrane is through monitoring the absorbance spectrum of the bacterial suspension. This is due to the colloidal nature of bacteria, where the absorbance of a bacterial suspension is related to the size and refractive index of the bacterial cells. Through a systematic study it was shown that there can be a significant change in the bacterial absorbance spectrum due to the presence of nonionic surfactants, with the effect a function of surfactant structure and concentration, solution ionic strength and cation valence. The effects were most pronounced with Na(+) as the cation, with surfactants having mid-range hydrophile-lipophile balance (HLB) values, and with surfactant concentrations above the CMC. The results indicate that measurement of the absorbance spectrum of bacterial cultures can provide a means to monitor the effects of nonionic surfactants on the bacterial cell membrane. In addition, depending on the specific application, appropriate selection of surfactant structure and media composition can be made to enhance or minimize the effects.
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Affiliation(s)
- D G Brown
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, USA
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43
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Brown DG, Duh JD. Reply to Huber. Estimating Markov transitions. J Environ Manage 2001; 62:233-236. [PMID: 11434034 DOI: 10.1006/jema.2001.0448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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44
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Brown DG, Jaffé PR. Spectrophotometric assay of POE nonionic surfactants and its application to surfactant sorption isotherms. Environ Sci Technol 2001; 35:2022-2025. [PMID: 11393983 DOI: 10.1021/es001807u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The operational range and suitability toward environmental samples of an iodine-iodide (I-I) assay for nonionic surfactants were assessed. The I-I assay provides a rapid and repeatable method for determining aqueous nonionic surfactant concentrations. Through a systematic examination of surfactant structure, the operational range of the assay was shown to be on the order of 10(-6) to 10(-3) MEO, where the concentration unit MEO is defined as the molar surfactant concentration multiplied by the number of ethylene oxide units in the surfactant molecule. For environmental samples, it was shown that the I-I assay can be applied to measurement of surfactant sorption isotherms to aquifer sands and bacteria cultures. A potential limitation of the I-I assay is interference with humic acids, with the magnitude of the interference dependent on the concentration of humic acids present. The main benefit of the I-I assay is that its high accuracy and ease of application allows measurement of low levels of surfactant sorption. Surfactant sorption to aquifer sand could be measured down to the range of 10(-9) mol/g.
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Affiliation(s)
- D G Brown
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, USA
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45
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Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921. [PMID: 11237011 DOI: 10.1038/35057062] [Citation(s) in RCA: 14499] [Impact Index Per Article: 630.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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Affiliation(s)
- E S Lander
- Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, MA 02142, USA.
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46
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Abstract
Large segmental duplications cover much of the Arabidopsis thaliana genome. Little is known about their origins. We show that they are primarily due to at least four different large-scale duplication events that occurred 100 to 200 million years ago, a formative period in the diversification of the angiosperms. A better understanding of the complex structural history of angiosperm genomes is necessary to make full use of Arabidopsis as a genetic model for other plant species.
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Affiliation(s)
- T J Vision
- USDA-ARS Center for Agricultural Bioinformatics, 604 Rhodes Hall, Cornell University, Ithaca, NY 14853, USA.
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Weinberg A, Wohl DA, Brown DG, Pott GB, Zhang L, Ray MG, van der Horst C. Effect of cryopreservation on measurement of cytomegalovirus-specific cellular immune responses in HIV-infected patients. J Acquir Immune Defic Syndr 2000; 25:109-14. [PMID: 11103040 DOI: 10.1097/00042560-200010010-00004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To determine the feasibility of cytomegalovirus (CMV)-specific cell-mediated immunity (CMI) studies using cryopreserved cells, we compared lymphocyte proliferation assays (LPA), responder cell frequency (RCF), interleukin-2 (IL-2) and interferon-gamma (IFN-gamma) production using fresh and cryopreserved peripheral blood mononuclear cells (PBMCs) from 53 HIV-infected patients and 15 uninfected controls. Qualitative CMV LPA results were concordant in >/=84% of the specimens from either HIV-infected patients or controls. Proliferation-based RCF, IL-2, and IFN-gamma comparisons showed that cryopreservation reduces the number of CMV-specific responders and decreases cytokine secretion, without changing the rank order of the results (p <.01). In contrast, the number of flow cytometry-enumerated IFN-gamma-producing CD4+ cells was not significantly changed by cryopreservation. In HIV-infected patients, the differences between fresh and frozen cell assays were not influenced by CD4 cell numbers or HIV viral load. These data indicate that cryopreserved cells are suitable for longitudinal studies of the CMV-specific immune response in HIV-infected patients and uninfected controls.
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Affiliation(s)
- A Weinberg
- University of Colorado Health Sciences Center, Denver, Colorado 80262, USA.
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Freathy C, Brown DG, Roberts RA, Cain K. Transforming growth factor-beta(1) induces apoptosis in rat FaO hepatoma cells via cytochrome c release and oligomerization of Apaf-1 to form a approximately 700-kd apoptosome caspase-processing complex. Hepatology 2000; 32:750-60. [PMID: 11003619 DOI: 10.1053/jhep.2000.18329] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In mammalian cells, non receptor-mediated apoptosis occurs via the cytochrome c-dependent assembly of a approximately 700-kd apoptotic protease-activating factor 1 (Apaf-1)/caspase-9 containing apoptosome complex. This initiates the postmitochondrial-mediated effector caspase cascade. We now show that receptor mediated transforming growth factor beta(1) (TGF-beta(1))-induced apoptosis in rat hepatoma cells is accompanied by processing and activation of caspases-2, -3, -7, and -8. Furthermore, we show that caspase activation is mediated via the release of cytochrome c and the oligomerization of Apaf-1 into an approximately 700-kd apoptosome complex. Similarly, in vitro activation of hepatoma cell lysates with 2'-deoxyadenosine 5'-triphosphate (dATP) results in the formation of the approximately 700-kd apoptosome complex, which recruits and processes caspases-3 and -7. Z-VAD.FMK [benzyloxycarbonyl-Val-Ala-Asp (OMe) fluoromethylketone], the pan-caspase inhibitor totally inhibits dATP-stimulated caspase activation but does not block the assembly of the large Apaf-1 containing apoptosome complex. However, the recruitment and subsequent processing of caspases-3 and -7 to the apoptosome is blocked. Similarly, in intact cells, although Z-VAD.FMK blocked TGF-beta(1)-induced apoptosis, it did not prevent the oligomerization of Apaf-1 into the apoptosome. However, recruitment and processing of caspases-3 and -7 were prevented by Z-VAD.FMK. These data show that TGF-beta(1) induces apoptosis via release of cytochrome c and activation of the Apaf-1 apoptosome complex, which initiates the caspase cascade.
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Affiliation(s)
- C Freathy
- MRC Toxicology Unit, Hodgkin Building, University of Leicester, Leicester, UK
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49
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Abstract
Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps.
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Affiliation(s)
- T J Vision
- Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA.
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50
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Cain K, Bratton SB, Langlais C, Walker G, Brown DG, Sun XM, Cohen GM. Apaf-1 oligomerizes into biologically active approximately 700-kDa and inactive approximately 1.4-MDa apoptosome complexes. J Biol Chem 2000; 275:6067-70. [PMID: 10692394 DOI: 10.1074/jbc.275.9.6067] [Citation(s) in RCA: 233] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apaf-1, by binding to and activating caspase-9, plays a critical role in apoptosis. Oligomerization of Apaf-1, in the presence of dATP and cytochrome c, is required for the activation of caspase-9 and produces a caspase activating apoptosome complex. Reconstitution studies with recombinant proteins have indicated that the size of this complex is very large in the order of approximately 1.4 MDa. We now demonstrate that dATP activation of cell lysates results in the formation of two large Apaf-1-containing apoptosome complexes with M(r) values of approximately 1.4 MDa and approximately 700 kDa. Kinetic analysis demonstrates that in vitro the approximately 700-kDa complex is produced more rapidly than the approximately 1.4 MDa complex and exhibits a much greater ability to activate effector caspases. Significantly, in human tumor monocytic cells undergoing apoptosis after treatment with either etoposide or N-tosyl-l-phenylalanyl chloromethyl ketone (TPCK), the approximately 700-kDa Apaf-1 containing apoptosome complex was predominately formed. This complex processed effector caspases. Thus, the approximately 700-kDa complex appears to be the correctly formed and biologically active apoptosome complex, which is assembled during apoptosis.
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Affiliation(s)
- K Cain
- MRC Toxicology Unit, University of Leicester, Lancaster Road, Leicester, LE1 9HN United Kingdom
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