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Minor W, Jaskolski M, Martin SJ, Dauter Z. Dr. Alexander Wlodawer-celebrating five decades of service to the structural biology community. FEBS J 2021; 288:4160-4164. [PMID: 34286923 DOI: 10.1111/febs.16064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022]
Abstract
This 75th birthday tribute to our Editorial Board member Alexander Wlodawer recounts his decades-long service to the community of structural biology researchers. His former and current colleagues tell the story of his upbringing and education, followed by an account of his dedication to quality and rigor in crystallography and structural science. The FEBS Journal Editor-in-Chief Seamus Martin further highlights Alex's outstanding contributions to the journal's success over many years.
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Affiliation(s)
- Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Seamus J Martin
- Department of Genetics, The Smurfit Institute, Trinity College, Dublin, Ireland
| | - Zbigniew Dauter
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
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Wlodawer A, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Minor W, Rupp B, Jaskolski M. Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank. FEBS J 2020; 287:3703-3718. [PMID: 32418327 PMCID: PMC7276724 DOI: 10.1111/febs.15366] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/02/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022]
Abstract
A bright spot in the SARS‐CoV‐2 (CoV‐2) coronavirus pandemic has been the immediate mobilization of the biomedical community, working to develop treatments and vaccines for COVID‐19. Rational drug design against emerging threats depends on well‐established methodology, mainly utilizing X‐ray crystallography, to provide accurate structure models of the macromolecular drug targets and of their complexes with candidates for drug development. In the current crisis, the structural biological community has responded by presenting structure models of CoV‐2 proteins and depositing them in the Protein Data Bank (PDB), usually without time embargo and before publication. Since the structures from the first‐line research are produced in an accelerated mode, there is an elevated chance of mistakes and errors, with the ultimate risk of hindering, rather than speeding up, drug development. In the present work, we have used model‐validation metrics and examined the electron density maps for the deposited models of CoV‐2 proteins and a sample of related proteins available in the PDB as of April 1, 2020. We present these results with the aim of helping the biomedical community establish a better‐validated pool of data. The proteins are divided into groups according to their structure and function. In most cases, no major corrections were necessary. However, in several cases significant revisions in the functionally sensitive area of protein–inhibitor complexes or for bound ions justified correction, re‐refinement, and eventually reversioning in the PDB. The re‐refined coordinate files and a tool for facilitating model comparisons are available at https://covid-19.bioreproducibility.org.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI, Frederick, MD, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI, Argonne National Laboratory, IL, USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.,Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Poland
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Bernhard Rupp
- k.-k. Hofkristallamt, San Diego, CA, USA.,Institute of Genetic Epidemiology, Medical University Innsbruck, Austria
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.,Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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