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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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Abstract
In this review, we describe how the interplay among science, technology and community interests contributed to the evolution of four structural biology data resources. We present the method by which data deposited by scientists are prepared for worldwide distribution, and argue that data archiving in a trusted repository must be an integral part of any scientific investigation.
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Affiliation(s)
- Helen M. Berman
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Catherine L. Lawson
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Brinda Vallat
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Margaret J. Gabanyi
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
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Owen RL, Juanhuix J, Fuchs M. Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 2016; 602:21-31. [PMID: 27046341 PMCID: PMC5505570 DOI: 10.1016/j.abb.2016.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/15/2022]
Abstract
Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.
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Affiliation(s)
- Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Jordi Juanhuix
- Alba Synchrotron, Carrer de la llum 2-26, Cerdanyola, 08192, Spain.
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Lab, Upton, NY, 11973, USA.
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Dauter Z, Wlodawer A. Progress in protein crystallography. Protein Pept Lett 2016; 23:201-10. [PMID: 26732246 PMCID: PMC6287266 DOI: 10.2174/0929866523666160106153524] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/26/2015] [Accepted: 01/03/2016] [Indexed: 11/22/2022]
Abstract
Macromolecular crystallography evolved enormously from the pioneering days, when structures were solved by "wizards" performing all complicated procedures almost by hand. In the current situation crystal structures of large systems can be often solved very effectively by various powerful automatic programs in days or hours, or even minutes. Such progress is to a large extent coupled to the advances in many other fields, such as genetic engineering, computer technology, availability of synchrotron beam lines and many other techniques, creating the highly interdisciplinary science of macromolecular crystallography. Due to this unprecedented success crystallography is often treated as one of the analytical methods and practiced by researchers interested in structures of macromolecules, but not highly competent in the procedures involved in the process of structure determination. One should therefore take into account that the contemporary, highly automatic systems can produce results almost without human intervention, but the resulting structures must be carefully checked and validated before their release into the public domain.
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Affiliation(s)
- Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD and Argonne, IL, USA.
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Jaskolski M, Dauter Z, Wlodawer A. A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits. FEBS J 2014; 281:3985-4009. [PMID: 24698025 PMCID: PMC6309182 DOI: 10.1111/febs.12796] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 11/28/2022]
Abstract
As a contribution to the celebration of the year 2014, declared by the United Nations to be 'The International Year of Crystallography', the FEBS Journal is dedicating this issue to papers showcasing the intimate union between macromolecular crystallography and structural biology, both in historical perspective and in current research. Instead of a formal editorial piece, by way of introduction, this review discusses the most important, often iconic, achievements of crystallographers that led to major advances in our understanding of the structure and function of biological macromolecules. We identified at least 42 scientists who received Nobel Prizes in Physics, Chemistry or Medicine for their contributions that included the use of X-rays or neutrons and crystallography, including 24 who made seminal discoveries in macromolecular sciences. Our spotlight is mostly, but not only, on the recipients of this most prestigious scientific honor, presented in approximately chronological order. As a summary of the review, we attempt to construct a genealogy tree of the principal lineages of protein crystallography, leading from the founding members to the present generation.
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Affiliation(s)
- Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University and Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Helliwell JR. The evolution of synchrotron radiation and the growth of its importance in crystallography. CRYSTALLOGR REV 2012. [DOI: 10.1080/0889311x.2011.631919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Abstract
Dedicated to the people who designed, built, and currently work at synchrotron beamlines.
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Affiliation(s)
- Cele Abad-Zapatero
- Department of Structural Biology, D-R46Y, AP-10, L-07, Protein Crystallography Laboratory, Abbott Laboratories, Abbott Park, IL 60064-6098 USA.
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Abstract
Is radiation damage to cryopreserved protein crystals strictly proportional to accumulated dose at the high-flux density of beams from undulators at third-generation synchrotron sources? The answer is "yes," for overall damage to several different kinds of protein crystals at flux densities up to 10(15) ph/sec/mm(2) (APS beamline 19-ID). We find that, at 12 keV (1 A wavelength), about ten absorbed photons are sufficient to "kill" a unit cell. As this corresponds to about one elastically scattered photon, each unit cell can contribute only about one photon to total Bragg diffraction. The smallest crystal that can yield a full data set to 3.5 A resolution has a diameter of about 20 microm (100 A unit cell).
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Affiliation(s)
- Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Affiliation(s)
- K C Holmes
- Max Planck Institut für medizinische Forschung, Heidelberg, Germany.
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Fourme R, Kahn R. A rotation camera used with a synchrotron radiation source. Methods Enzymol 1985; 114:281-99. [PMID: 4079770 DOI: 10.1016/0076-6879(85)14023-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Greenhough TJ, Helliwell JR. The uses of synchrotron X-radiation in the crystallography of molecular biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1983; 41:67-123. [PMID: 6340166 DOI: 10.1016/0079-6107(83)90026-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Helliwell J. The use of electronic area detectors for synchrotron X-radiation protein crystallography with particular reference to the Daresbury SRS. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/0167-5087(82)90023-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Schulz GE, Rosenbaum G. The multi-wire proportional chamber as an area detector for protein crystallography in comparison with photographic film; Guidelines for future development of area detectors. ACTA ACUST UNITED AC 1978. [DOI: 10.1016/0029-554x(78)90266-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Synchrotron radiation is intense electromagnetic radiation with a continuous spectral distribution emitted by high-energy electron (or positron) synchrotrons or storage rings in the visible, vacuum ultraviolet and X-ray regions. For a long time only an unwanted but inevitable by-product of ring accelerators in elementary particle research, synchrotron radiation is now becoming a most widely used tool in atomic, molecular and solid-state spectroscopy, surface physics, structural research on solids, soft X-ray microscopy, lithography. It is not yet clear how large the field of applications really is nor which line of research will prove to be the most fruitful one in the long run.
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