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Jacobs FJ, Helliwell JR, Brink A. Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development. IUCrJ 2024; 11:359-373. [PMID: 38639558 PMCID: PMC11067751 DOI: 10.1107/s2052252524002598] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.
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Affiliation(s)
- Francois J.F. Jacobs
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Helliwell JR. Dynamics and Kinetics in Structural Biology: Unravelling Function Through Time-Resolved Structural Analysis. By Keith Moffat and Eaton E. Lattman. Wiley, New York, 2023, pp. 288. ISBN 978-1-119-69628-5. Price USD 161 (hardback), USD 128 (Kindle). Acta Crystallogr D Struct Biol 2024; 80:S2059798324001451. [PMID: 38372590 DOI: 10.1107/s2059798324001451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
John Helliwell provides a review of the book Dynamics and Kinetics in Structural Biology: Unravelling Function Through Time-Resolved Structural Analysis by Keith Moffat and Eaton E. Lattman.
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Affiliation(s)
- John R Helliwell
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
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Kroon-Batenburg LMJ, Lightfoot MP, Johnson NT, Helliwell JR. Raw diffraction data and reproducibility. Struct Dyn 2024; 11:011301. [PMID: 38361661 PMCID: PMC10869167 DOI: 10.1063/4.0000232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
In recent years, there has been a major expansion in digital storage capability for hosting raw diffraction datasets. Naturally, the question has now arisen as to the benefits and costs for the preservation of such raw, i.e., experimental diffraction datasets. We describe the consultations made of the global structural chemistry, i.e., chemical crystallography community from the points of view of the International Union of Crystallography (IUCr) Committee on Data, of which JRH was the Chair until very recently, and the IUCrData Raw Data Letters initiative, for which LKB is the Main Editor. The monitoring by the CCDC of CSD depositions which cite the digital object identifiers of raw diffraction datasets provides interesting statistics by probe (x-ray, neutron, or electron) and by home lab vs central facility. Clearly, a better understanding of the reproducibility of current analysis procedures is at hand. Policies for publication requiring raw data have been updated in IUCr Journals for macromolecular crystallography, namely, that raw data should be made available for a new crystal structure or a new method as well as the wwPDB deposition. For chemical crystallography, such a step requiring raw data archiving has not yet been recommended by the IUCr Commission on Structural Chemistry.
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Affiliation(s)
- Loes M. J. Kroon-Batenburg
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Matthew P. Lightfoot
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Natalie T. Johnson
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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Brink A, Bruno I, Helliwell JR, McMahon B. The interoperability of crystallographic data and databases. IUCrJ 2024; 11:9-15. [PMID: 38131388 PMCID: PMC10833386 DOI: 10.1107/s2052252523010424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Interoperability of crystallographic data with other disciplines is essential for the smooth and rapid progress of structure-based science in the computer age. Within crystallography and closely related subject areas, there is already a high level of conformance to the generally accepted FAIR principles (that data be findable, accessible, interoperable and reusable) through the adoption of common information exchange protocols by databases, publishers, instrument vendors, experimental facilities and software authors. Driven by the success within these domains, the IUCr has worked closely with CODATA (the Committee on Data of the International Science Council) to help develop the latter's commitment to cross-domain integration of discipline-specific data. The IUCr has, in particular, emphasized the need for standards relating to data quality and completeness as an adjunct to the FAIR data landscape. This can ensure definitive reusable data, which in turn can aid interoperability across domains. A microsymposium at the IUCr 2023 Congress provided an up-to-date survey of data interoperability within and outside of crystallography, expounded using a broad range of examples.
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Affiliation(s)
- Alice Brink
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
| | - Ian Bruno
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Brian McMahon
- International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, United Kingdom
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Helliwell JR. Error estimates in atom coordinates and B factors in macromolecular crystallography. Curr Res Struct Biol 2023; 6:100111. [PMID: 38058355 PMCID: PMC10695842 DOI: 10.1016/j.crstbi.2023.100111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 12/08/2023] Open
Abstract
The overall diffraction precision index (DPI) of a biological macromolecule crystal structure was first described by Cruickshank in 1999. This topical review proceeds from this point and describes the subsequent elaboration of the index to individual atom coordinates. Additional developments were introduced by the availability of a webserver, which provides a transformed PDB entry with individual atom coordinate errors derived from applying the DPI method using the parameters provided by the authors and then subsequently added to the PDB file. This webserver has been extensively used and harnessed in describing non-covalent distance error estimates as well as assessing the significance, or otherwise, of atom movements in a variety of studies. The standard uncertainties on a biological macromolecule's atomic displacement parameters (the 'B factors') has been an entirely different challenge but is obviously important since the crystallographic community has developed the habit of quoting B factors to a false precision in papers. This can convey a false certainty in the dynamics of a structure. A method involving parallelisation of workflows for diffraction image data processing does however offer estimates of the precision of B factors.
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Helliwell JR. Observations on Laue diffraction within synchrotron radiation and neutron macromolecular crystallography research and developments. Struct Dyn 2023; 10:061301. [PMID: 38107246 PMCID: PMC10725304 DOI: 10.1063/4.0000225] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
A seminal contribution in the domain of physiologically relevant biological structure and function determination was by Keith Moffat, of Cornell and latterly of the University of Chicago proposing that synchrotrons should offer the option of a Laue method data collection mode. I enthusiastically joined in supporting this initiative. This proposal needed detailed methods development though; theoretical, experimental and software development. This work was added to the broad research and development program of synchrotron radiation at the UK's SRS. This whole program led to knowledge transfer from the UK's SRS to the ESRF as well as for neutron Laue protein crystallography to the reactor spallation sources and later to spallation neutron sources.
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Affiliation(s)
- John R. Helliwell
- School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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Massera C, Helliwell JR. Golden oldies: ten crystallography articles that we think must be read. Acta Crystallogr E Crystallogr Commun 2023; 79:580-591. [PMID: 37601583 PMCID: PMC10439429 DOI: 10.1107/s2056989023004619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/24/2023] [Indexed: 08/22/2023]
Abstract
We have selected a set of ten 'golden oldies', diverse crystallography articles to illustrate important moments in the development of our field of science and which form landmark papers in crystallography. They are a mixture of 'science pull and technology push'. For each of our choices, we firstly created a new title that emphasizes how the paper's importance worked out from today's perspective. Then we describe the core details and impacts of each paper, with some quotations and a selected figure or two. Ten is an arbitrary number of highlights and our choice is personal.
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Affiliation(s)
- Chiara Massera
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma - Viale delle Scienze 17/A, 43124 Parma, Italy
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, M13 9PL, United Kingdom
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Helliwell JR. Scientific Testimony. By Mikkel Gerken. Oxford University Press, 2022. Pp. 320. GBP 65. ISBN 9780198857273. J Appl Crystallogr 2023. [DOI: 10.1107/s1600576722010950] [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: 12/23/2022] Open
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Helliwell JR. The Knowledge Machine: How an Unreasonable Idea Created Modern Science. By Michael Strevens. Penguin, 2022. Pp. 368. Price GBP 7.99 (Kindle), GBP 9.95 (paperback). ISBN 9780141981260. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576722010275] [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: 11/06/2022] Open
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Helliwell JR. Relating protein crystal structure to ligand-binding thermodynamics. Acta Crystallogr F Struct Biol Commun 2022; 78:403-407. [PMID: 36458619 PMCID: PMC9716570 DOI: 10.1107/s2053230x22011244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
An important interface between biophysical chemistry and biological crystal structures involves whether it is possible to relate experimental calorimetry measurements of protein ligand binding to 3D structures. This has proved to be challenging. The probes of the structure of matter, namely X-rays, neutrons and electrons, have challenges of one type or another in their use. This article focuses on saccharide binding to lectins as a theme, yet after 25 years or so it is still a work in progress to connect 3D structure to binding energies. Whilst this study involved one type of protein (lectins) and one class of ligand (monosaccharides), i.e. it was specific, it was of general importance, as measured for instance by its wide impact. The impetus for writing this update now, as a Scientific Comment, is that a breakthrough in neutron crystal structure determinations of saccharide-bound lectins has been achieved. It is suggested here that this new research from neutron protein crystallography could improve, i.e. reduce, the errors in the estimated binding energies.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom,Correspondence e-mail:
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Helliwell JR, Massera C. The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability. J Appl Crystallogr 2022; 55:1351-1358. [PMID: 36249510 PMCID: PMC9533758 DOI: 10.1107/s1600576722007208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Across the sciences, generic monitors of trust in results from science are being introduced. As educators and researchers, the authors consider these terms within the context of biological and chemical crystal structure analyses. Within science, of which crystallography is a key part, there are questions posed to all fields that challenge the trust in results. The US National Academies of Sciences, Engineering and Medicine published a thorough report in 2019 on the Reproducibility and Replicability of Science: replicability being where a totally new study attempts to confirm if a phenomenon can be seen independently of another study. Data reuse is a key term in the FAIR data accord [Wilkinson et al. (2016). Sci. Data, 3, 160018], where the acronym FAIR means findable, accessible, interoperable and reusable. In the social sciences, the acronym FACT (namely fairness, accuracy, confidentiality and transparency) has emerged, the idea being that data should be FACTual to ensure trust [van der Aalst et al. (2017). Bus. Inf. Syst. Eng.59, 311–313]. A distinction also must be made between accuracy and precision; indeed, the authors’ lectures at the European Crystallography School ECS6 independently emphasized the need for use of other methods as well as crystal structure analysis to establish accuracy in biological and chemical/material functional contexts. The efforts by disparate science communities to introduce new terms to ensure trust have merit for discussion in crystallographic teaching commissions and possible adoption by crystallographers too.
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Helliwell JR. Raw diffraction data are our ground truth from which all subsequent workflows develop. Acta Crystallogr D Struct Biol 2022; 78:683-689. [PMID: 35647915 PMCID: PMC9159283 DOI: 10.1107/s2059798322003795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 11/11/2022] Open
Abstract
Defining best practice in science is challenging. International consensus is facilitated by the International Science Council via its members such as the International Union of Crystallography (IUCr). The crystallographic community has many decades of tradition linking articles with the underpinning data, and is admired across all sciences accordingly. Crystallography has always been at the forefront of harnessing new technology in the service of consensus. Technology has provided new vast data-archiving opportunities, allowing the preservation of raw diffraction data, along with article and database depositions of a model's coordinates and associated structure factors. The raw diffraction data, which can now be preserved, are the ground truth from which all subsequent workflows develop. Journal editorial boards provide a practical forum for setting the criteria to decide if a study's files are truly the version of record. Within that, reality involves a variance of reasonable workflows. But what is a reasonable variance? Workflows must be detailed carefully by authors in explaining what they have done. There is a great, and increasing, diversity of macromolecular crystallography analyses, and yet an increased constraint on how much can be written in an article about the workflow used. Raw data provide the ultimate reproducibility evidence. A part of reproducibility and replicability is using an agreed vocabulary; the meaning of words such as precision and accuracy and, more recently, the confidence of a protein structure prediction should feature in approaching `truth'.
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Hanau S, Helliwell JR. 6-Phosphogluconate dehydrogenase and its crystal structures. Acta Crystallogr F Struct Biol Commun 2022; 78:96-112. [PMID: 35234135 PMCID: PMC8900737 DOI: 10.1107/s2053230x22001091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
6-Phosphogluconate dehydrogenase (6PGDH; EC 1.1.1.44) catalyses the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate in the context of the oxidative part of the pentose phosphate pathway. Depending on the species, it can be a homodimer or a homotetramer. Oligomerization plays a functional role not only because the active site is at the interface between subunits but also due to the interlocking tail-modulating activity, similar to that of isocitrate dehydrogenase and malic enzyme, which catalyse a similar type of reaction. Since the pioneering crystal structure of sheep liver 6PGDH, which allowed motifs common to the β-hydroxyacid dehydrogenase superfamily to be recognized, several other 6PGDH crystal structures have been solved, including those of ternary complexes. These showed that more than one conformation exists, as had been suggested for many years from enzyme studies in solution. It is inferred that an asymmetrical conformation with a rearrangement of one of the two subunits underlies the homotropic cooperativity. There has been particular interest in the presence or absence of sulfate during crystallization. This might be related to the fact that this ion, which is a competitive inhibitor that binds in the active site, can induce the same 6PGDH configuration as in the complexes with physiological ligands. Mutagenesis, inhibitors, kinetic and binding studies, post-translational modifications and research on the enzyme in cancer cells have been complementary to the crystallographic studies. Computational modelling and new structural studies will probably help to refine the understanding of the functioning of this enzyme, which represents a promising therapeutic target in immunity, cancer and infective diseases. 6PGDH also has applied-science potential as a biosensor or a biobattery. To this end, the enzyme has been efficiently immobilized on specific polymers and nanoparticles. This review spans the 6PGDH literature and all of the 6PGDH crystal structure data files held by the Protein Data Bank.
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Brink A, Jacobs FJF, Helliwell JR. Trends in coordination of rhenium organometallic complexes in the Protein Data Bank. IUCrJ 2022; 9:180-193. [PMID: 35371500 PMCID: PMC8895017 DOI: 10.1107/s2052252522000665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Radiopharmaceutical development has similar overall characteristics to any biomedical drug development requiring a compound's stability, aqueous solubility and selectivity to a specific disease site. However, organometallic complexes containing 188/186Re or 99mTc involve a d-block transition-metal radioactive isotope and therefore bring additional factors such as metal oxidation states, isotope purity and half life into play. This topical review is focused on the development of radiopharmaceuticals containing the radioisotopes of rhenium and technetium and, therefore, on the occurrence of these organometallic complexes in protein structures in the Worldwide Protein Data Bank (wwPDB). The purpose of incorporating the group 7 transition metals of rhenium/technetium in the protein and the reasons for study by protein crystallography are described, as certain PDB studies were not aimed at drug development. Technetium is used as a medical diagnostic agent and involves the 99mTc isotope which decays to release gamma radiation, thereby employed for its use in gamma imaging. Due to the periodic relationship among group 7 transition metals, the coordination chemistry of rhenium is similar (but not identical) to that of technetium. The types of reactions the potential model radiopharmaceutical would prefer to partake in, and by extension knowing which proteins and biomolecules the compound would react with in vivo, are needed. Crystallography studies, both small molecule and macromolecular, are a key aspect in understanding chemical coordination. Analyses of bonding modes, coordination to particular residues and crystallization conditions are presented. In our Forward look as a concluding summary of this topical review, the question we ask is: what is the best way for this field to progress?
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Affiliation(s)
- Alice Brink
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Francois J. F. Jacobs
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
| | - John R. Helliwell
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
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Helliwell JR. Collecting Experiments. Making Big Data Biology. By Bruno J. Strasser. Chicago University Press, 2019. Pp. 392. Price USD 45.00. ISBN 9780226635040. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576721012140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
Like an article narrative is deemed by an editor and referees to be worthy of being a version of record on acceptance as a publication, so must the underpinning data also be scrutinized before passing it as a version of record. Indeed without the underpinning data, a study and its conclusions cannot be reproduced at any stage of evaluation, pre- or post-publication. Likewise, an independent study without its own underpinning data also cannot be reproduced let alone be considered a replicate of the first study. The PDB is a modern marvel of achievement providing an organized open access to depositor and user of the data held there opening numerous applications. Methods for modeling protein structures and for determination of structures are still improving their precision, and artifacts of the method exist. So their accuracy is realized if they are reproduced by other methods. It is on such foundations that reproducible data mining is based. Data rates are expanding considerably be they at synchrotrons, the X-ray free electron lasers (XFELs), electron cryomicroscopes (cryoEM), or at the neutron facilities. The work of a person as a referee or user with a narrative and its underpinning data may well be complemented in future by artificial intelligence with machine learning, the former for specific refereeing and the latter for the more general validation, both ideally before publication. Examples are described involving rhenium theranostics, the anti-cancer platins and the SARS-CoV-2 main protease.
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Affiliation(s)
- John R Helliwell
- Department of Chemistry, University of Manchester, Manchester, UK.
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Helliwell JR. The crystal structures of the enzyme hydroxymethylbilane synthase, also known as porphobilinogen deaminase. Acta Crystallogr F Struct Biol Commun 2021; 77:388-398. [PMID: 34726177 PMCID: PMC8561815 DOI: 10.1107/s2053230x2100964x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/16/2021] [Indexed: 12/03/2022] Open
Abstract
The enzyme hydroxymethylbilane synthase (HMBS; EC 4.3.1.8), also known as porphobilinogen deaminase, catalyses the stepwise addition of four molecules of porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane. Thirty years of crystal structures are surveyed in this topical review. These crystal structures aim at the elucidation of the structural basis of the complex reaction mechanism involving the formation of tetrapyrrole from individual porphobilinogen units. The consistency between the various structures is assessed. This includes an evaluation of the precision of each molecular model and what was not modelled. A survey is also made of the crystallization conditions used in the context of the operational pH of the enzyme. The combination of 3D structural techniques, seeking accuracy, has also been a feature of this research effort. Thus, SAXS, NMR and computational molecular dynamics have also been applied. The general framework is also a considerable chemistry research effort to understand the function of the enzyme and its medical pathologies in acute intermittent porphyria (AIP). Mutational studies and their impact on the catalytic reaction provide insight into the basis of AIP and are also invaluable for guiding the understanding of the crystal structure results. Future directions for research on HMBS are described, including the need to determine the protonation states of key amino-acid residues identified as being catalytically important. The question remains - what is the molecular engine for this complex reaction? Thermal fluctuations are the only suggestion thus far.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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Helliwell JR, Newman J, van Raaij MJ. Topical Reviews in Acta Crystallographica F Structural Biology Communications. Acta Crystallogr F Struct Biol Commun 2021; 77:385. [PMID: 34726175 PMCID: PMC8561818 DOI: 10.1107/s2053230x21011195] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Editors of Acta Cryst. F Structural Biology Communications discuss their plans for topical reviews.
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Affiliation(s)
- John R. Helliwell
- The University of Manchester, Brunswick Street, Manchester, M13 9PL, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J. van Raaij
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, E-28049, Madrid, Spain
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Helliwell JR. How should we teach crystallography? A review of teaching books’ contents pages. CRYSTALLOGR REV 2021. [DOI: 10.1080/0889311x.2021.1978080] [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: 10/20/2022]
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Helliwell JR. Respect the synchrotron beam strength: how to model it, measure it and mitigate it for various scientific fields. J Synchrotron Radiat 2021; 28:1275-1277. [PMID: 34475276 PMCID: PMC8415337 DOI: 10.1107/s1600577521008328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Extremely bright synchrotron radiation sources give extremely strong intensities at the sample. Lawrence Bright et al. (2021) [J. Synchrotron Rad. (2021), 28 , 1377–1385] dive into the details for materials science. I offer a Commentary including a historical context.
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Affiliation(s)
- John R. Helliwell
- Science and Engineering Research Council (now Science and Technology Facilities Council), Daresbury Laboratory, Warrington WA4 4AD, United Kingdom
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21
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Helliwell JR. The Beauty of Chemistry: Art, Wonder, and Science. By Philip Ball. Photographs by Wenting Zhu and Yan Liang. MIT Press, 2021. Pp. 308. Hardback price USD 49.45. ISBN 978-0262044417. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721005069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Helliwell JR. Triosephosphate isomerase: the perfect enzyme, but how does it work? IUCrJ 2021; 8:480-481. [PMID: 34257998 PMCID: PMC8256717 DOI: 10.1107/s205225252100573x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Insights are offered on the study by Kelpšas et al. [IUCrJ (2021). 8, 633-643], who have combined neutron and X-ray crystallography then QM (quantum mechanics) calculations on triosephosphate isomerase (TIM). The authors dissect three possible enzyme mechanisms of TIM that have arisen in the decades since the first X-ray crystal structure of this enzyme was published in 1975.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, United Kingdom
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Govada L, Saridakis E, Kassen SC, Bin-Ramzi A, Morgan RM, Chain B, Helliwell JR, Chayen NE. X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5. IUCrJ 2021; 8:678-683. [PMID: 34258015 PMCID: PMC8256702 DOI: 10.1107/s2052252521005340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. This led to the hypothesis that stimulating an antibody response would block HIV with minimal toxicity. Here, X-ray crystallographic studies of the anti-CCR5 antibody RoAb13 together with two peptides were undertaken: one peptide is a 31-residue peptide containing the PIYDIN sequence and the other is the PIDYIN peptide alone, where PIYDIN is part of the N-terminal region of CCR5 previously shown to be important for HIV entry. In the presence of the longer peptide (the complete N-terminal domain), difference electron density was observed at a site within a hypervariable CDR3 binding region. In the presence of the shorter core peptide PIYDIN, difference electron density is again observed at this CDR3 site, confirming consistent binding for both peptides. This may be useful in the design of a new biomimetic to stimulate an antibody response to CCR5 in order to block HIV infection.
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Affiliation(s)
- Lata Govada
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, United Kingdom
| | - Emmanuel Saridakis
- Structural and Supramolecular Chemistry Laboratory, Institute of Nanoscience and Nanotechnology, National Centre for Scientific Research ‘Demokritos’, 15310 Athens, Greece
| | - Sean C. Kassen
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ahmad Bin-Ramzi
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rhodri Marc Morgan
- Department of Life Sciences, Faculty of Natural Sciences, Sir Ernst Chain Building, Imperial College London, London SW7 2AZ, United Kingdom
| | - Benjamin Chain
- Division of Infection and Immunity, University College London, Gower Street, London, United Kingdom
| | - John R. Helliwell
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Naomi E. Chayen
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, United Kingdom
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Helliwell JR. Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies. Acta Crystallogr A Found Adv 2021; 77:173-185. [PMID: 33944796 PMCID: PMC8127390 DOI: 10.1107/s205327332100317x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/25/2021] [Indexed: 02/02/2023] Open
Abstract
The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure-function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, United Kingdom
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Helliwell JR, Yariv family. Joseph Yariv (1927–2021). J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721004453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Helliwell JR. The Science of Science. By Dashun Wang and Albert-László Barabási. Cambridge University Press, 2021. Pp. 308. Hardback price GBP 64.99, ISBN 9781108492669. Paperback price GBP 22.99, ISBN 9781108716956. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721002788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Nakagawa A, Helliwell JR, Yamagata Y. Diffraction structural biology - an introductory overview. Acta Crystallogr D Struct Biol 2021; 77:278-279. [PMID: 33645530 DOI: 10.1107/s2059798321001613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Atsushi Nakagawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John R Helliwell
- Department of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Yuriko Yamagata
- Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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Gillis RB, Solomon HV, Govada L, Oldham NJ, Dinu V, Jiwani SI, Gyasi-Antwi P, Coffey F, Meal A, Morgan PS, Harding SE, Helliwell JR, Chayen NE, Adams GG. Analysis of insulin glulisine at the molecular level by X-ray crystallography and biophysical techniques. Sci Rep 2021; 11:1737. [PMID: 33462295 PMCID: PMC7814034 DOI: 10.1038/s41598-021-81251-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Received: 03/31/2020] [Accepted: 12/09/2020] [Indexed: 11/16/2022] Open
Abstract
This study concerns glulisine, a rapid-acting insulin analogue that plays a fundamental role in diabetes management. We have applied a combination of methods namely X-ray crystallography, and biophysical characterisation to provide a detailed insight into the structure and function of glulisine. X-ray data provided structural information to a resolution of 1.26 Å. Crystals belonged to the H3 space group with hexagonal (centred trigonal) cell dimensions a = b = 82.44 and c = 33.65 Å with two molecules in the asymmetric unit. A unique position of D21Glu, not present in other fast-acting analogues, pointing inwards rather than to the outside surface was observed. This reduces interactions with neighbouring molecules thereby increasing preference of the dimer form. Sedimentation velocity/equilibrium studies revealed a trinary system of dimers and hexamers/dihexamers in dynamic equilibrium. This new information may lead to better understanding of the pharmacokinetic and pharmacodynamic behaviour of glulisine which might aid in improving formulation regarding its fast-acting role and reducing side effects of this drug.
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Affiliation(s)
- Richard B Gillis
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK.
| | - Hodaya V Solomon
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Lata Govada
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Shahwar Imran Jiwani
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Philemon Gyasi-Antwi
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Frank Coffey
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Andy Meal
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Paul S Morgan
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,Universitetet I Oslo, St. Olavs plass, Postboks 6762, 0130, Oslo, Norway
| | - John R Helliwell
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, UK
| | - Naomi E Chayen
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK.
| | - Gary G Adams
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK.
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Helliwell JR. Defining and Measuring Nature. The Make Of All Things. Second edition. By Jeffrey H. Williams. Institute of Physics Publishing, 2020. Price (hardcover) USD 50.00. ISBN 9780750331418. (Also available as ebook, 313 pp., price USD 40.00, ISBN 9780750331432.). J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720012674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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30
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Helliwell JR. A life among men, women and molecules memoirs of an Indian scientist. CRYSTALLOGR REV 2020. [DOI: 10.1080/0889311x.2020.1788005] [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: 10/23/2022]
Affiliation(s)
- John R. Helliwell
- Emeritus Professor of Chemistry, University of Manchester and DSc Physics, University of York, UK
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Helliwell JR. How To Be a Better Scientist. By Andrew C. Johnson and John P. Sumpter. Taylor and Francis, 2018. Pp. 248. Price GBP 15.19 ISBN 9781138731295 (paperback), GBP 76.00 ISBN 9781138731219 (hardback), GBP 12.34 ISBN 9781315189079 (ebook). J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720005646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Helliwell JR. Being an Interdisciplinary Academic: How Institutions Shape University Careers. By Catherine Lyall. Palgrave Pivot, 2019. Pp. 154. Price EUR 51.99 (hardcover). ISBN 978-3-030-18658-6. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720002630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Abstract
This chapter introduces this topic for the whole volume. It is not a review, rather it presents the basics, the key considerations and forward references to the other chapters. This starts by setting the scene of principles and overall strategy, moves onto planning an experiment including its feasibility and then outlines practicalities with options for the experiment. The crystal structure that results will lead to publication and associated with it, Protein Data Bank deposition.
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Helliwell JR. What is the structural chemistry of the living organism at its temperature and pressure? Acta Crystallogr D Struct Biol 2020; 76:87-93. [PMID: 32038039 PMCID: PMC7008516 DOI: 10.1107/s2059798320000546] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 12/02/2022] Open
Abstract
The three probes of the structure of matter (X-rays, neutrons and electrons) in biology have complementary properties and strengths. The balance between these three probes within their strengths and weaknesses is perceived to change, even dramatically so at times. For the study of combined states of order and disorder, NMR crystallography is also applicable. Of course, to understand biological systems the required perspectives are surely physiologically relevant temperatures and relevant chemical conditions, as well as a minimal perturbation owing to the needs of the probe itself. These remain very tough challenges because, for example, cryoEM by its very nature will never be performed at room temperature, crystallization often requires nonphysiological chemical conditions, and X-rays and electrons cause beam damage. However, integrated structural biology techniques and functional assays provide a package towards physiological relevance of any given study. Reporting of protein crystal structures, and their associated database entries, could usefully indicate how close to the biological situation they are, as discussed in detail in this feature article.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, England
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Helliwell JR. Broader Impacts of Science on Society. By Bruce J. MacFadden. Cambridge University Press, 2019. Pp. 320. Price GBP 19.99 (paperback). ISBN 9781108434287. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719014353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Helliwell JR. Why Trust Science?By Naomi Oreskes. Princeton University Press, 2019. Pp. 376. Price USD 24.95, GBP 22.00 (hardback). ISBN 9780691179001, ebook ISBN 9780691189932. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719013669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Helliwell JR. The Overproduction of Truth. Passion, Competition, and Integrity in Modern Science. By Gianfranco Pacchioni. Oxford University Press, 2018. Pp. 176. Price GBP 19.99 (hardback). ISBN 9780198799887. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719012147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Helliwell JR. What Science Is and How It Really Works.By James C. Zimring. Cambridge University Press, 2019. Pp. 402. Price USD 25.99. Paperback ISBN 9781108701648. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719011361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brink A, Helliwell JR. Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? IUCrJ 2019; 6:788-793. [PMID: 31576212 PMCID: PMC6760442 DOI: 10.1107/s2052252519010972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/06/2019] [Indexed: 05/06/2023]
Abstract
The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, Free State 9301, South Africa
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
- Correspondence e-mail:
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
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Helliwell JR. FACT and FAIR with Big Data allows objectivity in science: The view of crystallography. Struct Dyn 2019; 6:054306. [PMID: 31673568 PMCID: PMC6816445 DOI: 10.1063/1.5124439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/09/2019] [Indexed: 05/14/2023]
Abstract
A publication is an important narrative of the work done and interpretations made by researchers securing a scientific discovery. As The Royal Society neatly states though, "Nullius in verba" ("Take nobody's word for it"), whereby the role of the underpinning data is paramount. Therefore, the objectivity that preserving that data within the article provides is due to readers being able to check the calculation decisions of the authors. But how to achieve full data archiving? This is the raw data archiving challenge, in size and need for correct metadata. Processed diffraction data and final derived molecular coordinates archiving in crystallography have achieved an exemplary state of the art relative to most fields. One can credit IUCr with developing exemplary peer review procedures, of narrative, underpinning structure factors and coordinate data and validation report, through its checkcif development and submission system introduced for Acta Cryst. C and subsequently developed for its other chemistry journals. The crystallographic databases likewise have achieved amazing success and sustainability these last 50 years or so. The wider science data scene is celebrating the FAIR data accord, namely, that data be Findable, Accessible, Interoperable, and Reusable [Wilkinson et al., "Comment: The FAIR guiding principles for scientific data management and stewardship," Sci. Data 3, 160018 (2016)]. Some social scientists also emphasize more than FAIR being needed, the data should be "FACT," which is an acronym meaning Fair, Accurate, Confidential, and Transparent [van der Aalst et al., "Responsible data science," Bus Inf. Syst. Eng. 59(5), 311-313 (2017)], this being the issue of ensuring reproducibility not just reusability. (Confidentiality of data not likely being relevant to our data obviously.) Acta Cryst. B, C, E, and IUCrData are the closest I know to being both FACT and FAIR where I repeat for due emphasis: the narrative, the automatic "general" validation checks, and the underpinning data are checked thoroughly by subject specialists (i.e., the specialist referees). IUCr Journals are also the best that I know of for encouraging and then expediting the citation of the DOI for a raw diffraction dataset in a publication; examples can be found in IUCrJ, Acta Cryst D, and Acta Cryst F. The wish for a checkcif for raw diffraction data has been championed by the IUCr Diffraction Data Deposition Working Group and its successor, the IUCr Committee on Data.
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Affiliation(s)
- John R Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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Helliwell JR. Bias in Science and Communication. A Field Guide. By Matthew Welsh. IOP Publishing, 2018. Pp. 177. ISBN 978-0-7503-1312-4. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719006873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Helliwell JR. FACT and FAIR with big data allows objectivity in science: the view of crystallography. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s010876731909946x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brink A, Helliwell JR. Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging. IUCrJ 2019; 6:695-702. [PMID: 31316813 PMCID: PMC6608631 DOI: 10.1107/s2052252519006651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/09/2019] [Indexed: 05/22/2023]
Abstract
The fact that a protein crystal can serve as a chemical reaction vessel is intrinsically fascinating. That it can produce an electron-dense tetranuclear rhenium cluster compound from a rhenium tri-carbonyl tri-bromo starting compound adds to the fascination. Such a cluster has been synthesized previously in vitro, where it formed under basic conditions. Therefore, its synthesis in a protein crystal grown at pH 4.5 is even more unexpected. The X-ray crystal structures presented here are for the protein hen egg-white lysozyme incubated with a rhenium tri-carbonyl tri-bromo compound for periods of one and two years. These reveal a completed, very well resolved, tetra-rhenium cluster after two years and an intermediate state, where the carbonyl ligands to the rhenium cluster are not yet clearly resolved, after one year. A dense tetranuclear rhenium cluster, and its technetium form, offer enhanced contrast in medical imaging. Stimulated by these crystallography results, the unusual formation of such a species directly in an in vivo situation has been considered. It offers a new option for medical imaging compounds, particularly when considering the application of the pre-formed tetranuclear cluster, suggesting that it may be suitable for medical diagnosis because of its stability, preference of formation and biological compatibility.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
- Correspondence e-mail:
| | - John R. Helliwell
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. IUCrJ 2019; 6:341-343. [PMID: 31098014 PMCID: PMC6503929 DOI: 10.1107/s2052252519005918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
- The European Extreme Light Infrastructure, Institute of Physics, AS CR, Na Slovance 2, Prague 18221 8, Czech Republic
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. Acta Crystallogr F Struct Biol Commun 2019; 75:321-323. [PMID: 31045560 PMCID: PMC6497101 DOI: 10.1107/s2053230x19005909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. J Appl Crystallogr 2019; 52:495-497. [PMID: 31236090 PMCID: PMC6557178 DOI: 10.1107/s1600576719005922] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, UK
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden.,The European Extreme Light Infrastructure, Institute of Physics, AS CR, Na Slovance 2, Prague 18221 8, Czech Republic
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. Acta Crystallogr D Struct Biol 2019; 75:455-457. [PMID: 31063147 PMCID: PMC6503765 DOI: 10.1107/s2059798319004844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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Helliwell JR. Study and Communication Skills for the Biosciences, 3rd edition. By Stuart Johnson and Jon Scott. Oxford University Press, 2019. Pp. 262. Price (paperback) GBP 24.99. ISBN 978-0-19-879146-1. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719002292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Affiliation(s)
- John R. Helliwell
- Emeritus Professor, Department of Chemistry, University of Manchester, Manchester, UK
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Helliwell JR. Managing Science: Developing your Research, Leadership and Management Skills. By Ken Peach. Oxford University Press, 2017. Pp. 288. Hardback Price GBP 25.49. ISBN 9780198796077. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718013195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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