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Bijak V, Gucwa M, Lenkiewicz J, Murzyn K, Cooper DR, Minor W. Continuous Validation Across Macromolecular Structure Determination Process. NIHON KESSHO GAKKAI SHI 2023; 65:10-16. [PMID: 37416056 PMCID: PMC10321142 DOI: 10.5940/jcrsj.65.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia
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2
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Minor W, Cymborowski M, Borek D, Cooper DR, Chruszcz M, Otwinowski Z. Optimal structure determination from sub-optimal diffraction data. Protein Sci 2022; 31:259-268. [PMID: 34783106 PMCID: PMC8740829 DOI: 10.1002/pro.4235] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023]
Abstract
Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.
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Affiliation(s)
- Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Dominika Borek
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
| | - David R. Cooper
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Maksymilian Chruszcz
- Department of Chemistry and BiochemistryUniversity of South CarolinaColumbiaSouth Carolina
| | - Zbyszek Otwinowski
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
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3
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Gao Y, Ma C, Feng X, Liu Y, Haimiti X. BF12, a Novel Benzofuran, Exhibits Antitumor Activity by Inhibiting Microtubules and the PI3K/Akt/mTOR Signaling Pathway in Human Cervical Cancer Cells. Chem Biodivers 2020; 17:e1900622. [PMID: 31951313 DOI: 10.1002/cbdv.201900622] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/16/2020] [Indexed: 12/20/2022]
Abstract
BF12 [(2E)-3-[6-Methoxy-2-(3,4,5-trimethoxybenzoyl)-1-benzofuran-5-yl]prop-2-enoic acid], a novel derivative of combretastatin A-4 (CA-4), was previously found to inhibit tumor cell lines, with a particularly strong inhibitory effect on cervical cancer cells. In this study, we investigated the microtubule polymerization effects and apoptosis signaling mechanism of BF12. BF12 showed a potent efficiency against cervical cancer cells, SiHa and HeLa, with IC50 values of 1.10 and 1.06 μm, respectively. The cellular mechanism studies revealed that BF12 induced G2/M phase arrest and apoptosis in SiHa and HeLa cells, which were associated with alterations in the expression of the cell G2/M cycle checkpoint-related proteins (cyclin B1 and cdc2) and alterations in the levels of apoptosis-related proteins (P53, caspase-3, Bcl-2, and Bax) of these cells, respectively. Western blot analysis showed that BF12 inhibited the PI3 K/Akt/mTOR signaling pathway and induced apoptosis in human cervical cancer cells. BF12 was identified as a tubulin polymerization inhibitor, evidenced by the effective inhibition of tubulin polymerization and heavily disrupted microtubule networks in living SiHa and HeLa cells. By inhibiting the PI3 K/Akt/mTOR signaling pathway and inducing apoptosis in human cervical cancer cells, BF12 shows promise for use as a microtubule inhibitor.
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Affiliation(s)
- Yiting Gao
- Department of Medicinal and Organic Chemistry, School of Pharmacy, Xinjiang Medical University, Beijing Road 393#, Xinshi District, Urumqi, 830011, P. R. China
| | - Cheng Ma
- Department of Medicinal and Organic Chemistry, School of Pharmacy, Xinjiang Medical University, Beijing Road 393#, Xinshi District, Urumqi, 830011, P. R. China
| | - Xuezhao Feng
- Department of Medicinal and Organic Chemistry, School of Pharmacy, Xinjiang Medical University, Beijing Road 393#, Xinshi District, Urumqi, 830011, P. R. China
| | - Yang Liu
- Department of Medicinal and Organic Chemistry, School of Pharmacy, Xinjiang Medical University, Beijing Road 393#, Xinshi District, Urumqi, 830011, P. R. China
| | - Xiaohelaiti Haimiti
- Department of Medicinal and Organic Chemistry, School of Pharmacy, Xinjiang Medical University, Beijing Road 393#, Xinshi District, Urumqi, 830011, P. R. China
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4
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Svensson O, Gilski M, Nurizzo D, Bowler MW. A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples. IUCRJ 2019; 6:822-831. [PMID: 31576216 PMCID: PMC6760449 DOI: 10.1107/s2052252519008017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 05/12/2023]
Abstract
The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
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5
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Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W. Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. Biochemistry 2018; 57:963-977. [PMID: 29309127 PMCID: PMC6469932 DOI: 10.1021/acs.biochem.7b01137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site.
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Affiliation(s)
- Jan Kutner
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Dorota Matelska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 93 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Katarzyna B. Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Olga Gasiorowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Piotr Sroka
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Maria W. Gorna
- Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 93 Zwirki i Wigury, 02-089 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
| | - Krzysztof Wozniak
- Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Department of Chemistry, University of Warsaw, 1 Ludwika Pasteura, 02-093 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
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6
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Balasco N, Esposito L, Vitagliano L. Factors affecting the amplitude of the τ angle in proteins: a revisitation. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:618-625. [DOI: 10.1107/s2059798317007793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/25/2017] [Indexed: 11/10/2022]
Abstract
The protein folded state is the result of the fine balance of a variety of different forces. Even minor structural perturbations may have a significant impact on the stability of these macromolecules. Studies carried out in recent decades have led to the convergent view that proteins are endowed with a flexible spine. One of the open issues related to protein local backbone geometry is the identification of the factors that influence the amplitude of the τ (N—Cα—C) angle. Here, statistical analyses performed on an updated ensemble of X-ray protein structures by dissecting the contribution of the major factors that can potentially influence the local backbone geometry of proteins are reported. The data clearly indicate that the local backbone conformation has a prominent impact on the modulation of the τ angle. Therefore, a proper assessment of the impact of the other potential factors can only be appropriately evaluated when small (φ, ψ) regions are considered. Here, it is shown that when the contribution of the backbone conformation is removed by considering small (φ, ψ) areas, an impact of secondary structure, as defined byDSSP, and/or the residue type on τ is still detectable, although to a limited extent. Indeed, distinct τ-value distributions are detected for Pro/Gly and β-branched (Ile/Val) residues. The key role of the local backbone conformation highlighted here supports the use of variable local backbone geometry in protein refinement protocols.
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7
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Xu X, Bošnjaković-Pavlović N, Čolović MB, Krstić DZ, Vasić VM, Gillet JM, Wu P, Wei Y, Spasojević-de Biré A. A combined crystallographic analysis and ab initio calculations to interpret the reactivity of functionalized hexavanadates and their inhibitor potency toward Na(+)/K(+)-ATPase. J Inorg Biochem 2016; 161:27-36. [PMID: 27235271 DOI: 10.1016/j.jinorgbio.2016.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/16/2016] [Accepted: 04/25/2016] [Indexed: 02/02/2023]
Abstract
In vitro influence of five synthesized functionalized hexavanadates (V6) on commercial porcine cerebral cortex Na(+)/K(+)-ATPase activity has been studied. Dose dependent Na(+)/K(+)-ATPase inhibition was obtained for all investigated compounds. Calculated half maximal inhibitory concentration IC50 values, in mol/L, for Na(+)/K(+)-ATPase were 7.6×10(-5), 1.8×10(-5), 2.9×10(-5), 5.5×10(-5) for functionalized hexavanadates (V6) with tetrabutylammonium (TBA) [V6-CH3][TBA]2, [V6-NO2][TBA]2, [V6-OH][TBA]2 and [V6-C3][TBA]2 respectively. [V6-OH][Na]2 inhibited Na(+)/K(+)-ATPase activity up to 30% at maximal investigated concentration 1×10(-3)mol/L. This reactivity has been interpreted using a study of the non-covalent interactions of functionalized hexavanadate hybrids through Cambridge Structural Database (CSD) analysis. Bibliographic searching has led to 18 different structures and 99 contacts. We have observed that C-H⋯O contacts consolidate the structures. We have also performed density functional theory (DFT) calculations and have determined electrostatic potential values at the molecular surface on a series of functionalized V6. These results enlightened their chemical reactivity and their potential biological applications such as the inhibition of the ATPase.
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Affiliation(s)
- Xiao Xu
- Université Paris Saclay, CentraleSupélec, Campus de Châtenay, Grande Voie des Vignes, 92295 Châtenay-Malabry, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Grande Voie des Vignes, 92295 Châtenay-Malabry, France
| | | | - Mirjana B Čolović
- Department of Physical Chemistry, Vinča Institute of Nuclear Sciences, University of Belgrade, P.O.Box 522, Belgrade, Serbia
| | - Danijela Z Krstić
- University School of Medicine, Institute of Medical Chemistry, University of Belgrade, Višegradska 26, 11000 Belgrade, Serbia
| | - Vesna M Vasić
- Department of Physical Chemistry, Vinča Institute of Nuclear Sciences, University of Belgrade, P.O.Box 522, Belgrade, Serbia
| | - Jean-Michel Gillet
- Université Paris Saclay, CentraleSupélec, Campus de Châtenay, Grande Voie des Vignes, 92295 Châtenay-Malabry, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Grande Voie des Vignes, 92295 Châtenay-Malabry, France
| | - Pingfan Wu
- Institute of POM-based Materials, The Synergistic Innovation Center of Catalysis Materials of Hubei Province, Hubei University of Technology, 430086 Wuhan, Hubei Province, P. R. China
| | - Yongge Wei
- Department of Chemistry, Tsinghua University, 100084 Beijing, P.R. China
| | - Anne Spasojević-de Biré
- Université Paris Saclay, CentraleSupélec, Campus de Châtenay, Grande Voie des Vignes, 92295 Châtenay-Malabry, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Grande Voie des Vignes, 92295 Châtenay-Malabry, France
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8
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Groom CR, Bruno IJ, Lightfoot MP, Ward SC. The Cambridge Structural Database. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:171-9. [PMID: 27048719 PMCID: PMC4822653 DOI: 10.1107/s2052520616003954] [Citation(s) in RCA: 5835] [Impact Index Per Article: 729.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/08/2016] [Indexed: 05/03/2023]
Abstract
The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.
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Affiliation(s)
- Colin R. Groom
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Ian J. Bruno
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Matthew P. Lightfoot
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Suzanna C. Ward
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
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Zhou L, Li Q, Wang J, Huang C, Nice EC. Oncoproteomics: Trials and tribulations. Proteomics Clin Appl 2015; 10:516-31. [PMID: 26518147 DOI: 10.1002/prca.201500081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/19/2015] [Accepted: 10/27/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Qifu Li
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Jiandong Wang
- Department of Biomedical; Chengdu Medical College; Chengdu Sichuan Province P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
| | - Edouard C. Nice
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Australia
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10
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Baker EN. Biological crystallography: new methods, new challenges. IUCRJ 2015; 2:155-156. [PMID: 25866648 PMCID: PMC4392406 DOI: 10.1107/s2052252515003541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ability of crystallography to illuminate biology and contribute to medical advances continues to grow. Recent advances expand its reach while also asking questions of its practitioners.
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Affiliation(s)
- Edward N. Baker
- School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland, New Zealand
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