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Roy A, Tiwari S, Karmakar S, Anki Reddy K, Pandey LM. The effect of the stoichiometric ratio of zinc towards the fibrillation of Bovine Serum Albumin (BSA): A mechanistic insight. Int J Biol Macromol 2019; 123:409-419. [DOI: 10.1016/j.ijbiomac.2018.11.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023]
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53
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Coverdale JPC, Khazaipoul S, Arya S, Stewart AJ, Blindauer CA. Crosstalk between zinc and free fatty acids in plasma. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:532-542. [PMID: 30266430 PMCID: PMC6372834 DOI: 10.1016/j.bbalip.2018.09.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/23/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022]
Abstract
In mammalian blood plasma, serum albumin acts as a transport protein for free fatty acids, other lipids and hydrophobic molecules including neurodegenerative peptides, and essential metal ions such as zinc to allow their systemic distribution. Importantly, binding of these chemically extremely diverse entities is not independent, but linked allosterically. One particularly intriguing allosteric link exists between free fatty acid and zinc binding. Albumin thus mediates crosstalk between energy status/metabolism and organismal zinc handling. In recognition of the fact that even small changes in extracellular zinc concentration and speciation modulate the function of many cell types, the albumin-mediated impact of free fatty acid concentration on zinc distribution may be significant for both normal physiological processes including energy metabolism, insulin activity, heparin neutralisation, blood coagulation, and zinc signalling, and a range of disease states, including metabolic syndrome, cardiovascular disease, myocardial ischemia, diabetes, and thrombosis. Serum albumin binds and transports both free fatty acids and Zn2+ ions Elevated plasma free fatty acids impair Zn2+ binding by albumin through an allosteric mechanism The resulting changes in plasma zinc speciation are thought to impact blood coagulation and may promote thrombosis Increased free Zn2+ may lead to enhanced zinc export from plasma and dysregulation of zinc homeostasis in multiple tissues
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Affiliation(s)
| | | | - Swati Arya
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
| | - Alan J Stewart
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
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54
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Shabalin IG, Porebski PJ, Minor W. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. CRYSTALLOGR REV 2018; 24:236-262. [PMID: 30416256 DOI: 10.1080/0889311x.2018.1521805] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
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Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
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55
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Coverdale JPC, Katundu KGH, Sobczak AIS, Arya S, Blindauer CA, Stewart AJ. Ischemia-modified albumin: Crosstalk between fatty acid and cobalt binding. Prostaglandins Leukot Essent Fatty Acids 2018; 135:147-157. [PMID: 30103926 PMCID: PMC6109191 DOI: 10.1016/j.plefa.2018.07.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023]
Abstract
Myocardial ischemia is difficult to diagnose effectively with still few well-defined biochemical markers for identification in advance, or in the absence of myocardial necrosis. "Ischemia-modified albumin" (IMA), a form of albumin displaying reduced cobalt-binding affinity, is significantly elevated in ischemic patients, and the albumin cobalt-binding (ACB) assay can measure its level indirectly. Elucidating the molecular mechanism underlying the identity of IMA and the ACB assay hinges on understanding metal-binding properties of albumin. Albumin binds most metal ions and harbours four primary metal binding sites: site A, site B, the N-terminal site (NTS), and the free thiol at Cys34. Previous efforts to clarify the identity of IMA and the causes for its reduced cobalt-binding capacity were focused on the NTS site, but the degree of N-terminal modification could not be correlated to the presence of ischemia. More recent work suggested that Co2+ ions as used in the ACB assay bind preferentially to site B, then to site A, and finally to the NTS. This insight paved the way for a new consistent molecular basis of the ACB assay: albumin is also the main plasma carrier for free fatty acids (FFAs), and binding of a fatty acid to the high-affinity site FA2 results in conformational changes in albumin which prevent metal binding at site A and partially at site B. Thus, this review advances the hypothesis that high IMA levels in myocardial ischemia and many other conditions originate from high plasma FFA levels hampering the binding of Co2+ to sites A and/or B. This is supported by biophysical studies and the co-association of a range of pathological conditions with positive ACB assays and high plasma FFA levels.
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Affiliation(s)
| | - Kondwani G H Katundu
- School of Medicine, University of St Andrews, St Andrews, United Kingdom; College of Medicine, University of Malawi, Blantyre, Malawi
| | - Amélie I S Sobczak
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Swati Arya
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | | | - Alan J Stewart
- School of Medicine, University of St Andrews, St Andrews, United Kingdom.
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56
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Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W. Characterizing metal-binding sites in proteins with X-ray crystallography. Nat Protoc 2018; 13:1062-1090. [PMID: 29674755 PMCID: PMC6235626 DOI: 10.1038/nprot.2018.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.
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Affiliation(s)
- Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Ewa Niedzialkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
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57
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Iqbal S, Qais FA, Alam MM, Naseem I. Effect of glycation on human serum albumin–zinc interaction: a biophysical study. J Biol Inorg Chem 2018; 23:447-458. [DOI: 10.1007/s00775-018-1554-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/12/2018] [Indexed: 12/13/2022]
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58
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Soboleva SE, Guschina TA, Nevinsky GA. Human serum and milk albumins are metal-dependent DNases. IUBMB Life 2018; 70:501-510. [PMID: 29601140 DOI: 10.1002/iub.1741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 02/23/2018] [Accepted: 03/02/2018] [Indexed: 12/11/2022]
Abstract
It is known that that human serum albumin (HSA) and alpha-lactalbumin (LA) possess DNA-binding sites. Electrophoretically homogeneous HSA and LA containing no canonical enzymes were isolated from human sera and milk. Here we have analyzed for the first time the possibility of DNA hydrolysis by these proteins. It was shown that HSA possesses metal-dependent DNase activity, while LA cannot hydrolyze DNA. Several rigid criteria have been applied to show that DNase activity is an intrinsic property of HSA from human sera and milk. HSA preparations were inactive after their dialysis against EDTA or in the presence of EDTA, but were activated after addition of several external metal ions: Mn2+ > Mg2+ > Ca2+ . The best activation of HSA preparations was observed in the presence of two metal ions: Mg2+ +Ca2+ > Mn2+ + Ca2+ ≥ Mn2+ + Mg2+ . In contrast to DNases having only one pH optimum, HSA preparations demonstrated two well-pronounced optima at pH 5.7-5.9 and 6.9-7.1 as well as a weak optimum at pH 8.4-8.6. These results demonstrate the diversity of HSA in the DNA hydrolysis at various pHs and in activation by various metal cofactors. Possible reasons for the diversity of HSA preparations are discussed. © 2018 IUBMB Life, 70(6):501-510, 2018.
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Affiliation(s)
- Svetlana E Soboleva
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, 8 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Tat'yana A Guschina
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, 8 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, 8 Lavrentiev Ave, Novosibirsk, 630090, Russia
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59
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Synthesis and characterization of two new trans palladium (II) complexes containing benzylamine ligand: DNA/BSA interactions, molecular docking and in vitro cytotoxic activity. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.02.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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60
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Wang Y, Huang H, Chen G, Chen H, Xu T, Tang Q, Zhu H, Zhang Q, Zhang P. A novel iridium(iii) complex for sensitive HSA phosphorescence staining in proteome research. Chem Commun (Camb) 2018. [DOI: 10.1039/c8cc01597j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A novel iridium(iii) complex (Ir1) for sensitive HSA staining is reported. It is simpler and less time-consuming than Coomassie blue.
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Affiliation(s)
- Yi Wang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Huaiyi Huang
- Department of Chemistry
- University of Warwick
- Coventry
- UK
| | - Ge Chen
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Haijie Chen
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Tingting Xu
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Qian Tang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Hailiang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210046
- P. R. China
| | - Qianling Zhang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Pingyu Zhang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
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61
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Porebski PJ, Sroka P, Zheng H, Cooper DR, Minor W. Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps. Protein Sci 2017; 27:86-94. [PMID: 28815771 DOI: 10.1002/pro.3272] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 11/07/2022]
Abstract
Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼90% are an interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric. The possible consequences of basing research on suboptimal models make it imperative to inspect the agreement of a model with its experimental evidence. Molstack, a web-based interactive publishing platform for structural data, allows users to present density maps and structural models by displaying a collection of maps and models, including different interpretation of one's own data, re-refinements, and corrections of existing structures. Molstack organizes the sharing and dissemination of these structural models along with their experimental evidence as an interactive session. Molstack was designed with three groups of users in mind; researchers can present the evidence of their interpretation, reviewers and readers can independently judge the experimental evidence of the authors' conclusions, and other researchers can present or even publish their new hypotheses in the context of prior results. The server is available at http://molstack.bioreproducibility.org.
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Affiliation(s)
- Przemyslaw J Porebski
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - Piotr Sroka
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - Heping Zheng
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - David R Cooper
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - Wladek Minor
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
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62
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Similarities and differences of copper and zinc cations binding to biologically relevant peptides studied by vibrational spectroscopies. J Biol Inorg Chem 2017; 22:581-589. [DOI: 10.1007/s00775-017-1449-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/03/2017] [Indexed: 12/26/2022]
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63
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Nemashkalova EL, Permyakov EA, Permyakov SE, Litus EA. Modulation of linoleic acid-binding properties of human serum albumin by divalent metal cations. Biometals 2017; 30:341-353. [PMID: 28303360 DOI: 10.1007/s10534-017-0010-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/10/2017] [Indexed: 01/01/2023]
Abstract
Human serum albumin (HSA) is an abundant multiligand carrier protein, linked to progression of Alzheimer's disease (AD). Blood HSA serves as a depot of amyloid β (Aβ) peptide. Aβ peptide-buffering properties of HSA depend on interaction with its ligands. Some of the ligands, namely, linoleic acid (LA), zinc and copper ions are involved into AD progression. To clarify the interplay between LA and metal ion binding to HSA, the dependence of LA binding to HSA on Zn2+, Cu2+, Mg2+ and Ca2+ levels and structural consequences of these interactions have been explored. Seven LA molecules are bound per HSA molecule in the absence of the metal ions. Zn2+ binding to HSA causes a loss of one bound LA molecule, while the other metals studied exert an opposite effect (1-2 extra LA molecules are bound). In most cases, the observed effects are not related to the metal-induced changes in HSA quaternary structure. However, the Zn2+-induced decline in LA capacity of HSA could be due to accumulation of multimeric HSA forms. Opposite to Ca2+/Mg2+-binding, Zn2+ or Cu2+ association with HSA induces marked changes in its hydrophobic surface. Overall, the divalent metal ions modulate LA capacity and affinity of HSA to a different extent. LA- and Ca2+-binding to HSA synergistically support each other. Zn2+ and Cu2+ induce more pronounced changes in hydrophobic surface and quaternary structure of HSA and its LA capacity. A misbalanced metabolism of these ions in AD could modify interactions of HSA with LA, other fatty acids and hydrophobic substances, associated with AD.
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Affiliation(s)
- Ekaterina L Nemashkalova
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya Str., 7, Pushchino, Moscow region, Russia, 142290
| | - Eugene A Permyakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya Str., 7, Pushchino, Moscow region, Russia, 142290.,Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Science av., 3, Pushchino, Moscow region, Russia, 142290
| | - Sergei E Permyakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya Str., 7, Pushchino, Moscow region, Russia, 142290.,Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Science av., 3, Pushchino, Moscow region, Russia, 142290
| | - Ekaterina A Litus
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya Str., 7, Pushchino, Moscow region, Russia, 142290.
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64
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Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W. CheckMyMetal: a macromolecular metal-binding validation tool. Acta Crystallogr D Struct Biol 2017; 73:223-233. [PMID: 28291757 PMCID: PMC5349434 DOI: 10.1107/s2059798317001061] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/21/2017] [Indexed: 12/19/2022] Open
Abstract
Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.
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Affiliation(s)
- Heping Zheng
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - David R. Cooper
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Przemyslaw J. Porebski
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ivan G. Shabalin
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Katarzyna B. Handing
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Wladek Minor
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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