1
|
Neuhaus D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:62-105. [PMID: 36113918 PMCID: PMC7614390 DOI: 10.1016/j.pnmrs.2022.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/07/2023]
Abstract
Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.
Collapse
Affiliation(s)
- David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
2
|
Ensina A, Carvalho PM, Machado J, Carvalho ML, Casal D, Pais D, Santos JP, Dias AA, Pessanha S. Analysis of human tissues using Energy Dispersive X Ray Fluorescence - Dark matrix determination for the application to cancer research. J Trace Elem Med Biol 2021; 68:126837. [PMID: 34385034 DOI: 10.1016/j.jtemb.2021.126837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/24/2021] [Accepted: 08/05/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND X ray Fluorescence has been essayed as a suitable technique for the elemental quantification of trace element in human tissues, namely comparison of normal and cancerous tissue. However, accurate results depend on a robust quantification approach, namely correct evaluation of the samples' dark matrix. METHODS In order to determine the most suitable dark matrix composition for the quantification of such samples using the Fundamental Parameter approach, we have measured several Certified Reference Materials and essayed different dark matrix compositions to achieve the most accurate results. The resulting dark matrix was then applied to normal and tumor ovarian and prostate tissue samples, and the obtained results were compared with the ones obtained with a comparative method using external standard calibration curves. RESULTS Using a dark matrix composed of 10 % - H, 22 % - C, 3 % - N and 60 % - O yielded the best compromise in accuracy for the light and heavy elements. For the reduced sample size and conditions of this study, for both organs, the concentrations of transition metals decrease in tumor tissues, while the concentration of lighter elements, P and Cl, increases. On the other hand, there are elements that showed different behavior between the two types of tissue, namely Zn and S, that increase in prostate tumor tissue and decrease in ovarian tissue. CONCLUSION An increase in precision was one of the improvements found with the newly developed method, as the FP-approach contemplates matrix effects and the influence of other elements in the analytes' quantification. Additionally, the determined dark matrix can be employed in any tissue analysis application by means of EDXRF.
Collapse
Affiliation(s)
- Ana Ensina
- Physics Department, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal
| | - Patrícia M Carvalho
- Physics Department, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal; LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal
| | - Jorge Machado
- Physics Department, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal; LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal
| | - Maria Luísa Carvalho
- Physics Department, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal; LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal
| | - Diogo Casal
- LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal; Anatomy Department, NOVA Medical School, NOVA University Lisbon, 1169-056, Lisbon, Portugal
| | - Diogo Pais
- LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal; Anatomy Department, NOVA Medical School, NOVA University Lisbon, 1169-056, Lisbon, Portugal
| | - José Paulo Santos
- Physics Department, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal; LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal
| | - António A Dias
- Physics Department, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal; LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal
| | - Sofia Pessanha
- Physics Department, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal; LIBPhys - Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics, Portugal.
| |
Collapse
|
3
|
Valles M, Kamaruddin AF, Wong LS, Blanford CF. Inhibition in multicopper oxidases: a critical review. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00724b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This review critiques the literature on inhibition of O2-reduction catalysis in multicopper oxidases like laccase and bilirubin oxidase and provide recommendations for best practice when carrying out experiments and interpreting published data.
Collapse
Affiliation(s)
- Morgane Valles
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
- Department of Chemistry
| | - Amirah F. Kamaruddin
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
- Department of Materials
| | - Lu Shin Wong
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
- Department of Chemistry
| | - Christopher F. Blanford
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
- Department of Materials
| |
Collapse
|
4
|
Grime GW, Zeldin OB, Snell ME, Lowe ED, Hunt JF, Montelione GT, Tong L, Snell EH, Garman EF. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application. J Am Chem Soc 2019; 142:185-197. [PMID: 31794207 DOI: 10.1021/jacs.9b09186] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Metalloproteins comprise over one-third of proteins, with approximately half of all enzymes requiring metal to function. Accurate identification of these metal atoms and their environment is a prerequisite to understanding biological mechanism. Using ion beam analysis through particle induced X-ray emission (PIXE), we have quantitatively identified the metal atoms in 30 previously structurally characterized proteins using minimal sample volume and a high-throughput approach. Over half of these metals had been misidentified in the deposited structural models. Some of the PIXE detected metals not seen in the models were explainable as artifacts from promiscuous crystallization reagents. For others, using the correct metal improved the structural models. For multinuclear sites, anomalous diffraction signals enabled the positioning of the correct metals to reveal previously obscured biological information. PIXE is insensitive to the chemical environment, but coupled with experimental diffraction data deposited alongside the structural model it enables validation and potential remediation of metalloprotein models, improving structural and, more importantly, mechanistic knowledge.
Collapse
Affiliation(s)
- Geoffrey W Grime
- Ion Beam Centre, Advanced Technology Institute , University of Surrey , Guildford, Surrey GU2 7XH , United Kingdom
| | - Oliver B Zeldin
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| | - Mary E Snell
- Hauptman-Woodward Medical Research Institute , 700 Ellicott St. , Buffalo , New York 14203 , United States
| | - Edward D Lowe
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| | - John F Hunt
- Department of Biological Sciences , Columbia University , New York , New York 10027 , United States
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences , Rensselaer Polytechnic Institute , Troy New York 12180 United States
| | - Liang Tong
- Department of Biological Sciences , Columbia University , New York , New York 10027 , United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute , 700 Ellicott St. , Buffalo , New York 14203 , United States.,Materials Design and Innovation , SUNY Buffalo , 700 Ellicott St. , Buffalo , New York 14203 , United States
| | - Elspeth F Garman
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| |
Collapse
|