1
|
Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
Collapse
Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
2
|
Garman EF, Weik M. Radiation damage to biological macromolecules∗. Curr Opin Struct Biol 2023; 82:102662. [PMID: 37573816 DOI: 10.1016/j.sbi.2023.102662] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.
Collapse
Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
| |
Collapse
|
3
|
Kościuszko M, Buczyńska A, Krętowski AJ, Popławska-Kita A. Could Oxidative Stress Play a Role in the Development and Clinical Management of Differentiated Thyroid Cancer? Cancers (Basel) 2023; 15:3182. [PMID: 37370792 DOI: 10.3390/cancers15123182] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Increased oxidative stress (OS) has been implicated as a relevant risk factor for cancer progression. Furthermore, patients diagnosed with differentiated thyroid cancer (DTC) have been characterized by an increased OS status. Therefore, assessing OS status could potentially be considered a useful tool in DTC clinical management. This measurement could be particularly valuable in personalizing treatment protocols and determining new potential medical targets to improve commonly used therapies. A literature review was conducted to gather new information on DTC clinical management, with a particular focus on evaluating the clinical utility of OS. These meta-analyses concentrate on novel approaches that employ the measurement of oxidative-antioxidant status, which could represent the most promising area for implementing clinical management.
Collapse
Affiliation(s)
- Maria Kościuszko
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-274 Bialystok, Poland
| | - Angelika Buczyńska
- Clinical Research Center, Medical University of Bialystok, 15-274 Bialystok, Poland
| | - Adam Jacek Krętowski
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-274 Bialystok, Poland
- Clinical Research Center, Medical University of Bialystok, 15-274 Bialystok, Poland
| | - Anna Popławska-Kita
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-274 Bialystok, Poland
| |
Collapse
|
4
|
Sauer K, Zizak I, Forien JB, Rack A, Scoppola E, Zaslansky P. Primary radiation damage in bone evolves via collagen destruction by photoelectrons and secondary emission self-absorption. Nat Commun 2022; 13:7829. [PMID: 36539409 PMCID: PMC9768145 DOI: 10.1038/s41467-022-34247-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
X-rays are invaluable for imaging and sterilization of bones, yet the resulting ionization and primary radiation damage mechanisms are poorly understood. Here we monitor in-situ collagen backbone degradation in dry bones using second-harmonic-generation and X-ray diffraction. Collagen breaks down by cascades of photon-electron excitations, enhanced by the presence of mineral nanoparticles. We observe protein disintegration with increasing exposure, detected as residual strain relaxation in pre-stressed apatite nanocrystals. Damage rapidly grows from the onset of irradiation, suggesting that there is no minimal 'safe' dose that bone collagen can sustain. Ionization of calcium and phosphorous in the nanocrystals yields fluorescence and high energy electrons giving rise to structural damage that spreads beyond regions directly illuminated by the incident radiation. Our findings highlight photoelectrons as major agents of damage to bone collagen with implications to all situations where bones are irradiated by hard X-rays and in particular for small-beam mineralized collagen fiber investigations.
Collapse
Affiliation(s)
- Katrein Sauer
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, Department for Operative, Preventive and Pediatric Dentistry, Aßmannshauser Straße 4-6, 14197 Berlin, Germany
| | - Ivo Zizak
- grid.424048.e0000 0001 1090 3682Helmholtz-Zentrum Berlin, Department for Structure and Dynamics of Energy Materials (SE-ASD), Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Jean-Baptiste Forien
- grid.250008.f0000 0001 2160 9702Lawrence Livermore National Laboratory, Materials Science Division, 7000 East Ave, Livermore, CA 94550 USA
| | - Alexander Rack
- grid.5398.70000 0004 0641 6373ESRF - The European Synchrotron, Structure of Materials Group - ID19, CS 40220, F-38043, Grenoble, Cedex 9 France
| | - Ernesto Scoppola
- grid.461615.10000 0000 8925 2562Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam, Brandenburg Germany
| | - Paul Zaslansky
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, Department for Operative, Preventive and Pediatric Dentistry, Aßmannshauser Straße 4-6, 14197 Berlin, Germany
| |
Collapse
|
5
|
Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
| | | |
Collapse
|
6
|
Fan Y, Jia X, Xie T, Zhu L, He F. Radiosensitizing effects of c‑myc gene knockdown‑induced G2/M phase arrest by intrinsic stimuli via the mitochondrial signaling pathway. Oncol Rep 2020; 44:2669-2677. [PMID: 33125136 PMCID: PMC7640369 DOI: 10.3892/or.2020.7806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/18/2020] [Indexed: 11/06/2022] Open
Abstract
Osteosarcoma is the most common primary malignant bone tumor in children and adolescents and its long‑term survival rate has stagnated in the past decades. Previous studies have shown that tumors in the G2/M phase are more sensitive to radiotherapy. The proto‑oncogene c‑myc is a transformed member of the myc family and c‑myc‑interacting zinc finger protein‑1 (Miz‑1) is a poly‑Cys2His2 zinc finger (ZF) activator of cell cycle regulator genes, such as the cyclin‑dependent kinase inhibitor p21. C‑myc can repress the expression of p21 by binding to Miz‑1 and abolishing the interaction between Miz‑1 and its co‑activators, which induces G2/M phase arrest. Therefore, the present study investigated the radiosensitizing effects of the c‑myc gene and the sensitizing apoptosis pathway, aiming to identify a more effective combination radiotherapy treatment for osteosarcoma. The present study demonstrated that the c‑myc gene was overexpressed in osteosarcoma cells compared to osteoblasts. Following inhibition of c‑myc gene expression in osteosarcoma cells, tumor proliferation was significantly hindered after inducing G2/M phase arrest via regulating G2/M phase‑associated proteins. Additionally, it was revealed that inhibiting c‑myc gene expression combined with radiotherapy could significantly increase the apoptosis rate of osteosarcoma cells via the mitochondrial signaling pathway. In summary, the present study verified the radiosensitizing effects of c‑myc gene knockdown‑induced G2/M phase arrest, which was achieved by intrinsic stimuli through the mitochondrial signaling pathway.
Collapse
Affiliation(s)
- Yunpeng Fan
- The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaofeng Jia
- College of Life Science, China Jiliang University, Hangzhou, Zhejiang 310018, P.R. China
| | - Tao Xie
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Liulong Zhu
- The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Fan He
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| |
Collapse
|
7
|
Garman EF, Weik M. X-ray radiation damage to biological samples: recent progress. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:907-911. [PMID: 31274412 DOI: 10.1107/s1600577519009408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 05/20/2023]
Abstract
With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below.
Collapse
Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| |
Collapse
|