Article
Chemistry, Multidisciplinary
Selina L. S. Storm, Danny Axford, Robin L. Owen
Summary: A new study shows that using a high-energy X-ray data collection system can reduce the number of crystals needed, increase diffraction efficiency per unit dose, and provide more information. These findings suggest a brighter future for synchrotron-based macromolecular crystallography with high-energy X-rays.
Article
Chemistry, Multidisciplinary
Jangwoo Kim, Ki Hyun Nam
Summary: When X-rays pass through a material, heat is generated and transferred, which can affect the temperature of the sample and the experimental environment in serial crystallography experiments. This study investigated radiation damage and measured the level of heating near the X-ray interaction point. The findings provide valuable information for obtaining more accurate experimental parameters.
APPLIED SCIENCES-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Stavros Azinas, Marta Carroni
Summary: Cryo-EM is a major tool for determining protein structures, while AlphaFold2 enables high-confidence atomic models for polypeptide chains. Cryo-EM retains unique characteristics for determining structures of macromolecular complexes, allowing for near-atomic structures and exploring conformational panoramas. It also has the potential to develop a structural proteomic approach using ex vivo specimens.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sebastiaan Werten, Paul Waack, Gottfried J. Palm, Marie-Joelle Virolle, Winfried Hinrichs
Summary: TetR/AcrR-like transcription regulators enable bacteria to sense and adapt to chemical compounds. This study characterizes SCO3201, an atypical member of the TetR/AcrR family. SCO3201 strongly represses antibiotic production and morphological development in Streptomyces coelicolor under conditions of overexpression. The crystal structures reveal that in the absence of a ligand, SCO3201 is unable to span the distance between the two half-sites of its operator. Interaction with the ligand induces a major structural rearrangement, increasing the interdomain distance and potentially facilitating dimer-operator interaction. This 'reverse' induction mechanism expands the regulatory repertoire of the TetR/AcrR family and explains SCO3201's impact on antibiotic production and sporulation in S. coelicolor.
Article
Biochemistry & Molecular Biology
Nadine Werner, Sebastiaan Werten, Jens Hoppen, Gottfried J. Palm, Michael Goettfert, Winfried Hinrichs
Summary: Bradyrhizobium diazoefficiens, a bacterial symbiont of leguminous plants such as soybean, has a regulator protein FrrA that responds to isoflavonoids. The crystal structures of FrrA show a TetR-like fold with a flexible DNA-binding domain, and binding with genistein or naringenin does not induce conformational changes. Small-angle X-ray scattering experiments confirm the flexibility of the DNA-binding domain and lack of structural changes upon ligand binding.
Article
Materials Science, Characterization & Testing
Yang Liu, Jingyuan Ma, Weihua Liu, Fenggang Bian, Xiuhong Li, Zhongfeng Tang, Yuying Huang, Feng Tian
Summary: Synchrotron radiation X-ray was used as both the irradiation source and testing tool for PVDF membranes. The structural evolution of the PVDF membranes under irradiation was analyzed using in-situ and ex-situ characterization methods. The study demonstrated that the synchrotron radiation X-ray destroyed the long periodic structure and crystalline region of the PVDF membranes, leading to a decline in crystallinity.
Review
Crystallography
Katarzyna Kurpiewska, Joanna Slawek, Agnieszka Klonecka, Maciej Kozak
Summary: Since its introduction in the early 1970s, high pressure crystallography (HPX) has shown great potential for the investigation of different types of matter. This emerging technique has been rapidly implemented, making it available to biologists, and there is immense potential for utilizing this technique in biological systems in the future. The increase in the number of crystal structures of different macromolecules determined under high pressure over the last five decades can be ascribed mainly to the emergence of high-pressure cells with very large, open angles, and the advent of third generation synchrotron sources.
Article
Instruments & Instrumentation
Elspeth F. Garman, Martin Weik
Summary: The papers in this special issue cover various analyses on radiation damage effects in biological samples during structural analysis, with a focus on different imaging techniques such as X-ray diffraction and small-angle X-ray scattering. The studies also explore the efficacy of radical scavengers and the use of X-rays to induce OH radicals in water radiolysis for X-ray footprinting. Additionally, the issue includes papers on XFEL science and methods for improving dose efficiency in electron modalities.
JOURNAL OF SYNCHROTRON RADIATION
(2021)
Article
Multidisciplinary Sciences
Tai-Sing Wu, Sheng-Fu Chen, Shih-Chang Weng, Yun-Liang Soo
Summary: In this study, an unconventional effect of synchrotron X-ray irradiation on thermally annealed (Y, Co)-codoped CeO2 nanocrystal samples was reported. The experimental data indicated that instead of breaking the Co-O bonds, the X-ray irradiation formed new Co-O bonds by capturing escaping oxygen atoms from the X-ray-broken Ce-O bonds. This effect caused a transition of Co dopant atoms from the energetically-favored Co-O4 structure to the metastable Co-O6 environment, resulting in a fine-tuning of the band gap of the material.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Chinmayee Dash, Ramyaranjan Das, Deepak K. Sahu, Divyansh Upreti, T. Umasankar Patro, Dillip K. Bisoyi
Summary: The present study aims to establish a correlation between macromolecular parameters obtained from small angle X-ray scattering (SAXS) analysis of pretreated sunn hemp fibers and the dielectric and mechanical properties of their composites. Different pretreatment methods, including dewaxing, alkalization, and microwave irradiation, were used to modify the structure of the fibers, which in turn influenced the macromolecular parameters. The modified fibers showed improved mechanical and electrical properties in the reinforced composites.
Review
Multidisciplinary Sciences
Gisela Branden, Richard Neutze
Summary: Conformational changes within biological macromolecules regulate chemical reactions in living cells. Time-resolved crystallography can reveal these changes in detail, while serial crystallography approaches are now being routinely used for studying macromolecules. Recent progress includes visualizing ultrafast and slower time-scale structural changes in proteins like bacteriorhodopsin and photosystem II.
Review
Biophysics
Marcus Fischer
Summary: This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at room temperature, aiming to demystify preconceived impracticalities that freeze progress of routine room temperature data collection at synchrotron sources. Examples are provided as conceptual and experimental templates, illustrating the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics offers opportunities to advance basic and biomedical research.
QUARTERLY REVIEWS OF BIOPHYSICS
(2021)
Article
Multidisciplinary Sciences
Mehmet Gul, Esra Ayan, Ebru Destan, J. Austin Johnson, Alaleh Shafiei, Abdullah Kepceoglu, Merve Yilmaz, Fatma Betuel Ertem, Ilkin Yapici, Bilge Tosun, Niluefer Baldir, Nurettin Tokay, Zelis Nergiz, Gozde Karakadioglu, Seyide Seda Paydos, Cahine Kulakman, Cengiz Kaan Ferah, Omur Guven, Necati Atalay, Enver Kamil Akcan, Haluk Cetinok, Nazli Eylul Arslan, Kardelen Sabanoglu, Bengisu Asci, Serra Tavli, Helin Gumusboga, Sevde Altuntas, Masami Otsuka, Mikako Fujita, Saban Tekin, Halilibrahim Ciftci, Serdar Durdagi, Ezgi Karaca, Burcu Kaplan Turkoz, Burak Veli Kabasakal, Ahmet Kati, Hasan DeMirci
Summary: High-resolution biomacromolecular structure determination is crucial for understanding protein function and dynamics. Serial crystallography has limitations in terms of sample volume requirements and access to X-ray beamtime. To overcome these limitations, a plate-reader module adapted for a 72-well Terasaki plate is introduced for biomacromolecule structure determination using a home X-ray source. The first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight) provides valuable information about the structural dynamics of the lysozyme. Turkish DeLight offers robust and rapid ambient temperature biomacromolecular structure determination with minimal radiation damage.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Catia Barria, Diogo Athayde, Guillem Hernandez, Leonor Fonseca, Jorge Casinhas, Tiago N. Cordeiro, Margarida Archer, Cecilia M. Arraiano, Jose A. Brito, Rute G. Matos
Summary: Ribonucleases play a crucial role in RNA regulation by processing, degrading, and quality controlling cellular transcripts. Campylobacter jejuni, the main cause of human gastroenteritis, relies on the exoribonuclease PNPase (CjPNP) for low-temperature survival, virulence factor synthesis, and swimming, cell adhesion/invasion, and chick colonization abilities. The crystallographic structure of CjPNP, along with SAXS analysis, confirms its trimeric arrangement and provides insight into domain arrangement and flexibility. Mutations in highly conserved residues reveal unexpected RNA degradation activity even under conditions favoring polymerization. These findings have significant implications for the development of strategies to combat C. jejuni infections.
Article
Biochemistry & Molecular Biology
Franz Waibl, Klaus R. Liedl, Bernhard Rupp
Summary: Many macromolecular structure models in the PDB contain biologically relevant small molecule ligands with incorrect cis-trans stereochemistry. The errors may stem from deficiencies in stereochemical restraint files or negligence during model building. Awareness, identification, and correction of these errors are crucial to prevent inadvertent use of incorrect models.
Article
Biochemistry & Molecular Biology
Joshua L. Dickerson, Elspeth F. Garman
Summary: Microbeams and microcrystals are increasingly used in macromolecular crystallography experiments, but radiation damage remains a major concern. Accurate dose calculations are essential for optimizing experimental outcomes, and the RADDOSE-3D program helps estimate absorbed doses during MX data collection. Monte Carlo simulations show the importance of surrounding material composition on radiation damage and provide more accurate dose estimates.
Review
Biochemistry & Molecular Biology
Harshwardhan Poddar, Derren J. Heyes, Giorgio Schiro, Martin Weik, David Leys, Nigel S. Scrutton
Summary: Dynamic changes in protein structures are crucial for protein function and can be investigated with unprecedented temporal and spatial resolution using X-ray free electron lasers. Light-activated proteins are attractive targets for time-resolved structural studies, as they allow for visualization of early chemical changes and global structural changes.
Article
Chemistry, Physical
Nathalie K. Fernando, Andrew B. Cairns, Claire A. Murray, Amber L. Thompson, Joshua L. Dickerson, Elspeth F. Garman, Nayera Ahmed, Laura E. Ratcliff, Anna Regoutz
Summary: This paper presents systematic studies of X-ray-matter interactions on two industrially important catalysts through XRD and XPS experiments, revealing changes in structure and electronic structure due to X-ray exposure and allowing for comparisons of stability between the catalysts. Radiation dose was estimated using RADDOSE-3D software and applied to experiments, with further insights drawn from DFT. These methods have great potential for application to other small molecular systems of scientific or industrial relevance.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Biochemistry & Molecular Biology
Matthew Herdman, Andriko von Kugelgen, Danguole Kureisaite-Ciziene, Ramona Duman, Kamel El Omari, Elspeth F. Garman, Andreas Kjaer, Dimitrios Kolokouris, Jan Lowe, Armin Wagner, Phillip J. Stansfeld, Tanmay A. M. Bharat
Summary: In this study, the role of metal ions in the formation of Caulobacter crescentus S-layer was investigated. It was found that calcium ions facilitate S-layer lattice formation and cell-surface binding, and that bound metal ions are crucial for the S-layer lattice. The positions of metal ions in the S-layer were also mapped using advanced imaging techniques. These findings contribute to the understanding of S-layer formation and have implications for synthetic biology.
Editorial Material
Chemistry, Multidisciplinary
Edward N. Baker, Charles S. Bond, Elspeth F. Garman, Janet Newman, Randy J. Read, Mark J. van Raaij
Article
Multidisciplinary Sciences
Sarah Kono, Aafke van den Berg, Marco Simonetta, Ann Mukhortava, Elspeth F. Garman, Ingrid Tessmer
Summary: AGT is an important DNA repair protein that repairs highly mutagenic and cytotoxic alkylguanine lesions. Studies have revealed the interactions of AGT with alkyl lesions and its role in DNA repair mechanism. Surprisingly, AGT clusters do not enhance DNA translocation speed, suggesting a different role in AGT function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Kathryn L. Shelley, Elspeth F. Garman
Summary: This study introduces a new metric called B-net, which detects radiation damage in protein crystal structures. The metric provides a single value that summarizes the extent of damage and highlights features that are often overlooked by traditional statistics.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Kyprianos Hadjidemetriou, Nicolas Coquelle, Thomas R. M. Barends, Elke De Zitter, Ilme Schlichting, Jacques-Philippe Colletier, Martin Weik
Summary: By combining various techniques, researchers have elucidated the catalytic mechanism of fatty-acid photodecarboxylase, which converts free fatty acids into hydrocarbon compounds. The study faced challenges and further experiments are needed to identify the photoproducts and their movements during the catalytic cycle.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Martin Weik, Tatiana Domratcheva
Summary: This review highlights recent advances in studying structural changes of light-sensitive proteins using time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Elspeth F. Garman, Randy J. Read, Charles S. Bond
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Biographical-Item
Biochemical Research Methods
Elspeth F. Garman
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Editorial Material
Biochemical Research Methods
Randy J. Read, Edward N. Baker, Charles S. Bond, Elspeth F. Garman, Mark J. van Raaij
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Editorial Material
Biochemical Research Methods
Randy J. Read, Edward N. Baker, Charles S. Bond, Elspeth F. Garman, Mark J. van Raaij
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Editorial Material
Chemistry, Multidisciplinary
Randy J. Read, Edward N. Baker, Charles S. Bond, Elspeth F. Garman, Mark J. van Raaij
Article
Chemistry, Physical
Nathalie K. Fernando, Hanna L. B. Bostrom, Claire A. Murray, Robin L. Owen, Amber L. Thompson, Joshua L. Dickerson, Elspeth F. Garman, Andrew B. Cairns, Anna Regoutz
Summary: X-ray characterisation methods play a crucial role in materials research but face challenges of radiation-induced sample change and damage. This study investigates the structural stability of [Rh (COD) Cl] (2) using powder X-ray diffraction synchrotron beamlines at various photon energies. The absorbed X-ray dose and radiation hardness of the catalyst are discussed, emphasizing the importance of considering X-ray parameters before conducting diffraction on radiation-sensitive organometallic materials.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)