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
Chemistry, Multidisciplinary
Jun Zhang, Haoke Zhang, Junkai Liu, Jacky Wing Yip Lam, Ben Zhong Tang
Summary: This study utilized variable-temperature XRD characterization to investigate the static conformational change and dynamic trajectory of tetraphenylethylene in the solid state, shedding light on the aggregation-induced emission effect. The analysis revealed five types of molecular motions and provided insights into the AIE mechanism.
MATERIALS CHEMISTRY FRONTIERS
(2021)
Article
Biochemistry & Molecular Biology
Camila Campos-Escamilla, Dritan Siliqi, Luis A. Gonzalez-Ramirez, Carmen Lopez-Sanchez, Jose Antonio Gavira, Abel Moreno
Summary: The conformational changes of iron-free and iron-loaded transferrin at different pH values were studied using Macromolecular X-ray Crystallography and Small Angle X-ray Scattering techniques. While apo-Tf remained mostly globular in solution, holo-Tf showed a more elongated and flexible shape with co-existing closed, partially open, and open conformations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Nanoscience & Nanotechnology
Martina F. Ober, Adrian Mueller-Deku, Anna Baptist, Benjamin Ajanovic, Heinz Amenitsch, Oliver Thorn-Seshold, Bert Nickel
Summary: This study measures the thickness of photoswitchable lipid membranes using small-angle X-ray scattering and finds an unexpected dependency of photoswitching ratio on the aqueous phase composition. Additionally, it demonstrates that soft X-rays can quantitatively control the membrane while high energy X-rays do not affect the state of the photoswitches.
Article
Chemistry, Multidisciplinary
Daniel Bindl, Pradeep K. Mandal, Ivan Huc
Summary: This study synthesized a series of aromatic oligoamide foldamer sequences containing different proportions of three delta-amino acids. It was found that a canonical aromatic helix fold prevailed in almost all cases, and the helix stability depended critically on the ratio between rigid and flexible units. A fine-tuning of helix characteristics in aromatic delta-peptidic foldamers can be achieved by combining different yet compatible delta-amino acids.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
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
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.
Review
Chemistry, Multidisciplinary
Ha L. Nguyen
Summary: Reticular chemistry of covalent organic frameworks (COFs) focuses on linking discrete organic building units into extended structures through strong covalent bonds. Over the past decade, there has been rapid development in COF chemistry in terms of structural diversity and applications. Understanding the concept of reticular chemistry is essential for researching COFs and correlating their geometric structures and practical applications.
Review
Biochemistry & Molecular Biology
Solomon Tsegaye, Gobena Dedefo, Mohammed Mehdi
Summary: The main goal of structural biology is to model proteins and other biological macromolecules, linking structural information to function and dynamics. Understanding the conformational dynamics of protein molecules and nucleic acids is crucial for their biological functions. Various biophysical techniques such as X-ray crystallography, NMR, and cryo-EM are used to solve atomic-resolution structural information, providing insights into the mechanisms of action of biological macromolecules.
BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Tom Pan, Shikai Jin, Mitchell D. Miller, Anastasios Kyrillidis, George N. Phillips
Summary: This paper develops an initial pathway to a deep learning neural network approach for solving the phase problem in protein crystallography. It uses a synthetic dataset of small fragments derived from a well curated subset of solved structures in the Protein Data Bank (PDB), and produces electron density estimates of simple artificial systems directly from corresponding Patterson maps using a convolutional neural network architecture as a proof of concept.
Article
Physics, Applied
Jong Woo Kim, Mathew J. Cherukara, Ashish Tripathi, Zhang Jiang, Jin Wang
Summary: Coherent surface scattering imaging requires a mathematical conversion to visualize specimen structures, which can now be predicted using a deep learning neural network model to instantly obtain results from scattering patterns. This is highly beneficial for both experimental effectiveness and data analysis.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Mehran Amiri, Nicolas P. Martin, Ching-Lei Feng, Jacob Kreager Lovio, May Nyman
Summary: Polyoxometalates are molecular metal oxides that can be isolated without capping ligands, showing high negative charge. Carbonate can reassemble with highly reactive decaniobate to form new structures with strong interactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Cen Chen, Ziyuan Fang, Zhen Huang
Summary: Crystallization phasing and obtaining high-quality crystals are major challenges for X-ray crystallographic analysis of nucleic acids. In this study, the authors addressed these challenges by incorporating selenium atoms into DNA duplexes, which resulted in larger and higher quality crystals compared to standard DNA crystals. These findings provide a simple strategy to overcome crystallization challenges in nucleic acid crystallography.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Biochemistry & Molecular Biology
Jaroslaw Blaszczyk, Bogdan Bujnicki, Patrycja Pokora-Sobczak, Grazyna Mielniczak, Leslaw Sieron, Piotr Kielbasinski, Jozef Drabowicz
Summary: The aim of this research is to provide a detailed description of the synthesis of compounds containing a stereogenic heteroatom and to determine their structures through X-ray analysis. These compounds are potential candidates for use as chiral solvating agents, precursors of chiral ionic liquids, or ligands in organometallic catalysts.
Editorial Material
Plant Sciences
Veronique Hugouvieux, Chloe Zubieta
JOURNAL OF EXPERIMENTAL BOTANY
(2018)
Article
Biochemistry & Molecular Biology
Veronique Hugouvieux, Catarina S. Silva, Agnes Jourdain, Arnaud Stigliani, Quentin Charras, Vanessa Conn, Simon J. Conn, Cristel C. Carles, Francois Parcy, Chloe Zubieta
NUCLEIC ACIDS RESEARCH
(2018)
Article
Multidisciplinary Sciences
Emilie Vassal-Stermann, Manon Mottet, Corinne Ducournau, Frederic Iseni, Charles Vragniau, Hongjie Wang, Chloe Zubieta, Andre Lieber, Pascal Fender
SCIENTIFIC REPORTS
(2018)
Review
Biochemistry & Molecular Biology
Xuelei Lai, Leonie Verhage, Veronique Hugouvieux, Chloe Zubieta
Article
Chemistry, Multidisciplinary
R. Mizuta, J. M. Devos, J. Webster, W. L. Ling, T. Narayanan, A. Round, D. Munnur, E. Mossou, A. A. Farahat, D. W. Boykin, W. D. Wilson, S. Neidle, R. Schweins, P. Rannou, M. Haertlein, V. T. Forsyth, E. P. Mitchell
Article
Multidisciplinary Sciences
Rachel Fellows, Christopher M. Russo, Catarina S. Silva, Soon Goo Lee, Joseph M. Jez, John D. Chisholm, Chloe Zubieta, Max H. Nanao
SCIENTIFIC REPORTS
(2018)
Review
Plant Sciences
Xuelei Lai, Hicham Chahtane, Raquel Martin-Arevalillo, Chloe Zubieta, Francois Parcy
CURRENT OPINION IN PLANT BIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Enrico Junior Baldassarri, Maria Grazia Ortore, Francesco Spinozzi, Adam Round, Claudio Ferrero, Paolo Mariani
Article
Biochemistry & Molecular Biology
Xuelei Lai, Arnaud Stigliani, Jeremy Lucas, Veronique Hugouvieux, Francois Parcy, Chloe Zubieta
NUCLEIC ACIDS RESEARCH
(2020)
Article
Plant Sciences
Vitor da Silveira Falavigna, Edouard Severing, Xuelei Lai, Joan Estevan, Isabelle Farrera, Veronique Hugouvieux, Luis Fernando Revers, Chloe Zubieta, George Coupland, Evelyne Costes, Fernando Andres
Summary: A group of MADS transcription factors called DORMANCY-ASSOCIATED MADS-BOX (DAM) are believed to control temperature-mediated bud dormancy, forming complexes with MdSVPa essential for DNA binding. MdSVPa sequentially forms complexes with dominant MADS TFs at each dormancy phase, altering DNA binding specificity to regulate target gene transcription.
Editorial Material
Biochemistry & Molecular Biology
Stephanie Hutin, Chloe Zubieta
Article
Multidisciplinary Sciences
Tatiana N. Murugova, Oleksandr I. Ivankov, Yury L. Ryzhykau, Dmytro V. Soloviov, Kirill V. Kovalev, Daria V. Skachkova, Adam Round, Christian Baeken, Andrii V. Ishchenko, Oleksandr A. Volkov, Andrey V. Rogachev, Alexey V. Vlasov, Alexander I. Kuklin, Valentin I. Gordeliy
Summary: Despite remarkable progress in LCP and 'bicelle' crystallization, the lack of structural information remains a bottleneck in membrane protein research. This study uses small-angle scattering to investigate the evolution of the bicelle crystallization matrix during MP crystal growth and reveals the mechanisms of bicelle MP crystallization, providing support for rational design of crystallization.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Jaydeep Patel, Adam Round, Johan Bielecki, Katerina Doerner, Henry Kirkwood, Romain Letrun, Joachim Schulz, Marcin Sikorski, Mohammad Vakili, Raphael de Wijn, Andrew Peele, Adrian P. Mancuso, Brian Abbey
Summary: This article explores the application of liquid sample delivery systems in XFEL experiments and proposes an algorithm that uses machine vision to automatically align the X-ray beam and liquid jet. The performance of the algorithm is evaluated by comparing it with manual analysis, and it achieves a success rate of 0.98 in identifying hits among four different nozzle designs.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2022)
Article
Chemistry, Multidisciplinary
Jay Tinklepaugh, Britannia M. Smith, Etta Hanlon, Chloe Zubieta, Fadi Bou-Abdallah, Robert P. Doyle
Article
Plant Sciences
Daphne Ezer, Jae-Hoon Jung, Hui Lan, Surojit Biswas, Laura Gregoire, Mathew S. Box, Varodom Charoensawan, Sandra Cortijo, Xuelei Lai, Dorothee Stockle, Chloe Zubieta, Katja E. Jaeger, Philip A. Wigge