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
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
Multidisciplinary Sciences
Akimitsu Higuchi, Wataru Shihoya, Masae Konno, Tatsuya Ikuta, Hideki Kandori, Keiichi Inoue, Osamu Nureki
Summary: SzRs, a newly identified rhodopsin family in Asgard archaea, exhibit unique kinetic behaviors in inward H+ release compared to other H+ pumps. The crystal structure of SzR AM_5_00977 revealed that key residues and structural features are different from other microbial rhodopsins, suggesting a distinct mechanism for inward H+ release.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Hai Li, Chia-Ying Huang, Elena G. Govorunova, Oleg A. Sineshchekov, Adrian Yi, Kenneth J. Rothschild, Meitian Wang, Lei Zheng, John L. Spudich
Summary: The crystal structure of bromide-bound GtACR1 reveals structural changes that relax the constrictions of the channel and involve a novel salt-bridge switch mechanism. These findings suggest that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark, facilitating channel opening.
Article
Biochemistry & Molecular Biology
Sunbin Deng, Jiaxi Cai, Stephen C. Harrison, Huilin Zhou, Stephen M. Hinshaw
Summary: Successful mitosis relies on the correct attachment of chromosomes to microtubules. The kinetochore plays a crucial role in this process by recognizing specific chromatin and ensuring the formation of only one kinetochore per chromatid at the correct location. The crystal structure of the Cse4 peptide bound to the inner kinetochore Okp1-Ame1 complex provides insights into centromere recognition and the organization of the inner kinetochore.
Article
Chemistry, Multidisciplinary
Jiali Yang, Takahiro Mori, Xingxing Wei, Yudai Matsuda, Ikuro Abe
Summary: The novel isomerase NsrQ from Aspergillus novofumigatus plays a key role in the biosynthesis of fungal tetrahydroxanthones by catalyzing a two-step isomerization reaction. Through biochemical and structural characterizations, it was found that NsrQ and its homologue Dcr3 utilize Glu and His residues as acid-base catalysts and important hydrophobic residues for shaping the active site pocket for substrate binding. The crystal structures of NsrQ and Dcr3 revealed their cone-shaped alpha + beta barrel fold and similarities to the nuclear transport factor 2-like superfamily enzymes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Oliver F. Harder, Sarah V. Barrass, Marcel Drabbels, Ulrich J. Lorenz
Summary: Microsecond time-resolved cryo-EM allows for observation of fast protein dynamics, as demonstrated by the contraction of the CCMV capsid induced by a pH jump.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Filip Topic, Joseph M. Marrett, Tristan H. Borchers, Hatem M. Titi, Christopher J. Barrett, Tomislav Friscic
Summary: This study presents the first X-ray single crystal structures of hypochlorite and hypobromite salts, shedding light on the solid-state geometry and supramolecular chemistry of hypohalite ions through variable-temperature Raman spectroscopy and periodic density-functional theory calculations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Molly J. McBride, Sarah R. Pope, Kai Hu, C. Denise Okafor, Emily P. Balskus, J. Martin Bollinger, Amie K. Boal
Summary: The study identified the crucial role of SznF in the biosynthesis of streptozotocin, revealing the binding of two iron cofactors and addressing previous uncertainties about the cofactors. During the cofactor (dis)assembly process, dynamic changes in the core helix were observed, and an unexpected glutamate ligand was found to be involved.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Christo N. Nanev, Emmanuel Saridakis, Naomi E. Chayen
Summary: X-ray crystallography is currently the dominant method for determining the structure of proteins and biomolecules. However, it faces challenges in obtaining high-resolution data from small protein crystals. Serial crystallography using XFELs is a promising alternative method that can produce excellent structural data from weakly diffracting objects. In this study, the authors calculate the mean crystal size and growth time needed for batch crystallization, which is the main method for preparing microcrystalline slurries. They also consider the impact of impurities on the growth of microcrystals. Experimental results with lysozyme support the theoretical predictions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Alex Maolanon, Athanasios Papangelis, David Kawiecki, Tung-Chung Mou, Jed T. Syrenne, Feng Yi, Kasper B. Hansen, Rasmus P. Clausen
Summary: A versatile stereoselective route was developed for synthesizing new 2'-(S)-CCG-IV analogues, allowing for late stage diversification. The evaluation of these analogues demonstrated the potential for developing subtype-specific NMDA receptor agonists with varying potency and efficacy. The crystal structure analysis of the agonist binding domain provided insights into the structural determinants of agonist efficacy.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Thomas Zacharchenko, Till Dorendorf, Nicolas Locker, Evert Van Dijk, Anja Katzemich, Kay Diederichs, Belinda Bullard, Olga Mayans
Summary: Obscurins are large filamentous proteins that play crucial roles in muscle assembly, stability, and regulation. They contain tandem C-terminal kinase domains, PK1 and PK2, separated by a long intrinsically disordered sequence. PK1 from Drosophila obscurin is found to be a pseudokinase with features of CAM-kinase family, but lacks typical mechanosensory properties. It interacts with PK2, suggesting a functional relation, and the unstructured interkinase segment may now be responsible for mechanosensing properties.
Article
Chemistry, Inorganic & Nuclear
Lucy M. C. Luong, Xian B. Carroll, Christopher D. Lowe, Marilyn M. Olmstead, Alan L. Balch
Summary: The crystallization of two solvates of Au11(PPh3)7(SCN)3 revealed differences in the relative orientations of the thiocyanate ligands.
INORGANICA CHIMICA ACTA
(2022)
Article
Biochemistry & Molecular Biology
Yanmei Luo, Jin Li, Yuliang Zong, Mengxin Sun, Wan Zheng, Jiapeng Zhu, Liu Liu, Bing Liu
Summary: This study identifies a potent SHP2 allosteric inhibitor and provides insights into its structure-activity relationship through comparison of co-crystal structures. These results have implications for understanding the mode of action and designing other allosteric inhibitors of SHP2.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Xiuxiu Ma, Meng Wang, Fan Wang, Jiao Li, Zhengguang Zhang, Jiapeng Zhu, Bing Liu
Summary: In this study, a small-molecule BRD4 inhibitor named compound 3 was identified as an effective inhibitor of BRD4 activity. Co-crystal structure analysis revealed that compound 3 occupies the KAc recognition pockets of BRD4 by forming key hydrogen bonds with Asn140 and engaging in hydrophobic interactions, thereby hindering the binding of acetylated lysine to BRD4. These findings suggest that compound 3 can serve as a lead compound for the development of structurally novel BRD4 inhibitors.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Victor L. Lo, Richard L. Kingston, Rick P. Millane
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2015)
Article
Biochemistry & Molecular Biology
Victor L. Lo, Richard L. Kingston, Rick P. Millane
JOURNAL OF STRUCTURAL BIOLOGY
(2016)
Article
Chemistry, Multidisciplinary
Jaekyun Jeon, Xin Qiao, Ivan Hung, Alok K. Mitra, Ambroise Desfosses, Daniel Huang, Peter L. Gor'kov, Rebecca C. Craven, Richard L. Kingston, Zhehong Gan, Fangqiang Zhu, Bo Chen
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Multidisciplinary Sciences
Soumeya A. Jaballah, Graham D. Bailey, Ambroise Desfosses, Jaekyung Hyun, Alok K. Mitra, Richard L. Kingston
SCIENTIFIC REPORTS
(2017)
Article
Virology
Melissa N. Webby, Matthew P. Sullivan, Kavestri M. Yegambaram, Mazdak Radjainia, Jeremy R. Keown, Richard L. Kingston
Article
Biophysics
N. Herr, M. N. Webby, E. M. M. Bulloch, M. Schmitz, R. L. Kingston
BIOMOLECULAR NMR ASSIGNMENTS
(2019)
Article
Biochemical Research Methods
Jordan Douglas, Richard Kingston, Alexei J. Drummond
PLOS COMPUTATIONAL BIOLOGY
(2020)
Review
Virology
Jordan Douglas, Alexei J. Drummond, Richard L. Kingston
Summary: The phosphoprotein gene of paramyxoviruses encodes multiple protein products, with the P protein being essential and V protein sometimes encoded by default, requiring guanosines to be inserted to encode P.
Article
Virology
Melissa N. Webby, Nicole Herr, Esther M. M. Bulloch, Michael Schmitz, Jeremy R. Keown, David C. Goldstone, Richard L. Kingston
Summary: The paramyxoviral phosphoprotein plays a crucial role in RNA synthesis, with a stable structure and dynamic linker, facilitating interactions between the polymerase and genomic RNA. The protein's C-terminal region exhibits a gradual disorder-to-order transition at the interface between the structured binding domain and disordered linker.
Correction
Biochemical Research Methods
J. Douglas, R. Kingston, A. J. Drummond
PLOS COMPUTATIONAL BIOLOGY
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
Melissa Webby, Richard Kingston, Nicole Herr, Jeremy Keown, Michael Schmitz, Esther Bulloch
Article
Biophysics
Milka Doktorova, Frederick A. Heberle, Richard L. Kingston, George Khelashvili, Michel A. Cuendet, Yi Wen, John Katsaras, Gerald W. Feigenson, Volker M. Vogt, Robert A. Dick
BIOPHYSICAL JOURNAL
(2017)
Review
Biochemistry & Molecular Biology
Andrew C. Hausrath, Richard L. Kingston
CELLULAR AND MOLECULAR LIFE SCIENCES
(2017)
Article
Chemistry, Multidisciplinary
Matthew P. Sullivan, Michael Groessl, Samuel M. Meier, Richard L. Kingston, David C. Goldstone, Christian G. Hartinger
CHEMICAL COMMUNICATIONS
(2017)
Review
Virology
Jordan Douglas, Alexei J. Drummond, Richard L. Kingston
Summary: The phosphoprotein gene of paramyxoviruses encodes multiple protein products, with P, V, and W proteins generated by transcriptional slippage. Non-templated guanosine nucleosides are inserted to encode P, with variations in the editing process and evolutionary history observed between viruses. The physical mechanisms of cotranscriptional editing via slippage of the viral RNA polymerase are also reviewed.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)