Article
Biochemistry & Molecular Biology
Dorota Focht, Caroline Neumann, Joseph Lyons, Ander Eguskiza Bilbao, Rickard Blunck, Lina Malinauskaite, Ilona O. Schwarz, Jonathan A. Javitch, Matthias Quick, Poul Nissen
Summary: The flexibility of the GMG motif in the unwound region of MhsT is crucial for recognizing substrates of different sizes by tailoring the binding site shape and volume. Mutants with substitutions in the GMG loop and substrate binding pocket showed impaired transport of aromatic amino acids that require a larger binding site volume, indicating a common mechanism for substrate recognition and translocation by SLC6 transporters.
Article
Biochemistry & Molecular Biology
Yu Guo, Dan Zhou, Hui Zhang, Nan-Nan Zhang, Xiaoyu Qi, Xiaofang Chen, Qi Chen, Jing Li, Honghua Ge, Yan-Bin Teng
Summary: This study investigates the structural characteristics of MapA in HAPs and its substrate recognition mechanism. By analyzing the binding of the complex with inhibitors, a new substrate binding mode is revealed.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Michal Mayer, Yulia Matiuhin, Mickal Nawatha, Orly Tabachnikov, Inbar Fish, Nili Schutz, Hay Dvir, Meytal Landau
Summary: The bacterial tyrosine kinase BceF from Burkholderia cepacia is structurally characterized in this study and found to have unique variations compared to other BY-kinases, offering a potential for development of specific inhibitors targeting Burkholderia cepacia virulence.
Article
Chemistry, Medicinal
Siu Wai Wong, Lucy Vivash, Ramesh Mudududdla, Nghi Nguyen, Stefan J. Hermans, David M. Shackleford, Judith Field, Lian Xue, Andrea Aprico, Nancy C. Hancock, Mohammad Haskali, Michael A. Stashko, Stephen Frye, Xiaodong Wang, Michele D. Binder, Uwe Ackermann, Michael W. Parker, Trevor J. Kilpatrick, Jonathan B. Baell
Summary: A new [F-18] ligand with high affinity and selectivity for MERTK as a potential PET radiotracer was successfully developed in this study. The compound showed significant specific binding to MERTK, especially in specific regions of the brain, indicating potential clinical utility.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Elena Ostertag, Liujuan Zheng, Karina Broger, Thilo Stehle, Shu-Ming Li, Georg Zocher
Summary: Prenylation plays a crucial role in primary and secondary metabolism, contributing to chemical diversity in natural systems. Recent structural studies on prenyltransferases shed light on their catalytic mechanisms and key residues, but the control of regioselectivity and chemoselectivity remains a challenge. Site-directed mutagenesis has been successfully utilized to modify prenyl donor specificity and switch the regioselectivity of prenyltransferases, showing potential for production of novel prenylated compounds.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yihu Xie, Christopher L. Lord, Bradley P. Clarke, Austin L. Ivey, Pate S. Hill, W. Hayes McDonald, Susan R. Wente, Yi Ren
Summary: CTDK-1 is the primary RNA Pol II CTD Ser2 kinase complex in budding yeast, consisting of a CDK Ctk1, a cyclin Ctk2, and a unique subunit Ctk3 which activates Ctk1 by stabilizing the T-loop. Additionally, Ctk3 contributes to the assembly of CTDK-1 through interactions with both Ctk1 and Ctk2, and physically interacts with Gbp2, a serine/arginine-like protein. These findings reveal a regulatory mechanism of CDK complexes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Endocrinology & Metabolism
Michael C. Lawrence
Summary: The article describes the three-dimensional structure of insulin and its receptor, as well as their interactions, highlighting research gaps in structural understanding. A near-complete picture has been obtained of hormone receptor interactions, providing new insights and requiring revision of the existing hormone receptor engagement models.
MOLECULAR METABOLISM
(2021)
Article
Chemistry, Multidisciplinary
Yohei Katsuyama, Kaoru Sone, Ayaka Harada, Seiji Kawai, Naoki Urano, Naruhiko Adachi, Toshio Moriya, Masato Kawasaki, Kazuo Shin-ya, Toshiya Senda, Yasuo Ohnishi
Summary: The study determined the structure of FmoA3 using X-ray crystallography and cryogenic electron microscopy, revealing the accommodation of alpha-methyl-l-serine in the active site. The Cy domains of FmoA2 and FmoA3 catalyze different reactions, with the Cy domain of FmoA3 potentially losing its donor PCP binding activity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Gabriel Javitt, Alisa Kinzel, Nava Reznik, Deborah Fass
Summary: Zymogen granule membrane protein 16 (ZG16) is a protein produced in organs that secrete enzymes and other proteins into the digestive tract, with the ability to bind microbial pathogens. The CXXC motif on ZG16 contributes to its activity, and can be oxidized by specific enzymes to engage in redox reactions.
Article
Multidisciplinary Sciences
Gonzalo L. Gonzalez-Del Pino, Kunhua Li, Eunyoung Park, Anna M. Schmoker, Byung Hak Ha, Michael J. Eck
Summary: The dysregulation of the RAF/MEK/ERK pathway is associated with many cancers, making the proteins involved, like MEK, a focus of drug discovery efforts. Allosteric MEK inhibitors have complex effects on this pathway and are used in combination with BRAF inhibitors in malignant melanoma. Recent studies suggest that these inhibitors act most potently on BRAF/MEK complexes rather than on free active MEK.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Takaki Okamoto, Kazuya Yamanaka, Yoshimitsu Hamano, Shingo Nagano, Tomoya Hino
Summary: In this study, the crystal structure of the adenylation domain of epsilon-PL synthetase was determined, providing insights into the precise interactions between the enzyme and L-Lys and its analogs. The findings contribute to a better understanding of the epsilon-PL synthesis mechanism and have implications for the successful application of NRPS adenylation domains in bioengineering.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Angus J. Robertson, F. Aaron Cruz-Navarrete, Henry P. Wood, Nikita Vekaria, Andrea M. Hounslow, Claudine Bisson, Matthew J. Cliff, Nicola J. Baxter, Jonathan P. Waltho
Summary: Understanding the factors contributing to the high catalytic efficiencies of enzymes is crucial for catalysis and enzyme design. This study investigates the relationship between binding a phosphodianion group in a distal site, adopting a closed enzyme form, and catalytic proficiency. The results suggest that binding of a phosphodianion group in the distal site stimulates domain closure and stabilizes the closed active form, leading to high catalytic efficiencies.
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
Chemistry, Analytical
Avinash Kumar Sonkar, Abhishek Rai, Kamini Tripathi, Richa Yadav, Manjari Shukla, Brijesh Singh Chauhan, S. Srikrishna, Lallan Mishra
Summary: A new aggregation induced enhanced emission (AIEE) active probe was successfully synthesized and characterized in this study. The probe displayed selective detection of Cu2+ ions and enhanced fluorescence intensity upon addition of Zn2+ ions in nanoaggregates formed in H2O:CH3OH. Additionally, the probe showed switch on behavior of green fluorescence in larval gut tissues of Drosophila melanogaster in the presence of Zn2+ ions.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Biochemistry & Molecular Biology
B. M. Adams, Miranda N. Coates, S. RaElle Jackson, Melissa S. Jurica, Tara L. Davis
BIOCHEMICAL JOURNAL
(2015)
Article
Chemistry, Multidisciplinary
Moses Moustakim, Peter G. K. Clark, Laura Trulli, Angel L. Fuentes de Arriba, Matthias T. Ehebauer, Apirat Chaikuad, Emma J. Murphy, Jacqui Mendez-Johnson, Danette Daniels, Chun-Feng D. Hou, Yu-Hui Lin, John R. Walker, Raymond Hui, Hongbing Yang, Lucy Dorrell, Catherine M. Rogers, Octovia P. Monteiro, Oleg Fedorov, Kilian V. M. Huber, Stefan Knapp, Jag Heer, Darren J. Dixon, Paul E. Brennan
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2017)
Article
Biochemistry & Molecular Biology
Qi Zhang, Rachel Harding, Feng Hou, Aiping Dong, John R. Walker, Joseph Bteich, Yufeng Tong
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Cell Biology
Florence R. Wilson, Angus Ho, John R. Walker, Xu-Dong Zhu
JOURNAL OF CELL SCIENCE
(2016)
Article
Cell Biology
Patrick A. Williams, Michael S. Krug, Emily A. McMillan, Jasmine D. Peake, Tara L. Davis, Simon Cocklin, Todd I. Strochlic
MOLECULAR BIOLOGY OF THE CELL
(2016)
Article
Biochemistry & Molecular Biology
Chelsea L. Gustafson, Nicole C. Parsley, Hande Asimgil, Hsiau-Wei Lee, Christopher Ahlbach, Alicia K. Michael, Haiyan Xu, Owen L. Williams, Tara L. Davis, Andrew C. Liu, Carrie L. Partch
Article
Multidisciplinary Sciences
Nicole L. Batenburg, John R. Walker, Sylvie M. Noordermeer, Nathalie Moatti, Daniel Durocher, Xu-Dong Zhu
NATURE COMMUNICATIONS
(2017)
Article
Genetics & Heredity
Nicole L. Batenburg, Jian Qin, John R. Walker, Xu-Dong Zhu
Article
Biochemical Research Methods
Thanh G. Nguyen, Nicolette S. Honson, Steven Arns, Tara L. Davis, Sirano Dhe-Paganon, Suzana Kovacic, Nag S. Kumar, Tom A. Pfeifer, Robert N. Young
ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES
(2014)
Article
Multidisciplinary Sciences
Andreas Ernst, George Avvakumov, Jiefei Tong, Yihui Fan, Yanling Zhao, Philipp Alberts, Avinash Persaud, John R. Walker, Ana-Mirela Neculai, Dante Neculai, Andrew Vorobyov, Pankaj Garg, Linda Beatty, Pak-Kei Chan, Yu-Chi Juang, Marie-Claude Landry, Christina Yeh, Elton Zeqiraj, Konstantina Karamboulas, Abdellah Allali-Hassani, Masoud Vedadi, Mike Tyers, Jason Moffat, Frank Sicheri, Laurence Pelletier, Daniel Durocher, Brian Raught, Daniela Rotin, Jianhua Yang, Michael F. Moran, Sirano Dhe-Paganon, Sachdev S. Sidhu
Article
Biochemistry & Molecular Biology
Nicole Batenburg, John R. Walker, Yan Coulombe, Alana Sherker, Jean-Yves Masson, Xu-Dong Zhu
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Nicole L. Batenburg, Sofiane Y. Mersaoui, John R. Walker, Yan Coulombe, Ian Hammond-Martel, Hugo Wurtele, Jean-Yves Masson, Xu-Dong Zhu
Summary: CSB protein is recruited to stalled replication forks in a phosphorylation-dependent manner, and plays a role in promoting MRE11-mediated fork degradation in BRCA1/2-deficient cells. CSB also possesses ATP-dependent fork reversal activity and functions similarly to other fork reversal factors to regulate slowdown in fork progression under replication stress, indicating its importance in DNA repair pathways.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
John R. Walker, Xu-Dong Zhu
Summary: This article discusses the important role of CSB in resolving replication stress and maintaining genetic integrity through different pathways, and also explores the implications of CSB in cancer therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Qi Zhang, Zhongduo Wang, Feng Hou, Rachel Harding, Xinyi Huang, Aiping Dong, John R. Walker, Yufeng Tong
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2017)
Article
Biochemistry & Molecular Biology
Caroline Rajiv, S. RaElle Jackson, Simon Cocklin, Elan Z. Eisenmesser, Tara L. Davis
BIOCHEMICAL JOURNAL
(2017)