Article
Polymer Science
Dongyang Li, Wataru Takarada, Minoru Ashizawa, Takuya Yamamoto, Hidetoshi Matsumoto
Summary: Deuteration of polymeric nanofibers using deuterated solvents led to improved thermal and mechanical properties, as well as increased crystallinity. The partial exchange of amide linkages in PAs due to deuteration resulted in higher melting and glass transition points, along with substantially enhanced Young's moduli and tensile strengths of the NF sheets.
Article
Food Science & Technology
Fei Han, Qian Shen, Wei Zheng, Jingnan Zuo, Xinyu Zhu, Jingwen Li, Chao Peng, Bin Li, Yijie Chen
Summary: An air/water interface HDX-MS method was developed in this study to analyze the adsorption behavior of proteins at the air/water interface. The results indicated that specific peptide segments of bovine serum albumin (BSA) might interact with the interface through hydrophobic and electrostatic interactions. Furthermore, the conformational changes of these peptides could affect the structural properties related to protein foaming.
Article
Biochemistry & Molecular Biology
Helen T. Hobbs, Neel H. Shah, Jean M. Badroos, Christine L. Gee, Susan Marqusee, John Kuriyan
Summary: The catalytic activity of Syk-family tyrosine kinases is regulated by a tandem Src homology 2 module, which differs in conformational dynamics from ZAP-70, impacting the stability of its autoinhibited state and potentially influencing downstream signaling pathways in T cells.
Article
Biochemistry & Molecular Biology
Lijun Zhou, Defu Wang, Mehwish Iftikhar, Yinghong Lu, Min Zhou
Summary: The study investigated conformational changes of BtuF upon B-12 binding and release using hybrid approaches, highlighting the increased stability of BtuF with B-12 binding and the flexible regions within BtuF. The findings provide insights into the mechanism of B-12 recognition and deliverance by BtuF, showcasing the potential of hybrid methods in probing protein conformational dynamics.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Analytical
Ramin Ekhteiari Salmas, Antoni James Borysik
Summary: The quantification of hydrogen deuterium exchange (HDX) kinetics provides information on the stability of individual amino acids in proteins. The new programming tool HDXmodeller allows for optimization of low-resolution HDX-mass spectrometry (MS) data to understand exchange rates of individual amino acids. The tool also has a unique autovalidation method based on a covariance matrix for quantifying the accuracy of modeled exchange rates.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Pengfei Qian, Shilei Zhang, Fan Luo, Jiarui Wang, Xinyu Zhang, Xuejun Liu, Xiaodong Chen, Wei Wang, Xiaobei Chen
Summary: A co-catalyzed hydrogen-deuterium exchange method has been developed to selectively introduce deuterium at a specific position of enals. The protocol is mild and simple, allowing for high level deuterium incorporation in structurally diverse aromatic-derived enals and dienals.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Shuaihua Gao, Judith P. Klinman
Summary: With the growing acceptance of the importance of protein conformational ensembles in enzyme catalysis and regulation, research in protein dynamics is now focused on understanding the atomic properties and mechanisms behind protein dynamical networks. This includes the networks that communicate with the protein/water interface. Advances in experimental tools and biophysical methods have allowed for real-time visualization of dynamics in thermal activation pathways.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Laszlo L. P. Hosszu, Daljit Sangar, Mark Batchelor, Emmanuel Risse, Andrea M. Hounslow, John Collinge, Jonathan P. Waltho, Jan Bieschke
Summary: In prion replication, the conversion of cellular form of prion protein (PrPC) to its disease-associated fibrillar form is achieved through a full conformational transition. Transmembrane forms of PrP play a role in this structural conversion. Removing residues 119-136 of PrP, which includes the first β-strand and a large portion of the conserved hydrophobic region associated with the ER membrane, resulted in an open native-like conformer of PrPC with increased solvent exposure and enhanced fibril formation. These findings suggest a stepwise folding transition initiated by the conformational switch to this open form of PrPC.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Analytical
Neeleema Seetaloo, Monika Kish, Jonathan J. Phillips
Summary: Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a method for studying protein structures, which can be analyzed at different levels. However, the available software packages for HDX-MS data analysis can only handle different levels separately and lack the ability to combine them. Therefore, we developed a new standalone application (HDfleX) that allows the merging and analysis of HDX-MS data at different levels.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Carla Marie Stork, Remo Weck, Megane Valero, Henrik Kramp, Stefan Guessregen, Siegfried R. Waldvogel, Anna Sib, Volker Derdau
Summary: We have explored the application of highly selective homogeneous iridium-catalyzed hydrogen isotope exchange (HIE) using deuterium or tritium gas as an isotope source in aqueous media. By employing an improved water-soluble Kerr-type catalyst and conducting DFT calculations, we gained insights into the reactivity, transition states, and coordination complexes, guiding the scope and limitations of HIE reactions in water. Additionally, we successfully extended these findings to tritium chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Cell Biology
Juan Zeng, Shiwei Wang, Min Gao, Dian Lu, Shuang Song, Diyu Chen, Weimin Fan, Zhiliang Xu, Zhiguo Zhang, Xiaofang Sun
Summary: As a highly conserved and ubiquitously expressed kinase, PAK2 plays important roles in meiotic progression and chromosome alignment in mouse oocytes. Depletion of PAK2 leads to metaphase I arrest and meiotic chromosome alignment defects, partly due to the reduction of PLK1. The interaction between PAK2 and PLK1 protects PLK1 from degradation and promotes meiotic progression and bipolar spindle formation.
CELL DEATH & DISEASE
(2023)
Article
Materials Science, Paper & Wood
Yan Song, Wei Jiang, Haoxi Ben, Yuanming Zhang, Guangting Han, Arthur J. Ragauskas
Summary: Preparation of deuterium incorporated cellulose is important for investigating cellulose internal structure and expanding its application fields. The study successfully prepared cellulosic cotton fibers with anti-rehydration deuterium incorporation and characterized the process using nuclear magnetic resonance and spectroscopy. The results showed that the hydrogen-deuterium exchange occurred preferentially in the amorphous cellulose component and increased treatment time led to higher deuterium incorporation. Additionally, the isotope effect did not affect the cellulose microstructure, crystalline index, or degree of polymerization properties significantly.
Article
Chemistry, Analytical
Timothy R. R. O'Leary, Deepa Balasubramaniam, Kristin Hughes, Denisa Foster, Jeffrey Boyles, Kristina Coleman, Patrick R. R. Griffin
Summary: Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is used for epitope mapping of monoclonal antibodies (mAb) and understanding viral immune evasion. To overcome the limitation of glycan heterogeneity, a glycosidase was covalently immobilized on a resin and incorporated into an online HDX-MS workflow for post-HDX deglycosylation. This system allowed for full sequence coverage of the SARS-CoV-2 receptor-binding domain (RBD) and mapping of the glycosylated epitope of a glycan-binding mAb S309.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Faiz Ahmad, Angela Patterson, Jaigeeth Deveryshetty, Jenna R. Mattice, Nilisha Pokhrel, Brian Bothner, Edwin Antony
Summary: RPA binds to ssDNA and interacts with enzymes, acting as a recruitment hub for DNA metabolic processes. Recent evidence suggests that the dynamics of DBDs better define their roles. DBD-C plays a major role in stabilizing RPA on ssDNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Mahesh Kathania, Ritesh Kumar, Elviche Taskem Lenou, Venkatesha Basrur, Arianne L. Theiss, Jonathan Chernoff, K. Venuprasad
Summary: Dysregulated interleukin-17 expression and its downstream signaling is strongly linked to inflammatory bowel diseases. We identified that Pak2 directly interacts with ROR gamma t and regulates its activity through phosphorylation.