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
Multidisciplinary Sciences
Valeria Calvaresi, Antoni G. Wrobel, Joanna Toporowska, Dietmar Hammerschmid, Katie J. Doores, Richard T. Bradshaw, Ricardo B. Parsons, Donald J. Benton, Chloe Roustan, Eamonn Reading, Michael H. Malim, Steve J. Gamblin, Argyris Politis
Summary: In this study, the authors used hydrogen-deuterium exchange mass spectrometry to describe the evolution of the SARS-CoV-2 spike glycoprotein's structural dynamics features and receptor binding capability from the emergence of the original Wuhan isolate to the recent omicron variant. The findings shed light on the evolution of SARS-CoV-2 in the human population and the mechanisms of emergence of new variants.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Pablo M. Scrosati, Victor Yin, Lars Konermann
Summary: The study suggests that there may be major structural fluctuations in proteins that are weakly correlated with changes in hydrogen bonding, making them difficult to track using HDX-MS, potentially leading to an incomplete view of protein dynamics.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Didar Ciftci, Chloe Martens, Vishnu G. Ghani, Scott C. Blanchard, Argyris Politis, Gerard H. M. Huysmans, Olga Boudker
Summary: This study used single-molecule fluorescence microscopy to compare the timing of conformational transitions and substrate uptake in the transporter GltPh, finding that the movements of the substrate-loaded transport domain across membranes and substrate release are kinetically heterogeneous. Mutations that increase elevator transitions and reduce substrate affinity can diminish transport rate heterogeneities and boost transport efficiency, suggesting potential gain-of-function properties that impact transport rates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
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
Biochemical Research Methods
Irina Oganesyan, Cristina Lento, Anurag Tandon, Derek J. Wilson
Summary: Using time-resolved electrospray ionization hydrogen/deuterium exchange mass spectrometry (TRESI-HDX-MS), this study reveals different interaction modes of alpha SN with nanodisc membrane mimics. Interactions with nanodiscs containing lipids known to promote amyloidogenesis induce substantial and specific changes in the alpha SN conformational ensemble, particularly affecting residues 19-28 and 45-57. This supports the existing broken-helix model for asynuclein/membrane interactions but does not detect a helical extension thought to play a role in alpha SN aggregation.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
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: Nonlinear programming is utilized in protein biophysics to understand microscopic exchange kinetics in HDX-MS data. Despite the significant challenge of optimizing HDX-MS data due to a large number of variables and wide variable bounds, enhancing search for a minimum solution through selected constrained variables is considered effective. Local bounds optimization induces a large and surprisingly long-range global response on all variables, but can unpredictably decrease accuracy depending on constraint stringency.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Joseph Anacleto, Cristina Lento, Vladimir Sarpe, Ayesha Maqsood, Banafsheh Mehrazma, David Schriemer, Derek J. Wilson
Summary: Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a rapidly growing technique that provides information about the dynamic structural changes in proteins during biological function. The continuous flow injection setup for time-resolved HDX-MS (CFI-TRESI-HDX) introduced in this work allows for automated, continuous or discrete labeling time measurements from milliseconds to hours, with substantially reduced runtimes compared to conventional systems.
ANALYTICAL CHEMISTRY
(2023)
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, Analytical
Eric Largy, Matthieu Ranz
Summary: Hydrogen-deuterium exchange mass spectrometry (HDX/MS) is used for studying protein conformation dynamics and characterizing oligonucleotide conformations and their interactions with cations, small molecules, and proteins. OligoR is a web-based application that provides dedicated solutions for processing and visualizing native HDX/MS data of oligonucleotides. It offers a simple and robust approach to deconvoluting bimodal isotope distributions and can be extended to various analytes. The results are presented in interactive data tables and can be exported as publication-quality figures.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Applied
Hannah J. Mckerchar, Cristina Lento, Rachel Z. Bennie, Jennifer M. Crowther, Fabian Dolamore, Jolon M. Dyer, Stefan Clerens, Davide Mercadante, Derek J. Wilson, Renwick C. J. Dobson
Summary: The properties of milk proteins vary between different mammalian species. This study focuses on comparing the dynamics of beta-lactoglobulin (β lg) proteins from goat and cow milk at different pH levels. The dimeric states of the cow β lg B variant homologue exhibit more conformational flexibility than the goat β lg at lower pH, as observed through hydrogen/deuterium exchange experiments and molecular dynamics simulations. Understanding these dynamic differences in β lg homologues is crucial for understanding the variations in milk processing, human digestion, and immunogenicity.
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
Andrea Piserchio, Kimberly Long, Kwangwoon Lee, Eric A. Kumar, Rinat Abzalimov, Kevin N. Dalby, Ranajeet Ghose
Summary: In this study, the conformational changes during complex formation between CaM-activated eEF-2K and TR, as well as the effects of TR autophosphorylation at Thr348, were investigated using a combination of HXMS, solution-state NMR, and biochemical approaches. The results suggest that the C-lobe surface of CaM interacts with TR and the helix F of CaM responds to Thr348 phosphorylation and pH changes, playing a crucial role in inducing conformational changes in TR for efficient phosphorylation.
Article
Biochemistry & Molecular Biology
Xiang Zhou, Yuanyuan Wang, Wei Zheng, Guangxiu Deng, Fuyi Wang, Lan Jin
Summary: The aggregation of beta-amyloid peptide (Aβ) is one potential cause for Alzheimer's disease, and heparin can either promote or inhibit Aβ aggregation. The sulfation pattern and chain size of heparin determine its binding affinity to Aβ. By studying the glycosaminoglycan (GAG)-peptide complex and conducting an MTT assay, it was found that heparin oligosaccharides with defined sequences represent promising inhibitors of Aβ aggregation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Nicholas Vance, Neelie Zacharias, Mark Ultsch, Guangmin Li, Aimee Fourie, Peter Liu, Julien LaFrance-Vanasse, James A. Ernst, Wendy Sandoval, Katherine R. Kozak, Gail Phillips, Weiru Wang, Jack Sadowsky
BIOCONJUGATE CHEMISTRY
(2019)
Article
Medicine, Research & Experimental
Ayse Meric Ovacik, Ji Li, Marie Lemper, Dimitry Danilenko, Nicola Stagg, Mary Mathieu, Diego Ellerman, Vinita Gupta, Navdeep Kalia, Trung Nguy, Vicki Plaks, Clarissa David Johnson, Weiru Wang, Jochen Brumm, Bernard Fine, Teemu Junttila, Kedan Lin, Paul J. Carter, Saileta Prabhu, Christoph Spiess, Amrita V. Kamath
Article
Biochemistry & Molecular Biology
Ping Wu, Christopher J. Sneeringer, Keith E. Pitts, Eric S. Day, Bryan K. Chan, Binqing Wei, Isabelle Lehoux, Kyle Mortara, Hong Li, Jiansheng Wu, Yvonne Franke, John G. Moffat, Jane L. Grogan, Timothy P. Heffron, Weiru Wang
Article
Multidisciplinary Sciences
Jonathan M. Harnoss, Adrien Le Thomas, Anna Shemorry, Scot A. Marsters, David A. Lawrence, Min Lu, Yung-Chia Ariel Chen, Jing Qing, Klara Totpal, David Kan, Ehud Segal, Mark Merchant, Mike Reichelt, Heidi Ackerly Wallweber, Weiru Wang, Kevin Clark, Susan Kaufman, Maureen H. Beresini, Steven T. Laing, Wendy Sandoval, Maria Lorenzo, Jiansheng Wu, Justin Lyh, Tom De Bruyn, Amy Heidersbach, Benjamin Haley, Alvin Gogineni, Robby M. Weimer, Dong Lee, Marie-Gabrielle Braun, Joachim Rudolph, Michael J. VanWyngarden, Daniel W. Sherbenou, Patricia Gomez-Bougie, Martine Amiot, Diego Acosta-Alvear, Peter Walter, Avi Ashkenazi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Meagan Y. Nakarnoto, Johannes Rudolph, Deborah S. Wuttke, Karolin Luger
Article
Biochemistry & Molecular Biology
Johannes Rudolph, Jyothi Mahadevan, Karolin Luger
Article
Chemistry, Medicinal
Ramsay E. Beveridge, Heidi Ackerly Wallweber, Avi Ashkenazi, Maureen Beresini, Kevin R. Clark, Paul Gibbons, Elise Ghiro, Susan Kaufman, Alexandre Larivee, Melissa Leblanc, Jean-Philippe Leclerc, Alexandre Lemire, Cuong Ly, Joachim Rudolph, Jacob B. Schwarz, Sanjay Srivastava, Weiru Wang, Liang Zhao, Marie-Gabrielle Braun
ACS MEDICINAL CHEMISTRY LETTERS
(2020)
Article
Multidisciplinary Sciences
Elena Ferri, Adrien Le Thomas, Heidi Ackerly Wallweber, Eric S. Day, Benjamin T. Walters, Susan E. Kaufman, Marie-Gabrielle Braun, Kevin R. Clark, Maureen H. Beresini, Kyle Mortara, Yung-Chia A. Chen, Breanna Canter, Wilson Phung, Peter S. Liu, Alfred Lammens, Avi Ashkenazi, Joachim Rudolph, Weiru Wang
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Johannes Rudolph, Genevieve Roberts, Karolin Luger
Summary: PARP1 and PARP2 are key enzymes in the DNA damage response. HPF1 plays an essential role in modulating the PARylation of histones by forming a complex with both PARP1 and PARP2. Results show how HPF1 can affect the binding affinity of certain inhibitors to PARP1.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Johannes Rudolph, Genevieve Roberts, Uma M. Muthurajan, Karolin Luger
Summary: HPF1 redirects PARylation by PARP1 towards histones, leading to shorter PAR chains and production of free ADP-ribose. This switch from polymerase to hydrolase has important implications for DNA damage response mediated by PARP1 and raises questions about intracellular ADPR and depletion of NAD(+).
Article
Biochemistry & Molecular Biology
Laurel M. Pegram, Jake W. Anderson, Natalie G. Ahn
Summary: Recent research utilizing various techniques has unveiled the structural changes involved in protein kinase activation and ligand binding, deepening our understanding of these processes. This research demonstrates how activation mechanisms and ligand binding affect the internal motions of kinases, enabling allosteric coupling between distal regulatory regions and the active site.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Johannes Rudolph, Uma M. Muthurajan, Megan Palacio, Jyothi Mahadevan, Genevieve Roberts, Annette H. Erbse, Pamela N. Dyer, Karolin Luger
Summary: PARP1 is a key player in DNA damage response and a target for cancer treatment. The BRCT domain binds to DNA without activating the catalytic domain. The DNA-binding properties of the BRCT domain contribute to the monkey-bar mechanism for DNA transfer of PARP1.
Article
Biochemistry & Molecular Biology
Petra Stojanovic, Karolin Luger, Johannes Rudolph
Summary: Upon binding to DNA damage, PARP1 is activated to perform PARylation on itself and other proteins, leading to chromatin relaxation and DNA repair factor recruitment. HPF1 is a cofactor of PARP1 that directs preferential PARylation of histones. Understanding the dissociation of PARPi from the PARP1-HPF1 complex is important for the development of next-generation PARP inhibitors.