The substitution of Mg2+ by Mn2+ in the bacterial DnaB helicase from Helicobacter pylori, an ATP:Mg2+-fuelled protein engine, allows electron paramagnetic resonance (EPR) spectroscopy to be performed on this system. EPR experiments make it possible to monitor nucleotide binding and to estimate the fraction of bound Mn2+ through relaxation measurements. Furthermore, by measuring spin-spin distances we probe the geometry within such multimeric assemblies using ultra-wideband double electron-electron resonance (DEER) and relaxation induced dipolar modulation enhancement (RIDME). The extraction of distance distributions from RIDME experiments on high-spin paramagnetic centres is influenced by the presence of dipolar frequency overtones. We show herein that we can correct for these overtones by using a modified kernel function in Tikhonov regularization analysis routines, and that the overtone coefficients for Mn2+ in the DnaB helicase are practically the same as in the previously studied Mn2+-Mn2+ model compounds.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.2533/chimia.2018.216 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Structure and dynamics of monoclonal antibody domains determined using spins, scattering, and simulations.
ChemMedChem
January 2025
National Institute of Standards and Technology, Material Measurement Laboratory, UNITED STATES OF AMERICA.
Antibody-based pharmaceuticals are the leading biologic drug platform (> $75B/year). Despite a wealth of information collected on them, there is still a lack of knowledge on their inter-domain structural distributions, which impedes innovation and development. To address this measurement gap, we have developed a new methodology to derive biomolecular structure ensembles from distance distribution measurements via a library of tagged proteins bound to an unlabeled and otherwise unmodified target biologic.
View Article and Find Full Text PDFProbing Biomolecular Interactions with Paramagnetic Nuclear Magnetic Resonance Spectroscopy.
Chembiochem
January 2025
Institute for Drug Discovery, University of Leipzig, Brüderstr. 34, 04103, Leipzig, Germany.
Recent advances in computational methods like AlphaFold have transformed structural biology, enabling accurate modeling of protein complexes and driving applications in drug discovery and protein engineering. However, predicting the structure of systems involving weak, transient, or dynamic interactions, or of complexes with disordered regions, remains challenging. Nuclear Magnetic Resonance (NMR) spectroscopy offers atomic-level insights into biomolecular complexes, even in weakly interacting and dynamic systems.
View Article and Find Full Text PDFDirect Evaluation of Salivary Antioxidant Properties in Patients with Down Syndrome for assessment to Periodontal Disease and Premature Aging.
Free Radic Biol Med
January 2025
Department of Disaster Related Oral Health & Oxidative Stress/ESR Laboratories, Kanagawa Dental University, 82 Inaoka-cho, Yokosuka, Kanagawa 238-8580, Japan. Electronic address:
To evaluate oxidative stress involved in Down syndrome periodontal disease and pathological premature aging, reactive oxygen species (ROS) such as superoxide (O) and hydroxyl radical (HO) in human saliva were measured using electron spin resonance (ESR) spectroscopy. The groups consisted of 20 subjects in the Down syndrome (DS) child (DC) group (mean age 11.3 ± 4.
View Article and Find Full Text PDFComparison of lipid dynamics and permeability in styrene-maleic acid and diisobutylene-maleic acid copolymer lipid nanodiscs by electron paramagnetic resonance spectroscopy.
J Biol Inorg Chem
January 2025
Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA.
Lipid nanoparticles formed with copolymers are a new and increasingly powerful tool for studying membrane proteins, but the extent to which these systems affect the physical properties of the membrane is not completely understood. This is critical to understanding the caveats of these new systems and screening for structural and functional artifacts that might be caused in the membrane proteins they are used to study. To better understand these potential effects, the fluid properties of dipalmitoylphosphatidylcholine lipid bilayers were examined by electron paramagnetic resonance (EPR) spectroscopy with spin-labeled reporter lipids in either liposomes or incorporated into nanoparticles with the copolymers diisobutylene-maleic acid or styrene maleic acid.
View Article and Find Full Text PDFCatalyst-Free Nitrogen Fixation by Microdroplets through a Radical-Mediated Disproportionation Mechanism under Ambient Conditions.
J Am Chem Soc
January 2025
State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China.
Nitrogen fixation is essential for the sustainable development of both human society and the environment. Due to the chemical inertness of the N≡N bond, the traditional Haber-Bosch process operates under extreme conditions, making nitrogen fixation under ambient conditions highly desirable but challenging. In this study, we present an ultrasonic atomizing microdroplet method that achieves nitrogen fixation using water and air under ambient conditions in a rationally designed sealed device, without the need for any catalyst.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!