In-solution small-angle X-ray and neutron scattering (SAXS/SANS) have become popular methods to characterize the structure of membrane proteins, solubilized by either detergents or nanodiscs. SANS studies of protein-detergent complexes usually require deuterium-labeled proteins or detergents, which in turn often lead to problems in their expression or purification. Here, we report an approach whose novelty is the combined analysis of SAXS and SANS data from an unlabeled membrane protein complex in solution in two complementary ways. First, an explicit atomic analysis, including both protein and detergent molecules, using the program WAXSiS, which has been adapted to predict SANS data. Second, the use of MONSA which allows one to discriminate between detergent head- and tail-groups in an ab initio approach. Our approach is readily applicable to any detergent-solubilized protein and provides more detailed structural information on protein-detergent complexes from unlabeled samples than SAXS or SANS alone.
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http://dx.doi.org/10.1021/acs.jpclett.8b01598 | DOI Listing |
Int J Mol Sci
January 2025
Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia.
The Dps protein is the major DNA-binding protein of prokaryotes, which protects DNA during starvation by forming a crystalline complex. The structure of such an intracellular DNA-Dps complex is still unknown. However, the phenomenon of a decrease in the size of the Dps protein from 90 Å to 69-75 Å during the formation of a complex with DNA has been repeatedly observed, and no explanation has been given.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
Modeling inorganic glasses requires an accurate representation of interatomic interactions, large system sizes to allow for intermediate-range structural order, and slow quenching rates to eliminate kinetically trapped structural motifs. Neither first principles-based nor force field-based molecular dynamics (MD) simulations satisfy these three criteria unequivocally. Herein, we report the development of a machine learning potential (MLP) for a classic glass, B2O3, which meets these goals well.
View Article and Find Full Text PDFBioorg Med Chem Lett
January 2025
Department of Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan; Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
We describe here the design, synthesis, and X-ray structural studies of a new class of HIV-1 protease inhibitors containing 8-oxabicyclo[3.2.1]octanol-derived P2 ligands.
View Article and Find Full Text PDFScience
January 2025
Wolfson Catalysis Centre, Department of Chemistry, University of Oxford, Oxford, UK.
The distribution of substitutional aluminum (Al) atoms in zeolites affects molecular adsorbate geometry, catalytic activity, and shape and size selectivity. Accurately determining Al positions has been challenging. We used synchrotron resonant soft x-ray diffraction (RSXRD) at multiple energies near the Al K-edge combined with molecular adsorption techniques to precisely locate "single Al" and "Al pairs" in a commercial H-ZSM-5 zeolite.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt. Electronic address:
Alzheimer's disease (AD) is popularly believed to be triggered by the aggregation of amyloid beta 1-42 (Aβ - 42) peptides, eventually leading to neurodegeneration. Our study delves into the influential role played by Green Iron Oxide Nanoparticles (GIONP). GIONP are typically synthesized using a green chemistry approach, imposing curcumin as a biocompatible reducing and capping agent, leveraging its inherent antioxidant, anti-inflammatory, and neuroprotective attributes.
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