The recently developed efficient protocols to implicit [Grimme et al., J. Phys. Chem. A 125, 4039-4054 (2021)] and explicit quantum mechanical modeling of non-rigid molecules in solution [Katsyuba et al., J. Phys. Chem. B 124, 6664-6670 (2020)] are used to describe conformational equilibria of 1,2-dichloroethane and 1,2-dibromoethane in various media. Two approaches for evaluation of trans/gauche free energy differences, ΔG, are compared: (a) direct ΔG computation in implicit solution; (b) the use, together with experimental intensities, of infrared absorption coefficients and Raman scattering cross sections computed for each explicitly modeled solution. The same cluster model of a solute surrounded by the first solvation shell of solvent molecules was used to simulate both Raman and IR spectra. The good agreement between the two approaches indicates the reliability of both methods. The importance of using correct absorption coefficients and Raman scattering factors for each medium is discussed. The ΔG estimates from both implicit and explicit solvation simulations were combined with experimentally measured enthalpy differences ΔH available in the literature to obtain condensed-state ΔS estimates.
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http://dx.doi.org/10.1063/5.0126678 | DOI Listing |
J Am Chem Soc
January 2025
Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States.
The tau protein misfolds in neurodegenerative diseases such as Alzheimer's disease (AD). These pathological tau aggregates are associated with neuronal membranes, but molecular structural information about how disease-like tau fibrils interact with the lipid membrane is scarce. Here, we use solid-state NMR to investigate the structure of a tau construct bearing four AD-relevant phospho-mimetic mutations (4E tau) with cholesterol-containing high-curvature lipid membranes, which mimic the membrane of synaptic vesicles in neurons.
View Article and Find Full Text PDFSubcell Biochem
December 2024
IDIBE, Universidad Miguel Hernández, Elche, Alicante, Spain.
Nuclear magnetic resonance (NMR) is a spectroscopic technique based on the absorption of radiofrequency radiation by atomic nuclei in the presence of an external magnetic field. NMR has followed a "bottom-up" approach to solve the structures of isolated domains of viral proteins, including capsid protein subunits, or to provide information about other macromolecular partners with which such proteins interact. NMR has been instrumental in describing conformational changes in viral proteins and nucleic acids, showing the presence of dynamic equilibria which are thought to be important at different stages of the virus life cycle.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States.
It has been challenging to determine how a ligand that binds to a receptor activates downstream signaling pathways and to predict the strength of signaling. The challenge is compounded by functional selectivity, in which a single ligand binding to a single receptor can activate multiple signaling pathways at different levels. Spectroscopic studies show that in the largest class of cell surface receptors, 7 transmembrane receptors (7TMRs), activation is associated with ligand-induced shifts in the equilibria of intracellular pocket conformations in the absence of transducer proteins.
View Article and Find Full Text PDFRSC Chem Biol
January 2025
Novartis Biomedical Research Basel Switzerland
The design of potent RAS inhibitors benefits from a molecular understanding of the dynamics in KRAS and NRAS and their oncogenic mutants. Here we characterize switch-1 dynamics in GTP-state KRAS and NRAS by P NMR, by N relaxation dispersion NMR, hydrogen-deuterium exchange mass spectrometry (HDX-MS), and molecular dynamics simulations. In GMPPNP-bound KRAS and NRAS, we see the co-existence of two conformational states, corresponding to an "inactive" state-1 and an "active" state-2, as previously reported.
View Article and Find Full Text PDFProtein Sci
January 2025
Division of Biophysics, Department of Physiology, Jichi Medical University, Shimotsuke, Tochigi, Japan.
Much is known about how allosteric effectors influence the equilibrium between the relaxed (R) and tense (T) states of hemoglobin (Hb), but little is known about how and to what extent the effectors lower the intrinsic O affinity of each allosteric state, especially the R-state. Here, we provide a thorough characterization of the O equilibria of effector-bound and unbound R-quaternary form crystals of horse Hb without a quaternary structural switching. In the absence of effectors, R crystals of horse Hb were shown to bind O noncooperatively with a very high affinity virtually identical to that of R crystals of human Hb.
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