F NMR provides a way of monitoring conformational dynamics of G-protein coupled receptors (GPCRs) from the perspective of an ensemble. While X-ray crystallography provides exquisitely resolved high-resolution structures of specific states, it generally does not recapitulate the true ensemble of functional states. Fluorine (F) NMR provides a highly sensitive spectroscopic window into the conformational ensemble, generally permitting the direct quantification of resolvable states. Moreover, straightforward T- and T-based relaxation experiments allow for the study of fluctuations within a given state and exchange between states, on timescales spanning nanoseconds to seconds. Conveniently, most biological systems are free of fluorine. Thus, via fluorinated amino acid analogues or thiol-reactive fluorinated tags, F or CF reporters can be site specifically incorporated into proteins of interest. In this review, fluorine labeling protocols and F NMR experiments will be presented, from the perspective of small molecule NMR (i.e. drug or small molecule interactions with receptors) or macromolecular NMR (i.e. conformational dynamics of receptors and receptor-G-protein complexes).
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http://dx.doi.org/10.1016/j.coph.2023.102377 | DOI Listing |
J Chem Theory Comput
January 2025
Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains in order to develop a tool for data-assisted modeling of the conformational ensembles of multistate proteins, intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs), many of which are essential in cell biology. A numerically stable variant of molecular dynamics with time-averaged restraints has been introduced, in which the total energy is conserved in sections of a trajectory in microcanonical runs, the bath temperature is maintained in canonical runs, and the time-average-restraint-force components are scaled up with the length of the memory window so that the restraints affect the simulated structures. The new approach restores the conformational ensembles used to generate ensemble-averaged distances, as demonstrated with synthetic restraints.
View Article and Find Full Text PDFRSC Adv
January 2025
College of Agriculture and Biological Science, Dali University Dali 671000 China
The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models.
View Article and Find Full Text PDFAppl Spectrosc
January 2025
Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
Time-resolved, rapid-scan Fourier transform infrared (FT-IR) difference spectra have been recorded upon illumination on photosynthetic reaction centers (RCs) from under fixed hydration conditions (relative humidity = 76%). Two different illumination schemes were adopted. Whereas the use of a laser flash (duration: 7 ns) made it possible to follow the kinetics of recombination of the light-induced state PQ to the neutral state PQ, the use of a 20.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Reaction and interaction dynamics of azobenzene-tethered DNA (photoresponsive DNA) with T7 RNA polymerase (T7RNAP) were studied after photoisomerization of azobenzene from the - to -forms using the transient grating (TG) and time-resolved fluorescence polarization techniques. Two types of photoresponsive DNA were examined: AzoPBD, tethered at the protein binding site, and AzoTATA, tethered at the unwinding site. A diffusion change was observed after photoexcitation of -AzoPBD within 1 ms, and this change is explained in terms of a structural change from a bent to an extended conformation upon the -to- photoisomerization.
View Article and Find Full Text PDFFood Res Int
February 2025
Department of Food Science and Technology, Punjab Agricultural University, Ludhiana, Punjab 141 004, India. Electronic address:
In the present study, the impact of ultrasonication treatment (US) at varying time duration (10 and 20 min) on pearl millet protein (PMP) was evaluated. The native and ultrasonicated PMP were evaluated for techno-functional properties, zeta potential, particle size, SEM, FTIR, thermal properties and dynamic rheology. The significant (p < 0.
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