Vicinal proton-proton NMR couplings have been used to investigate whether the position of conformational equilibria is determined by intramolecular N-H hydrogen bonding for 2-(2'-pyridyl)ethylphosphonic acid 1 in its various possible ionization states in water, methanol, ethanol, and dimethyl sulfoxide (DMSO). With 1 in the form of its monoanion and dianion, the trans is favored, with the dianion being more trans than the monoanion for a given solvent, probably as the result of steric effects, possibly enhanced by repulsive electrostatic effects between the negatively charged phosphonic group and the lone pair on the pyridine nitrogen. For 1 and its conjugate acid, the gauche amounts, respectively, to 43% and 45% in water, 66% and 51% in methanol, 66% and 64% in ethanol, and 29% and 49% in DMSO. For these latter two species, electrostatic, steric, and hydrogen bonding-effects are all likely to play a role in determining the conformational equilibria.
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http://dx.doi.org/10.1002/chir.10064 | DOI Listing |
bioRxiv
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
November 2024
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.
View Article and Find Full Text PDFJ Chem Phys
November 2024
Department of Chemistry, Physics and Environmental and Soil Sciences and Agrotecnio, University of Lleida, Lleida, Catalonia, Spain.
Conformational and ionization equilibria of flexible weak polyelectrolytes (PEs) are, in general, strongly coupled. In this article, we analyze the effect of averaging over (or "contracting") the conformational degrees of freedom so that the original flexible molecule is replaced by an effective rigid object with the same ionization properties. As a result, one obtains the so-called Site Binding (SB) model, much easier to treat both theoretically and computationally, and extensively used to characterize the ionization properties of PE.
View Article and Find Full Text PDFBiophys J
December 2024
Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona. Electronic address:
Structural biology relies on several powerful techniques, but these tend to be limited in their ability to characterize protein fluctuations and mobility. Overreliance on structural approaches can lead to omission of critical information regarding biological function. Currently there is a need for complementary biophysical methods to visualize these mobile aspects of protein function.
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