Wheelergammelgaard7316

We show that the Cu2+ label functions efficiently within the standard PNA and the hydroxymethyl-modified PNA and that the MD parameters may be used to accurately reproduce our EPR findings. Through the combination of EPR and MD, we gain new insights into the PNA structure and conformations as well as into the mechanism of orientational selectivity in Cu2+ EPR at X-band. These results present for the first time a rigid Cu2+ spin label used for EPR distance measurements in PNA and the accompanying MD force fields for the spin label. Our studies also reveal that the spin labels have a low impact on the structure of the PNA duplexes. The combined MD and EPR approach represents an important new tool for the characterization of the PNA duplex structure and provides valuable information to aid in the rational application of PNA at large.Measuring the kinetics that govern ligand-receptor interactions is fundamental to our understanding of pharmacology. For ligand-gated ion channels, binding of an agonist triggers allosteric motions that open an integral ion-permeable pore. By mathematically modeling stochastic electrophysiological responses with high temporal resolution (ms), previous single channel studies have been able to infer the rate constants of ligands binding to these receptors. However, there are no reports of the direct measurement of the single-molecule binding events that are vital to how agonists exert their functional effects. For the first time, we report these direct measurements, the rate constants, and corresponding free energy changes, which describe the transitions between the different binding states. To achieve this, we use the super resolution technique points accumulation for imaging in nanoscale topography (PAINT) to observe binding of ATP to orthosteric binding sites on the P2X1 receptor. Furthermore, an analysis of time-resolved single-molecule interactions is used to measure elementary rate constants and thermodynamic forces that drive the allosteric motions. These single-molecule measurements unequivocally establish the location of each binding states of the P2X1 receptor and the stochastic nature of the interaction with its native ligand. The analysis leads to the measurement of the forward and reverse rates from a weak ligand-binding state to a strong ligand binding state that is linked to allosteric motion and ion pore formation. These rates (kα = 1.41 sec-1 and kβ = 0.32 sec-1) were then used to determine the free energy associated with this critical mechanistic step (3.7 kJ/mol). Importantly, the described methods can be readily applied to all ligand-gated ion channels, and more broadly to the molecular interactions of other classes of membrane proteins.This work deals with the solvation thermodynamics of systems containing extreme intermolecular interaction asymmetries, such as binary mixtures comprising ideal gas species plus other real species, and analyzes the composition dependence of relevant solvation properties from a rigorous molecular-based theoretical viewpoint. PF-841 It focuses on the effect of large intermolecular interaction asymmetries, involving simple model species for which we have available rigorous results, to advance our understanding of the true molecular-based origin of their unconventional solvation behavior. This effort involves a statistical mechanics approach to identify the thermodynamic constraints and microstructural manifestation underlying the nonmonotonous composition behavior of the species' partial molar properties, as well as to describe formally the explicit link between the intermolecular asymmetries and the observed anomalous behavior. The outcome of the analysis provides sound support to the depiction of the solvation of a weakly interacting solute in a real solvent, a scenario that facilitates the molecular thermodynamic interpretation of gas solvation characterized by low solubility and thermodynamic stability gaps. Moreover, this work illustrates direct comparisons between real aqueous systems and the ideal gas-aqueous system counterparts to highlight and discuss the usefulness of invoking the ideal gas species as a reference solute to gain understanding of the solvation of real gas species.The protein-osmolyte interaction has been shown experimentally to follow an additive construct, where the individual osmolyte-backbone and osmolyte-side-chain interactions contribute to the overall conformational stability of proteins. Here, we computationally reconstruct this additive relation using molecular dynamics simulations, focusing on sugars and polyols, including sucrose and sorbitol, as model osmolytes. A new set of parameters (ADD) is developed for this purpose, using the individual Kirkwood-Buff integrals for sugar-backbone and sugar-side-chain interactions as target experimental data. We show that the ADD parameters can reproduce the additivity of protein-sugar interactions and correctly predict sucrose and sorbitol self-association and their interaction with water. The accurate description of the separate osmolyte-backbone and osmolyte-side-chain contributions also automatically translates into a good prediction of preferential exclusion from the surface of ribonuclease A and α-chymotrypsinogen A. The description of sugar polarity is improved compared to previous force fields, resulting in closer agreement with the experimental data and better compatibility with charged groups, such as the guanidinium moiety. The ADD parameters are developed in combination with the CHARMM36m force field for proteins, but good compatibility is also observed with the AMBER 99SB-ILDN and the OPLS-AA force fields. Overall, exploiting the additivity of protein-osmolyte interactions is a promising approach for the development of new force fields.We report on the structure of dendritic polyelectrolytes accompanied by counterions in a good, salt-free, implicit solvent using Langevin dynamics simulations and a Flory-type approach. Our focus is on the modification of charged dendrimer conformations via the strength of electrostatic interactions and the counterion excluded volume. We study the effects caused by charges by varying the reduced Bjerrum length, λB*, between the extremes of weak and strong electrostatic interactions. The counterion excluded volume was controlled by the size of ions. We investigate counterions ranging from conventional ones, with the size comparable to the monomer size, to bulky ions. Our results indicate that, as compared to neutral dendrimers, dendritic polyelectrolytes exist in swollen conformations, and the degree of swelling changes non-monotonically with increasing λB*. For weak electrostatic couplings, counterion density within dendrimers is minor and their radius of gyration subtly exceeds the size of neutral dendrimers.