Analysis of binding centers in nicotinic receptors with the aid of synthetic peptides.

We studies the receptor-binding specificity of the synthetic peptide HAP (High Affinity Peptide) and its analogues, which are regarded as a model of the orthosteric site nicotinic acetylcholine receptors (nAChR). Using radioligand analysis, electrophysiology tests, and calcium imaging, we assessed the ability of HAP to interact with nAChR antagonists: long α-neurotoxins and α-conotoxins. A high affinity of HAP for α-bungarotoxin and the absence of its interaction with α-cobratoxin and α-conotoxins was found. The synthesized analogues of HAP in general retained the properties of the original peptide. Thus, HAP cannot be a model of a ligand-binding site.

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations.

Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded ß-sheet structure. The 1 µs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short (+)N-H⋯O(-) bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm(-1). It is caused by the asymmetric stretching vibrations of the (+)N-H⋯O(-) fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.

Charge-Transfer Mobility Parameters in Photoelectronic Devices: The Advanced Miller-Abrahams Computation.

The local hopping step of the electron transfer (ET) reaction is investigated for a real organic material composed of molecules M (N,N'-di(1-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine). This material is implemented in light-emitting photoelectronic devices. The conductivity effect is simulated and calculated at a molecular level. We have studied the ET mechanism alternative to that suggested by the usually employed Marcus-like polaron model. The ion-molecular binary complex M(+)M (for hole transfer) is considered as a reaction center. The reaction dynamics is carried through the low-frequency intermolecular vibration coordinate connecting its fragments (the promotion mode). Its coupling to the acoustic phonon bath serves for a dissipation of the reaction energy misfit. The high-frequency intramolecular vibrations (the reorganization modes) modulate the reaction kinetics via Franck-Condon factors induced by their polarization. The ET rate constants are evaluated in terms of the computational algorithm described earlier (Basilevsky, M. V.; et al. J. Chem. Phys. 2013 139, 234102). Standard quantum-chemical and molecular dynamical techniques are used for a calculation of all necessary parameters of this model. The macroscopic charge-carrier mobility of the material is estimated by properly averaging the rate constants over the total simulation cell.

Golden rule kinetics of transfer reactions in condensed phase: the microscopic model of electron transfer reactions in disordered solid matrices.

The algorithm for a theoretical calculation of transfer reaction rates for light quantum particles (i.e., the electron and H-atom transfers) in non-polar solid matrices is formulated and justified. The mechanism postulated involves a local mode (an either intra- or inter-molecular one) serving as a mediator which accomplishes the energy exchange between the reacting high-frequency quantum mode and the phonon modes belonging to the environment. This approach uses as a background the Fermi golden rule beyond the usually applied spin-boson approximation. The dynamical treatment rests on the one-dimensional version of the standard quantum relaxation equation for the reduced density matrix, which describes the frequency fluctuation spectrum for the local mode under consideration. The temperature dependence of a reaction rate is controlled by the dimensionless parameter ξ0 = ℏω0/k(B)T where ω0 is the frequency of the local mode and T is the temperature. The realization of the computational scheme is different for the high/intermediate (ξ0 < 1 - 3) and for low (ξ0 ≫ 1) temperature ranges. For the first (quasi-classical) kinetic regime, the Redfield approximation to the solution of the relaxation equation proved to be sufficient and efficient in practical applications. The study of the essentially quantum-mechanical low-temperature kinetic regime in its asymptotic limit requires the implementation of the exact relaxation equation. The coherent mechanism providing a non-vanishing reaction rate has been revealed when T → 0. An accurate computational methodology for the cross-over kinetic regime needs a further elaboration. The original model of the hopping mechanism for electronic conduction in photosensitive organic materials is considered, based on the above techniques. The electron transfer (ET) in active centers of such systems proceeds via local intra- and intermolecular modes. The active modes, as a rule, operate beyond the kinetic regimes, which are usually postulated in the existing theories of the ET. Our alternative dynamic ET model for local modes immersed in the continuum harmonic medium is formulated for both classical and quantum regimes, and accounts explicitly for the mode∕medium interaction. The kinetics of the energy exchange between the local ET subsystem and the surrounding environment essentially determine the total ET rate. The efficient computer code for rate computations is elaborated on. The computations are available for a wide range of system parameters, such as the temperature, external field, local mode frequency, and characteristics of mode/medium interaction. The relation of the present approach to the Marcus ET theory and to the quantum-statistical reaction rate theory [V. G. Levich and R. R. Dogonadze, Dokl. Akad. Nauk SSSR, Ser. Fiz. Khim. 124, 213 (1959); J. Ulstrup, Charge Transfer in Condensed Media (Springer, Berlin, 1979); M. Bixon and J. Jortner, Adv. Chem. Phys. 106, 35 (1999)] underlying it is discussed and illustrated by the results of computations for practically important target systems.

Association constants and distribution functions for ion pairs in binary solvent mixtures: application to a cyanine dye system.

The computations of the association constants K(ass) were performed at the microscopic level for the ion pair Cy(+)I(-) composed of the complex cyanine dye cation Cy(+) coupled to the negative iodine counterion. The wide array of K(ass) values is arranged by a variation of the composition of the binary solvent mixtures toluene/dimethylsulfoxide with the accompanying change of the solvent polarity. The potentials of mean force (PMFs) are calculated for a set of interionic separations R in the Cy(+)I(-) by a methodology which combines the quantum-chemical techniques for the treatment of the electronic structure of the Cy(+)I(-) system with the recent dielectric continuum approach which accounts for the solvation effects. For a given solute/solvent system the probability function P(R), which describes the distribution of interionic separations, is constructed in terms of the PMFs and implemented for the evaluation of the K(ass).

Decay kinetics of the excited S1 state of the cyanine dye Cy(+)I(-) (thiacarbocyanine iodide): the computation of quantum yields for different pathways.

This work explains the unordinary solvent effect which was observed in the photochemical decay kinetics for the cyanine dye thiacarbocyanine iodide (Cy(+)I(-)) in binary solvent mixtures toluene/dimethylsulfoxide. The interpretation is formulated in terms of the probability density F(R) describing the distribution of interionic distances R in the ion pair Cy(+)I(-) and depending on the solvent composition. The proper normalization of this distribution is expressed via the degree of association α for the ion pair in a given solvent mixture. The α values are, in turn, extracted by means of the mass action law from the ionic association constants computed in a separate publication. The detailed kinetic scheme includes the empirical parametrization of the R-dependent kinetic constants for different decay channels. The multiparameter fitting procedure represents, with the reasonable parameter values, the dependence of the observed quantum yields on the solvent composition.