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A. E. Sitnitsky

Publications and source records attributed to A. E. Sitnitsky.

23 records · Page 2Linked to original sources

Solvent viscosity dependence for enzymatic reactions

A mechanism for relationship of solvent viscosity with reaction rate constant at enzyme action is suggested. It is based on fluctuations of electric field in enzyme active site produced by thermally equilibrium rocking (cranckshaft motion) of the rigid plane (in which the dipole moment $\approx 3.6 D$ lies) of a favourably located and oriented peptide group (or may be a few of them). Thus the rocking of the plane leads to fluctuations of the electric field of the dipole moment. These fluctuations can interact with the reaction coordinate because the latter in its turn has transition dipole moment due to separation of charges at movement of the reacting system along it. The rocking of the plane of the peptide group is sensitive to the microviscosity of its environment in protein interior and the latter is a function of the solvent viscosity. Thus we obtain an additional factor of interrelationship for these characteristics with the reaction rate constant. We argue that due to the properties of the cranckshaft motion the frequency spectrum of the electric field fluctuations has a sharp resonance peak at some frequency and the corresponding Fourier mode can be approximated as oscillations. We employ a known result from the theory of thermally activated escape with periodic driving to obtain the reaction rate constant and argue that it yields reliable description of the preexponent where the dependence on solvent viscosity manifests itself. The suggested mechanism is shown to grasp the main feature of this dependence known from the experiment and satisfactorily yields the upper limit of the fractional index of a power in it.

q-bio.BM↗

Low frequency limit for thermally activated escape with periodic driving

The period-average rate in the low frequency limit for thermally activated escape with periodic driving is derived in a closed analytical form. We define the low frequency limit as the one where there is no essential dependence on frequency so that the formal limit $Ω\to 0$ in the appropriate equations can be taken. We develop a perturbation theory of the action in the modulation amplitude and obtain a cumbersom but closed and tractable formula for arbitrary values of the modulation ampitude to noise intensity ratio $A/D$ except a narrow region near the bifurcation point and a simple analytical formula for the limiting case of moderately strong modulation. The present theory yields analytical description for the retardation of the exponential growth of the escape rate enhancement (i.e., transition from a log-linear regime to more moderate growth and even reverse behavior). The theory is developed for an arbitrary potential with an activation barrier but is exemplified by the cases of cubic (metastable) and quartic (bistable) potentials.

cond-mat.stat-mech↗

Dynamical contribution into enzyme catalytic efficiency

A realistic physical model for the so called rate promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein dynamics, namely, by the so called discrete breather (DB) in secondary structure. The strength of interaction of the RPV with the reaction coordinate is evaluated and its effect on the reaction acceleration is assessed within the framework of modern theory for thermally activated escape rate at periodic driving. We reveal the phenomenon of resonant activation in our model elucidating why the frequency of the RPV in the range $100\div200 cm^{-1}$ was chosen by the evolution of enzymes as an optimal one. The effect of the RPV on the reaction acceleration is shown to vary from moderate one (up to $10^3\div10^4$) in the case of three-site DB to enormous (up to $10^6\div10^8$) in the case of five-site DB and thus can significantly contribute into enzyme catalytic efficiency. Also the model is shown to be compatible with the known functional dependence of enzymatic reaction rates on solvent viscosity.

cond-mat.soft↗

Discrete breathers in protein secondary structure

The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction characterizing the chain rigidity and the effective on-site potentials are calculated for three main types of protein secondary structure. The coupling interaction is found to be surprisingly weak for all of them but different in character: repulsive for alpha-helix and anti-parallel beta-sheet structures and attractive for parallel beta-sheet structure. The effective on-site potential is found to be a hard one for alpha-helix and anti-parallel beta-sheet and a soft one for parallel beta-sheet. In all three types of protein secondary structures a stable zig-zag shape discrete breather (DB) associated with the oscillations of torsional (dihedral) angles can exist due to weakness of the coupling interaction. However, since the absorption of far infrared radiation (IR) by proteins is known to require the existence of rather long chains of hydrogen bonds that takes place only in alpha-helicies, then one can conclude that the excitation of a DB in such a way is possible in alpha-helix and seems to be hardly possible in beta-sheet structures. The interpretation of the recent experiments of Xie et al. on far IR laser pulse spectroscopy of proteins is suggested. The frequency of a DB in an the alpha-helix is obtained in the region of 115 cm^{-1} in accordance with these experiments.

cond-mat.soft↗

Spin-lattice NMR relaxation by anomalous translational diffusion

A model-free theoretical framework for a phenomenological description of spin-lattice relaxation by anomalous translational diffusion in inhomogeneous systems based on the fractional diffusion equation is developed. The dependence of the spin-lattice relaxation time on the size of the pores in porous glass Vycor is experimentally obtained and found to agree well with our theoretical predictions. We obtain nonmonotonic behavior of the translational spin-lattice relaxation rate constant (it passes through a maximum) with the variation of the parameter referring to the extent of inhomogeneity of the system.

cond-mat.soft↗