Biomedical subjects

Alexey Krushelnitsky

Publications and source records attributed to Alexey Krushelnitsky.

6 recordsLinked to original sources

PubMed2006

Comparison of the internal dynamics of globular proteins in the microcrystalline and rehydrated lyophilized states.

Natural abundance solid-state 13C-NMR spin-lattice relaxation experiments in the laboratory (T1) and off-resonance rotating (T(1rho)) frames were applied for qualitative comparison of the internal molecular dynamics of barstar, hen egg white lysozyme and bacteriophage T4 lysozyme in both the microcrystalline and the rehydrated (water content is 50% of the protein mass) lyophilized states. The microcrystalline state of proteins provides a better spectral resolution; however, less is known about the local structure and dynamics in the different states. We found by visual comparison of both T1 and T(1rho) relaxation decays of various resonance bands of the CPMAS spectra that within the ns-mus range of correlation times there is no appreciable difference in the internal dynamics between rehydrated lyophilized and crystalline states for all three proteins tested. This suggests that the internal conformational dynamics depends weakly if at all on inter-protein interactions in the solid state. Hence, physical properties of globular proteins in a fully hydrated solid state seem to be similar to those in solution. This result at least partly removes concerns about biological relevance of studies of globular proteins in the solid state.

Animals↗

PubMed2006

15N spin diffusion rate in solid-state NMR of totally enriched proteins: the magic angle spinning frequency effect.

As demonstrated by means of the one-dimensional solid-state MAS exchange experiment (CODEX), the rate of the proton driven spin diffusion between backbone (15)N nuclei in totally enriched protein depends strongly on the magic angle spinning (MAS) frequency: spin diffusion at MAS frequency 16 kHz is about 4-5 times slower as compared to that at MAS frequency 1 kHz which is due to the averaging of the homo- and hetero-nuclear dipolar interactions by MAS. It is important that even at the highest MAS frequencies used in our experiments the spin diffusion rate is comparable or larger than typical values of the spin-lattice relaxation rates of backbone nitrogens in solid proteins. Thus, the precise quantitative analysis of (15)N T(1)'s in totally enriched solid proteins may lead to wrong quantitative results. On the other hand, the effectiveness of the (15)N-(15)N correlation and structure determination experiments making use of (15)N-(15)N distances can be increased by decreasing the MAS frequency as far as possible, which is counter intuitive to the commonly applied fast MAS conditions in order to reduce the dipolar-broadened line widths for increased spectral resolution.

Glycine↗

PubMed2006

Intermolecular electrostatic interactions and Brownian tumbling in protein solutions.

It is often implicitly assumed that the long-range intermolecular electrostatic interactions in homogeneous protein solutions either are negligible for affecting protein Brownian tumbling or cause its deceleration without changing the shape of rotational auto-correlation function. This review presents a wide set of experimental data (NMR relaxation, dielectric spectroscopy and Brownian dynamics simulations) demonstrating that the interprotein electrostatic steering leads to a complication of the rotational correlation function. The key point of this effect is the rotational anisotropy caused by the interaction of the electric dipole moment of a protein with the external electric field produced by charges of neighboring proteins. Taking this effect into account in some cases might be of critical importance for the correct interpretation of various experimental data.

Anisotropy↗

PubMed2005

Complex 1H,13C-NMR relaxation and computer simulation study of side-chain dynamics in solid polylysine.

The side-chain dynamics of solid polylysine at various hydration levels was studied by means of proton spin-lattice relaxation times measurements in the laboratory and tilted (off-resonance) rotating frames at several temperatures as well as Monte Carlo computer simulations. These data were analyzed together with recently measured carbon relaxation data (A. Krushelnitsky, D. Faizullin, and D. Reichert, Biopolymers, 2004, Vol. 73, pp. 1-15). The analysis of the whole set of data performed within the frame of the model-free approach led us to a conclusion about three types of the side-chain motion. The first motion consists of low amplitude rotations of dihedral angles of polylysine side chains on the nanosecond timescale. The second motion is cis-trans conformational transitions of the side chains with correlation times in the microsecond range for dry polylysine. The third motion is a diffusion of dilating defects described in (W. Nusser, R. Kimmich, and F. Winter, Journal of Physical Chemistry, 1988, Vol. 92, pp. 6808-6814). This diffusion causes almost no reorientation of chemical bonds but leads to a sliding motion of side chains with respect to each other in the nanosecond timescale. This work evidently demonstrates the advantages of the simultaneous quantitative analysis of data obtained from different experiments within the frame of the same mathematical formalism, providing for the detailed description of the nature and geometry of the internal molecular dynamics.

Carbon Isotopes↗

PubMed2004

Hydration dependence of backbone and side chain polylysine dynamics: a 13C solid-state NMR and IR spectroscopy study.

The molecular dynamics of solid poly-L-lysine has been studied by the following natural abundance (13)C-NMR relaxation methods: measurements of the relaxation times T(1) at two resonance frequencies, off-resonance T(1rho) at two spin-lock frequencies, and proton-decoupled T(1rho). Experiments were performed at different temperatures and hydration levels (up to 17% H(2)O by weight). The natural abundance (13)C-CPMAS spectrum of polylysine provides spectral resolution of all types of backbone and side chain carbons and thus, dynamic parameters could be determined separately for each of them. At the same time, the conformational properties of polylysine were investigated by Fourier transform infrared spectroscopy. The data obtained from the different NMR experiments were simultaneously analyzed using the correlation function formalism and model-free approach. The results indicate that in dry polylysine both backbone and side chains take part in two low amplitude motions with correlation times of the order of 10(-4) s and 10(-9) s. Upon hydration, the dynamic parameters of the backbone remain almost constant except for the amplitude of the slower process that increases moderately. The side chain dynamics reveals a much stronger hydration response: the amplitudes of both slow and fast motions increase significantly and the correlation time of the slow motion shortens by about five orders of magnitude, and at hydration levels of more than 10% H(2)O fast and slow side chain motions are experimentally indistinguishable. These changes in the molecular dynamics cannot be ascribed to any hydration-dependent conformational transitions of polylysine because IR spectra reveal almost no hydration dependence in either backbone or side chain absorption domains. The physical nature of the fast and slow motions, their correlation time distributions, and hydration dependence of microdynamic parameters are discussed.

Magnetic Resonance Spectroscopy↗

PubMed2002

Expanding the frequency range of the solid-state T1rho experiment for heteronuclear dipolar relaxation.

Solid-state spin-lattice relaxation in the rotating frame permits the investigation of dynamic processes with correlation times in the range of microseconds. The relaxation process in organic solids is driven by the fluctuation of the local magnetic field due to the dipole-dipole interaction of the probe nuclei (13C,15N) with 1H in close proximity. However, its effect is often hidden by a competing relaxation process due to the contact between the rotating frame 13C/15N Zeeman and 1H dipolar reservoirs. In most cases the latter process becomes superior for the commonly applied low and moderate spin-lock fields and practically does not provide information about the molecular dynamics. To suppress this undesired process and to expand the dynamic range of T1rho experiments, we present two approaches. The first one uses a resonance offset of the frequency of the spin-lock irradiation, which leads to a significant enhancement of the effective spin-lock frequency without the application of destructive high transmitter powers. We derive the theory and demonstrate the applicability of the method on various model compounds. The second approach utilizes heteronuclear 1H decoupling during the 13C/15N spin-lock irradiation which disrupts the contact between the 13C/15N Zeeman and 1H dipolar reservoirs. We demonstrate the method and discuss the results qualitatively.

Carbon Isotopes↗