Kazan Institute of Biochemistry and Biophysics

Kazan, Russia

Kazan Institute of Biochemistry and Biophysics

Kazan, Russia

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Sitnitsky A.E.,Kazan Institute of Biochemistry and Biophysics
Chemical Physics Letters | Year: 2017

We construct a double-well potential for which the Schrödinger equation can be exactly solved via reducing to the confluent Heun's one. Thus the wave function is expressed via the confluent Heun's function. The latter is tabulated in Maple so that the obtained solution is easily treated. The potential is infinite at the boundaries of the final interval that makes it to be highly suitable for modeling hydrogen bonds (both ordinary and low-barrier ones). We exemplify theoretical results by detailed treating the hydrogen bond in KHCO3 and show their good agreement with literature experimental data. © 2017 Elsevier B.V.

Ermakova E.,University of Minnesota | Ermakova E.,Kazan Institute of Biochemistry and Biophysics | Miller M.C.,University of Minnesota | Nesmelova I.V.,University of Minnesota | And 16 more authors.
Glycobiology | Year: 2013

The product of p53-induced gene 1 is a member of the galectin family, i.e., galectin-7 (Gal-7). To move beyond structural data by X-ray diffraction, we initiated the study of the lectin by nuclear magnetic resonance (NMR) and circular dichroism spectroscopies, and molecular dynamics (MD) simulations. In concert, our results indicate that lactose binding to human Gal-7 induces long-range effects (minor conformational shifts and changes in structural dynamics) throughout the protein that result in stabilization of the dimer state, with evidence for positive cooperativity. Monte Carlo fits of 15N-Gal-7 HSQC titrations with lactose using a two-site model yield K1 = 0.9 ± 0.6 × 103 M-1 and K2 = 3.4 ± 0.8 × 103 M-1. Ligand binding-induced stabilization of the Gal-7 dimer was supported by several lines of evidence: MD-based calculations of interaction energies between ligand-loaded and ligand-free states, gel filtration data and hetero-FRET spectroscopy that indicate a highly reduced tendency for dimer dissociation in the presence of lactose, CD-based thermal denaturation showing that the transition temperature of the lectin is significantly increased in the presence of lactose, and saturation transfer difference (STD) NMR using a molecular probe of the monomer state whose presence is diminished in the presence of lactose. MD simulations with the half-loaded ligand-bound state also provided insight into how allosteric signaling may occur. Overall, our results reveal long-range effects on Gal-7 structure and dynamics, which factor into entropic contributions to ligand binding and allow further comparisons with other members of the galectin family. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Nesmelova I.V.,University of Minnesota | Nesmelova I.V.,University of North Carolina at Charlotte | Ermakova E.,Kazan Institute of Biochemistry and Biophysics | Daragan V.A.,University of Minnesota | And 9 more authors.
Journal of Molecular Biology | Year: 2010

Galectins are a family of lectins with a conserved carbohydrate recognition domain that interacts with Β-galactosides. By binding cell surface glycoconjugates, galectin-1 (gal-1) is involved in cell adhesion and migration processes and is an important regulator of tumor angiogenesis. Here, we used heteronuclear NMR spectroscopy and molecular modeling to investigate lactose binding to gal-1 and to derive solution NMR structures of gal-1 in the lactose-bound and unbound states. Structure analysis shows that the Β-strands and loops around the lactose binding site, which are more open and dynamic in the unbound state, fold in around the bound lactose molecule, dampening internal motions at that site and increasing motions elsewhere throughout the protein to contribute entropically to the binding free energy. CD data support the view of an overall more open structure in the lactose-bound state. Analysis of heteronuclear single quantum coherence titration binding data indicates that lactose binds the two carbohydrate recognition domains of the gal-1 dimer with negative cooperativity, in that the first lactose molecule binds more strongly (K1=21±6×103 M-1) than the second (K2=4±2×103 M-1). Isothermal calorimetry data fit using a sequential binding model present a similar picture, yielding K1=20±10×103 M-1 and K2=1.67±0.07×103 M-1. Molecular dynamics simulations provide insight into structural dynamics of the half-loaded lactose state and, together with NMR data, suggest that lactose binding at one site transmits a signal through the Β-sandwich and loops to the second binding site. Overall, our results provide new insight into gal-1 structure-function relationships and to protein-carbohydrate interactions in general. © 2010.

PubMed | University Pierre and Marie Curie, Kazan Institute of Biochemistry and Biophysics, Akdeniz University, RAS Arbuzov Institute of Organic and Physical Chemistry and 4 more.
Type: Journal Article | Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience | Year: 2014

Terminal Schwann cells (TSCs) are key components of the mammalian neuromuscular junction (NMJ). How the TSCs sense the synaptic activity in physiological conditions remains unclear. We have taken advantage of the distinct localization of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) at the NMJ to bring out the function of different ACh receptors (AChRs). AChE is clustered by the collagen Q in the synaptic cleft and prevents the repetitive activation of muscle nicotinic AChRs. We found that BChE is anchored at the TSC by a proline-rich membrane anchor, the small transmembrane protein anchor of brain AChE. When BChE was specifically inhibited, ACh release was significant depressed through the activation of 7 nAChRs localized on the TSC and activated by the spillover of ACh. When both AChE and BChE were inhibited, the spillover increased and induced a dramatic reduction of ACh release that compromised the muscle twitch triggered by the nerve stimulation. 7 nAChRs at the TSC may act as a sensor for spillover of ACh adjusted by BChE and may represent an extrasynaptic sensor for homeostasis at the NMJ. In myasthenic rats, selective inhibition of AChE is more effective in rescuing muscle function than the simultaneous inhibition of AChE and BChE because the concomitant inhibition of BChE counteracts the positive action of AChE inhibition. These results show that inhibition of BChE should be avoided during the treatment of myasthenia and the pharmacological reversal of residual curarization after anesthesia.

Krushelnitsky A.,Kazan Institute of Biochemistry and Biophysics | Zinkevich T.,Kazan Physical Technical Institute | Reichert D.,Martin Luther University of Halle Wittenberg | Chevelkov V.,Leibniz Institute for Molecular Pharmacology | Reif B.,Leibniz Institute for Molecular Pharmacology
Journal of the American Chemical Society | Year: 2010

For the first time, we have demonstrated the site-resolved measurement of reliable (i.e., free of interfering effects) 15N R1ρ relaxation rates from a solid protein to extract dynamic information on the microsecond time scale. 15N R1ρ NMR relaxation rates were measured as a function of the residue number in a 15N, 2H-enriched (with 10-20% back-exchanged protons at labile sites) microcrystalline SH3 domain of chicken α-spectrin. The experiments were performed at different temperatures and at different spin-lock frequencies, which were realized by on- and off-resonance spin-lock irradiation. The results obtained indicate that the interfering spin-spin contribution to the R 1ρ rate in a perdeuterated protein is negligible even at low spin-lock fields, in contrast to the case for normal protonated samples. Through correlation plots, the R1ρ rates were compared with previous data for the same protein characterizing different kinds of internal mobility. © 2010 American Chemical Society.

Anisimov A.V.,Kazan Institute of Biochemistry and Biophysics | Dautova N.R.,Kazan Institute of Biochemistry and Biophysics
Review of Scientific Instruments | Year: 2010

This paper proposes a design for a system of temperature stabilization within the range from -10 to +80±0.5 °C for NMR spectrometers which is simple and affordable to fabricate in a laboratory. The design utilizes a closed system of circulation of an air heat carrier, twofold flow around the thermostabilized system, cooling element on Peltier thermal modules, and a proportional-integral-derivative regulator. © 2010 American Institute of Physics.

Sitnitsky A.E.,Kazan Institute of Biochemistry and Biophysics
Physica A: Statistical Mechanics and its Applications | Year: 2016

Exact analytic solution for the probability distribution function of the non-inertial rotational diffusion equation, i.e., of the Smoluchowski one, in a symmetric Maier-Saupe uniaxial potential of mean torque is obtained via the confluent Heun's function. Both the ordinary Maier-Saupe potential and the double-well one with variable barrier width are considered. Thus, the present article substantially extends the scope of the potentials amenable to the treatment by reducing Smoluchowski equation to the confluent Heun's one. The solution is uniformly valid for any barrier height. We use it for the calculation of the mean first passage time. Also the higher eigenvalues for the relaxation decay modes in the case of ordinary Maier-Saupe potential are calculated. The results obtained are in full agreement with those of the approach developed by Coffey, Kalmykov, Déjardin and their coauthors in the whole range of barrier heights. © 2016 Elsevier B.V. All rights reserved.

Kurbanov R.,Kazan Institute of Biochemistry and Biophysics | Zinkevich T.,Kazan Physical Technical Institute | Krushelnitsky A.,Martin Luther University of Halle Wittenberg
Journal of Chemical Physics | Year: 2011

The advantage of the solid state NMR for studying molecular dynamics is the capability to study slow motions without limitations: in the liquid state, if orienting media are not used, all anisotropic magnetic interactions are averaged out by fast overall Brownian tumbling of a molecule and thus investigation of slow internal conformational motions (e.g., of proteins) in solution can be conducted using only isotropic interactions. One of the main tools for obtaining amplitudes and correlation times of molecular motions in the μs time scale is measuring relaxation rate R1ρ. Yet, there have been a couple of unresolved problems in the quantitative analysis of the relaxation rates. First, when the resonance offset of the spin-lock pulse is used, the spin-lock field can be oriented under an arbitrary angle in respect to B0. Second, the spin-lock frequency can be comparable or even less than the magic angle spinning rate. Up to now, there have been no equations for R 1ρ that would be applicable for any values of the spin-lock frequency, magic angle spinning rate and resonance offset of the spin-lock pulse. In this work such equations were derived for two most important relaxation mechanisms: heteronuclear dipolar coupling and chemical shift anisotropy. The validity of the equations was checked by numerical simulation of the R1ρ experiment using SPINEVOLUTION program. In addition to that, the applicability of the well-known model-free approach to the solid state NMR relaxation data analysis was considered. For the wobbling in a cone at 30° and 90° cone angles and two-site jump models, it has been demonstrated that the auto-correlation functions G0(t), G 1(t), G2(t), corresponding to different spherical harmonics, for isotropic samples (powders, polycrystals, etc.) are practically the same regardless of the correlation time of motion. This means that the model-free approach which is widely used in liquids can be equally applied, at least assuming these two motional models, to the analysis of the solid state NMR relaxation data. © 2011 American Institute of Physics.

PubMed | University of North Carolina at Charlotte and Kazan Institute of Biochemistry and Biophysics
Type: Journal Article | Journal: Proteins | Year: 2015

Chemokines form a family of signaling proteins mainly responsible for directing the traffic of leukocytes, where their biological activity can be modulated by their oligomerization state. We characterize the dynamics and thermodynamic stability of monomer and homodimer structures of CXCL7, one of the most abundant platelet chemokines, using experimental methods that include circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy, and computational methods that include the anisotropic network model (ANM), molecular dynamics (MD) simulations and the distance constraint model (DCM). A consistent picture emerges for the effects of dimerization and Cys5-Cys31 and Cys7-Cys47 disulfide bonds formation. The presence of disulfide bonds is not critical for maintaining structural stability in the monomer or dimer, but the monomer is destabilized more than the dimer upon removal of disulfide bonds. Disulfide bonds play a key role in shaping the characteristics of native state dynamics. The combined analysis shows that upon dimerization flexibly correlated motions are induced between the 30s and 50s loop within each monomer and across the dimer interface. Interestingly, the greatest gain in flexibility upon dimerization occurs when both disulfide bonds are present, and the homodimer is least stable relative to its two monomers. These results suggest that the highly conserved disulfide bonds in chemokines facilitate a structural mechanism that is tuned to optimally distinguish functional characteristics between monomer and dimer.

PubMed | University of North Carolina at Charlotte and Kazan Institute of Biochemistry and Biophysics
Type: Journal Article | Journal: PloS one | Year: 2014

The reaction of DNA transposition begins when the transposase enzyme binds to the transposon DNA. Sleeping Beauty is a member of the mariner family of DNA transposons. Although it is an important tool in genetic applications and has been adapted for human gene therapy, its molecular mechanism remains obscure. Here, we show that only the folded conformation of the specific DNA recognition subdomain of the Sleeping Beauty transposase, the PAI subdomain, binds to the transposon DNA. Furthermore, we show that the PAI subdomain is well folded at low temperatures, but the presence of unfolded conformation gradually increases at temperatures above 15C, suggesting that the choice of temperature may be important for the optimal transposase activity. Overall, the results provide a molecular-level insight into the DNA recognition by the Sleeping Beauty transposase.

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