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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. Source


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. Source


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. Source


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. Source


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. Source

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