Ivan S. Podkorytov

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With the advent of ultra-long MD simulations it becomes possible to model microsecond time-scale protein dynamics and, in particular, the exchange broadening effects (R(ex)) as probed by NMR relaxation dispersion measurements. This new approach allows one to identify the exchanging species, including the elusive "excited states". It further helps to map out(More)
Site-directed spin labeling in combination with paramagnetic relaxation enhancement (PRE) measurements is one of the most promising techniques for studying unfolded proteins. Since the pioneering work of Gillespie and Shortle (J Mol Biol 1997;268:158), PRE data from unfolded proteins have been interpreted using the theory that was originally developed for(More)
Significant strides have been recently made to fold peptides and small proteins in silico using MD simulations. However, facilities are currently lacking to include disulfide bonding in the MD models of protein folding. To address this problem, we have developed a simple empirical protocol to model formation of disulfides, which is perturbation-free,(More)
A spin lock comprised of radiofrequency pulses with alternating phase, (x) (-x)(x) (-x) , is proposed as a new technique to probe microsecond time-scale dynamics. A series of R1rho measurements using different pulse duration tp allows one to determine exchange rate, kex, the product p(a)p(b)(Delta omega(ab))2 involving populations of the exchanging species,(More)
Antitumor GO peptides have been designed as dimerization inhibitors of prominent oncoprotein mucin 1. In this study we demonstrate that activity of GO peptides is independent of the level of cellular expression of mucin 1. Furthermore, these peptides prove to be broadly cytotoxic, causing cell death also in normal cells such as dermal fibroblasts and(More)
Two novel heterometallic octahedral clusters [Rh(4)Pt(2)(CO)(11)(dppm)(2)](1) and [Ru(2)Rh(2)Pt(2)(CO)(12)(dppm)(2)](2) were synthesized by the reaction of [Rh(2)Pt(2)(CO)(6)(dppm)(2)] with [Rh(6)(CO)(14)(NCMe)(2)] and Ru(3)(CO)(12), respectively. Solid state structures of 1 and 2 have been established by a single crystal X-ray diffraction study. Two dppm(More)
Experimental results (recent IR, DFT calculations and modern multinuclear NMR measurements on Rh-containing clusters, together with earlier VT multinuclear NMR measurements) show that the use of the Ligand Polyhedral Model (LPM) to provide a general mechanism for ligand fluxionality in Transition Metal Carbonyl Clusters (TMCCs) in solution cannot be(More)
We have investigated the behavior of second RNA-recognition motif (RRM2) of neuropathological protein TDP43 under the effect of oxidative stress as modeled in vitro. Toward this end we have used the specially adapted version of H/D exchange experiment, NMR relaxation and diffusion measurements, dynamic light scattering, controlled proteolysis, gel(More)
Tripyrrolylphosphine reacts with the cluster Rh6CO15(NCMe) to afford the disubstituted Rh6CO14(mu2)-P(NC4H4)3) derivative (2) via the Rh6CO15P(NC4H4)3 intermediate (1) with eta(1)-P coordination. In the solid state, 2 has the phosphine occupying a bridging position where it is bonded to two neighboring Rh atoms in the Rh(6) octahedron through the P-atom and(More)
A new version of one-dimensional (1)H experiment has been developed to probe ligand binding to macromolecular targets. The experiment, called transient NOE-exchange relay, is similar to the 'reverse NOE pumping' technique [A. Chen, M.J. Shapiro, J. Am. Chem. Soc. 122 (2000) 414-415]. The T(2) filter is used to erase protein magnetization, and the saturation(More)