Mapping chemical exchange in proteins with MW > 50 kD

Chemical exchange reveals motions in proteins that are critical for ligand binding, catalysis, and allosteric regulation at the microsecond to millisecond time scale. The detection of chemical exchange is inherently difficult in large proteins because of the fast transverse relaxation rate (R2) and spectral overlap. Here we report novel pulse sequences for the rapid identification of chemical exchange applicable to large deuterated proteins with MW greater than 30 kD. The success of our method is demonstrated in triosephosphate isomerase (TIM, MW = 54 kD).     

An anionic siloxane polymer as a pseudostationary phase for electrokinetic chromatography

A novel polymeric pseudostationary phase for electrokinetic chromatography is introduced and characterized. Siloxane polymers are of interest for this application because of the range of chemistries that could be developed based on these backbones, and because successful development of siloxane polymers would make it possible to employ much of the stationary phase chemistry developed in the past thirty years. A commercially available water-soluble siloxane with a hydroxy-terminated alkyl group was converted to the sulfate derivative. This siloxane polymer is water-soluble, effectively eliminating this limitation associated with siloxane polymers. When employed as a pseudostationary phase, this compound provided rapid, efficient, and selective separations. The electrophoretic mobility of the polymer was less than sodium dodecyl sulfate (SDS) and poly(sodium 10-undecenylsulfate), providing a compressed migration time range, which is the main limiting factor for this polymer. The chemical selectivity of the siloxane sulfate was somewhat different than SDS micelles. The siloxane was employed in buffers modified with a large amount of acetonitrile to separate a number of polynuclear aromatic hydrocarbons. The addition of acetonitrile caused an apparent discontinuity in the electrophoretic mobility of the polymer, which may indicate a change in the structure with increasing organic solvent content.     

Shallow implantation of "Size-Selected" Ag clusters into graphite

We have investigated the implantation of Ag(N) (N = 20-200) clusters into a graphite substrate over the range of energies (E) 0.75-6 keV using molecular dynamics simulations. We find that after implantation the silver clusters remain coherent, albeit amorphous, and rest at the bottom of an open tunnel in the graphite created by the impact. It is found that the implantation depth of the clusters varies linearly as E/N2/3. We conclude that the cluster is decelerated by a constant force proportional to its cross-sectional area. We also identify a threshold energy for surface penetration associated with elastic compression of the graphite substrate.     

Connections to fixed points and Sil’nikov saddle-focus homoclinic orbits in singularly perturbed systems

We consider a singularly perturbed system depending on two parameters with two (possibly the same) normally hyperbolic center manifolds. We assume that the unperturbed system has an orbit that connects a hyperbolic fixed point on one center manifold to a hyperbolic fixed point on the other. Then we prove some old and new results concerning the persistence of these connecting orbits and apply the results to find examples of systems in dimensions greater than three that possess Sil’nikov saddle-focus homoclinic orbits. Published in Ukrains’kyi Matematychnyi Zhurnal, Vol. 60, No. 1, pp. 28–55, January, 2008.     

Eine Methode zum Nachweis und zur qualitativen Trennung von Ferrocyaniden, Ferricyaniden und Rhodaniden

Ohne Zusammenfassung     

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Ohne Zusammenfassung     

Numerical Approximation of the Spectra of Phan-Thien Tanner Liquids

The linear stability of the linear Phan-Thien Tanner (PTT) fluid model is investigated for plane Poiseuille flow. The PTT model involves parameters that can be used to fit shear and extensional data, which makes it suitable for describing both polymer solutions and melts. The base flow is determined using a Chebyshev-tau method. The linear stability equations are also discretized using Chebyshev approximations to furnish a generalized eigenvalue problem. The spectrum is shown to comprise a continuous part and a discrete part. The theoretical and numerical results are validated for the UCM and Oldroyd-B models, which are special cases of the PTT model, by comparing with results in the literature. It is demonstrated that the linear PTT fluid is stable to infinitesimal disturbances with respect to the range of shear-thinning, extensional and elasticity parameters considered. The computational efficiency and accuracy of the numerical method are also investigated.     

The dynamics of gallamine: A potent neuromuscular blocker. A determination by quantum mechanics and molecular dynamics (i) in vacuo studies

The potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.