TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations

Summary We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework (http://inka.mssm.edu/~mezei/simulaid/) that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs.     

Effect of cholesterol on the properties of phospholipid membranes. 4. Interatomic voids

The properties of the interatomic voids present in fully hydrated dimyristoylphosphatidylcholine (DMPC)-cholesterol mixed membranes of different compositions are analyzed in detail using a generalized variant of the Voronoi-Delaunay method on the basis of computer simulation results. The systems investigated are chosen from both sides of the DMPC-cholesterol miscibility gap; the pure DMPC bilayer has also been included in the analysis as a reference system. The results obtained show that the empty space is organized in a more compact way, forming larger voids in the presence than in the absence of cholesterol. The voids located in the region of the rigid cholesterol rings become, on average, less spherical, oriented more parallel with the membrane normal axis with increasing cholesterol concentration, whereas an opposite effect of cholesterol is observed in the middle of the membrane among the chain terminal methyl groups. In general, the preferential orientation of the voids is found to strongly correlate with that of the molecules in the hydrocarbon phase of the membranes. The membranes are found to contain rather large voids, the volume of which can be an order of magnitude larger than the largest spherical cavities present in the systems. These voids are elongated or branching channels rather than big empty holes. The voids located among the DMPC and cholesterol molecules are lying preferably parallel with the membrane normal axis. The existence of such empty channels can be of great importance in the cross-membrane permeation of small, uncharged penetrants, in particular, of polar molecules.     

On an Extension Problem for Polynomials

Consider the following problem: given complex numbers a₁, ...,a_n, find an L function f of minimum norm whose Fourier coefficientsc_k(f) are equal to a_k for k between 0 and n. We show the uniquenessof this function, and we estimate its norm. The operator-valuedcase is also discussed. 2000 Mathematics Subject Classification30E05, 47A20, 47A56, 47A57.     

Pressure induced quantum critical point and non-fermi-liquid behavior in BaVS3

We report on experiments giving evidence for quantum effects of electromagnetic flux in barium alumosilicate glass. In contrast to expectation, below 100 mK the dielectric response becomes sensitive to magnetic fields. The experimental findings include both lifting of the dielectric saturation by weak magnetic fields and oscillations of the dielectric response in the low temperature resonant regime. As the origin of these effects we suggest that the magnetic induction field violates the time reversal invariance leading to a flux periodicity in the energy levels of tunneling systems. At low temperatures, this effect is strongly enhanced by the interaction between tunneling systems and thus becomes measurable.     

Analytical selenoamino acid studies by chromatography with interfaced atomic mass spectrometry and atomic emission spectral detection

Consumption of selenium enriched plants or yeast-based nutritional supplements has been reported to provide anticarcinogenic benefits which are selenium compound dependent. Separation and identification of these selenium compounds is critical to understand the activity. Plants and yeast convert inorganic selenium in the soil or growth media into organoselenium compounds, probably following a route similar to the sulfur assimilatory pathway. Non-volatile selenium compounds produced include selenoamino acids, some of which have shown anticarcinogenic activity. Volatile compounds produced by chemical reaction of involatile precursors have also been found. An ion pair chromatographic method with ICP-MS detection for the separation of selenoamino acid standards potentially present in real samples is given. The method allows separation of selenoamino acids including such analytes as the cis-trans isomers of Se-1-propenyl-dl-selenocysteine. The method also provides the capability of determining the presence of selenoxides and possibly selenones, and tracking of other functionalities and reactions by selective derivatization. Alternatively, selenoamino acids are treated with ethylchloroformate to produce stable volatile derivatives which are amenable to GC separation with element specific atomic emission detection (GC-AED). Results of total selenium determination and speciation of selenium enriched yeast-based nutritional supplements, selenium enriched allium vegetables and bioremediation samples are presented.     

Stability of nanodispersions: a model for kinetics of aggregation of nanoparticles

In the course of aggregation of very small colloid particles (nanoparticles) the overlap of the diffuse layers is practically complete, so that one cannot apply the common DLVO theory. Since nanopoarticles are small compared to the extent of the diffuse layer, the process is considered in the same way as for two interacting ions. Therefore, the Br?nsted concept based on the Transition State Theory was applied. The charge of interacting nanoparticles was calculated by means of the Surface Complexation Model and decrease of effective charge of particles was also taken into account. Numerical simulations were performed using the parameters for hematite and rutile colloid systems. The effect of pH and electrolyte concentration on the stability coefficient of nanosystems was found to be more pronounced but similar to that for regular colloidal systems. The effect markedly depends on the nature of the solid which is characterized by equilibrium constants of surface reactions responsible for surface charge, i.e., by the point of zero charge, while the specificity of counterions is described by their association affinity, i.e., by surface association equilibrium constants. The most pronounced is the particle size effect. It was shown that extremely small particles cannot be stabilized by an electrostatic repulsion barrier. Additionally, at the same mass concentration, nanoparticles aggregate more rapidly than ordinary colloidal particles due to thier higher number concentration.     

Copper(II) complexes of N-terminal protected tri- and tetra-peptides containing histidine residues

Copper(II) complexes of peptides containing two or three histidyl residues (Ac-HisGlyHis-OH, Ac-HisGlyHis-NHMe, Ac-HisHisGlyHis-OH and Ac-HisHisGlyHis-NHMe) have been studied by potentiometric, UV-Vis, EPR and CD spectroscopic measurements. The imidazole nitrogen atoms are described as the primary metal binding sites of all ligands resulting in the formation of various macrochelates in the pH range 4 to 7. The (Nim, N-, Nim)-co-ordinated [CuH-1L]0+ complexes were mainly detected in samples containing free carboxylates at the C-termini, whilst the [CuH-2L]-(0) complexes were the predominant species in slightly alkaline solution and their binding modes were described via 4N-co-ordination (Nim, N-, N-, Nim) in (7,5,6)-membered fused chelate rings. Deprotonation and co-ordination of the third amide nitrogens were detected above pH approximately 9 in all cases.     

Charging of silver bromide aqueous interface: Evaluation of enthalpy and entropy of interfacial reactions from surface potential data

Dependence of surface potential (electrostatic potential at the inner Helmholtz plane, Ψ(0)) at the silver bromide aqueous electrolyte interface was measured as a function of the activities of Br(-) and Ag(+) by using a single crystal silver bromide electrode (SCr-AgBr). Absolute values of surface potentials were obtained from electrode potentials of SCr-AgBr and isoelectric points. Measurements were performed at different temperatures in the range from 10 to 50°C. Corresponding equilibrium constants of interfacial reactions were obtained using the surface complexation model and interpreted via the van't Hoff equation. As a result of the interpretation for the binding of bromide ions leading to a negative surface charge, the thermodynamic parameters obtained were Δ(n)H(°)=-33kJmol(-1) and Δ(n)S(°)=-31Jmol(-1)K(-1); and for the binding of silver ions leading to a positive surface charge, Δ(p)H(°)=-72kJmol(-1) and Δ(p)S(°)=-196Jmol(-1)K(-1). Association of counterions (CI) with oppositely charged surface sites partially compensates the surface charge. Assuming approximately the same affinities for anions (NO(3)(-)) and cations (K(+)) thermodynamic parameters for their binding were obtained as Δ(CI)H(°)≈7kJmol(-1) and Δ(CI)S(°)≈105Jmol(-1)K(-1).