The lipidated membrane anchor of full length N-Ras protein shows an extensive dynamics as revealed by solid-state NMR spectroscopy

Many proteins involved in signal transduction are equipped with covalently attached lipid chains providing a hydrophobic anchor targeting these molecules to membranes. Despite the considerable biological significance of this membrane binding mechanism for 5-10% of all cellular proteins, to date very little is known about structural and dynamical features of lipidated membrane binding domains. Here we report the first comprehensive study of the molecular dynamics of the C-terminus of membrane-associated full-length lipidated Ras protein determined by solid-state NMR. Fully functional lipid-modified N-Ras protein was obtained by chemical-biological synthesis ligating the expressed water soluble N-terminus with a chemically synthesized (2)H or (13)C labeled lipidated heptapeptide. Dynamical parameters for the lipid chain modification at Cys 181 were determined from static (2)H NMR order parameter and relaxation measurements. Order parameters describing the amplitude of motion in the protein backbone and the side chain were determined from site-specific measurements of (1)H-(13)C dipolar couplings for all seven amino acids in the membrane anchor of Ras. Finally, the correlation times of motion were determined from temperature dependent relaxation time measurements and analyzed using a modified Lipari Szabo approach. Overall, the C-terminus of Ras shows a versatile dynamics with segmental fluctuations and axially symmetric overall motions on the membrane surface. In particular, the lipid chain modifications are highly flexible in the membrane.     

Reactivity studies of a disilene with N2O and elemental sulfur

In a previous contribution, we have reported on a convenient and high yield synthesis of the disilene trans-[(TMS)(2)N(η(1)-Me(5)C(5))Si═Si(η(1)-Me(5)C(5))N(TMS)(2)] (2). Herein, we show the reactions of 2 with N(2)O and S(8). The former reaction affords two isomeric (cis- and trans-) dioxadisiletane ring compounds. To the best of our knowledge, this is the first report where both cis-and trans-isomers are isolated from the same disilene precursor and characterized structurally by single-crystal X-ray diffraction (XRD) studies. The reaction of 2 with elemental sulfur yields only the trans-isomer. To investigate this dissimilar reaction pattern exhibited by 2, computational studies were performed. Density functional theory (DFT) calculations showed that the two dioxadisiletane ring isomers are isoenergetic, with the trans isomer being slightly more stable than the cis counterpart, by 3.3 kcal/mol, while that is not the case with sulfur. All the isolated compounds are characterized by single-crystal XRD studies, multinuclear NMR spectroscopy, and electron ionization-mass spectrometry (EI-MS).     

Assay Related Target Similarity (ARTS) - chemogenomics approach for quantitative comparison of biological targets

Computer-based chemogenomics approaches compare macromolecular drug targets based on their amino acid sequences or derived properties, by similarity of their ligands, or according to ligand-target interaction models. Here we present ARTS (Assay Related Target Similarity) as a quantitative index that estimates target similarity directly from measured affinities of a set of probe compounds. This approach reduces the risk of deducing artificial target relationships from mutually inactive compounds. ARTS implements a scoring scheme that matches intertarget similarity based on dose-response measurements. While all experimentally derived target similarities have a tendency to be data set-dependent, we demonstrate that ARTS depends less on the used data set than the commonly used Pearson correlation or Tanimoto index.     

The DMAP-catalyzed acetylation of alcohols--a mechanistic study (DMAP = 4-(dimethylamino)pyridine)

The acetylation of tert-butanol with acetic anhydride catalyzed by 4-(dimethylamino)pyridine (DMAP) has been studied at the Becke3 LYP/6-311 + G(d,p)//Becke3 LYP/6-31G(d) level of theory. Solvent effects have been estimated through single-point calculations with the PCM/UAHF solvation model. The energetically most favorable pathway proceeds through nucleophilic attack of DMAP at the anhydride carbonyl group and subsequent formation of the corresponding acetylpyridinium/acetate ion pair. Reaction of this ion pair with the alcohol substrate yields the final product, tert-butylacetate. The competing base-catalyzed reaction pathway can either proceed in a concerted or in a stepwise manner. In both cases the reaction barrier far exceeds that of the nucleophilic catalysis mechanism. The reaction mechanism has also been studied experimentally in dichloromethane through analysis of the reaction kinetics for the acetylation of cyclohexanol with acetic anhydride, in the presence of DMAP as catalyst and triethylamine as the auxiliary base. The reaction is found to be first-order with respect to acetic anhydride, cyclohexanol, and DMAP, and zero-order with respect to triethyl amine. Both the theoretical as well as the experimental studies strongly support the nucleophilic catalysis pathway.     

Membrane-mediated induction and sorting of K-Ras microdomain signaling platforms

The K-Ras4B GTPase is a major oncoprotein whose signaling activity depends on its correct localization to negatively charged subcellular membranes and nanoclustering in membrane microdomains. Selective localization and clustering are mediated by the polybasic farnesylated C-terminus of K-Ras4B, but the mechanisms and molecular determinants involved are largely unknown. In a combined chemical biological and biophysical approach we investigated the partitioning of semisynthetic fully functional lipidated K-Ras4B proteins into heterogeneous anionic model membranes and membranes composed of viral lipid extracts. Independent of GDP/GTP-loading, K-Ras4B is preferentially localized in liquid-disordered (l(d)) lipid domains and forms new protein-containing fluid domains that are recruiting multivalent acidic lipids by an effective, electrostatic lipid sorting mechanism. In addition, GDP-GTP exchange and, thereby, Ras activation results in a higher concentration of activated K-Ras4B in the nanoscale signaling platforms. Conversely, palmitoylated and farnesylated N-Ras proteins partition into the l(d) phase and concentrate at the l(d)/l(o) phase boundary of heterogeneous membranes. Next to the lipid anchor system, the results reveal an involvement of the G-domain in the membrane interaction process by determining minor but yet significant structural reorientations of the GDP/GTP-K-Ras4B proteins at lipid interfaces. A molecular mechanism for isoform-specific Ras signaling from separate membrane microdomains is postulated from the results of this study.     

Darstellung und Kristallstruktur von KSbS2

Preparation and Crystal Structure of KSbS₂ Red KSbS₂ was prepared in a aqueous solution of KHS and Sb₂S₃ under mild hydrothermal conditions. For crystallographic data see ?Inhaltsübersicht”?. There are SbS-chains, built up by ψ-trigonal bipyramids, which are connected by sharing edges. The K⁺-Ions between these chains have a nearly octaedric coordination.     

Darstellung und Kristallstruktur von Rb2Sb4S7

Preparation and Crystal Structure of Rb₂Sb₄S₇ The first thioantimonite of rubidium has been synthesized and its crystal structure determined. The substance crystallizes triclinic with spacegroup P1 . The lattice constants are a = 968.0(5) pm, b = 1193.4(5) pm, c = 723.1(5) pm, α = 87.68(5)°, β = 101.39(5)° and γ = 102.66(5)°. There are two formula units in the unit cell.     

TOSAR – A Topological Method for the Representation of Synthetic and Analytical Relations of Concepts

In mechanized systems used for searching in literature stores there is a steadily growing necessity not only to be able to formulate concepts as a search condition but also the characteristic connections under which these concepts appear in the inquiry. In this way the precision of the mechanized literature search is considerably increased. TOSAR has been developed in order to improve computerized literature searching in this respect.     

Thermal and mass spectrometric fragmentation of esters of deuterated long chain carboxylic acids

A method combining thermal fragmentation and mass spectrometry for the determination of the position of double bonds in an unsaturated ester is presented. The thermal fragmentation of methyl esters of deuterated long chain carboxylic acids yields a homologous series of olefins plus a homologous series of unsaturated esters. The positions of the deuterium atoms in the original ester are revealed by the deuterium content of its fragments as determined by mass spectrometry. Therefore, the positions of double bonds of a polyunsaturated acid can be determined by pyrolysis after saturation by deuterium. The structures of the unsaturated fragments are ascertained by mass spectrometric method, and the formation of the ion [M – 32] in the mass spectrometric fragmentation of unsaturated methyl esters is studied by means of deuterium labeling.