TreeDock: a tool for protein docking based on minimizing van der Waals energies

Predicting protein-protein and protein-ligand docking remains one of the challenging topics of structural biology. The main problems are (i) to reliably estimate the binding free energies of docked states, (ii) to enumerate possible docking orientations at a high resolution, and (iii) to consider mobility of the docking surfaces and structural rearrangements upon interaction. Here we present a novel algorithm, TreeDock, that addresses the enumeration problem in a rigid-body docking search. By representing molecules as multidimensional binary search trees and by exploring a sufficient number of docking orientations such that two chosen atoms, one from each molecule, are always in contact, TreeDock is able to explore all clash-free orientations at very fine resolution in a reasonable amount of time. Due to the speed of the program, many contact pairs can be examined to search partial or complete surface areas. The deterministic systematic search of TreeDock is in contrast to most other docking programs that use stochastic searches such as Monte Carlo or simulated annealing methods. At this point, we have used the Lennard-Jones potential as the only scoring function and show that this can predict the correct docked conformation for a number of protein-protein and protein-ligand complexes. The program is most powerful if some information is known about the location of binding faces from NMR chemical-shift perturbation studies, orientation information from residual dipolar coupling, or mutational screening. The approach has the potential to include docking-site mobility by performing molecular dynamics or other randomization methods of the docking site and docking families to families of structures. The performance of the algorithm is demonstrated by docking three complexes of immunoglobulin superfamily domains, CD2 to CD58, the V(alpha) domain of a T-cell receptor to its V(beta) domain, and a T-cell receptor to a pMHC complex as well as a small molecule inhibitor to a phosphatase.     

Synthese und Reaktionen von Bicyclo[6.4.0]dodecan-3-carbonsäure-Derivaten

Synthesis and Reactions of the Bicyclo[6.4.0]dodecane-3-carboxylic Acid Derivatives The synthesis and some consecutive reactions of the compounds 5-8 , derivatives of bicyclo[6.4.0]dodecane-3-carboxylic acid ( 1 ), are described. The esters 7 and 8 can be obtained by Baeyer-Villiger oxidation of 2-hydroxy-8-methyltricyclo[7.3.1.0^2,7]tridecan-13-one ( 4 ) and subsequent hydrolysis of the lactone 5 . The structure and configuration of these compounds has been evaluated by spectroscopic techniques (mainly 2D-NMR methods). The formation of 7 via 1,2-H shift and subsequent isomerization to 8 has been studied. The esters 11 and 13 are formed stereospecifically from 7 and 8 .     

Purification and analysis of partially alkylated cyclodextrins by liquid and gas chromatography

Complex mixtures of partially alkylated cyclodextrins can be analyzed by both HPLC and high temperature capillary GC. Because of the limited efficiency of LC, suitable analytical and preparative separations can be achieved only with systems of carefully optimized selectivity. Using LC it has been possible to isolate and purify single cyclodextrin species from very complex mixtures of components which contain unreacted hydroxyl groups in addition to the alkoxy groups. Analysis of the reaction mixtures and of fractions taken from LC separations can be performed with advantage by high resolution capillary GC at high temperatures between 300 and 400 °C. The thermal stability of partially alkylated cyclodextrins in high temperature GC is considerably increased by trimethylsilylation of the free hydroxyl groups. Fast atom bombardment mass spectrometry and proton NMR were used to identify species isolated from the preparative LC separations.     

Zur Lokalisierung funktioneller Gruppen mit Hilfe der Massenspektrometrie. XVII—Massenspektren von 3,6,20β-Trihydroxy-pregnanen

Mass spectra of 3,6,20β-trihydroxypregnanes differ greatly, depending upon the nature of the A/B ring fusion and the positions of the hydroxy groups. Of all the isomers only 3α,6β,20β-trihydroxy-5β-pregnane produces an intense, structurally significant, ion at m/e 263. For 3β,6α,20β-trihydroxy-5α-pregnane an ion of m/e 141 is typical.     

Chemie der Pleuromutiline,IX. Konfigurationsumkehr der Methylgruppe am Kohlenstoff 6 im tricyclischen Gerüst des Diterpens Pleuromutilin

The contact of pleuromutilin derivatives with the protein moiety of cytochrome P-450 as well as its orientation towards the heme iron is mainly dependent on the steric environment of the hydrindanone-part of the tricyclus. The apparent affinity between substrate and enzyme, which is correlated with the rate of metabolism can be reduced by inversion of configuration at carbon 6. This inversion is achieved by equilibrating the diastereomeric ketones12 and13 followed by a selective reduction of the keto group at position 7. The 6-methylgroup of14 was assigned α-configuration on the basis of spectroscopic data in comparison to those of the naturally configurated compound14a.     

Internal reactions of ion–neutral complexes from some disubstituted protonated benzaldehydes and acetophenones

Protonated benzaldehydes ‘a’ and protonated acetophenones ‘b’, substituted by a methoxymethyl group, a hydroxy-methyl group and a mercaptomethyl group, respectively, in position 3, in addition to a methoxymethyl side chain at position 5, have been prepared by electron impact induced dissociation from the corresponding benzylic alcohols. The spontaneous fragmentations of metastable ions of ‘a’ and ‘b’ have been investigated with the aid of specifically deuterated derivatives. Large signals arc observed for the loss of methanol induced by a proton migration across the aromatic ring. The competing loss of H₂O and H₂S, respectively, from the second side chain is less abundant, in agreement with the smaller PA's of HO? and HS? groups. The elimination of HCOX and CH₃COX (X = OCH₃, OH, SH), respectively, from ‘a’ and ‘b’ is also observed. The label distributions for these reactions are in agreement with a mechanism corresponding to an internal reaction of [CHO] ⁺ and [CH₃CO] ⁺, respectively, with the functional group of the side chains in an intermediary ion–neutral complex. In addition, fragmentations are observed arising from reactions between the two side chains at positions 3 and 5. The D labelling proves specific reactions without any H/D exchange and thus reaction channels separated from the methanol loss. The results are explained by internal ion-molecule reactions in an intermediary ion-neutral complex of a methoxymethyl cation, a hydroxymethyl cation and a mercaptomethyl cation, respectively, formed by a protolytic bond cleavage of the side chains.     

High performance liquid chromatographic separation of dipeptide and tripeptide enantiomers using a chiral crown ether stationary phase

A chiral stationary phase (CSP) based on (-)-(18-crown-6)-2,3,11,12-tetracarboxylic acid was evaluated for the direct resolution of the enantiomers of dipeptides and tripeptides. The type and concentration of the acid and the methanol content were optimized with regard to retention time and resolution using Ala-Phe as model peptide. A mobile phase consisting of 10 mM sulfuric acid in 70% aqueous methanol was applied to the separation of a set of 16 structurally diverse dipeptides and tripeptides. Generally, the configuration of the amino acid at the N-terminus determined the enantiomer elution order. With a few exceptions the LL- and LD-enantiomers interacted stronger with the CSP compared to the corresponding DD- or DL-enantiomers. The experimental conditions also allowed the simultaneous separation of all four stereoisomers of Ala-Phe. Addition of ammonium sulfate generally reduced retention times and enantiomer resolution. Addition of triethylamine as modifier led to an overall increase of the retention times while the resolution did not show a general trend, increasing in the case of Ala-Ala but decreasing in the case of Ala-Phe.     

On the synthesis of hypericin by oxidative trimethylemodin anthrone and emodin anthrone dimerization: Isohypericin

Summary The base catalyzed oxidative dimerization of emodin anthrone exclusively yields hypericin. However, on oxidative dimerization of trimethylemodinanthrone a mixture of hexamethylhypericin and hexamethylisohypericin was obtained. Chromatographic separation of the hexabenzoyl derivatives was achieved, and by saponification about equal amounts of hypericin and isohypericrin were produced. Isohypericin could be characterized for the first time by its spectroscopic data and its protonation and deprotonationpK _a andpK _a ^* values.

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Zur Synthese von Hypericin durch oxidative Dimerisierung von Trimethylemodinanthron und Emodinanthron: Isohypericin

Zusammenfassung Die basenkatalysierte oxidative Dimerisierung von Emodinanthron liefert ausschließlich Hypericin. Oxidative Dimerisierung von Trimethylemodinanthron ergibt jedoch ein Gemisch von Hexamethylhypericin und Hexamethylisohypericin. Die Hexabenzoylderivate wurden chromatographisch getrennt, und Hypericin und Isohypericin konnten aus diesen Derivaten durch Verseifung freigesetzt werden. Isohypercin konnte erstmals durch seine spektroskopischen Daten und seine Protonierungs- und Deprotonierungs-pK _aundpK _a ^* -Werte charakterisiert werden.

     

Permutation representations in molecular symmetry

The reducible representations of the point groups are generally studied because of their relevance to molecular orbital and vibration theory. Triple correlations within the polyhedra are described by group-theoretical invariants that are related to the permutation representations and termed polyhedral isoscalar factors. These invariants are applied in theorems on matrix elements referring to the symmetry-adapted bases at different centres. Further invariants or geometrical weight factors inter-relate different types of reduced matrix elements of irreducible tensors (generalization of the Wigner-Eckart theorem to the polycentric case). As a demonstration a complete tabulation is given for the point group C ₄.     

Development of a robust technique for sampling volatile metal(loid)s in wetlands

The formation of volatile organic and inorganic metals and metalloids in aquatic environments is a known, but not very intensively investigated, process. Several techniques have been developed over the past 10 years to determine these trace components. These techniques are of limited use in wetland environments, where samples have to be taken from the soil-water interface, and require an immediate sample analysis due to thermodynamic instabilities of the volatile metal(loid)s. This paper presents an innovative sampling technique for total concentrations of volatile metal(loid)s in wetlands, based on an in situ gas-water separation via a porous PTFE membrane and stabilising the volatile metal(loid)s in a liquid sorbent (NaOCl solution). Samples may thus be collected even at remote sites, where longer storage times have to be accounted for. The sampling system was tested by means of a laboratory facility simulating the generation of arsine and dimethyl arsine under abiotic conditions as well as under field conditions. Results for sampling efficiency, reproducibility, and long-term storage are presented. Application of the sampling system in the field is shown.