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.     

Tautomerism and stereochemistry of hypericin: Force field,NMR, and X-ray crystallographic investigations

Summary Stereochemistry and tautomerism of hypericin, pseudohypericin, and several of their partial structure models were investigated using an MM2 derived force field method. Besides the propeller type conformer, which was also found by the X-ray crystallographic study, the complicated energy hypersurface was shown to contain a novel double-butterfly conformer of similar stability. The upper limit interconversion barrier between these conformers and their enantiomers was found to be in the order of 115 kJ/mol.¹H-NMR experiments suggested a lower limit interconversion barrier of at least 80 kJ/mol. From the ten tautomers possible in principle, the 7,14-species was derived to be the most stable one by at least 48 kJ/mol.

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Tautomerie und Stereochemie von Hypericin: Untersuchungen mit Hilfe der Kraftfeld-Methodik, NMR-Spektroskopie und Röntgenstrukturanalyse

Zusammenfassung Die Stereochemie von Hypericin, Pseudohypericin und einigen seiner Partialstrukturmodelle wurde mit Hilfe einer von MM2 abgeleiteten Kraftfeldmethodik untersucht. In der komplizierten Energiehyperfläche wurde neben dem auch durch Röntgenstrukturanalyse gefundenen Propeller-Konformeren ein neues Doppelschmetterling-Konformer ähnlicher Stabilität aufgefunden. Die obere Grenze für die Interkonversionsbarrieren zwischen diesen Konformeren und ihren Enantiomeren sind in der Größenordnung von 115 kJ/mol. Aus¹H-NMR-Experimenten konnte eine untere Grenze von wenigstens 80 kJ/mol abgeleitet werden. Es wurde gefunden, daß von den zehn prinzipiell möglichen Tautomeren die 7,14-Spezies die um wenigstens 48 kJ/mol stabilste ist.

     

Orientational aspect of transient absorption in solutions

In picosecond spectroscopy transient absorption methods are utilized to measure ground-state repopulation kinetics. Since linearly polarized light pulses from mode-locked lasers are used, the transient absorption characteristics in solutions are governed by the rotational diffusion of the absorbing molecules, too. The theory for isotropic diffusion is given and compared to a measurement on the rhodamine 6G molecule dissolved in solvents of different viscosity using a novel pulse spectrophotometer.     

Facts and artifacts about aromatic stability estimation

The stability of a set of 105 five-membered π-electron systems (involving aromatic, non-aromatic and anti-aromatic species) was evaluated using six isodesmic reactions of which two belong to the subclass of homodesmotic reactions, which are based on cyclic and acyclic reference systems. We demonstrate that the ‘Resonance Energies’ derived from isodesmotic schemes have obvious flaws and do not correct or cancel other contributions to the energy, such as the changes of hybridization, homoconjugation of heterosubstituted cyclopentadienes, conjugative interactions of CC or CX (X=N or P) with a π or pseudo π orbital at Y (Y=O, S, NH, PH), strain, etc. as effectively as possible. Likewise, ‘aromatic stabilization energies (ASE)’ derived from homodesmotic schemes based on the acyclic reference compounds do not give satisfactory results. We strongly recommend that only cyclic reference compounds should be used for ASE and other aromaticity evaluations. The analysis is based on ab initio optimized geometries at B3LYP/6-311+G^∗∗.     

Ligand discrimination in the reaction of nitrones with [PtCl2(PhCN)2]. Selective formation of mono-oxadiazoline and mixed bis-oxadiazoline complexes under thermal and microwave conditions

[2+3] Cycloaddition of nitrones to the nitrile ligands in the complexes cis- or trans-[PtCl2(PhCN)2] occurs under ligand differentiation and allows for selective synthesis of complexes of the type cis- or trans-[PtCl2(oxadiazoline)(PhCN)]. Microwave irradiation enhances the reaction rates of the cycloaddition considerably and further favours the selectivity towards the mono-cycloadduct with respect to thermal conditions, because the first cycloaddition is accelerated to a higher extent than the second one. Reaction of the trans-substituted mono-oxadiazoline complexes with a nitrone different from the one used for the first cycloaddition step gives access to mixed bis-oxadiazoline compounds of the composition trans-[PtCl2(oxadiazoline-a)(oxadiazoline-b)]. The corresponding cis-configured complexes, however, do not undergo further cycloaddition. All reactions described occur without isomerisation of the stereochemistry around the platinum center, independently of whether thermal or microwave heating is applied.     

Microwave-assisted extraction of zearalenone from wheat and corn

A microwave-assisted extraction (MAE) method has been developed for determination of zearalenone in wheat and corn by LC-MS with an atmospheric pressure chemical ionization interface (APCI). Matrix effects were minimized by use of matrix-matched standard curves for quantification of the analyte. The limit of quantification (LOQ) of the method was 30 ng g(-1) in wheat and 20 ng g(-1) in corn. The rapid LC-MS method enabled analysis of the extracts without clean-up, thereby reducing analyte losses, the time required for the analytical procedure, and costs. A factorial design approach was used to examine the effect on extraction efficiency of the main extraction conditions - time, temperature, and solvent. On the basis of results from statistical assessment extraction was performed with 1:1 (v/v) methanol-acetonitrile at 80 degrees C for 5 min. When these extraction conditions were applied to a wheat sample from a recently conducted international proficiency test, 92% (103 ng g(-1)) of the assigned zearalenone concentration (112 ng g(-1)) in the test material was obtained. This result was within the uncertainty (u) range of the assigned value of the test material (u=+/-15.8 ng g(-1), alpha=0.05) thereby demonstrating the accuracy of the method was sufficient. The precision of the whole method was also confirmed to be adequate, because the observed relative standard deviation (RSD) of 12% (n=10) also fulfils the quality criteria recommended by European guidelines for in-house method validation.     

SIACON—Equipment for the on-line determination of the silicon content of coal

The paper describes an automatic equipment which allows to determine the silicon content of coal by neutron activation analysis. The technique is based on the measurement of gamma-ray intensity of the²⁸Al radionuclide, which is the result of the fast neutron reaction²⁸Si(n, p)²⁸ Al. The Activation part includes a Pu-238/Be neutron source which is located in the middle of the sample container; the measuring part includes two NaI(Tl)-scintillation counters. The total time of the anlysis of one sample amounts to a few minutes; the standard deviation of a single determination is 0.2% SiO₂.     

Delocalization resonance energy of the allylic radical from the geometrical isomerization of hexa-1,3,5-trienes

Thermal cis, trans geometrical isomerization theoretically involves a 90° twisted, singlet diradical-like transition state which may serve as a base for the examination of structural perturbations. Although thermal rearrangement of hexa-1, trans-3,5-triene (and all-trans octa-2,4,6-triene) to the cis isomer cannot be followed directly owing to subsequent cyclization and 1,5 hydrogen shifts, activation parameters for disappearance have been determined. Experimental complications and mechanistic uncertainties which make interpretation difficult are removed in the bicyclic hexatriene, cyclopentenylidenecyclopentene. These geometrical isomers undergo uncomplicated thermal cis, trans isomerization in vessels of lead-potash glass: log k₁ = 12·03±0·32?41·7±0·8/(0·004575T_abs). Extraction of a value for allylic delocalization energy from the behavior of hexa-1, trans-3,5-triene [log k₁ = 12·91 ± 0·47?44·3±1·2/(0·004575 T_abs)] requires corrections of the Dewar-Schmeising type for changes in hybridization of the σ bonds. Depending on whether ethylene or trans-butene is taken as standard, values of 12·2 and 13·1 kcal/mol are obtained (estimated uncertainty ± 2 kcal/mol).     

Proton-impact excitation of HeI triplet levels

We investigated the excitation of the λ(1s3d ³ D?1s2p ³ P)=588 nm line of atomic helium by proton and deuteron impact for projectile energies 10 keV≦E _p≦25 keV. In apparent contradiction to Wigner's spin conservation rule, the emission cross section does not vanish. By measuring the intensity of the impact radiation as a function of homogeneous magnetic and electric fields applied to the collision volume, it has been shown thatp- andd-impact excitation of the 1s3d ³ D level of HeI proceeds via 1snl states withl≧3, which populate the 3³ D states by cascade decays. The well-known strong singlet-triplet mixing of these 1snl states enables a population of triplet states in accord with Wigner's rule. Accordingly, we determine the excitation cross section of the 1s4f multiplet from the measured emission cross section of the 588 nm line. The field-dependent signals give evidence that predominantly substates with |m _L|≦1 are excited.