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.

     

Synthesis of 2-amino-4-pyrimidinones from resin-bound guanidines prepared using bis(allyloxycarbonyl)-protected triflylguanidine

We have synthesized novel heterocyclic compounds from resin-bound guanidines. For this purpose, an amine immobilized on a solid support was acylated with protected amino acids. Following the deprotection, the liberated amines were guanidinylated utilizing a new member of the family of diurethane-protected triflyl guanidine reagents, N,N'-bis(allyloxycarbonyl)-N' '-triflylguanidine. The deprotected guanidines were subsequently regioselectively cyclized with beta-keto esters yielding novel compounds containing heterocyclic structures in high purities.     

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.     

Substituent Effects on the C-C Bond Strength, 15[1] Geminal Substituent Effects, 7[2]. Thermochemistry and Thermal Decomposition of Alkyl-substituted Tricyanomethyl Compounds

The thermolysis reactions of the tricyanomethyl compounds 10a-c were studied in solution. 2,2-Dicyano-3-methyl-3-phenylbutyronitrile ( 10a ) and 2,2-dicyano-3-methyl-3-(4-nitrophenyl)butyronitrile ( 10b ) decomposed heterolytically into carbenium ions and (CN)₃C⁻ anions, while 9-methyl-9-(tricyanomethyl)fluorene ( 10c ) underwent about 11% homolytic C-C bond cleavage into 9-methyl-9-fluorenyl- and tricyanomethyl radicals. The rates of the homolysis were determined by a radical scavenger procedure under conditions of pseudozero order kinetics. From the temperature effect on the rate constants the activation parameters were determined [ΔH ( 10c ) = 155· 2 kJ mol⁻¹, ΔS ( 10c ) = 58· 5 J mol⁻¹ K⁻¹]. Standard enthalpies of formation ΔH (g) were determined for 2,2-dicyanopropionitrile ( 2 ) (422.45 kJ mol⁻¹), 2,2-dicyanohexanenitrile ( 3 ) (349.74 kJ mol⁻¹), 2,2-dicyano-3-phenylpropionitrile ( 4 ) (540.75 kJ mol⁻¹), 2-butyl-2-methylhexanentrile ( 5 ) (-133.20 kJ mol⁻¹), 2,2-dimethylpentanenitrile ( 6 ) (-45.78 kJ mol⁻¹), and 2-methylbutyronitrile ( 7 ) (2.44 kJ mol⁻¹) from the enthalpies of combustion and enthalpies of sublimation/vaporization. From these data and known Δ (g) values for alkanenitriles and -dinitriles, thermochemical increments for ΔH (g) were derived for alkyl groups with one, two, or three cyano groups attached. The comparison of these increments with those of alkanes reveals a strong geminal destabilization, which is interpreted by dipolar repulsions between the cyano groups. - From ΔH (g) of 10c and ΔH of its homolytic decomposition the radical stabilization enthalpy for the tricyanomethyl radical 1 RSE ( 1 ) = -18 kJ mol⁻¹ was determined. Thus, 1 is destabilized, in comparison with the RSEs of tertiary α-cyanalkyl (23 kJ mol⁻¹) and α,α-dicyanoalkyl (27 kJ mol⁻¹) radicals, which were recalculated from bond homolysis measurements^[4] and the new thermochemical data. This change of RSE on increasing the number of α-cyano groups is discussed as the result of the additive contributions by resonance stabilization and increasing destabilization by dipolar repulsion. The amount of the dipolar energies was estimated by molecular mechanics (MM2).     

Thermochemical study of aliphatic and phenyl-substituted geminal diacetates

The standard enthalpies of combustion _c H ^o of aliphatic diacetates1 and aromatic diacetates2 were measured calorimetrically. The enthalpies of vaporization _vap H ^o or sublimation _sub H ^o of1 and2 were obtained from the temperature function of the vapor pressure measured in a flow system. From _f H ^o(g) of1 and2 new values of group increments for the estimation of standard enthalpies of formation of these classes of compounds were derived. The geminal interaction energy between the geminal acyloxy groups shows no anomeric stabilization.Geminal Substituent Effects, Part 12, for part 11 see Ref. 7.     

Melting of icosahedral gold nanoclusters from molecular dynamics simulations

Molecular dynamics simulations show that gold clusters with about 600-3000 atoms crystallize into a Mackay icosahedron upon cooling from the liquid. A detailed surface analysis shows that the facets on the surface of the Mackay icosahedral gold clusters soften but do not premelt below the bulk melting temperature. This softening is found to be due to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size, so that the average shape of the cluster is nearly spherical at melting.     

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.