An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

分子力场进展

分子力学（简称ＭＭ）是近年来化学家常用的一种计算方法。与量子力学从头计算和半经验方法相比，用分子力学处理大分子可以大大节省计算时间，而且，在大多数情况下，用分子力学方法计算得到的分子几何构型参数与实验值之间的差值可在实验误差范围之内。所以，分子力学是研究生物化学体系的有效和可行的手段。分子力学的核心是分子力场。本文介绍了分子力场的量子力学背景、分子力场和光谱力场之间的关系。分子力场的一般形式、分力     

Study of poly(bisphenol A carbonate) relaxation kinetics at the glass transition temperature

In this work, the variations of the relaxation times are investigated above and below the glass transition temperature of a model amorphous polymer, the polycarbonate. Three different techniques (calorimetric, dielectric and thermostimulated currents) are used to achieve this goal. The relaxation time at the glass transition temperature was determined at the temperature dependence convergence of the relaxation times calculated with dynamic dielectric spectroscopy (DDS) for the liquid state and thermostimulated depolarisation currents (TSDC) for the vitreous state. We find a value of τ(T_g) = 110 s for PC samples. The knowledge of the temperature dependence, τ(T), and the value τ(T_g) enables to determine the glass-forming liquid fragility index, m. We find m = 178 ± 5.     

Dynamic kinetic resolution of secondary alcohols with a readily available ruthenium-based racemization catalyst

An easy to handle and stable racemization catalyst for secondary alcohols is obtained by an in situ mixture of readily available [Ru(cymene)Cl₂]₂ with chelating aliphatic diamines. Optimization of the reaction revealed that N,N,N′,N′-tetramethyl-1,3-propanediamine as ligand racemizes aromatic alcohols completely within 5 h. This easy to handle and stable catalytic system is combined with a lipase-catalyzed resolution to provide an efficient dynamic kinetic resolution of secondary alcohols.     

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

A large succinic acid (HOOC(CH₂)₂COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation. Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002     

Application of a dynamic method of minimisation in the study of reaction surfaces

This paper describes the application of Snyman's dynamic minimisation method to a fitted potential surface of H₃. Comparisons are made with conventional algorithms. A method is described to extend Snyman's method so that it will find only a particular kind of stationary point. It is emphasized that this method enables saddle points to be found without having to resort to approaches based on trial and error.     

On the determination of dynamic surface tensions by means of a modified bubble pressure method

A method for the determination of the dynamic surface tension of surfactant solutions is presented which allows to cover adsorption times down to 10 seconds. This method is based on the determination of the pressure inside two communicating bubbles. There is no deformation of the solution/air interface during the experimental procedure. Hence, in evaluating the kinetic data no surface area enlargement has to be taken into account. An automatically operating procedure should allow to cover adsorption times down to approximately one second and should improve the measuring accuracy substantially. Experimental investigations with aqueous n-decanoic acid solutions using the method proposed provided evidence that decanoic acid is adsorbed by a diffusioncontrolled mechanism.     

Growth of silica nanoparticles in methylmethacrylate-based water-in-oil microemulsions

The mechanism of silica particle formation in monomer microemulsions is studied using dynamic light scattering (DLS), atomic force microscopy, small-angle X-ray scattering (SAXS), and conductivity measurements. The hydrolysis of tetraethylorthosilicate (TEOS) in methylmethacrylate (MMA) microemulsions (MMA = methylmethacrylate) is compared with the formation of SiO₂ particles in heptane microemulsions. Stable microemulsions without cosurfactant were found for MMA, the nonionic surfactant Marlophen NP10, and aqueous ammonia (0.75 wt%). In the one-phase region of the ternary phase diagram, the water/surfactant ratio (R _w) could be varied from 6 to 18. The DLS and SAXS measurements show that reverse micelles form in these water-in-oil (w/o) microemulsions. The minimum water-to-surfactant molar ratio required for micelle formation was determined. Particle formation is achieved from the base-catalyzed hydrolysis of TEOS. According to atomic force microscopy measurements of particles isolated from the emulsion, the particle size can be effectively tailored in between 20 and 60 nm by varying R _w from 2–6 in heptane w/o microemulsions. For MMA-based microemulsions, the particle diameter ranges from 25 to 50 nm, but the polydispersity is higher. Tailoring of the particle size is not achieved with R _w, but adjusting the particle growth period produces particles between 10 and 70 nm.     

The first 1,2-dibora-[2]ferrocenophane and its dynamic behaviour in solution

1,2-Bis(dimethylamino)-1,2-dibora-[2]ferrocenophane (1) was prepared by the reaction of 1,1′-dilithioferrocene with 1,2-dichlorobis(dimethylamino)diborane(4). In addition to hindered rotation about the B-N bond (ΔG^‡ > 80 kJ mol⁻¹), another dynamic process was revealed by ¹H and ¹³C NMR in solution at low temperature, and interpreted as motion of the cyclopentadienyl rings between staggered and eclipsed conformations (ΔG_{(233 K)}^‡ = 44 ± 1 kJ mol⁻¹).     

Molecular mechanics (MM3) calculations on lithium amide compounds

The MM3 force field has been extended to deal with the lithium amide molecules that are widely used as efficient catalysts for stereoselective asymmetric synthesis. The MM3 force field parameters have been determined on the basis of the ab initio MP2/6-31G* and/or DFT (B3LYP/6-31G*, B3-PW91/6-31G*) geometry optimization calculations. To evaluate the electronic interactions specific to the lithium amides derived from the diamine molecules properly, the Lewis bonding potential term for the interaction between the lithium atom and the nonbonded adjacent electronegative atom such as nitrogen was introduced into the MM3 force field. The bond dipoles were evaluated correctly from the electronic charges on the atoms calculated by fitting to the electrostatic potential at points selected. The MM3 results on the molecular structures, conformational energies, and vibrational spectra show good agreement with those from the quantum mechanical calculations.