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.     

Random Copolymers of 1,5-Dioxepan-2-one

ABSTRACT

Copolymers of 1,5-dioxepan-2-one (DXO) and e-caprolactone (?-CL), δ-valerolactone (δ-VL) or L-lactide (LLA) have been synthesized and characterized. High molecular weight copolymers were obtained using stannous-2-ethyl hexanoate as catalyst in bulk. Reactivity ratios for the copolymerization of DXO and δ-VL were determined at 110°C as r_VL=0.5 and r_DXO=2.3. At high conversion, depolymerization of δ-VL occurred, resulting in lower molecular weight and variations in the copolymer composition.

Physical properties, such as crystallinity and melting temperature of the DXO-copolymers proved to be strongly dependent on the choice of comonomer and on the molar composition of the copolymers. DXO appears to be incorporated into the poly-?-caprolactone (PCL) crystals and to some extent into the poly-δ-valerolactone (PVL) crystals, resulting in a more gradual decrease in crystallinity with increasing amount of DXO.     

Control of defect concentrations within a semiconductor through adsorption

The technologically useful properties of a crystalline solid depend upon the concentration of defects it contains. Here we show that defect concentrations as deep as 0.5 microm within a semiconductor can be profoundly influenced by gas adsorption. Self-diffusion rates within silicon show that nitrogen atoms adsorbed at less than 1% of a monolayer lead to defect concentrations that vary controllably over several orders of magnitude. The results show that previous measurements of diffusion and defect thermodynamics in semiconductors may have suffered from neglect of adsorption effects.     

Secondary ion yields produced by keV atomic and polyatomic ion impacts on a self-assembled monolayer surface

A suite of keV polyatomic or 'cluster' projectiles was used to bombard unoxidized and oxidized self-assembled monolayer surfaces. Negative secondary ion yields, collected at the limit of single ion impacts, were measured and compared for both molecular and fragment ions. In contrast to targets that are orders of magnitude thicker than the penetration range of the primary ions, secondary ion yields from polyatomic projectile impacts on self-assembled monolayers show little to no enhancement when compared with monatomic projectiles at the same velocity. This unusual trend is most likely due to the structural arrangement and bonding characteristics of the monolayer molecules with the Au(111). Copyright 1999 John Wiley & Sons, Ltd.     

Fusion around the barrier for 7Li+12C

Fusion cross-sections for the ⁷Li + ¹²C reaction have been measured at energies above the Coulomb barrier by the direct detection of evaporation residues. The heavy evaporation residues with energies below 3 MeV could not be separated out from the α-particles in the spectrum and hence their contribution was estimated using statistical model calculations. The present work indicates that suppression of fusion cross-sections due to the breakup of ⁷Li may not be significant for ⁷Li + ¹²C reaction at energies around the barrier.     

Vibrational properties of the compressed and the relaxed 1,4,5,8-naphthalene-tetracarboxylic dianhydride monolayer on Ag(111)

Layers of 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA) grown on Ag(111) at about 80 K have been investigated using Fourier transform infrared spectroscopy, spot profile analysis low-energy electron diffraction, and temperature programmed desorption. Specifically, the compressed and the relaxed monolayer, as well as the transformation between the two ordered phases have been analyzed in detail. It is found that the two monolayer phases display distinctly different vibrational spectra and can thus be discriminated with high accuracy and sensitivity. For the NTCDA/Ag(111) monolayer strong in-plane vibrational modes point at a marked dynamic charge transfer between molecule and metal substrate and provide clear evidence for an efficient electronic coupling to the Ag(111) surface in conjunction with a partially filled electronic level at the Fermi energy. The bilayer, on the other hand, is largely electronically decoupled from the substrate and, according to the vanishing infrared-active in-plane vibrational modes, is oriented parallel to the surface. On the basis of spectroscopic data the metastable nature of the bilayer phase is identified as such, leading to an improved understanding of processes encountered in the course of layer preparation and resolving inconsistencies reported in the literature.     

Dynamics of surfactant-suspended single-walled carbon nanotubes in a centrifugal field

A hydrodynamic model is used to describe the motion of surfactant-suspended single-walled carbon nanotubes in a density gradient, while being subjected to a centrifugal field. The number of surfactant molecules adsorbed on each nanotube determines its effective density and, hence, its position in the gradient after centrifugation has been completed. Analysis of the spatial concentration distributions of CoMoCAT nanotubes suspended with 2 w/v% sodium cholate yielded 2.09, 2.14, and 2.08 surfactant molecules adsorbed per nanometer along the length of the (6,5), (7,5), and (8,7) nanotubes, respectively. The estimates are commensurate with experimental values reported in the literature and can be used to predict the fate of sodium cholate-suspended nanotubes in the separation process. Since the density of the surfactant-nanotube assembly is highly sensitive to the number of adsorbed molecules, a perturbation would cause it to be enriched at a different location in the gradient. The level of sensitivity is also reflected in the 95% confidence levels that are reported in this work.     

Real meromorphic functions and linear differential polynomials

We determine all real meromorphic functions f in the plane such that f has finitely many zeros, the poles of f have bounded multiplicities, and f and F have finitely many non-real zeros, where F is a linear differential polynomial given by F = f (k) +Σk-1j=0ajf(j) , in which k≥2 and the coefficients aj are real numbers with a0≠0.