Reduction and cyclization in biotransformation of carbonyl compounds by cultured cells of Taxus species

Cultured plant cells from Taxus brevifolia Nutt and Taxus globosa Schltdl were investigated as biocatalysts using exogenous substrates. Production of highly specific metabolites by these species prompted us to analyse their synthetic potential. Whole cells suspensions have the capacity to chemoselectively reduce ethyl acetoacetate to ethyl 3-hydroxybutyrate chemo- and stereoselectively reduce rac-2-benzoylcyclohexanone to (1R, 2S)- and (1S, 2S)-2-hydroxycyclohexylphenylmethanones, and to cyclize N-phthaloyl-L-glutamine to thalidomide.     

Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants

The use of computational modeling algorithms to guide the design of novel enzyme catalysts is a rapidly growing field. Force-field based methods have now been used to engineer both enzyme specificity and activity. However, the proportion of designed mutants with the intended function is often less than ten percent. One potential reason for this is that current force-field based approaches are trained on indirect measures of function rather than direct correlation to experimentally-determined functional effects of mutations. We hypothesize that this is partially due to the lack of data sets for which a large panel of enzyme variants has been produced, purified, and kinetically characterized. Here we report the k_cat and K_M values of 100 purified mutants of a glycoside hydrolase enzyme. We demonstrate the utility of this data set by using machine learning to train a new algorithm that enables prediction of each kinetic parameter based on readily-modeled structural features. The generated dataset and analyses carried out in this study not only provide insight into how this enzyme functions, they also provide a clear path forward for the improvement of computational enzyme redesign algorithms.     

Collective chain dynamics in lipid bilayers by inelastic x-ray scattering

We investigated the application of inelastic x-ray scattering (IXS) to lipid bilayers. This technique directly measures the dynamic structure factor S(q,omega) which is the space-time Fourier transform of the electron density correlation function of the measured system. For a multiatomic system, the analysis of S(q,omega) is usually complicated. But for multiple bilayers of lipid, S(q,omega) is dominated by chain-chain correlations within individual bilayers. Thus IXS provides a unique probe for the collective dynamics of lipid chains in a bilayer that cannot be obtained by any other method. IXS of dimyristoyl phosphatidylcholine and dimyristoyl phosphatidylcholine + cholesterol at two different concentrations were measured. S(q,omega) was analyzed by three-mode hydrodynamic equations, including a thermal diffusive mode and two propagating acoustic modes. We obtained the dispersion curves for the phonons that represent the collective in-plane excitations of lipid chains. The effect of cholesterol on chain dynamics was detected. Our analysis shows the importance of having a high instrument resolution as well as the requirement of sufficient signal-to-noise ratio to obtain meaningful results from such an IXS experiment. The requirement on signal-to-noise also applies to molecular dynamics simulations.     

Construction of biofilms with defined internal architecture using dielectrophoresis and flocculation

A novel approach was developed for the construction of biofilms with defined internal architecture using AC electrokinetics and flocculation. Artificial structured microbial consortia (ASMC) consisting of localized layered microcolonies of different cell types were formed by sequentially attracting different cell types to high field regions near microelectrodes using dielectrophoresis. Stabilization of the microbial consortia on the electrode surface was achieved by crosslinking the cells using the flocculant polyethyleneimine (PEI). Consortia of Escherichia coli, Micrococcus luteus, and Saccharomyces cerevisiae were made as model systems. Also, more natural consortia were made of the bacteria Pseudomonas putida, Clavibacter michiganense, and Methylobacterium mesophilum, which are found together in consortia during biodegradation of metal-cutting waste fluids.     

Glomerular and tubular responses to N(G)-nitro-L-arginine methyl ester are age dependent in conscious lambs

The present experiments were carried out to investigate the role of endogenously produced NO in modulating renal function during postnatal maturation under physiological conditions. In conscious, chronically instrumented lambs aged approximately 1 (n = 8) and approximately 6 wk (n = 8) of postnatal life, various parameters of glomerular and tubular function were measured for 1 h before and 1 h after intravenous injection of 20 mg/kg of N(G)-nitro-L-arginine methyl ester (L-NAME; experiment 1) or its inactive isomer D-NAME (experiment 2). After administration of L-NAME to 1-wk-old lambs, glomerular filtration rate (GFR) and filtration factor (FF) decreased by approximately 50% at 20 min, remaining decreased at 60 min. In 6-wk-old lambs, GFR and FF remained constant after L-NAME. Proximal fractional Na(+) reabsorption decreased after L-NAME administration to lambs aged 6 wk, resulting in a prompt natriuresis; this was sustained for 60 min. There were no effects of L-NAME on proximal fractional Na(+) reabsorption in 1-wk-old lambs. In 6-wk-old lambs, urinary flow rate increased by approximately 500%, free water clearance increased by approximately 50%, and urinary osmolality decreased by approximately 60% after L-NAME administration; no effects on these variables were measured in 1-wk-old lambs. The diuresis after L-NAME administration to 6-wk-old lambs was unaccompanied by any changes in plasma levels of arginine vasopressin. There were no effects of D-NAME on any of the measured variables. We conclude that endogenously produced nitric oxide modulates glomerular and tubular function in an age-dependent manner.     

Studies of short-wavelength collective molecular motions in lipid bilayers using high resolution inelastic X-ray scattering

We summarize a series of experimental results made with the newly developed high resolution X-ray scattering (IXS) instrument on two pure lipid bilayers, including dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) in both gel and liquid crystal phases, and lipid bilayers containing cholesterol. By analyzing the IXS data based on the generalized three effective eigenmode model (GTEE), we obtain dispersion relations of the high frequency density oscillations (phonons) of lipid molecules in these bilayers. We then compare the dispersion relations of pure lipid bilayers of different chain lengths among themselves and the dispersion relations of pure lipid bilayers with those of the cholesterol containing bilayers. We also compare our experimental results with collective dynamics data generated by computer molecular dynamics (MD) simulations for dipalmitoylphosphatidylcholine (DPPC) in gel phase and DMPC in liquid crystal phase.     

Nuclear forward scattering of synchrotron radiation by deoxymyoglobin

Nuclear forward scattering of synchrotron radiation is used to determine the quadrupole splitting and the mean square displacement of the iron atom in deoxymyoglobin in the temperature range between 50 K and 243 K. Above 200 K an abnormally fast decay of the forward scattered intensity at short times after the synchrotron flash is observed, which is caused by protein-specific motions. The results strongly support the picture that protein dynamics seen at the position of the iron can be understood by harmonic motions in the low temperature regime while in the physiological regime diffusive motions in limited space are present. The shape of the resonance broadening function is investigated. An inhomogeneous broadening with a Lorentzian distribution indicating dipole interactions results in a better agreement with the experimental data than the common Gaussian distribution. Received: 30 August 1999 / Revised version: 22 October 1999 / Accepted: 6 December 1999     

Fabricating tissues: Analysis of farming versus engineering strategies

Tissue Engineering has expanded rapidly towards target applications of tissue repair and regeneration, whilst generating surprisingly novel models to study tissue modelling. However, clinical success in producing effective engineered tissues such as bone, skin, cartilage, and tendon, have been rare and limited. Problems tend to focus on how to stimulate the replacement of initial scaffold with mechanically functional, native extracellular matrix (principally collagen). Typical approaches have been to develop perfused and mechanically active bioreactors, with the use of native collagen itself as the initial scaffold, though the idea remains that cells do the fabrication (i.e. a cultivation process). We have developed a new, engineering approach, in which the final collagen template is fabricatedwithout cell involvement. The first part of this biomimetic engineering involves a plastic compression of cellular native collagen gels to form dense, strong, collagenous neotissues (in minutes). Further steps can be used to orientate and increase collagen fibril diameter, again by non-cell dependent engineering. This allows operator control of cell or matrix density and material properties (influencing biological half life and fate). In addition, this (non-cultivation) approach can incorporate techniques to generate localised 3D structures and zones at a meso-scale. In conclusion, the use of biomimetic engineering based on native collagen, rather than cell-cultivation approaches for bulk matrix fabrication, produces huge benefits. These include speed of fabrication (minutes instead of weeks and months), possibility of fine control of composition and 3D nano-micro scale structure and biomimetic complexity.     

Selenium effects on arsenic cytotoxicity and protein phosphorylation in human kidney cells using chip-based nanoLC-MS/MS

Although arsenic toxicity is well known, little is known of how it exerts its effects at the proteome level. Protein phosphorylation is an important post-translational modification in the regulation of cell signaling. Despite the importance of protein phosphorylation, the identification and characterization of phosphorylated proteins, as influenced by interaction between arsenic and selenium species have not been fully studied. The aim of this study is to identify phosphorylation in arsenic toxified cells, with and without selenium present. Here, we identify the phosphorylated proteins related to post translational modifications (PTMs) after inorganic arsenic (iAs) and selenomethionine (SeMet) were inoculated together with HEK293 human kidney cells. In this study, using TiO(2)-based nanoLC-phosphochip? coupled to ESI-MS we observed phosphorylated peptide enrichment and significant reduction in sample complexity. The identification of phosphorylated proteins in highly complex digests of cell lysate were markedly different with As toxification only, or when in the presence of SeMet. Several phosphorylation sites and proteins are identified using Spectrum Mill and Mascot protein data base search engines. Cytotoxicity studies showed that SeMet significantly reduces the cytotoxic effect of iAs in HEK293 cells, while inorganic selenium did not.