Effects of pH on the Interactions and Conformation of Bovine Serum Albumin: Comparison between Chemical Force Microscopy and Small-Angle Neutron Scattering

The conformation of bovine serum albumin (BSA), as well as its interactions with negatively charged mica surfaces in saline solutions of different pH values, have been studied by small-angle neutron scattering (SANS) and chemical force microscopy (CFM), respectively. A new approach to extract the contribution of elementary interactions from the statistically averaged force-extension curves through self-consistent fitting was proposed and used to understand the effects of pH on the interactions and conformation of BSA in saline solutions. When pH increases, the SANS results reveal that the sizes of BSA molecules increase slightly, while the statistical analysis of the CFM results shows that the averaged pull-off force for the elongation monotonously decreases. The decrease of pull-off force with the increase of pH results from the decrease in the strength of hydrogen bonding and the number of interaction pairs, as well as the slight increase of the strength of van der Waals interaction. When pH approaches the isoelectric point (pI) of BSA, results from both SANS and CFM suggest a loss of long-range interactions in BSA molecules. Our results also suggest that the force-extension curve is mainly contributed by the van der Waals interaction. The combination of SANS and CFM provides new insight to understand the interactions and conformation of BSA molecules

Effects of polar group saturation on physical gelation of Amphiphilic polymer solutions

Monte Carlo simulation on the basis of the comblike coarse grained nonpolar/polar (NP) model has been carried out to study the polar group saturation effect on physical gelation of amphiphilic polymer solutions. The effects of polar group saturation due to hydrogen bonding or ion bridging on the sol-gel phase diagram, microstructure of aggregates, and chain conformation of amphiphilic polymer solutions under four different solvent conditions to either the nonpolar backbone or the polar side chain in amphiphilic polymer chains have been investigated. It is found that an increase of polar group saturation results in a monotonically decreased critical concentration of gelation point, which can be qualitatively supported by the dynamic theological measurements on pectin aqueous solutions. Furthermore, various solvent conditions to either the backbone or the side chain have significant impact on both chain conformation and microstructure of aggregates. When the solvent is repulsive to the nonpolar backbone but attractive to the polar side chain, the polymer chains are collapsed, and the gelation follows the mechanism of colloidal packing; at the other solvent conditions, the gelation follows the mechanism of random aggregation.

Effects of chain flexibility on polymer conformation in dilute solution studied by lattice Monte Carlo simulation

Effects of chain flexibility on the conformation of homopolymers in good solvents have been investigated by Monte Carlo simulation. Bond angle constraint coupled with persistence length of polymer chains has been introduced in the modified eight-site bond fluctuation simulation model. The study about the effects of chain flexibility on polymer sizes reveals that the orientation of polymer chains under confinement is driven by the loss of conformation entropy. The conformation of polymer chains undergoing a gradual change from spherical iso-diametric ellipsoid to rodlike iso-diametric ellipsoid with the decrease of polymer chain flexibility in a wide region has been clearly illustrated from several aspects. Furthermore, a comparison of the freely jointed chain (FJC) model and the wormlike chain (WLC) model has also been made to describe the polymer sizes in terms of chain flexibility and quasi-quantitative boundary toward the suitability of the models.

Investigation of sol-gel transition in Pluronic F127/D2O solutions using a combination of small-angle neutron scattering and Monte Carlo simulation

Physical gelation in the concentrated Pluronic F127/D2O solution has been studied by a combination of small-angle neutron scattering (SANS) and Monte Carlo simulation. A 15% F127/D2O solution exhibits a sol-gel transition at low temperature and a gel-sol transition at the higher temperature, as evidenced by SANS and Monte Carlo simulation studies. Our SANS and simulation results also suggest that the sol-gel transition is dominated by the formation of a percolated polymer network, while the gel-sol transition is determined by the loss of bound solvent. Furthermore, different diffusion behaviors of different bound solvents and free solvent are observed. We expect that this approach can be further extended to study phase behaviors of other systems with similar sol-gel phase diagrams.

How does solvent molecular size affect the microscopic structure in polymer solutions?

Monte Carlo simulation has been used to investigate the effects of linear solvent molecular size on polymer chain conformation in solutions. Increasing the solvent molecular size leads to shrinkage of the polymer chains and increase of the critical overlap concentrations. The root-mean-square radius of gyration of polymer chains (R-g) is less sensitive to the variation of polymer concentration in solutions of larger solvent molecules. In addition, the dependency of R-g on polymer concentration under normal solvent conditions and solvent molecular size is in good agreement with scaling laws. When the solvent molecular size approaches the ideal end-to-end distance of the polymer chain, an extra aggregation of polymer chains occurs, and the solvent becomes the so-called medium-sized solvent. When the size of solvent molecules is smaller than the medium size, the polymer chains are swollen or partially swollen. However, when the size of solvent molecules is larger than the medium size, the polymer coils shrink and segregate, enwrapped by the large solvent molecules.

Electron collision cross sections and rate coefficients for the Na-like Cu ion

Collision cross sections are calculated using the R-matrix method for excitations between the three lowest LS states for Na-like Cu ion. The complex resonance structures are investigated. The collision rate coefficients have been calculated assuming a Maxwellian distribution of electron-impact energies. The results of the collision cross sections are in good agreement with those of the other theory.

Polyunsaturated eicosapentaenoic acid changes lipid composition in lipid rafts

Background Polyunsaturated fatty acids (PUFAs) modulate immune responses particularly by affecting T cell function and are applied clinically as adjuvant immunosuppressants in the treatment of various inflammatory diseases. However, the molecular mechanisms of PUFA-induced immunosuppressive effects are not yet elucidated. Membrane lipid rafts are functional plasma membrane microdomains characterized by a unique lipid environment. Since lipid interactions are crucial for the formation of lipid rafts, the immunomodulatory effects of PUFAs may be due to changes of fatty acid composition in lipid rafts.

Expression of C-reactive protein in human lung epithelial cells and up-regulation by cytokines and carbon particles.

C-reactive protein (CRP) is the prototypic human acute-phase protein and is found at increased levels in the blood during episodes of inflammation. CRP was generally thought to be produced only by hepatocytes; however, several studies have shown extrahepatic synthesis of CRP. A previous study showed that PM10 and ultrafine carbon black (ufCB) were able to induce CRP expression in A549 cells. This study aims to examine the factors that lead to the production of CRP in A549 cells. A549 human lung epithelial cells were treated with cytokines (interleukin 6, tumor necrosis factor , interferon , or interleukin 1) or carbon particles (CB and ufCB) for 18 h. It was found that CRP could be expressed within the cells and that CRP was secreted from the cells particularly with tumor necrosis factor , CB and ufCB treatments. It was also found that this expression of CRP with CB and ufCB treatments was dependent on nuclear factor kappa B (NFB). The expression of CRP in A549 cells may indicate an important role for CRP expression and secretion from lung epithelial cells in response to inflammatory stimuli.

Analysis of the mechanism and regulation of lactose transport and metabolism in Clostridium acetobutylicum ATCC 824.

Although the acetone-butanol-ethanol (ABE) fermentation of Clostridium acetobutylicum is currently uneconomic, the ability of the bacterium to metabolise a wide range of carbohydrates offers the potential for revival based on the use of cheap, low grade substrates. We have investigated the uptake and metabolism of lactose, the major sugar in industrial whey waste, by C. acetobutylicum ATCC 824. Lactose is taken up via a phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) comprising both soluble and membrane-associated components, and the resulting phosphorylated derivative is hydrolysed by a phospho--galactosidase. These activities are induced during growth on lactose, but are absent in glucose-grown cells. Analysis of the C. acetobutylicum genome sequence identified a gene system, lacRFEG, encoding a transcriptional regulator of the DeoR family, IIA and IICB components of a lactose PTS, and phospho--galactosidase. During growth in medium containing both glucose and lactose, C. acetobutylicum exhibited a classical diauxic growth, and the lac operon was not expressed until glucose was exhausted from the medium. The presence upstream of lacR of a potential catabolite responsive element (cre) encompassing the transcriptional start site is indicative of the mechanism of carbon catabolite repression characteristic of low-GC Gram-positive bacteria. A pathway for the uptake and metabolism of lactose by this industrially important organism is proposed.

Ambiguities and Deviations in Qualitative Circuit Analysis

Lee M.H., Bell J. and Coghill G.M., Ambiguities and Deviations in Qualitative Circuit Analysis, in Proc. QR?2001, 15th Int. Workshop on Qualitative Reasoning, San Antonio, Texas, May 2001, pp51-58.

Many-Valued Logic and Qualitative Modelling of Electrical Circuits

Lee M.H., Many-Valued Logic and Qualitative Modelling of Electrical Circuits, in Proc. QR?2000, 14th Int. Workshop on Qualitative Reasoning, Morelia, Mexico June 3rd - 7th 2000.

Qualitative Modelling of Linear Networks in ECAD Applications

Lee M.H., Qualitative Modelling of Linear Networks in ECAD Applications, Expert Update, Vol. 3, Num. 2, pp23-32, BCS SGES, Summer 2000. Qualitative modeling of linear networks in ecad applications (1999) by M Lee Venue: Pages 146?152 of: Proceedings 13th international workshop on qualitative reasoning, QR ?99

Qualitative Modelling of Linear Networks in ECAD Applications

Lee M.H., Qualitative Modelling of Linear Networks in ECAD Applications, Proc. 13th Int. Workshop on Qualitative Reasoning, (QR'99), Loch Awe, Scotland, 1999, pp146-52.

On the use of qualitative reasoning to simulate and identify metabolic pathways

King, R.D., Garrett, S.M., Coghill, G.M. (2005). On the use of qualitative reasoning to simulate and identify metabolic pathways. Bioinformatics 21(9):2017-2026 RAE2008