Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model

Residues at the binding sites of the ligand and receptor of several enzyme-inhibitor and antibody-antigen complexes are predicted from the slowest (for the ligand) and fastest (for the receptor) modes of motion by the Gaussian Network Model applied to unbound molecules.     

Electrostatically driven protein aggregation: beta-lactoglobulin at low ionic strength

The aggregation of beta-lactoglobulin (BLG) at ambient temperature was studied using turbidimetry and dynamic light scattering in the range 3.8相似文献   

High-temperature electrocatalysis using thermophilic P450 CYP119: dehalogenation of CCl4 to CH4

The use of a thermophilic cytochrome P450, CYP119, in electrocatalytic dehalogenations of C1 halocarbon solvents is studied. Temperature stable enzyme-modified electrodes were constructed using sol-gel and polymeric surfactant approaches. CYP119 deposited in a dimethyldidodecylammonium poly(p-styrene sulfonate) (DDAPSS) film has good retention of electrochemical activity up to 80 degrees C. At potentials approaching the FeII/I couple, the CYP119/DDAPSS films demonstrate high catalytic dehalogenations of the C1 chloromethanes CCl4, CHCl3, and CH2Cl2. Product analysis identified mixtures of sequentially dechlorinated products up to methane; no evidence for radical-coupled products was observed. The yield of methane from the CYP119-catalyzed reduction of CCl4 is increased 35-fold from 25 degrees C to 55 degrees C. In combination with the lack of C2 products, the facility of an overall eight-electron reductive dehalogenation suggests that the substrate is constrained within the protein during electrocatalytic turnover.     

Method for obtaining the rate coefficient of a second-order gas evolving reaction

The method is based on the measurement of pressures produced by collection of the gas during equal time intervals. It was applied to HCOOH decomposition in H₂SO₄.     

Electrocatalytic reductions of nitrite, nitric oxide, and nitrous oxide by thermophilic cytochrome P450 CYP119 in film-modified electrodes and an analytical comparison of its catalytic activities with myoglobin

Previous investigations of nitrite and nitric oxide reduction by myoglobin in surfactant film modified electrodes characterized several distinct steps in the denitrification pathway, including isolation of a nitroxyl adduct similar to that proposed in the P450nor catalytic cycle. To investigate the effect of the axial ligand on these biomimetic reductions, we report here a comparison of the electrocatalytic activity of myoglobin (Mb) with a thermophilic cytochrome P450 CYP119. Electrocatalytic nitrite reduction by CYP119 is very similar to that by Mb: two catalytic waves at analogous potentials are observed, the first corresponding to the reduction of nitric oxide, the second to the production of ammonia. CYP119 is a much more selective catalyst, giving almost exclusively ammonia during the initial half-hour of reductive electrolysis of nitrite. More careful investigations of specific steps in the catalytic cycle show comparable rates of nitrite dehydration and almost identical potentials and lifetimes for ferrous nitroxyl intermediate (Fe(II)-NO(-)) in CYP119 and Mb. The catalytic efficiency of nitric oxide reduction is reduced for CYP119 as compared to Mb, attributable to both a lower affinity of the protein for NO and a decreased rate of N-N coupling. Isotopic labeling studies show ammonia incorporation into nitrous oxide produced during nitrite reduction, as has been termed co-denitrification for certain bacterial and fungal nitrite reductases. Mb has a much higher co-denitrification activity than CYP119. Conversely, CYP119 is shown to be slightly more efficient at the two-electron reduction of N(2)O to N(2). These results suggest that thiolate ligation does not significantly alter the catalytic reactivity, but the dramatic difference in product distribution may suggest an important role for protein stability in the selectivity of biocatalysts.     

Numerical modeling of a non-linear viscous flow in order to determine how parameters in constitutive relations influence the entropy production

Some rheological materials, such as melting polymers, cosmetic creams, ketchup, toothpaste, can be modeled as non-NEWTONian fluids by using a non-linear constitutive relation. An incompressible flow of this kind of amorphous matter can be considered as a thermodynamic process, and a solution for the pressure, velocity and temperature fields describe it fully. Since such flow processes are generally irreversible, entropy is produced leading to dissipation in the system. This energy loss can be measured indirectly in a cone/plate viscometer which is used to determine viscosity of a BINGHAM fluid. While dissipation is an observable quantity we also want to be able to calculate it. Thus the goal of this work is to explain briefly how to compute a transient flow of a viscous fluid in two-dimensional channel under a sinusoidal traction and calculate the dissipated energy for non-NEWTONian fluids. (© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Molecular mass dependence of adsorbed amount and hydrodynamic thickness of polyelectrolyte layers

Highly charged polyelectrolytes adsorbed on oppositely charged colloidal particles are investigated by electrophoresis and dynamic light scattering. The dependence of the adsorbed amount and of the hydrodynamic layer thickness on the molecular mass and the salt level is analyzed. The adsorbed amount increases with increasing salt level and decreases with increasing molecular mass. The hydrodynamic layer thickness is independent of the molecular mass at low salt levels, but increases with the molecular mass as a power law with an exponent 0.10 ± 0.01 at high salt. The same behavior was observed for different polyelectrolytes and substrates and therefore is suspected to be generic. Due to semi-quantitative agreement with computer simulations carried out by Kong and Muthukumar in 1998, the observed behavior is interpreted with conformational changes of single adsorbed polyelectrolyte chains.     

Quantification of the degree of irreversibility in terms of material parameters by using Ziegler's non-linear constitutive relation for the stress-velocity gradient relationship

The non-trivial task of an engineer is to derive or at least to use a constitutive relation which leads to a solvable equation but still expresses the system behavior adequately, so that the solution for the motion is accurate. Often the system has solid-like or fluid-like behavior, and an appropriate relation is chosen. In the so-called Bingham-Ilyushin matter both regimes occur simultaneously. This can be expressed by using a tensor-linear constitutive relation with a nonlinear (viscosity) term and even be solved in a specific case of material parameters (b = 0 ). The analytical solution for the velocity distribution in a channel with moving walls is presented here. The velocity gradients lead to an increase in temperature. The internal friction due to the (nonlinear) viscosity contributes to the entropy production and accounts for the irreversibility of the process. The aim is to analyze the role of each material parameter in the entropy production which might be used as a measure of irreversibility of the process. (© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Verification of deforming polarized structure computation by using a closed-form solution

Various engineering systems exploit the conversion between electromagnetic and mechanical work. It is important to compute this coupling accurately, and we present a method for solving the governing equations simultaneously (at once) without a staggering scheme. We briefly present the theory for coupling the elecgoverning equations as well as the variational formulation that leads to the weak form. This weak form is nonlinear and couples various fields. In order to solve the weak form, we use the finite element method in space and the finite difference method in time for the discretization of the computational domain. Numerical problems are circumvented by selecting the field equations carefully, and the weak form is assembled using standard shape functions. In order to examine the accuracy of the method, for the case of a linear elastic material under small deformations, we present and use an analytic solution. Comparison of the computation to the closed-form solution shows that the computational approach is reliable and models the jump of the electromagnetic fields across the interface between two different materials.