			Home About us Contact

Electrostatic Analysis (electrostatic + analysis)

Distribution by Scientific Domains

Chemistry	60%

Selected Abstracts

Electrostatic analysis of charge interactions in proteins

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2010
G. P. Tsironis
Abstract We model proteins as continuous electrostatic media immersed in water to investigate charge mediated processes in their interior. We use a Green's function formalism and find analytical expressions for the electrostatic energy in the vicinity of the protein surfaces. We find that due to image charges generated by the protein dielectric medium embedded in water, the effective electrostatic interaction between the two charges in the interior of the protein has an energy larger than the thermal energy. We focus specifically on kinesin to asses the strength of the electrostatic interaction between ATP and ADP molecules. It is known experimentally that ADP expulsion is correlated to ATP kinesin binding while both processes are essential for the kinesin walk. We estimate that the Bjerrum length in the interior of the kinesin dimer protein is of the order of 4 nm and that the pure electrostatic ATP,ADP interaction is of the order of 3,5 kBT. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]

A fast boundary cloud method for 3D exterior electrostatic analysis

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 15 2004
Vaishali Shrivastava
Abstract An accelerated boundary cloud method (BCM) for boundary-only analysis of 3D electrostatic problems is presented here. BCM uses scattered points unlike the classical boundary element method (BEM) which uses boundary elements to discretize the surface of the conductors. BCM combines the weighted least-squares approach for the construction of approximation functions with a boundary integral formulation for the governing equations. A linear base interpolating polynomial that can vary from cloud to cloud is employed. The boundary integrals are computed by using a cell structure and different schemes have been used to evaluate the weakly singular and non-singular integrals. A singular value decomposition (SVD) based acceleration technique is employed to solve the dense linear system of equations arising in BCM. The performance of BCM is compared with BEM for several 3D examples. Copyright © 2004 John Wiley & Sons, Ltd. [source]

XPS study of surface potential in AlGaN/GaN heterostructure with Cat-CVD SiN passivation

PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 7 2007
N. Onojima
Abstract AlGaN surface potentials in AlGaN/GaN heterostructures with and without SiN passivation were investigated using x-ray photoelectron spectroscopy (XPS). SiN films were formed on AlGaN surfaces by catalytic chemical vapor deposition (Cat-CVD), which has already been found to increase two-dimensional electron gas (2DEG) density. Based on a simple electrostatic analysis, the 2DEG density is expected to increase as the AlGaN surface potential decreases. This study experimentally demonstrates that a reduction in the AlGaN surface potential is actually induced by Cat-CVD SiN passivation. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid

PROTEIN SCIENCE, Issue 2 2008
Freddie R. Salsbury Jr
Abstract Cysteine sulfenic acid (Cys-SOH), a reversible modification, is a catalytic intermediate at enzyme active sites, a sensor for oxidative stress, a regulator of some transcription factors, and a redox-signaling intermediate. This post-translational modification is not random: specific features near the cysteine control its reactivity. To identify features responsible for the propensity of cysteines to be modified to sulfenic acid, a list of 47 proteins (containing 49 known Cys-SOH sites) was compiled. Modifiable cysteines are found in proteins from most structural classes and many functional classes, but have no propensity for any one type of protein secondary structure. To identify features affecting cysteine reactivity, these sites were analyzed using both functional site profiling and electrostatic analysis. Overall, the solvent exposure of modifiable cysteines is not different from the average cysteine. The combined sequence, structure, and electrostatic approaches reveal mechanistic determinants not obvious from overall sequence comparison, including: (1) pKas of some modifiable cysteines are affected by backbone features only; (2) charged residues are underrepresented in the structure near modifiable sites; (3) threonine and other polar residues can exert a large influence on the cysteine pKa; and (4) hydrogen bonding patterns are suggested to be important. This compilation of Cys-SOH modification sites and their features provides a quantitative assessment of previous observations and a basis for further analysis and prediction of these sites. Agreement with known experimental data indicates the utility of this combined approach for identifying mechanistic determinants at protein functional sites. [source]