The Role of Electrostatic Interactions in Protease Surface Diffusion and the Consequence for Interfacial Biocatalysis

Langmuir ◽  
2010 ◽  
Vol 26 (24) ◽  
pp. 18916-18925 ◽  
Author(s):  
Bob E. Feller ◽  
James T. Kellis ◽  
Luis G. Cascão-Pereira ◽  
Channing R. Robertson ◽  
Curtis W. Frank
Keyword(s):  
Surface Diffusion ◽  
Electrostatic Interactions

scholarly journals On the role of surface diffusion in determining the shape or morphology of noble-metal nanocrystals

2013 ◽  
Vol 110 (17) ◽  
pp. 6669-6673 ◽  
Author(s):  
X. Xia ◽  
S. Xie ◽  
M. Liu ◽  
H.-C. Peng ◽  
N. Lu ◽  
...  
Keyword(s):  
Surface Diffusion ◽  
Noble Metal ◽  
Metal Nanocrystals

scholarly journals Role of Dispersion Attraction in Differential Geometry Based Nonpolar Solvation Models

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Zhan Chen
Keyword(s):  
Differential Geometry ◽  
Electrostatic Interactions ◽  
Polar Component ◽  
Great Success ◽  
Free Energies ◽  
Dispersion Interactions ◽  
Solvation Models ◽  
Nonpolar Solvation ◽  
Solvation Analysis

AbstractDifferential geometry (DG) based solvation models have shown their great success in solvation analysis by avoiding the use of ad hoc surface definitions, coupling the polar and nonpolar free energies, and generating solvent-solute boundary in a physically self-consistent fashion. Parameter optimization is a key factor for their accuracy, predictive ability of solvation free energies, and other applications. Recently, a series of efforts have been made to improve the parameterization of these new implicit solvent models. In thiswork, we aim at studying the role of dispersion attraction in the parameterization of our DG based solvation models. To this end, we first investigate the necessity of van derWaals (vdW) dispersion interactions in the model and then carry out systematic parameterization for the model in the absence of electrostatic interactions. In particular, we explore how the changes in Lennard-Jones (L-J) potential expression, its decomposition scheme, and choices of some fixed parameter values affect the optimal values of other parameters as well as the overall modeling error. Our study on nonpolar solvation analysis offers insights into the parameterization of nonpolar components for the full DG based models by eliminating uncertainties from the electrostatic polar component. Therefore, it can be regarded as a step towards better parameterization for the full DG based model.

Solvent effect on the conformational behavior of substituted spiro[4.5]decanes and spiro[5.5]undecanes

1995 ◽  
Vol 73 (5) ◽  
pp. 703-709 ◽  
Author(s):  
S. Sağ Erdem ◽  
T. Varnali ◽  
V. Aviyente ◽  
M.F. Ruiz-Lopez
Keyword(s):  
Solvent Effect ◽  
Electrostatic Interactions ◽  
Multipole Moment ◽  
Semiempirical Methods ◽  
Main Role ◽  
Solvent Interactions ◽  
Reaction Field ◽  
Solvent Models ◽  
Conformational Equilibria

We studied the relatively complex polar systems 6-substituted-1,4-dioxospiro[4.5]decanes and 7-substituted-1,5-dioxospiro[5.5]undecanes with substituents X = CH3, F, Cl, CN, OH, OCH3, and NO2. Solvent effects on the equilibrium have been analysed by means of a Self-Consistent-Reaction-Field model and the PM3 method. Complete geometry optimizations have been carried out for all the structures in the gas phase and in solution. For some substituents, a set of rotamers have been separately optimized. The discussion of the results is focussed on the effects arising from structural aspects and from steric and electrostatic interactions on the axial/equatorial relative stability. The role played by multipole moment is considered. In general, good agreement with available experimental data and with previous theoretical studies has been obtained. Though the use of semiempirical methods and simple solvent models prevents us from reaching definitive conclusions, this approach seems to be very useful in predicting the main role of solute–solvent interactions in conformational equilibria of complex systems for which ab initio calculations cannot be performed. Keywords: conformational equilibria, spiro decanes and undecanes, cavity model, SCRF, solvent effect, PM3 calculations.

On the Role of Surface Diffusion in Stress Relaxation During Electromigration

1995 ◽  
Vol 391 ◽  
Author(s):  
L.M. Klinger ◽  
L. Levin ◽  
E.E. Glickman
Keyword(s):  
Stress Relaxation ◽  
Surface Diffusion ◽  
Hydrostatic Stress ◽  
Stress Gradient ◽  
Film Surface ◽  
Diffusional Creep ◽  
Atomic Diffusion ◽  
Material Transport ◽  
Diffusional Flux

AbstractWe report on the role of surface diffusion involved in relaxation of electromigration (EM) induced compressive stresses in relation to hillock growth and EM behavior of interconnects. Two competing mechanisms of EM stress relaxation by material transport onto the surface are considered. The first is hillocking by threshold diffusional creep (TCH), with rather large blocks of material (grains or group of grains) involved in plastic flow. The second mechanism, atomic diffusion hillocking (ADH), is presumed to be a nonthreshold one, and represents atomic grain boundary (GB) diffusion stimulated by the hydrostatic stress gradient in the direction normal to the film surface. The latter process involves surface diffusion because GB diffusional flux onto the surface must be coupled with the flux of redistribution of the atoms over the surface. If ADH acts rapidly, this should prevent the build-up of the matter at the down-wind (anode) end of the stripe, and thus, eliminate the Blech EM threshold resulting from the stress-gradient along the stripe. The question as to whether GB diffusion capable of transporting atoms pushed by electron wind along the stripe is also effective in relieving compressive stress by GB migration of the surplus atoms in the normal direction, has remained open up to now. The problem is especially acute for short or/and narrow lines separated into short polycrystalline segments, where the Blech threshold effects are critical to EM reliability.We derived the main features of the EM behavior in drift velocity test geometry assuming that both TCH and ADH are operative. The result can be compared with available and future experimental observations in order to reveal if and when the ADH mechanism with surface diffusion involved works.

scholarly journals Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall

2018 ◽  
Author(s):  
Alister T. Boags ◽  
Firdaus Samsudin ◽  
Syma Khalid
Keyword(s):  
Cell Wall ◽  
Electrostatic Interactions ◽  
Cell Envelope ◽  
Binding Domain ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
E Coli ◽  
Non Covalent Interactions ◽  
Covalent Interactions

SUMMARYWe present a molecular modeling and simulation study of the of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. We show that non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. When OmpA is truncated to remove the peptidoglycan binding domain, TolR is able to pull the cell wall down towards the inner membrane. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.

scholarly journals The role of individual lysine residues in the basic patch on turnip cytochrome f for electrostatic interactions with plastocyanin in vitro

2000 ◽  
Vol 267 (12) ◽  
pp. 3461-3468 ◽  
Author(s):  
Xiao-Song Gong ◽  
Jiang Qi Wen ◽  
Nicholas E. Fisher ◽  
Simon Young ◽  
Christopher J. Howe ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Cytochrome F ◽  
Lysine Residues
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