scholarly journals Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

2014 ◽  
Vol 118 (14) ◽  
pp. 3805-3813 ◽  
Author(s):  
Kushal Bagchi ◽  
Susmita Roy
Keyword(s):  
Electrostatic Interactions ◽  
Water Dynamics ◽  
Monomeric Insulin

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 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.

scholarly journals Biogeomorphic feedbacks and the ecosystem engineering of recently deglaciated terrain

2018 ◽  
Vol 43 (1) ◽  
pp. 24-45 ◽  
Author(s):  
Hannah R Miller ◽  
Stuart N Lane
Keyword(s):  
Environmental Stress ◽  
Ecosystem Engineer ◽  
Abiotic Factors ◽  
Ecosystem Engineering ◽  
Soil Development ◽  
Water Dynamics ◽  
Biotic Factors ◽  
Successional Stage ◽  
Abiotic And Biotic Factors

Matthews’ 1992 geoecological model of vegetation succession within glacial forefields describes how following deglaciation the landscape evolves over time as the result of both biotic and abiotic factors, with the importance of each depending on the level of environmental stress within the system. We focus in this paper on how new understandings of abiotic factors and the potential for biogeomorphic feedbacks between abiotic and biotic factors makes further development of this model important. Disturbance and water dynamics are two abiotic factors that have been shown to create stress gradients that can drive early ecosystem succession. The subsequent establishment of microbial communities and vegetation can then result in biogeomorphic feedbacks via ecosystem engineering that influence the role of disturbance and water dynamics within the system. Microbes can act as ecosystem engineers by supplying nutrients (via remineralization of organic matter and nitrogen fixation), enhancing soil development, either decreasing (encouraging weathering) or increasing (binding sediment grains) geomorphic stability, and helping retain soil moisture. Vegetation can act as an ecosystem engineer by fixing nitrogen, enhancing soil development, modifying microbial community structure, creating seed banks, and increasing geomorphic stability. The feedbacks between vegetation and water dynamics in glacial forefields are still poorly studied. We propose a synthesized model of ecosystem succession within glacial forefields that combines Matthews’ initial geoecological model and Corenblit's model to illustrate how gradients in environmental stress combined with successional time drive the balance between abiotic and biotic factors and ultimately determine the successional stage and potential for biogeomorphic feedbacks.

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

scholarly journals Graphene oxide for high-efficiency separation membranes: Role of electrostatic interactions

Carbon ◽  
2016 ◽  
Vol 110 ◽  
pp. 56-61 ◽  
Author(s):  
Gonggang Liu ◽  
Hongqi Ye ◽  
Antai Li ◽  
Chenyuan Zhu ◽  
Heng Jiang ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Electrostatic Interactions ◽  
High Efficiency ◽  
Separation Membranes
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