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Conduction Properties of KcsA Measured Using Brownian Dynamics with Flexible Carbonyl Groups in the Selectivity Filter
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ABSTRACT
In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihe...
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; ABSTRACT It is now widely accepted that protein function depends not only on structure, but also on flexibility. However, the way mechanical properties contribute to catalytic mechanisms remains unclear. Here, we propose a method for investigating local flexibility within protein structures that
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Conduction Properties of KcsA Measured Using Brownian Dynamics with Flexible Carbonyl Groups in the Selectivity Filter
Biophysical Journal
; ABSTRACT In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics
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Intrachain reactions of supercoiled DNA simulated by Brownian dynamics
Biophysical Journal
; ABSTRACT We considered an irreversible biochemical intrachain reaction of supercoiled DNA as a random event that occurs, with certain probability, at the instant of collision between two reactive groups bound to distant DNA sites. Using the Brownian dynamics technique, we modeled this process for a
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Biophysical Journal
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Biophysical Journal
; ABSTRACT A comparative analysis of two models of anisotropic reactivity in bimolecular diffusion-controlled reaction kinetics is presented. One is the conventional model of reactive patches (MRP), where the surface of a molecule is assumed to be reactive over a certain region (circular patch) with
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Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels
Biophysical Journal
; ABSTRACT The recognition of the scorpion toxin maurotoxin (MTX) by the voltage-gated potassium (Kv1) channels, Kv1.1, Kv1.2, and Kv1.3, has been studied by means of Brownian dynamics (BD) simulations. All of the 35 available structures of MTX in the Protein Data Bank (httpwww.rcsb.org/pdb)
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Biophysical Journal
; ABSTRACT We investigate the validity of continuum electrostatics in the gramicidin A channel using a recently determined high-resolution structure. The potential and electric field acting on ions in and around the channel are computed by solving Poisson's equation. These are then used in Brownian
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Probing Protein Mechanics: Residue-Level Properties and Their Use in Defining Domains
Biophysical Journal
; ABSTRACT It is becoming clear that, in addition to structural properties, the mechanical properties of proteins can play an important role in their biological activity. It nevertheless remains difficult to probe these properties experimentally. Whereas single-molecule experiments give access to
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Hierarchical approach to predicting permeation in ion channels
Biophysical Journal
; ABSTRACT A hierarchical computational strategy combining molecular modeling, electrostatics calculations, molecular dynamics, and Brownian dynamics simulations is developed and implemented to compute electrophysiologically measurable properties of the KcsA potassium channel. Models for a series of
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Homology Model of the GABA^sub A^ Receptor Examined Using Brownian Dynamics
Biophysical Journal
; ... produce a homology model of the GABA^sub A^ receptor. This model, consisting of two α1, two β2, and one γ2 subunit, maps the majority of the native receptor, with the exception of the intracellular vestibule. Our initial model is then molded in a ...
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