Access resistance in protein nanopores. A structure-based computational approach.

08:00 EDT 3rd September 2019 | BioPortfolio

Summary of "Access resistance in protein nanopores. A structure-based computational approach."

Single-channel conductance measurements in biological pores have demonstrated the importance of interfacial effects in nanopores, particularly in protein channels with low aspect ratio (length over aperture radius). Access resistance (AR), the contribution to the total measured resistance arising from the electrodiffusive limitation that ions experience in passing from bulk solution to confinement within the pore, becomes essential in the description of ionic transport across these biological channels. Common analytical estimates of AR are based on idealized nanopore models, cylindrical in shape, electrically neutral and embedded in a neutral substrate. Here we calculate the AR of five protein channels by using their atomic structure and a mean-field approach based on solving 3D Poisson and Nernst-Planck equations. Our approach accounts for the influence of the protein charged ionizable residues, the geometry of the pore mouth and the ion concentration gradients near the pore. We compare numerical calculations with the few available AR measurements and show for several protein channels that analytical predictions tend to overestimate AR for physiological concentrations and below. We also discuss the relationship between AR and the size of the channel aperture in single-pore channels and three-pore channels and demonstrate that in the latter case, there is an enhancement of AR.


Journal Details

This article was published in the following journal.

Name: Bioelectrochemistry (Amsterdam, Netherlands)
ISSN: 1878-562X
Pages: 107371


DeepDyve research library

PubMed Articles [41942 Associated PubMed Articles listed on BioPortfolio]

1/f noise in solid-state nanopores is governed by access and surface regions.

The performance of solid-state nanopores as promising biosensors is severely hampered by low-frequency 1/f noise in the through-pore ionic current recordings. Here, we develop a model for the 1/f nois...

POsitive Multistate Protein design.

Structure-based Computational Protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to identify amino acid sequences th...

Computational algorithms for in silico profiling of activating mutations in cancer.

Methods to catalog and computationally assess the mutational landscape of proteins in human cancers are desirable. One approach is to adapt evolutionary or data-driven methods developed for predicting...

Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores.

The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state an...

The structure of Erwinia amylovora AvrRpt2 provides insight into protein maturation and induced resistance to fire blight by Malus × robusta 5.

The AvrRpt2 protein of the phytopathogenic bacterium Erwinia amylovora (AvrRpt2) is a secreted type III effector protein, which is recognised by the FB_MR5 resistance protein of Malus × robusta 5...

Clinical Trials [13501 Associated Clinical Trials listed on BioPortfolio]

Computational Simulation of Patellar Instability

Computational simulation will be performed to represent motion of knees with a dislocating kneecap. Common surgical treatment methods will be simulated and anatomical parameters commonly a...

Plant-based Dietary Protein and Resistance-training Adaptations

Dietary protein consumption maximizes the anabolic response during resistance training (RT) by triggering muscle protein synthesis and providing the indispensable amino acids for a net pos...


The molecular nature of insulin resistance in human muscle is still incompletely defined. Our data indicate that acetylation of mitochondrial proteins in humans is regulated by muscle cont...

Meat and Whey Protein Supplementation in Athletes

The aim of this project is to investigate the potential benefits of combining a new protein meat hydrolysates extract with a regular resistance training programme on (a) body composition (...

Protein Requirements in Resistance-trained Males

In this study, the investigators will use the minimally invasive indicator amino acid oxidation (IAAO) technique to determine protein requirements in resistance-trained males. It is hypoth...

Medical and Biotech [MESH] Definitions

A hemostatic disorder characterized by a poor anticoagulant response to activated protein C (APC). The activated form of Factor V (Factor Va) is more slowly degraded by activated protein C. Factor V Leiden mutation (R506Q) is the most common cause of APC resistance.

Approach to improve the quality of care by selectively encouraging or discouraging the use of specific health care services, based on their potential benefit to patients' health, relative to their cost. One element is lowering beneficiary cost sharing or out-of-pocket spending to increase medication adherence.

Differential treatment or unequal access to opportunities, based on group membership such as origin or ethnicity.

Surgical excision of the gingiva at the level of its attachment, thus creating new marginal gingiva. This procedure is used to eliminate gingival or periodontal pockets or to provide an approach for extensive surgical interventions, and to gain access necessary to remove calculus within the pocket. (Dorland, 28th ed)

Biased behaviors or attitudes, differential treatment, unequal access to social participation or opportunities based on age.

Quick Search

DeepDyve research library

Relevant Topics

Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...

Biological Therapy
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...

Searches Linking to this Article