Influence of protein flexibility on the electrostatic energy landscape in gramicidin A

Ben Corry, S-H. Chung

Research output: Contribution to journalArticlepeer-review

16 Citations (Web of Science)

Abstract

We describe an electrostatic model of the gramicidin A channel that allows protein atoms to move in response to the presence of a permeating ion. To do this, molecular dynamics simulations are carried out with a permeating ion at various positions within the channel. Then an ensemble of atomic coordinates taken from the simulations are used to construct energy profiles using macroscopic electrostatic calculations. The energy profiles constructed are compared to experimentally-determined conductance data by inserting them into Brownian dynamics simulations. We find that the energy landscape seen by a permeating ion changes significantly when we allow the protein atoms to move rather than using a rigid protein structure. However, the model developed cannot satisfactorily reproduce all of the experimental data. Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel.
Original languageEnglish
Pages (from-to)208-216
JournalEuropean Biophysics Journal
Volume34
Issue number3
DOIs
Publication statusPublished - 2005

Fingerprint

Dive into the research topics of 'Influence of protein flexibility on the electrostatic energy landscape in gramicidin A'. Together they form a unique fingerprint.

Cite this