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CAPTURING THE COMPLEXITY OF ION CHANNELS: SIMULATIONS OF
LONG-TIME DYNAMICS, CONFORMATIONAL CHANGES AND THE
EFFECT OF THE MEMBRANE POTENTIAL
by
Anatoly Dryga
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Ful llment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(CHEMISTRY)
May 2012
Copyright 2012 Anatoly Dryga
Object Description
| Title | Capturing the complexity of ion channels: simulations of long-time dynamics, conformational changes and the effect of the membrane potential |
| Author | Dryga, Anatoly |
| Author email | dryga@usc.edu;anatolydryga@gmail.com |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Chemistry |
| School | College of Letters, Arts And Sciences |
| Date defended/completed | 2012-03-20 |
| Date submitted | 2012-05-08 |
| Date approved | 2012-05-09 |
| Restricted until | 2012-05-09 |
| Date published | 2012-05-09 |
| Advisor (committee chair) | Warshel, Arieh |
| Advisor (committee member) | Nakano, Aiichiro |
| Abstract | The relationship between the membrane potential and the gating of voltage-activated ion channels, as well as ion current through pores, is currently a problem of great interest. For example, simulations of conformational changes during the voltage-induced transition and ion current represent a major challenge that cannot be overcome at present by brute-force molecular dynamics approaches. To progress on this front, we developed and validated a renormalization approach and extended our previously developed coarse grained (CG) model so that it can describe the effect of the membrane potential and electrolyte solutions. Here we apply our model in realistic simulations of the energetics of the Kv1.2 channel. The simulations reproduce the observed experimental trend for both the gating charge and the effect of the membrane potential on the stability of the closed and open conformations. This indicates that our CG modeling offers a powerful tool for simulating voltage-activated channels. |
| Keyword | coarse-grain; Kv1.2; Langevin dynamics; molecular dynamics; renormalization |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m |
| Rights | Dryga, Anatoly |
| Access conditions | The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the author, as the original true and official version of the work, but does not grant the reader permission to use the work if the desired use is covered by copyright. It is the author, as rights holder, who must provide use permission if such use is covered by copyright. The original signature page accompanying the original submission of the work to the USC Libraries is retained by the USC Libraries and a copy of it may be obtained by authorized requesters contacting the repository e-mail address given. |
| Repository name | University of Southern California Digital Library |
| Repository address | USC Digital Library, University of Southern California, University Park Campus MC 7002, 106 University Village, Los Angeles, California 90089-7002, USA |
| Repository email | cisadmin@usc.edu |
| Archival file | uscthesesreloadpub_Volume4/etd-DrygaAnato-824.pdf |
Description
| Title | Page 1 |
| Full text | CAPTURING THE COMPLEXITY OF ION CHANNELS: SIMULATIONS OF LONG-TIME DYNAMICS, CONFORMATIONAL CHANGES AND THE EFFECT OF THE MEMBRANE POTENTIAL by Anatoly Dryga A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Ful llment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (CHEMISTRY) May 2012 Copyright 2012 Anatoly Dryga |
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