RESEARCH ARTICLE
Multiple Unfolding Intermediates Obtained by Molecular Dynamic Simulations under Stretching for Immunoglobulin-Binding Domain of Protein G
Anna V Glyakina1, Nikolai K Balabaev1, Oxana V Galzitskaya*, 2
Article Information
Identifiers and Pagination:
Year: 2009Volume: 3
First Page: 66
Last Page: 77
Publisher ID: TOBIOCJ-3-66
DOI: 10.2174/1874091X00903010066
Article History:
Received Date: 1/9/2009Revision Received Date: 20/10/2009
Acceptance Date: 30/10/2009
Electronic publication date: 23/11/2009
Collection year: 2009
open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.
Abstract
We have studied the mechanical properties of the immunoglobulin-binding domain of protein G at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process can occur either in a single step or through intermediate states. Analysis of the trajectories from the molecular dynamic simulations showed that the mechanical unfolding of the immunoglobulin-binding domain of protein G is triggered by the separation of the terminal β-strands and the order in which the secondary-structure elements break is practically the same in two- and multi-state events and at the different extension velocities studied. It is seen from our analysis of 24 trajectories that the theoretical pathway of mechanical unfolding for the immunoglobulin-binding domain of protein G does not coincide with that proposed in denaturant studies in the absence of force.
