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
1 Institute of Mathematical Problems of Biology, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
2 Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia


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© Glyakina et al.; Licensee Bentham Open.

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.

* Address correspondence to this author at the Institute of Protein Research, Russian Academy of Sciences, Institutskaya str., 4 Pushchino, Moscow, Region, 142290, Russia; E-mail: ogalzit@vega.protres


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.

Keywords: Molecular dynamics, mechanical unfolding pathway, denaturant unfolding pathway, intermediate state, ensemble of transition states, explicit model of water.