Two-, Three-, and Four-State Events Occur in the Mechanical Unfolding of Small Protein L Using Molecular Dynamics Simulations

Title: Two-, Three-, and Four-State Events Occur in the Mechanical Unfolding of Small Protein L Using Molecular Dynamics Simulations

Volume: 17 Issue: 1

Author(s): Anna V. Glyakina, Nikolay K. Balabaev and Oxana V. Galzitskaya

Affiliation:

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

Abstract: Mechanical properties of (protein L)5 have been recently investigated by single-molecule force spectroscopy. It has been demonstrated that the unfolding of individual domains proceeds through a two-state mechanism. Here, we study mechanical properties of protein L at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process of protein L can occur either in a single step or through short living and quite native like intermediate states, which was not observed in previous studies. Analysis of the 24 trajectories from molecular dynamics simulations with explicit water showed that the mechanical unfolding of protein L occurs through at least two pathways. These pathways coincide in two- and multi-state events and at different extension velocities studied (0.125, 0.0625 and 0.005 Å.ps-1).

Cite this article as:

Glyakina V. Anna, Balabaev K. Nikolay and Galzitskaya V. Oxana, Two-, Three-, and Four-State Events Occur in the Mechanical Unfolding of Small Protein L Using Molecular Dynamics Simulations, Protein & Peptide Letters 2010; 17 (1) . https://dx.doi.org/10.2174/092986610789909449