Computational investigation of the effect of thermal perturbation on the mechanical unfolding of titin I27

Abstract

The emergence of single-molecule force measurement experiments has facilitated a better understanding of protein folding pathways and the thermodynamics involved. Computational methods such as steered molecular dynamics (SMD) simulations are helpful in providing atomistic level information on the unfolding pathways. Recent experimental studies have showed that combinations of single-molecule experiments with traditional methods such as chemical and/or thermal denaturation yield additional insights into the folding phenomenon. In this study, we report results from extensive computations (a total of about 60 SMD simulations with a total length of about 0.4 μs) that address the effect of thermal perturbation on the mechanical stability of the I27 domain of the protein titin. A wide range of temperatures (280-340 K) were considered for the pulling, which was done at both constant velocity and constant force using SMD simulations. Good agreement with experimental data, such as for the trends in changes in average force and the maximum force with respect to the temperature, was obtained. This study identifies two competing pathways for the mechanical unfolding of I27, and illustrates the significance of combining various techniques to examine protein folding.

Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State

“…These configurations of the protein were then resolvated in each of the six pre-equilibrated solvent environments (water and 8 M aqueous urea at 300, 400, and 500 K). Previous studies have suggested that combination of two or more perturbations (chemical, thermal, and mechanical) helps examine different aspects of the protein folding problem that may not be accessible individually. ,− The size of the solvation box for all the umbrella sampling simulations (74 × 74 × 74 Å 3 ) was chosen based on the initial configuration of the last window so that the box extended at least 12 Å on all sides. Each of the windows was then subjected to short energy minimization and equilibration followed by 50 ns MD simulations, resulting in a cumulative sampling time of about 4.2 μs.…”

Using simulations to provide the framework for experimental protein folding studies

“…Steered MD provides an atomistic view for experimental results obtained with single-molecule atomic force microscopy (AFM)-based force spectroscopy [87]. One well-studied model system is the immunoglobulin domain I27 of titin, a giant protein (about 30,000 amino acid residues) responsible for the contraction and extension of muscles [88–90]. In particular, the height of the potential energy barrier [89] and the additional effect of temperature during pulling was determined [88].…”

“…One well-studied model system is the immunoglobulin domain I27 of titin, a giant protein (about 30,000 amino acid residues) responsible for the contraction and extension of muscles [88–90]. In particular, the height of the potential energy barrier [89] and the additional effect of temperature during pulling was determined [88]. Steered MD and force spectroscopy have also recently cooperated to reveal multiple pathways in the unfolding of a slipknotted protein [91].…”