Reconstructing the free energy landscape of a mechanically unfolded model protein

Abstract

The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a range of temperatures around the ``folding transition'' we find a good quantitative agreement between the free energies obtained via EJE and IS approaches. This indicates that the two methodologies are consistent and able to reproduce equilibrium properties of the examined system. Moreover, for the studied model the structural transitions induced by pulling can be related to thermodynamical aspects of folding.

References in corpus (4)

• Experimental Free Energy Surface Reconstruction From Single-Molecule Force Spectroscopy Using Jarzynski's Equality
• An Ising-Like model for protein mechanical unfolding
• Evaluation of free energy landscapes from manipulation experiments
• Thermally activated processes in polymer dynamics

Cited by in corpus (7)

• Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength
• Reconstructing the free energy landscape of a polyprotein by single-molecule experiments
• Discrete Breathers in a Realistic Coarse-Grained Model of Proteins
• Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction
• Exact Nonequilibrium Work Generating Function for a Small Classical System
• Geometry of the energy landscape and folding transition in a simple model of a protein
• Mechanical Unfolding of a Simple Model Protein Goes Beyond the Reach of One-Dimensional Descriptions