Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction
arXiv:0803.1811 · doi:10.1103/PhysRevE.78.031907
Abstract
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the inherent structure (IS) formalism. A comparison of the free energies estimated with these two schemes with equilibrium results obtained via the umbrella sampling technique reveals a good quantitative agreement among all the approaches in a range of temperatures around the ``folding transition'' for the two examined sequences. In particular, for the sequence with good foldability properties, the mechanically induced structural transitions can be related to thermodynamical aspects of folding. Moreover, for the same sequence the knowledge of the landscape profile allows for a good estimation of the life times of the native configuration for temperatures ranging from the folding to the collapse temperature. For the random sequence, mechanical and thermal unfolding appear to follow different paths along the landscape.
Latex manuscript, 20 pages, 23 figures, submitted to Physical Review E
References in corpus (11)
- Experimental Free Energy Surface Reconstruction From Single-Molecule Force Spectroscopy Using Jarzynski's Equality
- Distribution of work in isothermal non-equilibrium processes
- Optimized free energies from bidirectional single-molecule force spectroscopy
- An Ising-Like model for protein mechanical unfolding
- Work probability distribution in systems driven out of equilibrium
- Reconstructing the free energy landscape of a polyprotein by single-molecule experiments
- Work distribution and path integrals in general mean-field systems
- Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators
- Reconstructing the free energy landscape of a mechanically unfolded model protein
- Thermally activated processes in polymer dynamics
- Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity