Theory of force-extension curve for modular proteins and DNA hairpins

Abstract

We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control, and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices.

major revision, accepted for publication in PRE; 20 pages, 13 figures

References in corpus (7)

• Glassy dynamics of kinetically constrained models
• Single-molecule derivation of salt dependent base-pair free energies in DNA
• Path-integral analysis of fluctuation theorems for general Langevin processes
• Calorimetric glass transition explained by hierarchical dynamic facilitation
• Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles
• Spin-oscillator model for DNA/RNA unzipping by mechanical force
• Protein unfolding and refolding as transitions through virtual states

Cited by in corpus (9)

• Statistical Mechanics of Systems with Negative Temperature
• Thermal control of nucleation and propagation transition stresses in discrete lattices with non-local interactions and non-convex energy
• Thermal effects on fracture and brittle-to-ductile transition
• Designing hyperchaos and intermittency in semiconductor superlattices
• Global stability and $H$-theorem in lattice models with non-conservative interactions
• Understanding the dependence on the pulling speed of the unfolding pathway of proteins
• Relevance of the speed and direction of pulling in simple modular proteins
• Modelling the unfolding pathway of biomolecules: theoretical approach and experimental prospect
• Buckling in a rotationally invariant spin-elastic model