Eur. Phys. J. E (2005) 18: 1-13
https://doi.org/10.1140/epje/i2005-10024-8

Original Article

Force spectroscopy of single multidomain biopolymers: A master equation approach

II. Institut für Theoretische Physik, Universität Stuttgart, 70550, Stuttgart, Germany

^* e-mail: useifert@theo2.physik.uni-stuttgart.de

Received: 9 February 2005
Accepted: 21 June 2005
Published online: 20 September 2005

Abstract

Experiments using atomic force microscopy for unfolding single multidomain biopolymers cover a broad range of time scales from equilibrium to non-equilibrium. A master equation approach allows to identify and treat coherently three dynamical regimes for increasing linear ramp velocity: i) an equilibrium regime, ii) a transient regime where refolding events still occur, and iii) a saw-tooth regime without any refolding events. For each regime, analytical approximations are derived and compared to numerically investigated examples. We analyze in the framework of this model also a periodic experimental protocol instead of a linear ramp. In this case, a major simplification arises if the dynamics can be restricted to an effectively two-dimensional subspace. For transitions with an intermediate meta-stable state, like Immunoglobulin27, a refined model allows to extract previously unknown molecular parameters related to this meta-stable state.