Force spectroscopy of single multidomain biopolymers: A master equation approach
II. Institut für Theoretische Physik, Universität Stuttgart, 70550, Stuttgart, Germany
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Accepted: 21 June 2005
Published online: 20 September 2005
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.
PACS: 87.15.-v Biomolecules: structure and physical properties – / 87.64.Dz Scanning tunneling and atomic force microscopy –
© EDP Sciences, Società Italiana di Fisica and Springer-Verlag, 2005