Extraction COIL-1 model

Abstract. Various ways of extracting information on the conformational structure, dynamics and correlations between them from single-molecule measurements of florescence resonance energy transfer are surveyed. The information obtained via those various ways is then analyzed in detail in the case of an off-lattice model of a two-stranded coiled-coil polypeptide that follows Langevin dynamics. The analysis includes a consideration of the cases of a freely diffusing and surface-immobilized polypeptide as well as the effect of different types of surface and denaturation conditions. 

Most macro molecules in solution are neither as stiff as the rigid rod nor as flexible as the Gaussian coil. For particular systems of interest a dynamical model should be made and the corresponding spectrum (or time correlation function) calculated. Measurement of the spectrum and a fit to the theoretical form then allows extraction of the model dynamic constants. These dynamic constant may then be related to equilibrium structural properties of the molecule (end-to-end distances, backbone curvature, etc.). 

The described theoretical model involves a basic molecular actuator constituted by an ideal and lineal polymeric chain. We can imagine this basic chain coimected to a metallic electrode and immersed in an electrolyte (Figure 16.5). The strong intramolecular interactions produce a coil-compact structure of the chain. During oxidation, consecutive electrons are extracted from the chain, positive charges are... 

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