A computational study of the conformational structure and dynamics of biopolymers in relation to single molecule fluorescence resonance energy transfer measurements

The development of single molecule spectroscopy over the last two decades has made it possible to probe the conformational structure and dynamics of biomolecules with an unprecedented level of detail. Room-temperature Single-Molecule Fluorescence Resonance Energy Transfer (SM-FRET), in particular, provides the ability to probe intra- and inter-molecular distances as a function of time in a direct manner. These experiments also give rise to many new theoretical questions regarding the behavior of single molecules as apposed to averages over large ensembles.; Previous theoretical work on SM-FRET has been based on relatively simple phenomenological stochastic models. In this thesis, we take the next step by attempting to provide a more molecular view of the conformational structure and dynamics underlying SM-FRET experiments. To this end, we use combination of Langevin Dynamics simulations of the biopolymer together with kinetic Monte Carlo simulations of the photon statistics. The analysis focuses on quantities which are particularly relevant to SM-FRET experiments, such as the distribution of donor-acceptor distance and its displacement. Emphasis is put on the unique ability of those experiments to provide information on the correlations between conformational structure and dynamics. We also explore the effect of immobilizing the biopolyiner on surface or trapping it in a pore.; Our investigation focuses on two off-lattice models, one of a freely-joined homopolymer and another of a polyypeptide. In the homopolymer case, we consider the conformational structure and dynamics in good and poor solvents, as well as the effect of immobilization on attractive or repulsive surfaces. The polypeptide model is designed to mimic the two-stranded coiled-coil from the yeast transcription factor GCN4 that was studied in the pioneering SM-FILET experiment by Hochstrasser and co-workers[46, 47]. In this case, we consider itninobilizations on repulsive and attractive surfaces as well as encapsulation inside of a pore with varying sizes and shapes. We also consider two types of denaturated states that differ with respect to the amount of residual secondary structure.; Finally, we propose a new way for extracting the dine scales of conformational dynamics from single-molecule single-photon fluorescence statistics. To this end, we derive a general relation between the autocorrelation function of the time-delay, between excitation and single photon emission and the autocorrelation function of the fluorescence life-time. We also examine the conditions under which there is a direct relation between the decay of the delay-time autocorrelation function and the time scale of conformational dynamics. We demonstrate how the time scales of conformational dynamics can be extracted from the time-delay autocorrelation function via applications to the above-mentioned homopolyner and polypeptide models.