In this reporting period, papers dealing with the following topics appeared in print or have been accepted for publication: (1)Influence of diffusion on the kinetics of excited state association dissociation chemical reactions, (2) Enhancement of association rates by nonspecific binding to DNA and cell membranes (3) Ensemble of transition states for two state protein folding from the eigenvectors of rate matrices and (4) The theory of photon statistics in single molecule Forster resonance energy transfer . The first paper deals with testing the predictions of our general theory or reversible diffusion influenced reactions against the result of many-body computer simulations. In the second paper, we apply this theory to examine the influence of nonspecific binding on the kinetics of binding to receptors on cell membranes and to DNA. In the third paper we propose a new method to analyze kinetic models of protein folding in order to provide insigh into the mechanism. The last and most important paper deals with the theory required to interpret Forster resonance energy transfer experiments on protein folding. In these experiments the number of photons emitted by a donor and an acceptor are monitoried. These contain structural information because the efficiency of energy transfer between tne donor and acceptor depend on the distance between them. Given an arbitrary dynamical scheme we showed how to calculate the probability distribution of the energy transfer obtained for fixed time windows. We have considered the contribution due to shot noise, to conformational dynamics and to translational diffusion in and out of the laser spot. This kind of complete analysis of all contributing factors is essential for the meanigful interpretation of experiments.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Intramural Research (Z01)
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U.S. National Inst Diabetes/Digst/Kidney
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Berezhkovskii, Alexander; Hummer, Gerhard; Szabo, Attila (2009) Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys 130:205102
Gopich, Irina V; Nettels, Daniel; Schuler, Benjamin et al. (2009) Protein dynamics from single-molecule fluorescence intensity correlation functions. J Chem Phys 131:095102
Bezrukov, Sergey M; Berezhkovskii, Alexander M; Szabo, Attila (2007) Diffusion model of solute dynamics in a membrane channel: mapping onto the two-site model and optimizing the flux. J Chem Phys 127:115101
Dudko, Olga K; Mathe, Jerome; Szabo, Attila et al. (2007) Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophys J 92:4188-95
Berezhkovskii, Alexander; Szabo, Attila (2006) Perturbation theory of Phi-value analysis of two-state protein folding: relation between p fold and Phi values. J Chem Phys 125:104902
Dudko, Olga K; Hummer, Gerhard; Szabo, Attila (2006) Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett 96:108101
Gopich, Irina; Szabo, Attila (2005) Fluorophore-quencher distance correlation functions from single-molecule photon arrival trajectories. J Phys Chem B 109:6845-8
Berezhkovskii, Alexander; Szabo, Attila (2005) One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions. J Chem Phys 122:14503
Gopich, Irina V; Szabo, Attila (2005) Photon counting histograms for diffusing fluorophores. J Phys Chem B 109:17683-8
Gopich, Irina; Szabo, Attila (2005) Theory of photon statistics in single-molecule Forster resonance energy transfer. J Chem Phys 122:14707

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