Multiscale complex network of protein conformational fluctuations in single-molecule time series Export

@article{citeulike:2238511, abstract = {10.1073/pnas.0707378105 Conformational dynamics of proteins can be interpreted as itinerant motions as the protein traverses from one state to another on a complex network in conformational space or, more generally, in state space. Here we present a scheme to extract a multiscale state space network (SSN) from a single-molecule time series. Analysis by this method enables us to lift degeneracy\^{a}€”different physical states having the same value for a measured observable\^{a}€”as much as possible. A state or node in the network is defined not by the value of the observable at each time but by a set of subsequences of the observable over time. The length of the subsequence can tell us the extent to which the memory of the system is able to predict the next state. As an illustration, we investigate the conformational fluctutation dynamics probed by single-molecule electron transfer (ET), detected on a photon-by-photon basis. We show that the topographical features of the SSNs depend on the time scale of observation; the longer the time scale, the simpler the underlying SSN becomes, leading to a transition of the dynamics from anomalous diffusion to normal Brownian diffusion.}, author = {Li, Chun-Biu and Yang, Haw and Komatsuzaki, Tamiki}, citeulike-article-id = {2238511}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0707378105}, citeulike-linkout-1 = {http://www.pnas.org/content/105/2/536.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/105/2/536.full.pdf}, citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/105/2/536}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18178627}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18178627}, day = {15}, doi = {10.1073/pnas.0707378105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {cmn, markov, out\_of\_equilibrium}, month = {January}, number = {2}, pages = {536--541}, posted-at = {2009-07-21 15:16:32}, priority = {2}, title = {Multiscale complex network of protein conformational fluctuations in single-molecule time series}, url = {http://dx.doi.org/10.1073/pnas.0707378105}, volume = {105}, year = {2008} }

TY - JOUR ID - citeulike:2238511 L3 - citeulike-article-id:2238511 N2 - 10.1073/pnas.0707378105 Conformational dynamics of proteins can be interpreted as itinerant motions as the protein traverses from one state to another on a complex network in conformational space or, more generally, in state space. Here we present a scheme to extract a multiscale state space network (SSN) from a single-molecule time series. Analysis by this method enables us to lift degeneracy—different physical states having the same value for a measured observable—as much as possible. A state or node in the network is defined not by the value of the observable at each time but by a set of subsequences of the observable over time. The length of the subsequence can tell us the extent to which the memory of the system is able to predict the next state. As an illustration, we investigate the conformational fluctutation dynamics probed by single-molecule electron transfer (ET), detected on a photon-by-photon basis. We show that the topographical features of the SSNs depend on the time scale of observation; the longer the time scale, the simpler the underlying SSN becomes, leading to a transition of the dynamics from anomalous diffusion to normal Brownian diffusion. IS - 2 JF - Proceedings of the National Academy of Sciences EP - 541 TI - Multiscale complex network of protein conformational fluctuations in single-molecule time series VL - 105 SP - 536 KW - cmn KW - markov KW - out_of_equilibrium AU - Li, Chun-Biu AU - Yang, Haw AU - Komatsuzaki, Tamiki PY - 2008/01/15/ UR - http://dx.doi.org/10.1073/pnas.0707378105 ER -