@article{3414, abstract = {Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter.}, author = {Kedrov, Alexej and Harald Janovjak and Ziegler, Christine and Kühlbrandt, Werner and Mueller, Daniel J}, journal = {Journal of Molecular Biology}, number = {1}, pages = {2 -- 8}, publisher = {Elsevier}, title = {{Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli}}, doi = {10.1016/j.jmb.2005.10.028}, volume = {355}, year = {2006}, } @misc{3415, author = {Harald Janovjak and Kedrov, Alexej and Cisneros, David and Sapra, Tanuj K and Struckmeier, Jens and Mueller, Daniel J}, booktitle = {Neurobiology of Aging}, pages = {546 -- 561}, publisher = {Elsevier}, title = {{Imaging and detecting molecular interactions of single membrane proteins}}, doi = {10.1016/j.neurobiolaging.2005.03.031}, volume = {27}, year = {2006}, } @article{3437, abstract = {The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models.}, author = {Betancourt, Andrea J and Jonathan Bollback}, journal = {Current Opinion in Genetics & Development}, number = {6}, pages = {618 -- 623}, publisher = {Elsevier}, title = {{Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution}}, doi = {10.1016/j.gde.2006.10.006}, volume = {16}, year = {2006}, } @unpublished{3431, abstract = {Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses.}, author = {Gasper Tkacik and Schneidman, E. and Berry, M. J. and Bialek, William S}, booktitle = {ArXiv}, pages = {1 -- 4}, publisher = {ArXiv}, title = {{Ising models for networks of real neurons}}, year = {2006}, } @inproceedings{3449, abstract = {We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control.}, author = {Krishnendu Chatterjee and Jagadeesan, Rhada and Pitcher, Corin}, pages = {70 -- 82}, publisher = {IEEE}, title = {{Games for controls}}, doi = {10.1109/CSFW.2006.14}, year = {2006}, }