@article{908, abstract = {Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.}, author = {Alkalaeva, Elena Z and Eliseev, Boris D and Ambrogelly, Alexandre and Vlasov, Peter K and Fyodor Kondrashov and Gundllapalli, Sarath B and Frolova, Ludmila Y and Söll, Dieter G and Kisselev, Lev L}, journal = {FEBS Letters}, number = {21}, pages = {3455 -- 3460}, publisher = {Elsevier}, title = {{Translation termination in pyrrolysine-utilizing archaea}}, doi = {10.1016/j.febslet.2009.09.044}, volume = {583}, year = {2009}, } @article{9147, abstract = {As part of an ongoing effort to develop a parameterization of wave-induced abyssal mixing, the authors derive an heuristic model for nonlinear wave breaking and energy dissipation associated with internal tides. Then the saturation and dissipation of internal tides for idealized and observed topography samples are investigated. One of the main results is that the wave-induced mixing could be more intense and more confined to the bottom than previously assumed in numerical models. Furthermore, in this model wave breaking and mixing clearly depend on the small scales of the topography below 10 km or so, which is below the current resolution of global bathymetry. This motivates the use of a statistical approach to represent the unresolved topography when addressing the role of internal tides in mixing the deep ocean.}, author = {Muller, Caroline J and Bühler, Oliver}, issn = {1520-0485}, journal = {Journal of Physical Oceanography}, keywords = {Oceanography}, number = {9}, pages = {2077--2096}, publisher = {American Meteorological Society}, title = {{Saturation of the internal tides and induced mixing in the abyssal ocean}}, doi = {10.1175/2009jpo4141.1}, volume = {39}, year = {2009}, } @article{9148, abstract = {Several observational studies have shown a tight relationship between tropical precipitation and column‐integrated water vapor. We show that the observed relationship in the tropics between column‐integrated water vapor, precipitation, and its variance can be qualitatively reproduced by a simple and physically motivated two‐layer model. It has previously been argued that features of this relationship could be explained by analogy with the theory of continuous phase transitions. Instead, our model explicitly assumes that the onset of precipitation is governed by a stability threshold involving boundary‐layer water vapor. This allows us to explain the precipitation‐humidity relationship over a broader range of water vapor values, and may explain the observed temperature dependence of the relationship.}, author = {Muller, Caroline J and Back, Larissa E. and O'Gorman, Paul A. and Emanuel, Kerry A.}, issn = {0094-8276}, journal = {Geophysical Research Letters}, keywords = {General Earth and Planetary Sciences, Geophysics}, number = {16}, publisher = {American Geophysical Union}, title = {{A model for the relationship between tropical precipitation and column water vapor}}, doi = {10.1029/2009gl039667}, volume = {36}, year = {2009}, } @article{9453, abstract = {Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.}, author = {Hsieh, Tzung-Fu and Ibarra, Christian A. and Silva, Pedro and Zemach, Assaf and Eshed-Williams, Leor and Fischer, Robert L. and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5933}, pages = {1451--1454}, publisher = {American Association for the Advancement of Science}, title = {{Genome-wide demethylation of Arabidopsis endosperm}}, doi = {10.1126/science.1172417}, volume = {324}, year = {2009}, } @inproceedings{964, abstract = {A theory of the fluctuation-induced Nernst efl'ect is developed for a two-dimensional superconductor in a perpendicular magnetic field. First, we derive a simple phenomenological formula for the Nernst coefficient, which naturally explains the giant Nernst signal due to fluctuating Cooper pairs. The latter signal is shown to be large even far from the transition and may exceed by orders of magnitude the Fermi liquid terms. We also present a complete microscopic calculation of the Nernst coefficient for arbitrary magnetic fields and temperatures, which is based on the standard definition of heat current vertices. It is shown that the magnitude and the behavior of the Nernst signal observed experimentally in disordered superconducting films can be well understood on the basis of superconducting fluctuation theory.}, author = {Maksym Serbyn and Skvortsov, Mikhail A and Varlamov, Andrei A and Galitski, Victor M}, pages = {140 -- 145}, publisher = {American Institute of Physics}, title = {{Giant nernst effect due to fluctuating cooper Pairs in superconductors}}, doi = {10.1063/1.3149485}, volume = {1134}, year = {2009}, } @article{1038, abstract = {One possible way to produce ultra-cold, high-phase-space-density quantum gases of molecules in the rovibronic ground state is given by molecule association from quantum-degenerate atomic gases on a Feshbach resonance and subsequent coherent optical multi-photon transfer into the rovibronic ground state. In ultra-cold samples of Cs2 molecules, we observe two-photon dark resonances that connect the intermediate rovibrational level |v=73,J=2 with the rovibrational ground state |v=0,J=0 of the singlet X 1 ∑ g + ground-state potential. For precise dark resonance spectroscopy we exploit the fact that it is possible to efficiently populate the level |v=73,J=2 by two-photon transfer from the dissociation threshold with the stimulated Raman adiabatic passage (STIRAP) technique. We find that at least one of the two-photon resonances is sufficiently strong to allow future implementation of coherent STIRAP transfer of a molecular quantum gas to the rovibrational ground state |v=0,J=0.}, author = {Mark, Manfred and Danzl, Johann G and Haller, Elmar and Gustavsson, Mattias and Bouloufa, Nadia and Dulieu, Olivier and Salami, Houssam and Bergeman, Thomas and Ritsch, Helmut and Hart, Russell and Nägerl, Hanns}, journal = {Applied Physics B: Lasers and Optics}, number = {2}, pages = {219 -- 225}, publisher = {Springer}, title = {{Dark resonances for ground-state transfer of molecular quantum gases}}, doi = {10.1007/s00340-009-3407-1}, volume = {95}, year = {2009}, } @article{1040, abstract = {Ultracold atomic physics offers myriad possibilities to study strongly correlated many-body systems in lower dimensions. Typically, only ground-state phases are accessible. Using a tunable quantum gas of bosonic cesium atoms, we realized and controlled in one-dimensional geometry a highly excited quantum phase that is stabilized in the presence of attractive interactions by maintaining and strengthening quantum correlations across a confinement-induced resonance. We diagnosed the crossover from repulsive to attractive interactions in terms of the stiffness and energy of the system. Our results open up the experimental study of metastable, excited, many-body phases with strong correlations and their dynamical properties.}, author = {Haller, Elmar and Gustavsson, Mattias and Mark, Manfred and Danzl, Johann G and Hart, Russell and Pupillo, Guido and Nägerl, Hanns}, journal = {Science}, number = {5945}, pages = {1224 -- 1227}, publisher = {American Association for the Advancement of Science}, title = {{Realization of an excited, strongly correlated quantum gas Phase}}, doi = {10.1126/science.1175850}, volume = {325}, year = {2009}, } @article{1041, abstract = {We demonstrate efficient transfer of ultracold molecules into a deeply bound rovibrational level of the singlet ground state potential in the presence of an optical lattice. The overall molecule creation efficiency is 25%, and the transfer efficiency to the rovibrational level |v = 73, J = 2) is above 80%. We find that the molecules in |v = 73, J = 2) are trapped in the optical lattice, and that the lifetime in the lattice is limited by optical excitation by the lattice light. The molecule trapping time for a lattice depth of 15 atomic recoil energies is about 20 ms. We determine the trapping frequency by the lattice phase and amplitude modulation technique. It will now be possible to transfer the molecules to the rovibrational ground state |v = 0, J = 0) in the presence of the optical lattice.}, author = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Hart, Russell and Liem, Andreas and Zellmer, Holger and Nägerl, Hanns}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Deeply bound ultracold molecules in an optical lattice}}, doi = {10.1088/1367-2630/11/5/055036}, volume = {11}, year = {2009}, } @article{1043, abstract = {One possibility for the creation of ultracold, high phase space density quantum gases of molecules in the rovibronic ground state relies on first associating weakly-bound molecules from quantum-degenerate atomic gases on a Feshbach resonance and then transferring the molecules via several steps of coherent two-photon stimulated Raman adiabatic passage (STIRAP) into the rovibronic ground state. Here, in ultracold samples of Cs2 Feshbach molecules produced out of ultracold samples of Cs atoms, we observe several optical transitions to deeply-bound rovibrational levels of the excited 0 u+ molecular potentials with high resolution. At least one of these transitions, although rather weak, allows efficient STIRAP transfer into the deeply-bound vibrational level v = 73> of the singlet X 1Σg+ ground state potential, as recently demonstrated (J. G. Danzl, E. Haller, M. Gustavsson, M. J. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, and H.-C. Nägerl, Science, 2008, 321, 1062). From this level, the rovibrational ground state v = 0, J = 0> can be reached with one more transfer step. In total, our results show that coherent ground state transfer for Cs2 is possible using a maximum of two successive two-photon STIRAP processes or one single four-photon STIRAP process.}, author = {Danzl, Johann G and Mark, Manfred and Haller, Elmar and Gustavsson, Mattias and Bouloufa, Nadia and Dulieu, Olivier and Ritsch, Helmut and Hart, Russell and Nägerl, Hanns}, journal = {Faraday Discussions}, pages = {283 -- 295}, publisher = {Royal Society of Chemistry}, title = {{Precision molecular spectroscopy for ground state transfer of molecular quantum gases}}, doi = {10.1039/b820542f}, volume = {142}, year = {2009}, } @inproceedings{11799, abstract = {We study the problem of matching bidders to items where each bidder i has general, strictly monotonic utility functions u i,j (p j ) expressing her utility of being matched to item j at price p j . For this setting we prove that a bidder optimal outcome always exists, even when the utility functions are non-linear and non-continuous. Furthermore, we give an algorithm to find such a solution. Although the running time of this algorithm is exponential in the number of items, it is polynomial in the number of bidders.}, author = {Dütting, Paul and Henzinger, Monika H and Weber, Ingmar}, booktitle = {5th International Workshop on Internet and Network Economics}, isbn = {9783642108402}, issn = {1611-3349}, location = {Rome, Italy}, pages = {575--582}, publisher = {Springer Nature}, title = {{Bidder optimal assignments for general utilities}}, doi = {10.1007/978-3-642-10841-9_58}, volume = {5929}, year = {2009}, } @inproceedings{11905, abstract = {Given only the URL of a web page, can we identify its topic? This is the question that we examine in this paper. Usually, web pages are classified using their content, but a URL-only classifier is preferable, (i) when speed is crucial, (ii) to enable content filtering before an (objection-able) web page is downloaded, (iii) when a page's content is hidden in images, (iv) to annotate hyperlinks in a personalized web browser, without fetching the target page, and (v) when a focused crawler wants to infer the topic of a target page before devoting bandwidth to download it. We apply a machine learning approach to the topic identification task and evaluate its performance in extensive experiments on categorized web pages from the Open Directory Project (ODP). When training separate binary classifiers for each topic, we achieve typical F-measure values between 80 and 85, and a typical precision of around 85. We also ran experiments on a small data set of university web pages. For the task of classifying these pages into faculty, student, course and project pages, our methods improve over previous approaches by 13.8 points of F-measure.}, author = {Baykan, Eda and Henzinger, Monika H and Marian, Ludmila and Weber, Ingmar}, booktitle = {18th International World Wide Web Conference}, isbn = {978-1-60558-487-4}, location = {New York, NY, United States}, pages = {1109--1110}, publisher = {Association for Computing Machinery}, title = {{Purely URL-based topic classification}}, doi = {10.1145/1526709.1526880}, year = {2009}, } @inproceedings{11906, abstract = {In the origin detection problem an algorithm is given a set S of documents, ordered by creation time, and a query document D. It needs to output for every consecutive sequence of k alphanumeric terms in D the earliest document in $S$ in which the sequence appeared (if such a document exists). Algorithms for the origin detection problem can, for example, be used to detect the "origin" of text segments in D and thus to detect novel content in D. They can also find the document from which the author of D has copied the most (or show that D is mostly original.) We concentrate on solutions that use only a fixed amount of memory. We propose novel algorithms for this problem and evaluate them together with a large number of previously published algorithms. Our results show that (1) detecting the origin of text segments efficiently can be done with very high accuracy even when the space used is less than 1% of the size of the documents in $S$, (2) the precision degrades smoothly with the amount of available space, (3) various estimation techniques can be used to increase the performance of the algorithms.}, author = {Abdel Hamid, Ossama and Behzadi, Behshad and Christoph, Stefan and Henzinger, Monika H}, booktitle = {18th International World Wide Web Conference}, isbn = {978-160558487-4}, location = {Madrid, Spain}, pages = {61--70}, publisher = {Association for Computing Machinery}, title = {{Detecting the origin of text segments efficiently}}, doi = {10.1145/1526709.1526719}, year = {2009}, } @inproceedings{11912, abstract = {As the World Wide Web is growing rapidly, it is getting increasingly challenging to gather representative information about it. Instead of crawling the web exhaustively one has to resort to other techniques like sampling to determine the properties of the web. A uniform random sample of the web would be useful to determine the percentage of web pages in a specific language, on a topic or in a top level domain. Unfortunately, no approach has been shown to sample the web pages in an unbiased way. Three promising web sampling algorithms are based on random walks. They each have been evaluated individually, but making a comparison on different data sets is not possible. We directly compare these algorithms in this paper. We performed three random walks on the web under the same conditions and analyzed their outcomes in detail. We discuss the strengths and the weaknesses of each algorithm and propose improvements based on experimental results.}, author = {Baykan, Eda and Henzinger, Monika H and Keller, Stefan F. and de Castelberg, Sebastian and Kinzler, Markus}, booktitle = {26th International Symposium on Theoretical Aspects of Computer Science}, isbn = {978-3-939897-09-5}, issn = {1868-8969}, location = {Freiburg, Germany}, pages = {13--30}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{A comparison of techniques for sampling web pages}}, doi = {10.4230/LIPICS.STACS.2009.1809}, volume = {3}, year = {2009}, } @article{12654, abstract = {We investigate the transferability of an enhanced temperature-index melt model that was developed and tested on Haut Glacier d’Arolla, Switzerland, in the 2001 season. The model’s empirical parameters (temperature factor, TF, and shortwave radiation factor, SRF) are recalibrated for: (1) other locations on Haut Glacier d’Arolla; (2) subperiods of distinct meteorological conditions; (3) different years on Haut Glacier d’Arolla; and (4) other glaciers in different years. The model parameters are optimized against simulations of an energy-balance model validated against ablation observations. Results are compared with those obtained with the original parameters. The model works very well when applied to other sites, seasons and glaciers, with the exception of overcast conditions. Differences are due to underestimation of high melt rates. The parameter values are associated with the prevailing energy-balance conditions, showing that high SRF are obtained on clear-sky days, whereas higher TF are typical of locations where glacier winds prevail and turbulent fluxes are high. We also provide a range of parameters clearly associated with the site’s location and its meteorological characteristics that could help to assign parameter values to sites where few data are available.}, author = {Carenzo, Marco and Pellicciotti, Francesca and Rimkus, Stefan and Burlando, Paolo}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {190}, pages = {258--274}, publisher = {Cambridge University Press}, title = {{Assessing the transferability and robustness of an enhanced temperature-index glacier-melt model}}, doi = {10.3189/002214309788608804}, volume = {55}, year = {2009}, } @article{12655, abstract = {We discuss the inclusion of the subsurface heat-conduction flux into the calculation of the energy balance and ablation at the glacier–atmosphere interface. Data from automatic weather stations are used to force an energy-balance model at several locations on alpine glaciers and at one site in the dry Andes of central Chile. The heat-conduction flux is computed using a two-layer scheme, assuming that 36% of the net shortwave radiation is absorbed by the surface layer and that the rest penetrates into the snowpack. We compare simulations conducted with and without subsurface heat flux. Results show that assuming a surface temperature of zero degrees leads to a larger overestimation of melt at the sites in the accumulation area (10.4–13.3%) than in the ablation area (0.5–2.8%), due to lower air temperatures and the presence of snow. The difference between simulations with and without heat conduction is also high at the beginning and end of the ablation season (up to 29% for the first 15 days of the season), when air temperatures are lower and snow covers the glacier surface, while they are of little importance during periods of sustained melt at all the locations investigated.}, author = {Pellicciotti, Francesca and Carenzo, Marco and Helbing, Jakob and Rimkus, Stefan and Burlando, Paolo}, issn = {1727-5644}, journal = {Annals of Glaciology}, number = {50}, pages = {16--24}, publisher = {International Glaciological Society}, title = {{On the role of subsurface heat conduction in glacier energy-balance modelling}}, doi = {10.3189/172756409787769555}, volume = {50}, year = {2009}, } @article{1302, abstract = {The nervous system of seeing animals derives information about optic flow in two subsequent steps. First, local motion vectors are calculated from moving retinal images, and second, the spatial distribution of these vectors is analyzed on the dendrites of large downstream neurons. In dipteran flies, this second step relies on a set of motion-sensitive lobula plate tangential cells (LPTCs), which have been studied in great detail in large fly species. Yet, studies on neurons that convey information to LPTCs and neuroanatomical investigations that enable a mechanistic understanding of the underlying dendritic computations in LPTCs are rare. We investigated the subcellular distribution of nicotinic acetylcholine receptors (nAChRs) on two sets of LPTCs: vertical system (VS) and horizontal system (HS) cells in Drosophila melanogaster. In this paper, we describe that both cell types express Dα7-type nAChR subunits specifically on higher order dendritic branches, similar to the expression of gamma aminobutyric acid (GABA) receptors. These findings support a model in which directional selectivity of LPTCs is achieved by the dendritic integration of excitatory, cholinergic, and inhibitory GABA-ergic input from local motion detectors with opposite preferred direction. Nonetheless, whole-cell recordings in mutant flies without Dα7 nAChRs revealed that direction selectivity of VS and HS cells is largely retained. In addition, mutant LPTCs were responsive to acetylcholine and remaining nAChR receptors were labeled by α-bungarotoxin. These results in LPTCs with genetically manipulated excitatory input synapses suggest a robust cellular implementation of dendritic processing that warrants direction selectivity. The underlying mechanism that ensures appropriate nAChR-mediated synaptic currents and the functional implications of separate sets or heteromultimeric nAChRs can now be addressed in this system.}, author = {Raghu, Shamprasad V and Maximilian Jösch and Sigrist, Stephan J and Borst, Alexander and Reiff, Dierk F}, journal = {Journal of Neurogenetics}, number = {1-2}, pages = {200 -- 209}, publisher = {Informa Healthcare}, title = {{Synaptic organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors}}, doi = {10.1080/01677060802471684}, volume = {23}, year = {2009}, } @article{337, abstract = {The formation of hollow vs solid particles by means of the oxidation reaction of solid metal particles depends on the differential self-diffusivities of the reactants through the composite shell, the reaction probabilities at each interface, and the concentration and diffusivity of the element in solution. By means of a kinetic model of the oxidation process, we determine the phase diagrams for the geometry of the oxidized particles and propose four shell growth regimes. We experimentally illustrate the different growth scenarios by changing the conditions of oxidation of cadmium spherical crystals using different chalcogen precursors. }, author = {Cabot, Andreu and Ibáñez, Maria and Guardia, Pablo and Alivisatos, Paul}, journal = {Journal of the American Chemical Society}, number = {32}, pages = {11326 -- 11328}, publisher = {ACS}, title = {{Reaction regimes on the synthesis of hollow particles by the Kirkendall effect}}, doi = {10.1021/ja903751p}, volume = {131}, year = {2009}, } @article{3398, abstract = {Why is a particular architecture for a pathway chosen over seemingly equivalent alternatives? Çağatay et al. (2009) use a synthetic biology approach to show that fluctuations—or noise—in protein levels may play a key role in determining which network design is selected during evolution.}, author = {Bollenbach, Tobias and Kishony, Roy}, journal = {Cell}, number = {3}, pages = {460 -- 461}, publisher = {Cell Press}, title = {{Quiet gene circuit more fragile than its noisy peer}}, doi = {10.1016/j.cell.2009.10.005}, volume = {139}, year = {2009}, } @phdthesis{3400, abstract = {Invasive fungal infections pose a serious threat to immunocompromised people. Most of these infections are caused by either Candida or Aspergillus species, with A. fumigatus being the predominant causative agent of Invasive Aspergillosis. Affected people comprise mainly haematopoietic stem cell or solid organ transplant patients who receive either high-dose corticosteroids or immunosuppressants. These risk factors predispose to the development of Invasive Aspergillosis which is lethal in 20 to 80 % of the cases, largely due to insufficient efficacy of current antifungal therapy. Thus one major aim in current mycological research is the identification of new drug targets. The polysaccharide-based fungal cell wall is both essential to fungi and absent from human cells which makes it appear an attractive new target. Notably, many components of the A. fumigatus cell wall, including the polysaccharide galactomannan, glycoproteins, and glycolipids, contain the unusual sugar galactofuranose (Galf). In contrast to the other cell wall monosaccharides, Galf does not occur on human cells but is known as component of cell surface molecules of many pathogenic bacteria and protozoa, such as Mycobacterium tuberculosis or Leishmania major. These molecules are often essential for virulence or viability of these organisms which suggested a possible role of Galf in the pathogenicity of A. fumigatus. To address the importance of Galf in A. fumigatus, the key biosynthesis gene glfA, encoding UDPgalactopyranose mutase (UGM), was deleted. In different experimental approaches it was demonstrated that the absence of the glfA gene led to a complete loss of Galf-containing glycans. Analysis of the DeltaglfA phenotype revealed growth and sporulation defects, reduced thermotolerance and an increased susceptibility to antifungal drugs. Electron Microscopy indicated a cell wall defect as a likely cause for the observed impairments. Furthermore, the virulence of the DeltaglfA mutant was found to be severely attenuated in a murine model of Invasive Aspergillosis. The second focus of this study was laid on further elucidation of the galactofuranosylation pathway in A. fumigatus. In eukaryotes, a UDP-Galf transporter is likely required to transport UDP-Galf from the cytosol into the organelles of the secretory pathway, but no such activity had been described. Sixteen candidate genes were identified in the A. fumigatus genome of which one, glfB, was found in close proximity to the glfA gene. In vitro transport assays revealed specificity of GlfB for UDP-Galf suggesting that glfB encoded indeed a UDP-Galf transporter. The influence of glfB on galactofuranosylation was determined by a DeltaglfB deletion mutant, which closely recapitulated the DeltaglfA phenotype and was likewise found to be completely devoid of Galf. It could be concluded that all galactofuranosylation processes in A. fumigatus occur in the secretory pathway, including the biosynthesis of the cell wall polysaccharide galactomannan whose subcellular origin was previously disputed. Thus in the course of this study the first UDP-Galf specific nucleotide sugar transporter was identified and its requirement for galactofuranosylation in A. fumigatus demonstrated. Moreover, it was shown that blocking the galactofuranosylation pathway impaired virulence of A. fumigatus which suggests the UDP-Galf biosynthesis enzyme UGM as a target for new antifungal drugs.}, author = {Philipp Schmalhorst}, pages = {1 -- 72}, publisher = {Gottfried Wilhelm Leibniz Universität Hannover}, title = {{Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus}}, year = {2009}, } @article{3408, abstract = {Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes.}, author = {Szymczak, Piotr and Harald Janovjak}, journal = {Journal of Molecular Biology}, number = {3}, pages = {443 -- 456}, publisher = {Elsevier}, title = {{Periodic forces trigger a complex mechanical response in ubiquitin}}, doi = {10.1016/j.jmb.2009.04.071}, volume = {390}, year = {2009}, }