--- _id: '8022' abstract: - lang: eng text: Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Wulfram full_name: Gerstner, Wulfram last_name: Gerstner citation: ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406. doi:10.1016/j.neuron.2014.04.045 apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045 chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045. ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient dynamics in balanced networks supports generation of complex movements,” Neuron, vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014. ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 82(6), 1394–1406. mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045. short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406. date_created: 2020-06-25T13:07:37Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T08:16:35Z day: '18' doi: 10.1016/j.neuron.2014.04.045 extern: '1' external_id: pmid: - '24945778' intvolume: ' 82' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/ month: '06' oa: 1 oa_version: Submitted Version page: 1394-1406 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Optimal control of transient dynamics in balanced networks supports generation of complex movements type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 82 year: '2014' ... --- _id: '809' abstract: - lang: eng text: The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position. acknowledgement: 'The authors thank Leonardo Trabuco for help with running MDFF, Maria Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber (robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal screening, and the European Molecular Biology Laboratory (EMBL) Information Technology Services Unit and Frank Thommen for technical support. This study was supported by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship (to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL and the Chica und Heinz Schaller Stiftung. ' author: - first_name: Tanmay full_name: Bharata, Tanmay A last_name: Bharata - first_name: Luis full_name: Menendez, Luis R last_name: Menendez - first_name: Wim full_name: Hagena, Wim J last_name: Hagena - first_name: Vanda full_name: Luxd, Vanda last_name: Luxd - first_name: Sebastien full_name: Igonete, Sebastien last_name: Igonete - first_name: Martin full_name: Schorba, Martin last_name: Schorba - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Hans full_name: Kraüsslich, Hans Georg last_name: Kraüsslich - first_name: John full_name: Briggsa, John A last_name: Briggsa citation: ama: Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 2014;111(22):8233-8238. doi:10.1073/pnas.1401455111 apa: Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M., … Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1401455111 chicago: Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete, Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1401455111. ieee: T. Bharata et al., “Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly,” PNAS, vol. 111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014. ista: Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 111(22), 8233–8238. mla: Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS, vol. 111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:10.1073/pnas.1401455111. short: T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K. Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238. date_created: 2018-12-11T11:48:37Z date_published: 2014-06-03T00:00:00Z date_updated: 2021-01-12T08:16:50Z day: '03' doi: 10.1073/pnas.1401455111 extern: 1 intvolume: ' 111' issue: '22' month: '06' page: 8233 - 8238 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6838' quality_controlled: 0 status: public title: Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 111 year: '2014' ... --- _id: '8244' abstract: - lang: eng text: Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer. article_processing_charge: No article_type: original author: - first_name: J. full_name: Singer, J. last_name: Singer - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: W. full_name: Wang, W. last_name: Wang - first_name: M. full_name: Weichselbaumer, M. last_name: Weichselbaumer - first_name: M. full_name: Matz, M. last_name: Matz - first_name: A. full_name: Mader, A. last_name: Mader - first_name: W. full_name: Steinfellner, W. last_name: Steinfellner - first_name: S. full_name: Meitz, S. last_name: Meitz - first_name: D. full_name: Mechtcheriakova, D. last_name: Mechtcheriakova - first_name: Y. full_name: Sobanov, Y. last_name: Sobanov - first_name: M. full_name: Willmann, M. last_name: Willmann - first_name: T. full_name: Stockner, T. last_name: Stockner - first_name: E. full_name: Spillner, E. last_name: Spillner - first_name: R. full_name: Kunert, R. last_name: Kunert - first_name: E. full_name: Jensen-Jarolim, E. last_name: Jensen-Jarolim citation: ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288 apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A., … Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288 chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics. American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288. ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics, vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014. ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E, Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 13(7), 1777–1790. mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics, vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288. short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner, R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790. date_created: 2020-08-10T11:54:29Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T08:17:42Z day: '01' doi: 10.1158/1535-7163.mct-13-0288 extern: '1' intvolume: ' 13' issue: '7' language: - iso: eng month: '07' oa_version: None page: 1777-1790 publication: Molecular Cancer Therapeutics publication_identifier: issn: - 1535-7163 - 1538-8514 publication_status: published publisher: American Association for Cancer Research quality_controlled: '1' status: public title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2014' ... --- _id: '8459' abstract: - lang: eng text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis. article_processing_charge: No article_type: original author: - first_name: Sébastien full_name: Morin, Sébastien last_name: Morin - first_name: Troels E full_name: Linnet, Troels E last_name: Linnet - first_name: Mathilde full_name: Lescanne, Mathilde last_name: Lescanne - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Gary S full_name: Thompson, Gary S last_name: Thompson - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger - first_name: Kaare full_name: Teilum, Kaare last_name: Teilum - first_name: Stéphane full_name: Gagné, Stéphane last_name: Gagné - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Christian full_name: Griesinger, Christian last_name: Griesinger - first_name: Martin full_name: Blackledge, Martin last_name: Blackledge - first_name: Edward J full_name: d’Auvergne, Edward J last_name: d’Auvergne citation: ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166' apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btu166' chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics. Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.' ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.' ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.' mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.' short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220. date_created: 2020-09-18T10:08:07Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/bioinformatics/btu166 extern: '1' intvolume: ' 30' issue: '15' keyword: - Statistics and Probability - Computational Theory and Mathematics - Biochemistry - Molecular Biology - Computational Mathematics - Computer Science Applications language: - iso: eng month: '08' oa_version: None page: 2219-2220 publication: Bioinformatics publication_identifier: issn: - 1367-4803 - 1460-2059 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/bioinformatics/btz397 status: public title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2014' ... --- _id: '8458' abstract: - lang: eng text: The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Sébastien full_name: Triboulet, Sébastien last_name: Triboulet - first_name: Cédric full_name: Laguri, Cédric last_name: Laguri - first_name: Catherine M. full_name: Bougault, Catherine M. last_name: Bougault - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Morgane full_name: Callon, Morgane last_name: Callon - first_name: Michel full_name: Arthur, Michel last_name: Arthur - first_name: Jean-Pierre full_name: Simorre, Jean-Pierre last_name: Simorre citation: ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987 apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon, M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987 chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja5105987. ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan,” Journal of the American Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860, 2014. ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 136(51), 17852–17860. mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60, doi:10.1021/ja5105987. short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon, M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014) 17852–17860. date_created: 2020-09-18T10:07:52Z date_published: 2014-11-27T00:00:00Z date_updated: 2021-01-12T08:19:24Z day: '27' doi: 10.1021/ja5105987 extern: '1' intvolume: ' 136' issue: '51' language: - iso: eng month: '11' oa_version: None page: 17852-17860 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2014' ... --- _id: '8460' abstract: - lang: eng text: The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states. article_processing_charge: No article_type: original author: - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Jens D. full_name: Haller, Jens D. last_name: Haller - first_name: Jérémy full_name: Zajakala, Jérémy last_name: Zajakala - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Dieter full_name: Willbold, Dieter last_name: Willbold - first_name: Jérôme full_name: Boisbouvier, Jérôme last_name: Boisbouvier - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275 apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201311275 chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275. ieee: P. Ma et al., “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014. ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317. mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275. short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317. date_created: 2020-09-18T10:08:53Z date_published: 2014-03-18T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '18' doi: 10.1002/anie.201311275 extern: '1' intvolume: ' 53' issue: '17' language: - iso: eng month: '03' oa_version: None page: 4312-4317 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2014' ... --- _id: '8501' abstract: - lang: eng text: In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation. article_processing_charge: No article_type: original author: - first_name: Abed full_name: Bounemoura, Abed last_name: Bounemoura - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203 apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203 chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203. ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014. ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203. mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203. short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203. date_created: 2020-09-18T10:47:09Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T08:19:43Z day: '01' doi: 10.17323/1609-4514-2014-14-2-181-203 extern: '1' external_id: arxiv: - '1304.3050' intvolume: ' 14' issue: '2' keyword: - General Mathematics language: - iso: eng month: '04' oa_version: Preprint page: 181-203 publication: Moscow Mathematical Journal publication_identifier: issn: - 1609-3321 - 1609-4514 publication_status: published publisher: Independent University of Moscow quality_controlled: '1' status: public title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '8500' abstract: - lang: eng text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way. article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Mark full_name: Levi, Mark last_name: Levi - first_name: Maria full_name: Saprykina, Maria last_name: Saprykina citation: ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509 apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21509 chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley, 2014. https://doi.org/10.1002/cpa.21509. ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley, pp. 748–775, 2014. ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775. mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:10.1002/cpa.21509. short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775. date_created: 2020-09-18T10:47:01Z date_published: 2014-05-01T00:00:00Z date_updated: 2022-08-25T13:58:13Z day: '01' doi: 10.1002/cpa.21509 extern: '1' intvolume: ' 67' issue: '5' keyword: - Applied Mathematics - General Mathematics language: - iso: eng month: '05' oa_version: None page: 748-775 publication: Communications on Pure and Applied Mathematics publication_identifier: issn: - 0010-3640 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Arnol′d diffusion in a pendulum lattice type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2014' ... --- _id: '852' abstract: - lang: eng text: 'Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. ' author: - first_name: Oriol full_name: Rosello, Oriol P last_name: Rosello - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955. doi:10.1093/gbe/evu159 apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evu159 chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159. ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” Genome Biology and Evolution, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014. ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955. mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159. short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955. date_created: 2018-12-11T11:48:51Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:51Z day: '01' doi: 10.1093/gbe/evu159 extern: 1 intvolume: ' 6' issue: '8' month: '08' page: 1949 - 1955 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6797' quality_controlled: 0 status: public title: Long-Term asymmetrical acceleration of protein evolution after gene duplication tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2014' ... --- _id: '856' abstract: - lang: eng text: The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network. acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.' author: - first_name: Ksenia full_name: Pougach, Ksenia S last_name: Pougach - first_name: Arnout full_name: Voet, Arnout R last_name: Voet - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Karin full_name: Voordeckers, Karin last_name: Voordeckers - first_name: Joaquin full_name: Christiaens, Joaquin F last_name: Christiaens - first_name: Bianka full_name: Baying, Bianka last_name: Baying - first_name: Vladimı́R full_name: Bénès, Vladimı́r last_name: Bénès - first_name: Ryo full_name: Sakai, Ryo last_name: Sakai - first_name: Jan full_name: Aerts, Jan A last_name: Aerts - first_name: Bo full_name: Zhu, Bo last_name: Zhu - first_name: Patrick full_name: Van Dijck, Patrick last_name: Van Dijck - first_name: Kevin full_name: Verstrepen, Kevin J last_name: Verstrepen citation: ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 2014;5. doi:10.1038/ncomms5868 apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms5868 chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868. ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5. mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications, vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868. short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014). date_created: 2018-12-11T11:48:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:20:01Z day: '01' doi: 10.1038/ncomms5868 extern: 1 intvolume: ' 5' month: '01' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '6790' quality_controlled: 0 status: public title: Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 5 year: '2014' ...