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Physique théorique des systèmes biologiques
(25) Production(s) de l'année 2018
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Looping and Clustering: a statistical physics approach to protein-DNA complexes in bacteria
Auteur(s): Walliser N.-O.
(Séminaires)
L2C, Université de Montpellier (Montpellier, FR), 2018-02-15 |
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Looping and Clustering: a statistical physics approach to protein-DNA complexes in bacteria
Auteur(s): Walliser N.-O.
Conference: Chromatin Meets South (Montpellier, FR, 2018-06-12)
Ref HAL: hal-01939901_v1
Exporter : BibTex | endNote
Résumé: The DNA shows a high degree of spatial and dynamical organization over a broad range of length scales. It interacts with different populations of proteins and can form protein-DNA complexes that underlie various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, an essential component of a widely spread mechanism for DNA segregation in bacteria. Recent studies suggest that DNA-bound ParB proteins interact with each other and condense into large clusters with multiple extruding DNA-loops. In my talk, I present the Looping and Clustering model, a simple statistical physics approach to describe how proteins assemble into a protein-DNA cluster with multiple loops. Our analytic model predicts binding profiles of ParB proteins in good agreement with data from high precision ChIP-sequencing – a biochemical technique to analyze the interaction between DNA and proteins at the level of the genome. The Looping and Clustering framework provides a quantitative tool that could be exploited to interpret further experimental results of ParB-like protein complexes and gain some new insights into the organization of DNA.
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Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome
Auteur(s): Walliser N.-O.
Conference: Réunion annuelle du GdR ADN (Millau, FR, 2018-04-09)
Ref HAL: hal-01939895_v1
Exporter : BibTex | endNote
Résumé: The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate parS binding site.
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DNA-loops and the organization of protein-DNA complexes in bacteria
Auteur(s): Walliser N.-O.
Conference: Journées de Physique Statistique 2018 (Paris, FR, 2018-01-25)
Ref HAL: hal-01939889_v1
Exporter : BibTex | endNote
Résumé: The DNA shows a high degree of spatial and dynamical organization over a broad range of length scales. It interacts with different populations of proteins and can form protein-DNA complexes that underlie various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, an essential component of a widely spread mechanism for DNA segregation in bacteria. Recent studies suggest that DNA-bound ParB proteins interact with each other and condense into large clusters with multiple extruding DNA-loops. In my talk, I present the Looping and Clustering model, a simple statistical physics approach to describe how proteins assemble into a protein-DNA cluster with multiple loops. Our analytic model predicts binding profiles of ParB proteins in good agreement with data from high precision ChIP-sequencing – a biochemical technique to analyze the interaction between DNA and proteins at the level of the genome. The Looping and Clustering framework provides a quantitative tool that could be exploited to interpret further experimental results of ParB-like protein complexes and gain some new insights into the organization of DNA.
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Looping and Clustering: a statistical physics approach to protein-DNA complexes in bacteria
Auteur(s): Walliser N.-O.
Conference: Labex EpiGenMed & Numev & Grisbi joint meetin (Montpellier, FR, 2018-04-03)
Ref HAL: hal-01939883_v1
Exporter : BibTex | endNote
Résumé: The DNA shows a high degree of spatial and dynamical organization over a broad range of length scales. It interacts with different populations of proteins and can form protein-DNA complexes that underlie various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, an essential component of a widely spread mechanism for DNA segregation in bacteria. Recent studies suggest that DNA-bound ParB proteins interact with each other and condense into large clusters with multiple extruding DNA-loops. In my talk, I present the Looping and Clustering model, a simple statistical physics approach to describe how proteins assemble into a protein-DNA cluster with multiple loops. Our analytic model predicts binding profiles of ParB proteins in good agreement with data from high precision ChIP-sequencing – a biochemical technique to analyze the interaction between DNA and proteins at the level of the genome. The Looping and Clustering framework provides a quantitative tool that could be exploited to interpret further experimental results of ParB-like protein complexes and gain some new insights into the organization of DNA.
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Surfing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning
Auteur(s): Walter J.-C.
Conference: DNA Transactions & Physical and Molecular Biology of Chromosomes (Egmond-Aan-Zee, NL, 2018-09-20)
Texte intégral en Openaccess :
Ref HAL: hal-01931229_v1
Exporter : BibTex | endNote
Résumé: Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.
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Transport of ions in solution through single-walled carbon nanotubes
Auteur(s): Yazda K., Tahir S., Michel T., Loubet Bastien, Manghi Manoel, Bentin Jérémy, Picaud Fabien, Palmeri J., Henn F., Jourdain V.
Conference: Chemontubes 2018 (Biarritz, FR, 2018-04-22)
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