Papers by Damien Lariviere
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany, 2008
Thanks to NMR, X-ray crystallography and electron microscopy, it is possible to resolve 3D struct... more Thanks to NMR, X-ray crystallography and electron microscopy, it is possible to resolve 3D structure of most cell components. Even though many softwares help biologists to visualize the 3D shape of individual molecules, several authors have been calling for a visual discovery tool which can link the individual component view with the system view [1, 2] (Fig.1).
English Abstract—Biologists need simple spatial modeling tools to help in understanding the role ... more English Abstract—Biologists need simple spatial modeling tools to help in understanding the role of objects ’ relative position in the functionning of the cell. In this context, we report on a tool for DNA modeling. An english version of this text is available on the authors ’ webpages.
FEMS Microbiology Reviews, 2011
Formerly regarded as small 'bags' of nucleic acids with randomly diffusing enzymes, bacteria are ... more Formerly regarded as small 'bags' of nucleic acids with randomly diffusing enzymes, bacteria are organized by a sophisticated and tightly regulated molecular machinery. Here, we review qualitative and quantitative data on the intracellular organization of bacteria and provide a detailed inventory of macromolecular structures such as the divisome, the degradosome and the bacterial 'nucleolus' . We discuss how these metabolically active structures manage the spatial organization of the cell and how macromolecular crowding influences them. We present for the first time a visualization program, LIFEEXPLORER, that can be used to study the interplay between metabolism and spatial organization of a prokaryotic cell.
Journal of Biological Chemistry, 2011
The ternary complex comprising MutS, MutL, and DNA is a key intermediate in DNA mismatch repair. ... more The ternary complex comprising MutS, MutL, and DNA is a key intermediate in DNA mismatch repair. We used chemical cross-linking and fluorescence resonance energy transfer (FRET) to study the interaction between MutS and MutL and to shed light onto the structure of this complex. Via chemical cross-linking, we could stabilize this dynamic complex and identify the structural features of key events in DNA mismatch repair. We could show that in the complex between MutS and MutL the mismatch-binding and connector domains of MutS are in proximity to the N-terminal ATPase domain of MutL. The DNA- and nucleotide-dependent complex formation could be monitored by FRET using single cysteine variants labeled in the connector domain of MutS and the transducer domain of MutL, respectively. In addition, we could trap MutS after an ATP-induced conformational change by an intramolecular cross-link between Cys-93 of the mismatch-binding domain and Cys-239 of the connector domain.
The GraphiteLifeExplorer tool enables biologists to reconstruct 3D cellular complexes built from ... more The GraphiteLifeExplorer tool enables biologists to reconstruct 3D cellular complexes built from proteins and DNA molecules. Models of DNA molecules can be drawn in an intuitive way and assembled to proteins or others globular structures. Real time navigation and immersion offer a unique view to the reconstructed biological machinery. Citation: Hornus S, Lévy B, Larivière D, Fourmentin E (2013) Easy DNA Modeling and More with GraphiteLifeExplorer. PLoS ONE 8(1): e53609.
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Papers by Damien Lariviere