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Large Multiprotein Structures Modeling and Simulation: The Need for Mesoscopic Models

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Functional Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 484))

Abstract

Recent observational techniques based upon confocal microscopy make it possible to observe cells at a scale that has never been probed before: the mesoscopic scale. In the eukaryotic cell nucleus, many objects demonstrating phenomena occurring at this scale, such as nuclear bodies, are current subjects of investigations. But from a modeling perspective, this scale has not been widely explored, and hence there is a lack of suitable models for such studies. By reviewing higher and lower scale modeling techniques, we analyze their relevance in the context of mesoscale phenomena. We emphasize important characteristics that should be included in a mesoscopic model: an explicit continuous three-dimensional space with discrete simplified molecules that still have the characteristics of steric volume exclusion and realistic distant interaction forces. Then we present 3DSPI, a model dedicated to studies of nuclear bodies based on a simple formalism inspired from molecular dynamics and coarse-grained models: particles interacting through a potential energy function and driven by an overdamped Langevin equation. Finally, we present the features expected to be included in the model, pointing out the difficulties that might arise.

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Author information

Authors and Affiliations

  1. Université de Lyon, Lyon, France

    Antoine Coulon & Olivier Gandrillon

  2. Centre de Génétique Moléculaire et Cellulaire, UMR CNRS 5534, Villeurbanne, France

    Antoine Coulon

  3. Laboratoire d’InfoRmatique en Images et Systèmes d’information (LIRIS, UMR CNRS 5205), INSA-Lyon, Villeurbanne, France

    Guillaume Beslon

Authors
  1. Antoine Coulon
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  2. Guillaume Beslon
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  3. Olivier Gandrillon
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Editor information

Editors and Affiliations

  1. Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France

    Julie D. Thompson

  2. Department of Protein Science Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany

    Marius Ueffing

  3. LSMBO, ECPM, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France

    Christine Schaeffer-Reiss

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© 2008 Humana Press, Totowa, NJ

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Coulon, A., Beslon, G., Gandrillon, O. (2008). Large Multiprotein Structures Modeling and Simulation: The Need for Mesoscopic Models. In: Thompson, J.D., Ueffing, M., Schaeffer-Reiss, C. (eds) Functional Proteomics. Methods in Molecular Biology, vol 484. Humana Press. https://doi.org/10.1007/978-1-59745-398-1_32

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  • DOI: https://doi.org/10.1007/978-1-59745-398-1_32

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-971-0

  • Online ISBN: 978-1-59745-398-1

  • eBook Packages: Springer Protocols

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