Modeling Macromolecular Complexes: A Journey Across Scales

  • Frédéric Cazals
  • Tom Dreyfus
  • Charles H. Robert
Chapter

Abstract

While proteins and nucleic acids are the fundamental components of an organism, Biology itself is based on the interactions they make with each other. Analyzing macromolecular interactions typically requires handling systems involving from two to hundreds of polypeptide chains. After a brief overview of the modeling challenges faced in computational structural biology, this chapter presents concepts and tools aiming at improving our understanding of the link between the static structures of macromolecular complexes and their biophysical/biological properties. We discuss geometrical approaches suited to atomic-resolution complexes and to large protein assemblies; for each, we also present examples of their successful application in quantifying and interpreting biological data. This methodology includes state-of-the-art geometric analyses of surface area, volume, curvature, and topological properties (isolated components, cavities, voids, cycles) related to Voronoï constructions in the context of structure analysis. On the applied side, we present novel insights into real biological problems gained thanks to these modeling tools.

Keywords

Delaunay Triangulation Protein Type Nuclear Pore Complex Hasse Diagram Toleranced Model 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

Joël Janin is acknowledged for insightful discussions.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Frédéric Cazals
    • 1
  • Tom Dreyfus
    • 1
  • Charles H. Robert
    • 2
  1. 1.Inria Sophia Antipolis MéditerranéeABS project-teamSophia AntipolisFrance
  2. 2.Laboratoire de Biochimie Théorique – UPR 9080 CNRS, Institut de Biologie Physico ChimiqueUniversité Paris Diderot Sorbonne Paris CitéParisFrance

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