A variety of computer studies have attempted to predict bi-molecular protein complexes and biomolecular interactions automatically, with varying degrees of success. However, applying these methods to the more difficult challenge of computing the structure and function of multi-meric proteins has numerous drawbacks. The most important derives from the problem's combinatorial element, which entails predicting the dynamic sequence in which the subunits interact (the interaction path). The scale of these molecules, which can number in the thousands of atoms, necessitates the use of advanced computer tools.
The efforts of a recent study aimed at the automatic elucidation of protein multimeric configurations, and therefore the dynamic order of multimeric protein complex formation, are summarised in this chapter. The research is based on the creation of a genuine strategy that demands the isolated structures of each of the subunits that make up the multimeric complex as distinct information. The method is based on an original protocol we developed to infer protein surface contact locations. Attempts to overcome this important topic in protein function elucidation have so far been limited to three-body dockings and molecular dynamic simulations. The goal is to deduce complex configurations and dynamic orders of creation from monomers that make up a multimeric complex, revealing active areas on protein surfaces and intermediate complexes. We present three case studies and show that analysing the surface characteristics of the interacting monomers can provide important insights into the formation mechanisms of these multimeric complexes, which can help with the docking and energy calculations involved in the prediction of their configurations in a later stage.
Author (s) Details
Carlos A. Del Carpio
Department of Molecular Biology School of Medicine Nagoya City University Mizuho-ku, Nagoya 467-8601, Japan and Drosophila Genetic Resource Center. Kyoto Institute of Technology. Saga, Ippongi-cho, Ukyo-ku, Kyoto, 616-8354, Japan.
Eiichiro Ichiishi
International University of Health and Welfare Hospital (IUHW Hospital) 537 Iguchi, Nasushiobara-City, Tochigi Pref. 329-2763, Japan.
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