Inference of Structure and Dynamic Order of Formation of Multimeric Protein Complexes

Abstract

Automatic prediction of bi-molecular protein complexes and biomolecular interactions has been the object of a diversity of computational studies and with different degrees of success. Extrapolating these methodologies to treat the harder problem of computing the structure and function of multi-meric proteins, however, poses several complications. The most relevant stems from the combinatorial aspect of the problem, which involves the prediction of the dynamic order in which the subunits interact (the interaction path). A second, not less important, is the size of these molecules which account for thousands of atoms, and thus require sophisticated computational platforms. In this chapter we entail the efforts of a recent study oriented to the automatic elucidation of protein multimeric configurations and thereby the dynamic order of multimeric protein complex formation. The study is namely based on the development of a genuine approach that requires as unique information that of the isolated structures of each of the subunits constituting the multimeric complex. The method is based on an original protocol we have implemented to infer interaction sites on protein surfaces. Hitherto attempts to solve this relevant problem in protein function elucidation have been limited to three body dockings using conventional docking algorithms and molecular dynamic simulations. Here the aim is to infer complex configurations and dynamic orders of formation from the monomers known to constitute a multimeric complex unveiling active regions on the surfaces of the proteins and intermediate complexes. We present three case studies and show that important insights into the formation mechanisms of this type of multimeric complexes can be gained from the analysis of the surface characteristics of the interacting monomers which can facilitate, in a further stage, the docking and energy calculations involved in the prediction of the configurations of these complexes.