MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases.
A new paradigm is proposed for modeling biomacromolecular interactions and complex formation in solution (protein-protein interactions so far in this report) that constitutes the scaffold of the automatic system MIAX (acronym for Macromolecular Interaction Assessment X). It combines in a rational way a series of computational methodologies, the goal being the prediction of the most native-like protein complex that may be formed when two isolated (unbound) protein monomers interact in a liquid environment. The overall strategy consists of first inferring putative precomplex structures by identification of binding sites or epitopes on the proteins surfaces and a simultaneous rigid-body docking process using geometric instances alone. Precomplex configurations are defined here as all those decoys the interfaces of which comply substantially with the inferred binding sites and whose free energy values are lower. Retaining all those precomplex configurations with low energies leads to a reasonable number of decoys for which a flexible treatment is amenable. A novel algorithm is introduced here for automatically inferring binding sites in proteins given their 3-D structure. The procedure combines an unsupervised learning algorithm based on the self-organizing map or Kohonen network with a 2-D Fourier spectral analysis. To model interaction, the potential function proposed here plays a central role in the system and is constituted by empirical terms expressing well-characterized factors influencing biomacromolecular interaction processes, essentially electrostatic, van der Waals, and hydrophobic. Each of these procedures is validated by comparing results with observed instances. Finally, the more demanding process of flexible docking is performed in MIAX embedding the potential function in a simulated annealing optimization procedure. Whereas search of the entire configuration hyperspace is a major factor precluding hitherto systems from efficiently modeling macromolecular interaction modes and complex structures, the paradigm presented here may constitute a step forward in the field because it is shown that a rational treatment of the information available from the 3-D structure of the interacting monomers combined with conveniently selected computational techniques can assist to elude search of regions of low probability in configuration space and indeed lead to a highly efficient system oriented to solve this intriguing and fundamental biologic problem.
Del Carpio-Muñoz
Carlos Adriel
CA
Laboratory for Bioinformatics, Department of Ecological Engineering, Toyohashi University of Technology, Tempaku, Toyohashi, Japan. carlos@translell.eco.tut.ac.jp
Ichiishi
Eiichiro
E
Yoshimori
Atsushi
A
Yoshikawa
Toshikazu
T
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D002919:Chymotrypsinogen / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D019272:Leukocyte Elastase / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D046911:Macromolecular Substances; D008958:Models, Molecular; D015394:Molecular Structure; D010059:Ovomucin / Q000737:chemistry; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014359:Trypsin Inhibitor, Kazal Pancreatic / Q000737:chemistry / Q000378:metabolism; D014452:Ubiquitins / Q000737:chemistry / Q000378:metabolism
D000596:Amino Acids; D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins; D012997:Solvents; D014452:Ubiquitins; C039345:ovomucoid inhibitors; D010059:Ovomucin; D014359:Trypsin Inhibitor, Kazal Pancreatic; D002919:Chymotrypsinogen; D019272:Leukocyte Elastase