Modeling AAA+ ring complexes from monomeric structures.
AAA+ proteins form large, ring-shaped complexes, which act as energy-dependent unfoldases of macromolecules. Many crystal structures of proteins in this superfamily have been determined, but mostly in monomeric or non-physiological oligomeric forms. The assembly of ring-shaped complexes from monomer coordinates is, therefore, of considerable interest. We have extracted structural features of complex formation relating to the distance of monomers from the central axis, their relative orientation and the molecular contacts at their interfaces from experimentally determined oligomers and have implemented a semi-automated modeling procedure based on RosettaDock into the iMolTalk server (http://protevo.eb.tuebingen.mpg.de/iMolTalk). As examples of this procedure, we present here models of Apaf-1, MalT and ClpB. We show that the recent EM-based model of the apoptosome is not compatible with the conserved structural features of AAA+ complexes and that the D1 and D2 rings of ClpB are most likely offset by one subunit, in agreement with the structure proposed for ClpA.
Diemand
Alexander V
AV
Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany.
Lupas
Andrei N
AN
D000251:Adenosine Triphosphatases / Q000737:chemistry* / Q000378:metabolism* / Q000648:ultrastructure; D000465:Algorithms; D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D049071:Endopeptidase Clp / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009711:Nucleotides / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry; D017386:Sequence Homology, Amino Acid
D029968:Escherichia coli Proteins; D009711:Nucleotides; D021122:Protein Subunits; D049071:Endopeptidase Clp; D000251:Adenosine Triphosphatases