Premium
Modeling oligomers with C n or D n symmetry: Application to CAPRI target 10
Author(s) -
Berchanski Alexander,
Segal Dadi,
Eisenstein Miriam
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20558
Subject(s) - trimer , oligomer , monomer , protein subunit , docking (animal) , crystallography , chemistry , icosahedral symmetry , molecular dynamics , computational chemistry , biological system , dimer , biology , polymer chemistry , medicine , biochemistry , nursing , organic chemistry , gene , polymer
The abundance of oligomeric proteins makes them a frequent target for structure prediction. However, homologous proteins sometimes adopt different oligomerization states, rendering the prediction of structures of whole oligomers beyond the scope of comparative modeling. This obstacle can be overcome by combining comparative modeling of the single subunit of an oligomer with docking techniques, designed for predicting subunit–subunit interfaces. We present here algorithms for predicting the structures of homo‐oligomers with C n or D n ( n > 2) symmetry. The prediction procedure includes a symmetry‐restricted docking step followed by a C n or D n oligomer‐forming step, in which the dimers from the docking step are assembled to oligomers. The procedure is applied to each of the crystallographically independent subunits in 8 C n and 3 D n oligomers, producing very accurate predictions. It is further applied to a single monomer of the tick‐borne encephalitis virus coat protein E (Target 10 of the CAPRI experiment). The predicted trimer ranked 30, obtained via rigid‐body geometric–hydrophobic docking followed by C n oligomer formation, is very similar to the experimentally observed trimer formed by domain II of this protein. Furthermore, the predicted trimer formed from the separated domain I is also close to the experimental structure. Proteins 2005;60:202–206. © 2005 Wiley‐Liss, Inc.