Structural characterization of assemblies from overall shape and subcomplex compositions.
We suggest structure characterization of macromolecular assemblies by combining assembly shape determined by electron cyromicroscopy with information about subunit proximity determined by affinity purification. To achieve this aim, structure characterization is expressed as a problem in satisfaction of spatial restraints that (1) represents subunits as spheres, (2) encodes information about the subunit excluded volume, assembly shape, and pulldowns in a scoring function, and (3) finds subunit configurations that satisfy the input restraints by an optimization of the scoring function. Testing of the approach with model systems suggests its feasibility.
Alber
Frank
F
Department of Biopharmaceutical Sciences and, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California 94143, USA.
Kim
Michael F
MF
Sali
Andrej
A
D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020285:Cryoelectron Microscopy; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism
D046912:Multiprotein Complexes; D021122:Protein Subunits; D046988:Proteasome Endopeptidase Complex