Structural characterization of assemblies from overall shape and subcomplex compositions

Frank Alber; Michael F Kim; Andrej Sali

doi:10.1016/j.str.2005.01.013

Structural characterization of assemblies from overall shape and subcomplex compositions

Structure. 2005 Mar;13(3):435-45. doi: 10.1016/j.str.2005.01.013.

Authors

Frank Alber¹, Michael F Kim, Andrej Sali

Affiliation

¹ Department of Biopharmaceutical Sciences and, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California 94143, USA.

PMID: 15766545
DOI: 10.1016/j.str.2005.01.013

Abstract

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.

MeSH terms

Computational Biology / methods*
Computer Simulation
Cryoelectron Microscopy*
Models, Molecular
Multiprotein Complexes / chemistry*
Multiprotein Complexes / metabolism
Proteasome Endopeptidase Complex / chemistry
Proteasome Endopeptidase Complex / metabolism
Protein Conformation
Protein Subunits / chemistry
Protein Subunits / metabolism

Substances

Multiprotein Complexes
Protein Subunits
Proteasome Endopeptidase Complex

Grants and funding

R33 CA89810/CA/NCI NIH HHS/United States