1. Structure-based assembly of protein complexes in yeast.
- Author
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Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, and Russell RB
- Subjects
- Chaperonins chemistry, Chaperonins metabolism, Computational Biology, Image Processing, Computer-Assisted, Microscopy, Electron, Models, Biological, Models, Molecular, Nuclear Proteins chemistry, Nuclear Proteins metabolism, Protein Binding, Protein Conformation, Protein Structure, Tertiary, RNA Polymerase II chemistry, RNA Polymerase II metabolism, Ribonuclease P chemistry, Ribonuclease P metabolism, Saccharomyces cerevisiae chemistry, Saccharomyces cerevisiae ultrastructure, Saccharomyces cerevisiae Proteins chemistry, Transcription Factors chemistry, Transcription Factors metabolism, Protein Interaction Mapping, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins metabolism
- Abstract
Images of entire cells are preceding atomic structures of the separate molecular machines that they contain. The resulting gap in knowledge can be partly bridged by protein-protein interactions, bioinformatics, and electron microscopy. Here we use interactions of known three-dimensional structure to model a large set of yeast complexes, which we also screen by electron microscopy. For 54 of 102 complexes, we obtain at least partial models of interacting subunits. For 29, including the exosome, the chaperonin containing TCP-1, a 3'-messenger RNA degradation complex, and RNA polymerase II, the process suggests atomic details not easily seen by homology, involving the combination of two or more known structures. We also consider interactions between complexes (cross-talk) and use these to construct a structure-based network of molecular machines in the cell.
- Published
- 2004
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