Condensed-Matter Physics Seminar

Proteins, nucleic acids, and small molecules form a dense network of molecular interactions in a cell. Molecules are nodes of this network and the interactions between them are edges. The architecture of molecular networks can reveal important principles of cellular organization and function, similarly to the way that protein structure tells us about the function and organization of a protein.

1) We analyzed the network of protein-protein interactions in yeast and found several densely interconnected modules. Comparison with the experimental data and functional annotation of genes showed that these modules correspond either to protein complexes (splicing machinery, transcription factors, etc.) or to dynamic functional units (signaling cascades, cell-cycle regulation, etc.).

2) We integrated a metabolic network of E.coli with data on
functional associations (genomic co-localization, domain fusion, etc.) between the enzymes and analyzed it on three scales. The macroscale analysis focuses on general properties of the network such as the correlation between pathway distance and enzyme co-regulation. We found that reactions short pathway distance apart on the metabolic network are more likely to be catalyzed by the same enzymes or by co-regulated enzymes. On the mesoscale level, using our search algorithms we identified several non-overlapping metabolic modules. Finally, the microscale analysis focuses on patterns of associations exhibited by motifs of a few enzymes that correspond to a particular architecture of
chemical reactions.