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791_ak_lecture7 - 7.91 Amy Keating The Protein Interactome...

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The Protein Interactome A critical framework underlying systems biology 1. Overview - the many levels of systems biology 2. Experimental methods for measuring protein-protein interactions, and their limitations 3. Data sources for information about proteins and their interactions 4. Computational methods for assessing and predicting protein-protein interactions. 7.91 Amy Keating
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Spectrum of Systems Biology detailed models - describe rates, concentrations, structure low-resolution models - describe information flow, logic, mechanism circuitry logic/control - positive and negative regulation connectivity/topology - who talks to who? interaction scaffold parts list - protein and DNA sequences (& structures) Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262
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Spectrum of Systems Biology detailed models - differential equations comparison with data low-resolution models - Boolean & Markov models circuitry logic/control - Bayesian networks connectivity/topology - graph theory parts list - databases Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262
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Spectrum of Systems Biology detailed models - rates of individual reactions, protein concentrations in the cell, extent of phosphorylation, diffusion rates low-resolution models - which elements are most crucial? combinatorial dependencies. circuitry logic/control - Expression profiling, post-translational modifications in response to different stimuli. Identify pathways and clusters; does an interaction activate or repress; are multiple components required? connectivity/topology - protein-protein, protein-DNA and protein-small molecule interactions parts list - genome sequencing projects, gene finding algorithms, EST libraries Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262
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Spectrum of Systems Biology detailed models YAFFE low-resolution models - not covering this topic much this year circuitry logic/control - BURGE connectivity/topology - KEATING (today) parts list BURGE Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262
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Protein-protein and protein-DNA interactions at the genomic level Saccharomyces cerevisiaeas a model organism. A very simple eukaryote - “yeast as a model for human” Genome 12,053 kb sequenced in 1996. ~5800 protein-coding genes. Easy to do genetics in yeast. Many regulatory and metabolic pathways are at least partly conserved between yeast and higher eukaryotes. Many human disease genes have yeast orthologs. Saccharomyces cerevisiae image from SGD , provided by Peter Hollenhorst and Catherine Fox. Used with permission.
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Small-scale interaction experiments Protein-protein interactions pull-down (GST, Ni affinity, co-immunoprecipitation) cross-linking more biophysical & quantitative: fluorescence, CD, calorimetry, surface plasmon resonance Protein-DNA interactions mostly by gel shift assay Many, many thousands of such experiments have been done and
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This note was uploaded on 11/11/2011 for the course BIO 20.410j taught by Professor Rogerd.kamm during the Spring '03 term at MIT.

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791_ak_lecture7 - 7.91 Amy Keating The Protein Interactome...

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