Introduction to biological networks

protein-gene interactions protein-protein interactions PROTEOME GENOME Citrate Cycle METABOLISM Bio-chemical reactions

Types of biological network Genetic regulatory network Protein-protein interaction network Metabolic network Signal transduction network

Gene Regulation Network Regulatory proteins Promoter 1Promoter 3Promoter 2

Transcription network activator repressor

Node: protein Edge: protein-protein interaction Protein-Protein Interaction Network Saccharomyces cerevisiae

Metabolic Network Node: Chemicals or Proteins Edge: Chemical reaction Metabolic Pathway

cAMP signaling transduction of Dictyostelium discoideum Dictyostelium discoideum

High throughput experiments to identify interaction in network

Experiments for Protein- Protein Interaction

Saccharomyces Cerevisiae Nature, 415, 180, (2001) Nature, 415, 141, (2001) Cellzome is a private Corporation in German HMS-PCI TAP tag

Helicobacter Pylori

Drosophila melanogaster Science, 5 Dec, 302, 1727, (2003) Two hybrid

Caenorhabditis elegans (Worm)

Experimetal Methods HMS-PCI(High-throughput mass spectrometric protein complex identification) TAP (Tandem Affinity Purification) Yeast two hybrid Immunoprecipitation Phage display Fluorescence resonance energy transfer (FRET)

TAP tag TAP tag contains 1. two IgG binding domains of Staphylococcus aureus protein A (ProtA) 2. Calmodulin binding petide (CBP) 3. TEV protease cleavage site TAP tag Purification

TAP tag

Advantage: Detects in physiological condition, high- throughput Disavantage: Tag may disturb protein interaction miss the protein complexes that are not present in such condition

HMS-PCI High-throughput mass spectrometric protein complex indentification Use epitope tag

Yeast Two Hybrid Method

Advantage : In vivo experiment, transient and unstable interactions could be detected Disadvantage: many false positive, only two proteins were detected at a time it take place in the nucleus, so many protein interactions are not detected in their native environment

Immunoprecipitation

Advantages of this approach This approach can test the protein associations in nature condition in the cell. The isolated proteins (or complex) can be used to do other functional assay.

Phage Display

Advanage: high throughput Can be used to elucidate nuclear protein interaction.

When the donor and acceptor come close to 10~100, the donor will transmit energy to acceptor, we could monotor the protein interaction by fluorescence. Fluorescence Resonance Energy Transfer (FRET)

Protein-Protein Interaction Database BIND: Biomolecular Interaction Network Database DIP: Database of Interacting Protein Genome Website:

☺ About interactions between yeast proteins are available from high-throughput methods. ☺ Only ~2400 interactions are supported by more than two methods. ☺ Possible reasons are ® the methods may not have reached saturation ® many methods may produce false positives ® some methods has difficulties for certain types of interaction. Yeast protein-protein interaction

Assign interactions of 5400 yeast proteins a confidence value interactions with high and medium confidence among 2617 proteins

Biological significance of protein- protein interaction? Assemble proteins together into protein complex Bring the proteins(signaling proteins) to its activate or function place Binding of one protein to another can induce conformational change that affect activity or accessibility of additional binding domain

MycMax Mad PromoterGene Sequence Burkitt lymphoma neuroblastomas small cell lung cancers

Cdc28 YBR160W Cln Cdc28 YBR160W Clb Sic1 Partner Specific Yeast cell cylce Cyclin-CDK (Cyclin-dependent kinases) complexes

Scaffold Protein E1E2 E3 Product Reactants Scaffold E1E2E3 Reactants E1E2 E3 Reactants Product Protein complex

Experiments for genetic regulation interaction

Protein-DNA interaction Chromatin Inmmunoprecipitation (ChIP)

Science 298, 799, (2002).

Yeast cell cycle regulatory network

Mathematical modeling of biological networks as a graph

Protein-protein interaction network

Node: protein Edge: interaction

Node: protein Edge: protein-protein interaction Protein-Protein Interaction Network Saccharomyces cerevisiae

Metabolic network Node: protein or chemicals Edge: chemical reaction Substrates linked to all its products

Biochemical reduction Pathway map Graph representation Reduced graph representation

E. coli metabolic network with biochemical reduction

Topological reduction Remove hair nodes, and replacing arc with single link

E. coli metabolic network with topological reduction

Both protein-protein interaction network and metabolic network are modeling as undirected graphs.

Adjacency Matrix A ij = 1 if ith protein interacts with jth protein A ij =0 otherwise A ij =A ji (undirected graph) A ij is a sparse matrix, most elements of A ij are zero

Gene Regulation Network Regulatory proteins Promoter 1Promoter 3Promoter 2

Control element I: Transcriptional Control Gene A repressor activator Multiple inputs; combinatorial Transcription factors

Control element II Protein-Protein Interaction — kinase and phosphatase On-off switch Multiple sites Location control (nuclear entry) Tags for degradation Signal transduction P P kinase phosphatase P P kinase phosphatase

Protein interactions On-off switching upon binding Partner-specific Cdc28 Cln Cdc28 Clb Sic1 — protein-protein binding

Integrated genetic network A C B A activates B A inhibits C A is the activator of B A is the inhibitor of C

Integrated genetic network A C B A activates B A inhibits C A is the activator of B A is the inhibitor of C

Integrated genetic network Green arrow: activate interaction Red arrow: inhibitive interaction

Adjacency Matrix A ij = 1 for activated interaction (green arrow) A ij =-1 for inhibitive interaction (red arrow) A ij ≠A ij (directed graph) A ij =0 otherwise

課 堂 練 習課 堂 練 習 Write down the adjacency matrix for the following graph.