1. Introduction to biological networks

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

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

4. Gene Regulation Network Regulatory proteins Promoter 1Promoter 3Promoter 2

5. Transcription network activator repressor

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

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

8. cAMP signaling transduction of Dictyostelium discoideum Dictyostelium discoideum

9. High throughput experiments to identify interaction in network

10. Experiments for Protein- Protein Interaction

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

12. Helicobacter Pylori

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

14. Caenorhabditis elegans (Worm)

15. 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)

16. 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

18. TAP tag

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

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

21. Yeast Two Hybrid Method

22. 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

23. Immunoprecipitation

24. 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.

25. Phage Display

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

27. 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)

28. Protein-Protein Interaction Database BIND: Biomolecular Interaction Network Database http://www.blueprint.org/bind/bind.php DIP: Database of Interacting Protein Genome Website: http://www.hgmp.mrc.ac.uk/GenomeWeb/

31. ☺ About 80000 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

32. Assign 80000 interactions of 5400 yeast proteins a confidence value 11855 interactions with high and medium confidence among 2617 proteins

33. 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

34. MycMax Mad PromoterGene Sequence Burkitt lymphoma neuroblastomas small cell lung cancers

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

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

37. Experiments for genetic regulation interaction

38. Protein-DNA interaction Chromatin Inmmunoprecipitation (ChIP)

39. Science 298, 799, (2002).

40. Yeast cell cycle regulatory network

41. Mathematical modeling of biological networks as a graph

42. Protein-protein interaction network

43. Node: protein Edge: interaction

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

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

46. Biochemical reduction Pathway map Graph representation Reduced graph representation

47. E. coli metabolic network with biochemical reduction

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

49. E. coli metabolic network with topological reduction

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

51. 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

52. Gene Regulation Network Regulatory proteins Promoter 1Promoter 3Promoter 2

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

54. 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

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

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

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

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

60. 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

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