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 1

Promoter 3

Promoter 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 CerevisiaeNature, 415, 180, (2001)

Nature, 415, 141, (2001)

Cellzome is a private Corporation in German

HMS-PCITAP tag

Helicobacter Pylori

Drosophila melanogaster

Science, 5 Dec, 302, 1727, (2003)

Two hybrid

Caenorhabditis elegans (Worm)Caenorhabditis elegans (Worm)

Experimetal Methods • HMS-PCI(High-throughput mass spectro

metric 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 p

rotein A (ProtA)

2. Calmodulin binding petide (CBP)

3. TEV protease cleavage site

TAP tag Purification

TAP tag

• Advantage: Detects in physiological condition, high-t

hroughput

• Disavantage: Tag may disturb protein interaction

miss the protein complexes that are not present in such condition

HMS-PCI• High-throughput mass spectrometric pr

otein 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.

A

Fluorescence Resonance Energy Transfer (FRET)

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/

☺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

Assign 80000 interactions of 5400 yeast proteins a confidence

value11855 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

Myc Max

Mad

Promoter Gene Sequence

Burkitt lymphoma

neuroblastomas

small cell lung cancers

Cdc28YBR160W

Cln

Cdc28YBR160W

Clb

Sic

1

Partner Specific

Yeast cell cylce

Cyclin-CDK (Cyclin-dependent kinases) complexes

Scaffold Protein

E1 E2 E3 ProductReactants

ScaffoldE1 E2 E3

Reactants

E1 E2

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

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 representatio

n

Reduced graph

representation

E. coli metabolic network with biochemical reduction

Topological reductionRemove 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

• Aij= 1 if ith protein interacts with jth protein

• Aij=0 otherwise

• Aij=Aji (undirected graph)

• Aij is a sparse matrix, most elements of Aij are zero

Gene Regulation Network

Regulatory proteins

Promoter 1

Promoter 3

Promoter 2

Control element I:

Transcriptional Control

Gene Arepressor activator

Multiple inputs; combinatorial

Transcription factors

Control element IIProtein-Protein Interaction

— kinase and phosphatase

• On-off switch• Multiple sites• Location control (nuclear entry)• Tags for degradation• Signal transduction

P

Pkinase

phosphataseP

Pkinase

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

• Aij= 1 for activated interaction (green arrow)

• Aij=-1 for inhibitive interaction (red arrow)

• Aij ≠Aij (directed graph)

• Aij=0 otherwise

課 堂 練 習• Write down the adjacency matrix

for the following graph.