Protein-protein interactions

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Protein-protein interactions
Lecture series in systems biology
Department of Bioinfomatics Shanghai Jiao Tong
University
Woo Mao-Ying ricket_at_sjtu.edu.cn
http//202.120.45.17/course/intro/ppi.htm
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Outline

• Why protein-protein interactions?.
• Experimental methods for discovering PPIs
• Yeast-two-hybrid(?????)
• AP-MS(????-????)
• PPIs databases
• DIP
• MIPs
• Computational prediction of PPIs
• Phylogenetic based method(???????)
• Expression correlation based method (???????)
• STRING (EMBL)

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Why protein-protein interactions (PPI)?

• Gene is the basic unit of heredity. Genomes are
  availabe.

• Proteins, the working molecules of a cell, carry
  out many biological activities

• Proteins function by interacting with other
  proteins.

genome
Proteome(????)
interactome
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Why protein-protein interactions (PPI)?

• PPIs are involved in many biological processes
• Signal transduction (????)
• Protein complexes or molecular machinery
  (??????????)
• Protein carrier (?????)
• Protein modifications (phosphorylation) (??????)
• PPIs help to decipher the molecular mechanisms
  underlying the biological functions, and enhance
  the approaches for drug discovery

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High throughput experimental methods for
discovering PPIs

• Yeast-two-hybrid (Y2H,?????)
• Ito T. et al., 2001
• Uetz P. et al., 2000
• Affinity purification followed by mass
  spectrometry (AP-MS,????-????)
• Gavin AC et al., 2002, 2006
• Ho Y. et al., 2002
• Krogan NJ et al., 2006

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Y2H experiments

• Idea
• Bait ????(prey????) protein is fused to the
  binding domain (activation domain).
• If bait and prey proteins interact, the
  transcription of the reporter gene is initiated.
• High throughput screening the interactions
  between the bait and the prey library.
• In yeast nucleus

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AP-MS experiments

• Fuse a TAP tag consisting of protA (IgG binding
  peptides) and calmodulin binding peptide (CBP)
  separated by TEV protease cleavage site to the
  target protein
• After the first AP step (???????) using an IgG
  (?????) matrix, many contaminants are
  eliminated.
• In the second AP step(???????), CBP binds tightly
  to calmodulin coated beads. After washing which
  removes remained contaminants and the TEV
  protease, the bound meterial is released under
  mild condition with EGTA (??????????? ).
• Proteins are identified by mass spectrometry

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PPIs Databases.

• DIP- Database of Interacting Protein.
• (http//dip.doe-mbi.ucla.edu/ )
• MIPS-Munich Information center for Protein
  Sequences.
• (http//mips.gsf.de/ )

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DIP

• Protein function
• Protein-protein relationship
• Evolution of protein-protein interaction
• The network of interacting proteins
• Unknown protein-protein interaction
• The best interaction conditions

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DIP-Statistics

• Number of proteins 20731
• Number of organisms 274
• Number of interactions 57687
• Number of distinct experiments describing an
  interaction 65735
• Number of data sources (articles) 3915

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DIP-Searching information
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Find information about your protein
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DIP Node (DIP1143N)
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Graph of PPIs around DIP1143N

• Nodes are proteins
• Edges are PPIs
• The center node is DIP1143N
• Edge width encodes the number of independent
  experiments identyfying the interaction.
• Green (red) is used to draw core (unverified)
  interactions.
• Click on each node (edge) to know more about the
  protein (interaction).

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List of interacting partners of DIP1143N
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MIPS

• Services
• Genomes
• Databanks retrieval systems
• Analysis tools
• Expression analysis
• Protein protein interactions
• MPact the MIPS protein interaction resource on
  yeast.
• MPPI the MIPS Mammalian Protein-Protein
  Interaction Database.
• Protein complexes
• Mammalian protein complexes at MIPS

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MPact the MIPS protein interaction resource on
yeast

• Query all PPIs of a yeast protein

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MPact the MIPS protein interaction resource on
yeast
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MPact Interaction Visualization
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MPPI the MIPS Mammalian Protein-Protein
Interaction Database

• Query PPIs of a mamalian protein. You can use
  x-ref, for example Uniprot accession number.

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Results for PPI search

• In short format

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Results for PPI search

• In full format

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Mammalian protein complexes at MIPS
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(No Transcript)
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Search information of complexes
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Assessment of largescale data sets of PPIs

• The overlap between the individual methods is
  surprisingly small
• The methods may not have reached saturation.
• Many of the methods may produce a significant
  fraction of false positives.
• Some methods may have difficulties for certain
  types of interactions

Von Mering C, et al. Nature, (2002) 417 399403
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Functional biases

• AP-MS discovers few PPIs involved in transport
  and sensing
• Y2H detects few PPIs involved in translation.
• Different methods complement each other

Von Mering C, et al. Nature, (2002) 417 399403
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Coverage and Accuracy

• Limited and biased coverage (False Negatives)
• High error rate (False Positives)
• Expensive, time-consuming and labor-intensive

Von Mering C, et al. Nature, (2002) 417 399403
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Computational methods of prediction

• Current approaches
• Genomic methods
• Biological context methods
• Structural based methods

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Genomic methods

• Protein a and b whose genes are close in
  different genomes are predicted to interact.
• Protein a and b are predicted to interact if they
  combine (fuse) to form one protein in another
  organism.
• Protein a and c are predicted to interact if they
  have similar phylogenetic profiles.

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Biological context methods

• Gene expression Two protein whose genes exhibit
  very similar patterns of expression across
  multiple states or experiments may then be
  considered candidates for functional association
  and posibly direct physical interaction.
• GO annotations two interacting proteins likely
  have the same GO term annotations.
• Machine learning techniques are adopted for PPI
  classification by intergrating all known
  information.

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STRING Search Tool for the Retrieval of
Interacting Genes/Proteins

• A database of known and predicted protein
  interactions
• Direct (physical) and indirect (functional)
  associations
• The database currently covers 2,483,276 proteins
  from 630 organisms
• Derived from these sources

• Supported by

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Searching information

• Query infomation via protein names or protein
  sequences.

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Graph of PPIs

• Nodes are proteins
• Lines with color is an evidence of interaction
  between two proteins. The color encodes the
  method used to detect the interaction.
• Click on each node to get the information of the
  corresponding protein.
• Click on each edge to get information of the
  interaction between two proteins.

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List of predicted partners

• Partners with discription and confidence score.
• Choose different types of views to see more detail

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Neighborhood View

• The red block is the queried protein and others
  are its neighbors in organisms. Click on the
  blocks to obtain the information about
  corresponding proteins.
• The close organisms show the similar protein
  neighborhood patterns.
• Help to find out the close genes/proteins in
  genomic region.

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Occurence Views

• Represents phylogenetic profiles of proteins.
• Color of the boxes indicates the sequence
  similarity between the proteins and their
  homologus protein in the organisms.
• The size of box shows how many members in the
  family representing the reported sequence
  similarity.
• Click on each box to see the sequence alignment.

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Gene Fusion View

• This view shows the individual gene fusion events
  per species
• Two different colored boxes next to each other
  indicate a fusion event.
• Hovering above a region in a gene gives the gene
  name clicking on a gene gives more detailed
  information

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References

• Ito T et.al A comprehensive two-hybrid analysis
  to explore the yeast protein interactome. Proc.
  Natl Acad. Sci. USA 2001, 984569-4574.
• Uetz P et. al A comprehensive analysis
  protein-protein interactions in Saccharomyces
  cerevisiae. Nature 2000, 403623-627.
• Gavin AC et.al Functional organization of the
  yeast proteome by systematic analysis of protein
  complexes. Nature 2002, 415141-147.
• Gavin AC et.al Proteome survey reveals
  modularity of the yeast cell machinery. Nature
  2006, 440631-636.
• Ho Y et.al Systematic identification of protein
  complexes in Saccharomyces cerevisiae by mass
  spectrometry. Nature 2002, 415180-183.
• Von Mering C et.al Comparative assessment of
  large-scale data sets of protein-protein
  interactions. Nature 2002, 417399-403.

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Thank you for your attention