Download Lecture: Protein-Protein Interactions

Lecture series in systems biology
Protein-protein
interactions
Department of Bioinfomatics
Shanghai Jiao Tong University
Woo Mao-Ying
[email protected]
http://202.120.45.17/course/intro/ppi.htm
Outline
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Why protein-protein interactions?.
Experimental methods for discovering PPIs:
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PPIs databases:
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Yeast-two-hybrid（酵母双杂交）
AP-MS（亲和纯化-质谱串联）
DIP
MIPs
Computational prediction of PPIs
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Phylogenetic based method（基于进化的手段）
Expression correlation based method （基于表达相关性）
STRING (EMBL)
Why protein-protein interactions (PPI)?
Gene is the basic
unit of heredity.
Genomes are
availabe.
genome
Proteins, the working
molecules of a cell,
carry out many
biological activities
Proteome（蛋白质组）
Proteins function by
interacting with other
proteins.
interactome
Why protein-protein interactions (PPI)?
PPIs are involved in many biological processes:
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Signal transduction (信号传递)
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Protein complexes or molecular machinery （蛋白复合物或分子体系）
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Protein carrier （蛋白的运输）
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Protein modifications (phosphorylation) （蛋白质的修饰）
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…
PPIs help to decipher the molecular mechanisms underlying the
biological functions, and enhance the approaches for drug discovery
High throughput experimental methods
for discovering PPIs
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Yeast-two-hybrid (Y2H，酵母双杂交）
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Ito T. et al., 2001
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Uetz P. et al., 2000
Affinity purification followed by mass
spectrometry (AP-MS，亲和纯化-质谱串联）

Gavin AC et al., 2002, 2006
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Ho Y. et al., 2002
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Krogan NJ et al., 2006
Y2H experiments
Idea:
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Bait 诱饵蛋白(prey捕获蛋白)
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
AP-MS experiments
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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
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After the first AP step （亲和纯化第一步） using an
IgG (免疫球蛋白) matrix, many contaminants are
eliminated.
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In the second AP step（亲和纯化第二步）, 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 (乙二醇二乙醚二胺
四乙酸 ).
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Proteins are identified by mass spectrometry
PPIs Databases.
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DIP- Database of Interacting Protein.
(http://dip.doe-mbi.ucla.edu/ )
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MIPS-Munich Information center for Protein
Sequences.
(http://mips.gsf.de/ )
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
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Number of proteins:
20731
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Number of organisms:
274
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Number of interactions: 57687
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Number of distinct experiments describing an interaction:
65735
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Number of data sources (articles):
3915
DIP-Searching information
Find information about your protein
DIP Node (DIP:1143N)
Graph of PPIs around DIP:1143N
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Nodes are proteins
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Edges are PPIs
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The center node is DIP:1143N
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Edge width encodes the number
of independent experiments
identyfying the interaction.
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Green (red) is used to draw core
(unverified) interactions.
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Click on each node (edge) to
know more about the protein
(interaction).
List of interacting partners of
DIP:1143N
MIPS
Services:
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Genomes
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Databanks retrieval systems
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Analysis tools
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Expression analysis
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Protein protein interactions
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MPact: the MIPS protein interaction resource on yeast.
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MPPI: the MIPS Mammalian Protein-Protein Interaction Database.
Protein complexes
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Mammalian protein complexes at MIPS
MPact: the MIPS protein interaction
resource on yeast
Query all PPIs of a yeast protein
MPact: the MIPS protein interaction
resource on yeast
MPact: Interaction Visualization
MPPI: the MIPS Mammalian Protein-Protein
Interaction Database
Query PPIs of a mamalian protein. You can use x-ref, for example Uniprot
accession number.
Results for PPI search
In short format
Results for PPI search
In full format
Mammalian protein complexes at MIPS
Search information of complexes
Assessment of large–scale data sets of
PPIs
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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 : 399–403
Functional biases
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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 : 399–403
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 : 399–403
Computational methods of prediction
Current approaches:
 Genomic
methods
 Biological
context methods
 Structural
based methods
Genomic methods
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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.
Biological context methods
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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.
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GO annotations: two interacting proteins likely have
the same GO term annotations.
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Machine learning techniques are adopted for PPI
classification by intergrating all known information.
STRING: Search Tool for the Retrieval of
Interacting Genes/Proteins
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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:
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Supported by
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Searching information
Query infomation via protein names or protein sequences.
Graph of PPIs
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Nodes are proteins
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Lines with color is an evidence of
interaction between two proteins.
The color encodes the method
used to detect the interaction.
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Click on each node to get the
information of the corresponding
protein.
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Click on each edge to get
information of the interaction
between two proteins.
List of predicted partners
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Partners with discription and confidence score.
Choose different types of views to see more detail
Neighborhood View
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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.
Occurence Views
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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.
Gene Fusion View
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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
References
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Ito T et.al: A comprehensive two-hybrid analysis to explore the yeast protein
interactome. Proc. Natl Acad. Sci. USA 2001, 98:4569-4574.
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Uetz P et. al: A comprehensive analysis protein-protein interactions in
Saccharomyces cerevisiae. Nature 2000, 403:623-627.
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Gavin AC et.al: Functional organization of the yeast proteome by systematic
analysis of protein complexes. Nature 2002, 415:141-147.
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Gavin AC et.al: Proteome survey reveals modularity of the yeast cell
machinery. Nature 2006, 440:631-636.
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Ho Y et.al: Systematic identification of protein complexes in Saccharomyces
cerevisiae by mass spectrometry. Nature 2002, 415:180-183.
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Von Mering C et.al: Comparative assessment of large-scale data sets of
protein-protein interactions. Nature 2002, 417:399-403.
Thank you for your
attention