Protein-Protein Interactions in Health and...
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Franca Fraternali
Randall Division of Cellular and Molecular Biophysics
Protein-Protein Interactions in Health and Disease
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GENOME
PROTEOME
METABOLISM
bio-chemical reactions
protein-protein interactions
protein-gene interactions
Interactions inside the cell...
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ATOMISTIC
MOLECULAR
CELLULAR
TOPOLOGICAL
A Multiscale view of Protein-Protein Interactions
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Lu, Fornili & Fraternali: Protein-protein interaction networks studies and importance of 3D structure
knowledge. Expert Rev Proteomics 10, 511–520 (2013).
Satoh T, et al.S: B-RAF mutant alleles associated with Langerhans cell histiocytosis, a granulomatous
pediatric disease. PLoS One 7(4):e33891(2012).
Carlin LM et al. A targeted siRNA screen identifies regulators of Cdc42 activity at the
natural killer cell immunological synapse.
Sci Signal. 2011 Nov 29;4(201):ra81.
Vaz F et al. Mutation of the RAD51C gene in a Fanconi anemia-like
disorder.
Nat Genet. 2010 May;42(5):406-9.
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First Focus: topological level
Protein-Protein Interaction (PPI) Networks
interaction matrix all interactions
a1 a2 a3 …
a1 1 1 0 …
a2 1 0 0 …
a3 0 0 1 …
…
Useful for: •Studying inter-relationships of proteins (essential, crucial) •The study of protein functions •Detecting disease-related interactions (sub-networks) •Mapping protein sub-networks to pathways •Extracting phenotype-related sub-networks •Complementing large scale siRNA screenings
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Network Definition
The degree k of protein i
in interaction network c
is defined as:
Degree Distribution
i.e. probability of a protein
to have degree k.
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Degree-Degree Correlation
Relative degree-degree correlation DDC,
i.e. the probability of two proteins
with degree k and k’ to be found linked in the graph.
The normalised DDC function (k, k′) of the network is defined as the ratio between
the probability that two randomly picked nodes in c with degrees (k, k′) are found
to be connected, divided by what this probability would have been in large
random networks with the same degree distribution as c.
The probabilities for large random networks can be calculated analytically.
This results in the following definition for the normalised DDC function :
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Interaction Data
Recent analyses of PPINs sparked a debate about the influence of the experimental
method on the quality and biological relevance of the interaction data.
Current experimental techniques, such as yeast two-hybrid (Y2H) and co–affinity
purification combined with mass spectrometry (AP–MS), sample subsets of the
interaction data space.
These subsets show very limited overlap.
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Degree-Degree Correlation Yeast
Ito et al.
2001 Yu et al. 2008
Gavin et
al.
2006
Krogan et al.
2006
Relative degree-degree correlation DDC
i.e. the probability of two proteins
with degree k and k’ to be found linked in the graph
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Network Distance DAB
Annibale A, Coolen A, Fernandes L, Fraternali F, Kleinjung J.
Tailored graph
ensembles as proxies or null models for real networks I: tools
for quantifying structure. J Phys A Math Gen. 2009 Dec
4;42(48). doi:pii: 485001.
Fernandes LP, Annibale A, Kleinjung J, Coolen AC, Fraternali F. Protein
networks reveal detection bias and species consistency when analysed by
information-theoretic methods. PLoS One. 2010 Aug 18;5(8):e12083. doi:
10.1371/journal.pone.0012083.
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Analysis of PPINs using loop network motifs
Protein-protein interaction Network
Analysis by short loops of length 3, 4, 5, 6
Randomised Null Model Markov Chain Graph Dynamics
I II III
IV V VI
Species Method
C.elegans I Y2H
C.elegans II Y2H
C.jejuni Y2H
H.pylori Y2H
H.sapiens I Y2H
H.sapiens II Y2H
H.sapiens VIII Y2H
M.loti Y2H
P.falciparum Y2H
S.cerevisiae I Y2H
S.cerevisiae II Y2H
S.cerevisiae III Y2H
S.cerevisiae XII Y2H
Synechocystis Y2H
T.pallldum Y2H
E.coli AP-MS
H.sapiens III AP-MS
S.cerevisiae IV AP-MS
S.cerevisiae VI AP-MS
S.cerevisiae VIII AP-MS
S.cerevisiae IX AP-MS
S.cerevisiae X AP-MS
H.sapiens V BP-MS
S.cerevisiae XI PCA
D.melanogaster Database
H.sapiens IV Database
S.cerevisiae V Data Integration
S.cerevisiae VII Data Integration
H.sapiens VI Database
H.sapiens VII Database
edge swap
Constraints :
i) degree distribution
ii) degree-degree
correlation
H. sapiens V (BP-MS)
Reproduced from (Havugimana et al., 2012)
1. Topological analysis
2. Functional analysis
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Classification of PPINs by Topological Properties
No. Species Method
1 C.elegans I Y2H
2 C.elegans II Y2H
3 C.jejuni Y2H
4 H.pylori Y2H
5 H.sapiens I Y2H
6 H.sapiens II Y2H
7 H.sapiens VIII Y2H
8 M.loti Y2H
9 P.falciparum Y2H
10 S.cerevisiae I Y2H
11 S.cerevisiae II Y2H
12 S.cerevisiae III Y2H
13 S.cerevisiae XII Y2H
14 Synechocystis Y2H
15 T.pallldum Y2H
16 E.coli AP-MS
17 H.sapiens III AP-MS
18 S.cerevisiae IV AP-MS
19 S.cerevisiae VI AP-MS
20 S.cerevisiae VIII AP-MS
21 S.cerevisiae IX AP-MS
22 S.cerevisiae X AP-MS
23 H.sapiens V BP-MS
24 S.cerevisiae XI PCA
25 D.melanogaster Database
26 H.sapiens IV Database
27 S.cerevisiae V Data Integration
28 S.cerevisiae VII Data Integration
29 H.sapiens VI Database
30 H.sapiens VII Database
Loop Resilience
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Core Cluster of PPIN from Resilient Loops
Ribosome
ATP-dependent helicase
Interleukin enhancer
binding factors
U2 snRNP splicing
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Functional Consensus in H. Sapiens V (BP-MS) using Gene Ontology (GO)
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Functional Enrichment in loop motifs
H. Sapiens V (BP-MS) - Ribosomal proteins
H. Sapiens V (BP-MS) •mRNA metabolism •gene expression •viral process
•cell cycle / cell death •regulation processes •antigen processing
•organismal and •developmental processes •DNA-templated transcription
•biosynthetis •protein complex subunit •localization (transport)
x-axis : Network, Loop3, Loop4, Loop5 y-axis : Frequency of GO terms
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•biosynthetis •protein complex subunit •localization (transport)
•cell cycle / cell death •regulation processes •antigen processing
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Structural Coverage of Human PPINs
Single protein structures
Stein, A., Mosca, R. & Aloy, P. Three-dimensional modeling of protein interactions and complexes is going ‘omics. Curr. Opin. Struct. Biol. 21, 200–208 (2011).
Interaction protein pair structures
Mosca R, Céol A, Aloy P. Interactome3D: adding structural details to proteinnetworks. Nat Methods. 2012 Dec 16;10(1):47-53.
http://interactome3d.irbbarcelona.org/
Second Focus: Molecular
Second Focus: Molecular Complexes
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Protein Binding Mechanism
Integrating 3D Structure Information
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Identify Partner Proteins with Structures
A B (partner protein of A)
HMMER3
PSI-Blast
Pfam
PDB
Homolog structures of
protein A and B are in
the same PDB
(biological unit) ?
Discard partner
protein B
No
Yes
Identify surface and interface
region of protein A and B by
calculating solvent-accessible
surface area (SASA).
(Kleinjung, J. and Fraternali, F.,
2005 Nuleic Acids Research)
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From BIG to SMALLER data with atomic resolution
BIG data
•Large-scale genome
sequencing projects as:
the 1000 Genomes Project
International HapMap Project
the NHLBI Exome Sequencing
Project
CHARGE Consortium
Cancer Genome Project
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Implications at the molecular level
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• General nsSNPs (nsSNPsC)
• Germ-line disease nsSNPs (nsSNPsGD)
• Somatic cancer nsSNVs (nsSNVsSC)
Missense Variants
WT
Mut
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nsSNPsC nsSNPsGD nsSNVsSC
Enrichment measurement
Confirming previous work: Nat Biotechnol. 2012 Jan 15;30(2):159-64. doi: 10.1038/nbt.2106.
Three-dimensional reconstruction of protein networks provides insight into human genetic disease.
Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H.
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Polyphen-2 prediction
nsSNPsGD
nsSNPsC
Germ-line disease variants on structured regions
are predicted damaging
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enrichment close to PTM sites
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enrichment- secondary structure
cancer-interface
GD-cancer-core
‘flexible’ regions
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SCOP-Domains Functional annotation: GD
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SCOP-Domains Functional annotation SC
•RNA binding •DNA-binding •Kinases/phosphatases •Signal transduction •Other regulatory function •Receptor activity
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Goh, K.-I. et al., Natl. Acad. Sci. U.S.A. (2007).
The Human Disease Network
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Summary
• Both germ-line disease and cancer variants have tendency to occur at the interface region of proteins.
• Germ-line disease and cancer variants of the interface tend to be mostly located at flexible structural regions.
• A high number of disordered region variants locate close to PTM sites; for germ-line diseases and cancer the variants are close to ordered region PTM sites.
• The type of disease that a gene variant underpins may be intimately related to the function of the protein/domain implicated.
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Conclusions
We have developed a new generation of precise and user-friendly computational
tools to quantify PPIN topologies particularly useful for testing new protocols for the
removal of experimental biases from PPIN datasets
We have shown by a large-scale analysis of publicly available datasets that the
present protein network data are strongly biased by their experimental methods,
while still exhibiting species-specific similarity and reproducibility.
Introduced a new strategy to identify regulators of a signalling pathway in immune
cells
Devised a targeted screen using bioinformatics databases identified PI3K-p85α and
AKT1 as novel regulators of the oscillatory increase in CDC42 activity and prevent
polarisation at the immunological synapse.
Characterised dynamical properties of Hub proteins and observed higher
conformational flexibility for multi-partner residues in unbound proteins. Stronger
communication exists between multi-partner residues.
Analysed the propensity for the localization of human missense variants on protein
structures;
highlighted different trends in germ-line diseases vs somatic cancer mutations,
hypotheses on disease-protein-function relationships.
MACROSCOPIC-TOPOLOGICAL
MOLECULAR- SIGNALLING
ATOMISTIC- DYNAMICS
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Thanks to.....
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Luis Fernandez PhD 2011 Ton Coolen, Alessia Annibale IMMB KCL Tony Ng, Leo Carlin Cancer Studies, KCL Jens Kleinjung NIMR London