Network analysis of Network analysis of proteomesproteomes

Peter AndrasPeter AndrasSchool of Computing ScienceSchool of Computing Science

University of NewcastleUniversity of Newcastlepeter.andras@ncl.ac.ukpeter.andras@ncl.ac.uk

OverviewOverview IntroductionIntroductionThe dataThe dataNetwork analysisNetwork analysisProtein interaction networksProtein interaction networksAnalysis of protein interaction networksAnalysis of protein interaction networksComputational drug target discoveryComputational drug target discovery

MotivationMotivationSearch for new antibiotics, drugs for Search for new antibiotics, drugs for

genetic and prion diseasesgenetic and prion diseasesDestroying and restoring the functionality Destroying and restoring the functionality

of cellsof cellsHow to do this ?How to do this ?eXSys projecteXSys project

Cells – 1 Cells – 1

Cells – 2 Cells – 2

Analysing cellsAnalysing cellsAnalysing and understanding cells by Analysing and understanding cells by

analysing their protein interaction networkanalysing their protein interaction network Ideally: dynamic analysisIdeally: dynamic analysisSimplified version: static analysisSimplified version: static analysis

Proteomics dataProteomics dataYeast-two-hybrid dataYeast-two-hybrid dataGene co-expression based predicted dataGene co-expression based predicted dataOther experimental dataOther experimental data

Web databasesWeb databases DIP (Database of Interacting Proteins) – DIP (Database of Interacting Proteins) –

experimentally validated data, mostly for yeastexperimentally validated data, mostly for yeast STRING (Search Tool for the Retrieval of STRING (Search Tool for the Retrieval of

Interacting Genes/Proteins) – large amount of Interacting Genes/Proteins) – large amount of predicted data based on gene expression datapredicted data based on gene expression data

KEGG – metabolic cycle descriptionsKEGG – metabolic cycle descriptions EBI – Proteome – full proteomesEBI – Proteome – full proteomes Swiss – Prot – general protein informationSwiss – Prot – general protein information

Data collectionData collectioneXSys data management engineeXSys data management engineCollects and updates automatically data Collects and updates automatically data

from web databasesfrom web databasesExtracts information about protein Extracts information about protein

interactions and stores this in proprietary interactions and stores this in proprietary formatformat

Allows to get specific data about selected Allows to get specific data about selected proteins from web databasesproteins from web databases

NetworksNetworksGraphs: nodes and edgesGraphs: nodes and edges

Scale-free networksScale-free networks

Damaging scale-free networksDamaging scale-free networksRobustness to random damageRobustness to random damageHigh sensitivity to targeted damageHigh sensitivity to targeted damage

Important nodesImportant nodesHubs: high connectivity nodesHubs: high connectivity nodes

Bottlenecks: nodes connecting clustersBottlenecks: nodes connecting clusters

Other important nodesOther important nodesElementary cycle number of nodesElementary cycle number of nodesEffect of deletion on the characteristic Effect of deletion on the characteristic

polynomialpolynomial

Integrity measuresIntegrity measuresAverage minimum path length: how close Average minimum path length: how close

are in average the nodes of the graphare in average the nodes of the graph

Clustering coefficient: how densely Clustering coefficient: how densely clustered is the graphclustered is the graph

Number of isolated clustersNumber of isolated clusters

Other integrity measuresOther integrity measuresComparison of characteristic polynomials Comparison of characteristic polynomials

of the damaged and non-damaged of the damaged and non-damaged networksnetworks

Informational measuresInformational measures

Comparative integrity measuresComparative integrity measures Integrity measures calculated for well Integrity measures calculated for well

specified targeted damage or random specified targeted damage or random damagedamage

E.g., top 10% hub nodes deleted, average E.g., top 10% hub nodes deleted, average damage by 10% of randomly selected damage by 10% of randomly selected nodes deletednodes deleted

Network analysisNetwork analysisEvaluation and categorisation of nodesEvaluation and categorisation of nodes

Evaluation of damaging capacity of nodes Evaluation of damaging capacity of nodes and node combinationsand node combinations

Selection of nodes to achieve a desired Selection of nodes to achieve a desired level of damagelevel of damage

Protein interaction systemsProtein interaction systemsProtein interaction systems can be viewed Protein interaction systems can be viewed

as networksas networks

Static picture of the cell, ignores the Static picture of the cell, ignores the temporal activation of sub-networks of the temporal activation of sub-networks of the full protein interaction networkfull protein interaction network

Protein interaction networksProtein interaction networks

E. coli

P. aeruginosa

Analysis of protein interaction Analysis of protein interaction networks – 1 networks – 1

Protein interaction networks are scale-free Protein interaction networks are scale-free networks networks high sensitivity to targeted high sensitivity to targeted damage, low sensitivity to random damagedamage, low sensitivity to random damage

Earlier work shows that hub proteins are Earlier work shows that hub proteins are likely to be essential proteinslikely to be essential proteins

Analysis of protein interaction Analysis of protein interaction networks – 2networks – 2

Conjecture: graph theoretic network Conjecture: graph theoretic network integrity is related to functional integrity of integrity is related to functional integrity of the protein interaction systemthe protein interaction system

Objective: determine important nodes and Objective: determine important nodes and node combinations that can cause node combinations that can cause significant integrity damagesignificant integrity damage

Analysis of protein interaction Analysis of protein interaction networks – 3networks – 3

Lists of hubs, bottlenecks, elementary Lists of hubs, bottlenecks, elementary cycle nodes and other important nodescycle nodes and other important nodes

Calculation of comparative damage Calculation of comparative damage measuresmeasures

Analysis of protein interaction Analysis of protein interaction networks – 4networks – 4

Calculation of optimal combination of Calculation of optimal combination of nodes that have damage potential above a nodes that have damage potential above a pre-specified limitpre-specified limit

Cocktails of target proteins; blocking the Cocktails of target proteins; blocking the activity of target proteins causes activity of target proteins causes significant integrity damage to the protein significant integrity damage to the protein interaction networkinteraction network

Analysis of protein interaction Analysis of protein interaction networks – 5networks – 5

Checking potential targets for toxicityChecking potential targets for toxicity

BLAST comparison of targets with BLAST comparison of targets with important proteins of host organismimportant proteins of host organism

Selection of admissible targets and target Selection of admissible targets and target combinationscombinations

Protein network analysisProtein network analysiseXSys network analysis engineeXSys network analysis engine

Takes data files generated by the eXSys Takes data files generated by the eXSys data management enginedata management engine

Performs network analysis and generates Performs network analysis and generates suggested target protein cocktails of suggested target protein cocktails of admissible targetsadmissible targets

Analysis of B. subtilisAnalysis of B. subtilis

B. subtilis

Important nodes for B. subtilis – 1 Important nodes for B. subtilis – 1

Id Swiss-Prot Id

Protein Name Gene Name

Function

355 P35164

Sensor protein resE

RESE Member of the two-component regulatory system resd/rese involved in the global regulation of aerobic and anaerobic respiration. Probably phosphorylates resd.

378 P16497

Sporulation kinase A

KINA Phosphorylates the sporulation-regulatory proteins spo0a and spo0f. It also autophosphorylates in the presence of atp.

391 Q45614

Sensor protein yycG

YYCG Essential Member of the two-component regulatory system yycG/yycF involved in the regulation of the ftsAZ operon. Probably phosphorylates yycF.

392 O31661

YKRQ protein YKRQ

393 P39764

Sporulation kinase C

KINC Phosphorylates the sporulation-regulatory protein spo0a.

Hub nodes

Important nodes for B. subtilis – 2Important nodes for B. subtilis – 2

Id- Swiss-Prot Id

Protein Name Gene Name Significance Function

121 P05652 DNA gyrase subunit B

GYRB Essential DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.

122 Q45066 Topoisomerase IV subunit A

PARC/GRLA Essential Topoisomerase IV is essential for chromosome segregation. It has relaxation of supercoiled DNA activity. Performs the decatenation events required during the replication of a circular DNA molecule

123 P05653 DNA gyrase subunit A

GYRA Essential DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.

124 Q59192 Topoisomerase IV subunit B

PARE Essential Topoisomerase IV is essential for chromosome segregation. It has relaxation of supercoiled DNA activity. Performs the decatenation events required during the replication of a circular DNA molecule

453 O07622 Hypothetical protein yhw

YHFW

Bottleneck nodes

Important nodes for B. subtilis – 3Important nodes for B. subtilis – 3

Id Swiss-Prot Id

Protein Name Gene Name

Significance Function

52 P16336 Preprotein translocase secY subunit

SECY Essential Involved in protein export. Interacts with secA and secE to allow the translocation of proteins across the plasma membrane, by forming part of a channel.

34 P42920 50S ribosomal protein L3 RPLC Essential This protein binds directly to 23S ribosomal RNA and may participate in the formation of the peptidyltransferase center of the ribosome

35 P42921 50S ribosomal protein L4 RPLD Essential This protein binds directly and specifically to 23S rRN

36 P42924 50S ribosomal protein L23 RPLW Essential Binds to a specific region on the 23S rRNA

37 P42919 50S ribosomal protein L3 RPLC Essential This protein binds directly to 23S ribosomal RNA and may participate in the formation of the peptidyltransferase center of the ribosom

Other important nodes

Target list for B. subtilisTarget list for B. subtilis

Id Swiss-Prot Id

Protein Name Gene Name Significance

55 P05647 50S ribosomal protein L34 RPMH Essential

56 O06492 Glutamyl tRNA amidotransferase subunit C GATC Essential

374 Q45614 Sensor protein yycG YYCG Essential

410 P42924 Preprotein translocase secY subunit SECY Essential

776 P42060 50S ribosomal protein L22 RL22 Essential

Target nodes validated against human proteome

eXSys proteome analysis system – 1 eXSys proteome analysis system – 1

Components:Components:eXSys data management engineeXSys data management engineeXSys network analysis engineeXSys network analysis engineeXSys user interface and network eXSys user interface and network

visualisation toolvisualisation toolPerforms data collection, analysis of Performs data collection, analysis of

protein interaction networks, provides user protein interaction networks, provides user interface and network visualisation interface and network visualisation

eXSys proteome analysis system – 2 eXSys proteome analysis system – 2

Computational search for new Computational search for new antibiotic targetsantibiotic targets

Bacterial proteome + host proteomeBacterial proteome + host proteome

Analysis of bacterial proteome with BLAST Analysis of bacterial proteome with BLAST validation against the host proteomevalidation against the host proteome

List of potential antibiotic targets that can List of potential antibiotic targets that can cause significant damage to the bacteria cause significant damage to the bacteria while are likely to not damage the hostwhile are likely to not damage the host

New antibioticsNew antibioticsUsual antibiotics target a single protein or Usual antibiotics target a single protein or

a related class of proteins (e.g., penicillin a related class of proteins (e.g., penicillin targeting PBPs, ribosomal antibiotics targeting PBPs, ribosomal antibiotics targeting ribosomal subunits)targeting ribosomal subunits)

New antibiotics: multiple target proteins, New antibiotics: multiple target proteins, achieving effect by combined damageachieving effect by combined damage

Computational search for drug targets Computational search for drug targets for prion and genetic diseases – 1 for prion and genetic diseases – 1

Prions and mutated genes produce wrong Prions and mutated genes produce wrong protein interactions within the protein protein interactions within the protein interaction networkinteraction network

Restoring the functionality of the cells Restoring the functionality of the cells might be done by adding or changing might be done by adding or changing existing proteins such that the functional existing proteins such that the functional integrity of the protein interaction system is integrity of the protein interaction system is restoredrestored

Computational search for drug targets Computational search for drug targets for prion and genetic diseases – 2for prion and genetic diseases – 2

Analysing protein interaction systems of Analysing protein interaction systems of diseased cells can lead to the prediction of diseased cells can lead to the prediction of likely interventions that may lead to the likely interventions that may lead to the restoration of functional integrity of the restoration of functional integrity of the protein interaction systemprotein interaction system

Summary – 1 Summary – 1 Cells can be perceived as protein Cells can be perceived as protein

interaction systemsinteraction systemsProtein interaction systems can be Protein interaction systems can be

analysed as networksanalysed as networksProtein interaction networks are scale-free Protein interaction networks are scale-free

networks, which are resistant to random networks, which are resistant to random damage but highly sensitive to targeted damage but highly sensitive to targeted damagedamage

Summary – 2 Summary – 2 The eXSys protein interaction network The eXSys protein interaction network

analysis system can collect data about analysis system can collect data about proteomes and analyse them to detect proteomes and analyse them to detect potential new drug target proteinspotential new drug target proteins

Computational drug target discovery may Computational drug target discovery may lead to new antibiotics and new drugs to lead to new antibiotics and new drugs to restore the functionality of diseased cellsrestore the functionality of diseased cells

eXSys project teameXSys project teamProject leaders: Project leaders:

Peter Andras Peter Andras Malcolm P YoungMalcolm P Young

Project members:Project members:Olusola IdowuOlusola IdowuSteven LyndenSteven LyndenPanos PeriorellisPanos Periorellis