Macromolecular complexes – A new Online Portal (under construction!)

Birgit Meldal

(IntAct)

Overview• Aims & Definitions

• Data Sources

• Issues and Challenges:

• Nomenclature

• Sets

• ‘Transient’ complexes

• GO

• Confidence scores

• Inference

• Visualisation

• Search Parameters and Filters

• Status quo

Project Aim

• To design a Online Portal to search and visualise protein complexes

• Including cross-referencing to source databases and beyond

• Export to interested parties in a format of their choice

• Incorporate the data into network analysis tools

• To curate a ‘starter set’ of protein complexes for 4 major model organisms, chosen to span the taxonomic range –

• Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli

• Which will be expanded to a second set of organisms –

• Mus musculus, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces pombe

• IntAct provides the data structure

Long-term Strategy

• Create stable complex identifiers

• Joined curation effort

benefit to all collaborating databases:

• Resource sharing

• Elimination of redundancies

benefit to user:

• One central resource that links to all source databases

Definition: stable protein complexes

A stable set (2 or more) of interacting protein molecules which

• can be co-purified and

• have been shown to exist as a functional unit in vivo.

Non-protein molecules (e.g. small molecules, nucleic acids) may also be present in the complex.

What is not a stable complex?

• Enzyme/substrate or any similar transient interaction• Two proteins associated in a pulldown /

coimmunoprecipitation with no functional link

Source Databases

• Reactome – human (EBI), Gramene – arabidopsis , Microme – bacteria (EBI)

• PDBe (EBI) – mainly human

• ChEMBL (EBI)

• MatrixDB (Sylvie Richard-Blum)

• Mining UniProt – yeast (Bernd Roechert, SIB – manually)

• Unmaintained web resources – CYGD (yeast), CORUM (human), E. coli website, 3D Complexes (Sarah Teichmann, EBI)

• Manual curation from IMEx DBs & the literature (Sandra & Birgit)

Issues -

• Currently, complexes are shoe-horned into an interaction which is part of a dummy publication and dummy experiment

• New, complex-specific functionality, parameters and tools are needed

Issues - Nomenclature

• Most complexes have no ‘common’ name, or the ‘common’ name is defined differently depending on authors or host organism.

• One name can describe multiple complexes (e.g. AP1 describes ~25 different homo/heterodimers)

• Reactome makes a string of all components by gene name but this can become too long for our short-label.

• We will need both ‘recommended’ and ’systematic’ name.

• List of synonyms already available as free-text.

• Collaboration with GO, Reactome, HGNC

Issues – open/fuzzy sets

• Complexes where the identity of one or more participants is unknown, i.e. participant(s) are only identified to a set of (related) proteins

• Stoichiometry: often not known or ‘average’ (e.g. ion channel pore proteins)

• Only sub-set of a given complex curated because functional assays often focus on interactions between catalytic subunits

Issues – indirect activation & transient complexes

• Complexes that are activated without direct ligand interaction− e.g. through change of pH

− transient interactions

• Kim van Roey, Heidelberg: coorperative interactions

Different complex? Same participants!

GO:0043234 – protein complex (> 400)

Issues - Gene Ontology

• Currently, complexes mostly children of GO:0043234 protein complex (> 400) – lacking hierarchal structure

• Collaboration with GO to provide structured annotation

• New terms should capture all potential complexes from all species for which a parental term is appropriate

• E.g. DNA Polymerase complex

• Needs to allow for (open) sets of proteins / protein families

Issues - Confidence

• We need to define confidence scores:

• Do we know all participants of the complex?

• Do we have (open) sets of participants?

• How do we indicate the depth of data available, i.e. compare Reactome import vs. manual curation?

• e.g. using Evidence Code Ontology (ECO)

• only qualitative description

• Need a quantitative identifier

Issues – Inference data

• Do we use inference/modelling data (e.g. Compara)?

• Where is the cut-off for ‘model organisms’?

• e.g. function remains but participants change

Issues – Visualisation

• Flexible display of 2D and 3D options to capture complexity

• The majority of complexes has 5 participants, average size 2.3

• For large complexes it needs to be dynamic:

• use zoom-in/-out functionality on demand,

• display only main participants or subcomplexes by default and expand on demand,

• This might be achieved by assigning confidence scores to different levels of the complex by which it collapses/expands…

• Most biological network packages, e.g. Cytoscape, not up to it

• BioLayout 3D, ONDEX

• For crystal structures link to PDB (e.g. BioJS widget)

Bubble diagram

Protein A

Protein B

Protein C

Protein C

Weak evidenceof Ix

Strong evidenceof Ix

Hyperlink to IMEx Ix AC

Hyperlink to binding site (IMEx/InterPro)

Small Molecule

Protein D

?

Unknown which participant is direct interactor

Gene name in bubble with hyperlink to UniProtKB

Search for all Ix or Cx containing one or more

of these participants

Ix = Interaction, Cx = Complex

Ix

Ix Ix

Ix

Ix

Ix

*

*

* Need to query hyperlinks from whole database on the fly rather than having a static link to just one Ix

*

Issues – Search Parameters

Simple Search:

• UniprotKB ID / protein name

• Gene ID / name

• Small molecule ID / name

• InterPro Domain

• GO term

• PMID

• Complex ID / name

• Drug

Advanced Search Filters:• Stoichiometry

• Binding sites

• Biological role

• Source DB

• Host organism

• Interactor type (protein, small mol., NA)

• ECO

• Process/Pathway

• Stable vs. transient

• Confidence score

• Orthology

• Disease

• No. of participants

- Already searchable- New search parameters- Most important new search parameter!

Status quo?

• > 550 complexes already curated (Sandra, Bernd, Birgit), many imported (e.g. MatrixDB from Sylvie)

• Exporter for Reactome working (David Croft)

• PDB export under construction (Jose Dana)

• ChEMBL xref list available (Yvonne Light)

• Not all necessary features incorporated into Editor breaks release!

• e.g. complexes can’t be participants

• JAMI under construction (Marine!)

• It’s a complex project which needs collaboration!!!

Acknowledgements

Proteomics Services

• Henning Hermjakob

IntAct

• Sandra Orchard

• Marine Dumousseau

• Noemi del Toro Ayllón

• Rafael Jimenez

• Pablo Porras

• Margaret Duesbury

SIB

• Bernd Roechert

MatrixDB

• Sylvie-Ricard-Blum

Reactome

• Steve Jupe

• David Croft

ChEMBL

• Anna Gaulton

• Yvonne Light

PDBe

• Sameer Velankar

• Jose Dana

GO

• Jane Lomax

• Rachel Huntley

• Heiko Dietze