MarkUsA Function Annotation Server for Protein Structures

Markus Fischer, Donald Petrey, and Barry Honig

Columbia UniversityCenter for Computational Biology and Bioinformatics

NorthEast Structural Genomics Consortium

The importance of exploiting structure-function relationships

5

304

115

146

1

PSI-BLASTPfamStructure

571

Sequence analysis and

structure analysis

List of neighborsList of target properties

AYWLMKSEPDEFSISDLQ LYWL-KSEPDLFSIT-LVIYFLFKT--DTFSIDTLK

1.

2.

3.

Prediction of function

keywords

Static annotation

pages

Not designed for hypothesis-driven queries

How to identify false positives?

Sequence Analysis

Query: 1 AYWLMKSEPDEFSISDLQ AYWL K+EPD FSI L+Sbjct: 2 AYWLFKTEPDTFSIDTLK

Sequence neighbors

Protein families and motifs

InterPro

Structure Analysis

Structural neighbors

Skan

Electrostatic surface potentials

DelPhi

Residue conservation

ConSurf

Solvent accessible cavities

Screen

Interactive Annotation Map Gene Ontology

UniProt

Ligand contacts

ChEBI Ontology

Integrate Structure

Two example applications for the MarkUs server

1. Testing a hypothesis on protein function

Does NESG target 2eve interact with tRNA?

2. Identification of a binding site

Where does sugar bind to VP8?

General introduction to the MarkUs interface

Display cavities

High Low

Map residue conservation

Negative Positive

Map electrostatic potentials

NESG target PsR62 (PDB 2eve)

ASCH family

PUA domains

YTH domains

connected to RNAmetabolism

known to interactwith tRNA

potential mRNA binding domains

Structural neighbors

Hypothesis: 2eve binds RNA

How to identify RNA binding structural neighbors

How to define a subset of structural neighbors

Identify a structural neighbor of interest

Superimpose a structural neighbor

NESG target2eve

PUA domain1j2b

Residue conservation Electrostatic potentials

High Low Negative Positive

Testing the hypothesis

VP8* carbohydrate-recognizing domain From porcine CRW-8 rotavirus

How to identify a postulated sugar binding site?

Identify sugar binding structural neighbors

Identify sugar binding structural neighbors

Identify sugar binding structural neighbors

Identify sugar binding structural neighbors

Identify sugar binding structural neighbors

Define subset of sugar binding structural neighbors

Define a subset of structural neighbors

Identify sugar binding sites

postulated 2nd binding site

NESG software and databases

SkylineHigh throughput modeling

PudgeRefined models

MarkUshttp://luna.bioc.columbia.edu/honiglab/mark-us/

SkybaseModels database

(NESG, PDB)

MarkUsRepository

(NESG, PDB)

NESG software and databases

SkylineHigh throughput modeling

PudgeRefined models

MarkUshttp://luna.bioc.columbia.edu/honiglab/mark-us/

SkybaseModels database

(NESG, PDB)

MarkUsRepository

(NESG, PDB)

geWorkbench -> genomic data

Conclusions

• System for hypothesis-driven protein function annotation by comparison of local functional features

• Interactive system guided by biological knowledge

• Fast access to function annotations for protein structures

Acknowledgements

National Institutes of Health

Thanks to the

HonigLab

and

for financial support

(grant U54-GM074958)