M.S. Thesis Defense

Protein Structure Database for Structural Genomics Group

Jessica Lau December 13, 2004

• • • • • • • • Bioinformatics is Analysis of biological data: gene expression, DNA sequence, protein sequence. Data mining and management of biological information through database systems.

• • • At the Northeast Structural Genomics Consortium, database management systems play a large role in its daily operation Data collection and mining of experimental results Track target progress – status milestones Exchange information with rest of the world My thesis presents work in database management systems at the NESG.

Part 1: ZebaView Part 2: Worm Structure Gallery Part 3: Prototype of NESG Structure Gallery

• Zebaview is the official target list of the Northeast Structural Genomics Consortium • Display summary table of NESG targets.

– Status milestones – Protein properties: DNA and protein sequences, molecular weight, isoelectric point • New targets are curated and then uploaded to SPiNE. • 11,284 targets from 88 organisms.

Family View

NESG Families • Unfolded • Membrane • Core 50 • Nf-kB

Target Summary Statistics

Selected  Cloned  Expressed X-ray or NMR data collection   Soluble  In PDB Purified  90 35 80 30 70 25 60 50 20 Prokaryotic Eukaryotic Prokaryotic Eukaryotic • 4,418 targets cloned • 141 structures • 3.4% successful targets 40 15 30 10 20 5 10 0 0

GO, Cellular Localization, and SignalP

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Search for targets that have

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any of the three GO ontologies defined

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no GO ontologies defined at all

116 NESG structures do not have Molecular Function defined

LOCTarget

Bovine ribonuclease A has four disulfide bonds to stabalize its 3-D structure.

Mahesh Narayan, et al. (2000) Acc. Chem. Res., 33 (11), 805 -812. • Secretory proteins require formation of disulfide bonds • Oxidative Folding needed for proper native folding • 2,132 “Extracellular” NESG targets

SignalP

Lodish et al. Molecular Cell Biology 4 th 7.1 (2000) edition, Figure • mRNA are translated with signal peptide for cellular localization • Peptide is cleaved upon destination • SignalP predicts cleavage of signal peptide • Removal of signal peptide gives proper native fold

Part 2 – Worm Structure Gallery

Caenorhabditis elegans

– Widely studied model organism • 2-3 weeks life span, small size (1.5-mm-long), ease of laboratory cultivation, transparent body • Small genome, yet has complex organ systems similar to higher organisms: digestive, excretory, neuromuscular, reproductive systems Donald Riddle et al, C. elegans II (1997) Altun Z F and Hall DH. , Atlas of C. elegans Anatomy, Wormatlas (2002-2004)

System Components

• 22,653 C. elegans proteins • 42 experimentally determined • 4 are from NESG • 24 homology models • 14 are from NESG • 960 C. elegans proteins potentially modeled • Uniprot: Pfam domain, Gene name, ORF name • PDB Coordinates • Structure Validation Report • Sequence similarities to proteins in PDB

Protein Structure Validation Software

• Suite of quality validation software – PROCHECK • Quality of experimental data • Distribution of φ, ψ angles in Ramachandran plot – MolProbity Clashscore • Number of H atom clashes per 1,000 atoms • With respect to a set of scores from 129 high resolution X-ray crystal structures • < 500 residues, of resolution <= 1.80 Å, R-factor <= 0.25 and R-free <= 0.28; Bahattacharya, A et al. to be published

Homology Modeling Automatically (HOMA)

• Algorithm based on alignment between query and template sequences.

– Regions of conserved residues forms a set of constraints for modeling • Sequence identity of 40% or more • Good quality template

Bad alignment  Bad model

Poor quality template  Poor quality model

Quality scores of 3-D structures

-10

Quality Z-scores - Homology Models vs. Experimentally Determined Structures

-8 -6 -4 -2 -10 -15 -20 -25 -30 -35 -40 -45 5 0 -5 0 Homology Models Experimentally Determined Structures

Procheck (all) z-score

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Search

• Search for C. elegans proteins in local database.

• Keyword: “Ubiquitin” in any field Results: 72 C. elegans proteins 2 Experimentally determined structures 1 Homology model 11 Potential models

System Architecture

• Java, Tomcat, MySQL, Perl.

Three-tier architecture • Client: Web browser • Application: JSP, Logic components, Data access components • Data: MySQL

Part 3 – NESG Structure Gallery

• Structure files submitted by automated pipeline • ADIT integrated with SPiNE for uniform format • PSVS and images automatically generated • Structure information from PSVS directly into SPiNE • Archives structure files.

• Structure files submitted by individual groups • Structure information is entered into SPiNE manually • Manually run PSVS and MolScript

• Downloads – Structure Validation Report – Structure related files • Atomic coordinates • NMR constraints • NMR peak lists • Chemical shifts • Structure factor • Annotation – Functional annotation provided by other NESG members – Uniprot – PDB coordinates file • Reusing Java components from Worm Structure Gallery

– Enhance ZebaView performance to handle increased load and functionalities – Integrate annotation from other protein and structure databases. – Make modules available for other java-based applications within structural genomics.

– Develop a gallery for other organisms: yeast, fruit fly, human – Continue specifications for the new NESG Structure Gallery

Advisor: Dr. Gaetano Montelione Thanks to everyone at the Protein NMR lab and NESG!

Aneerban Bhattacharya John Everett All the scientists who solved the structures!