Protein Structure Database for Structural Genomics Group
description
Transcript of Protein Structure Database for Structural Genomics Group
Protein Structure Database for Structural Genomics
GroupJessica Lau
December 13, 2004
M.S. Thesis Defense
• 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
In PDB / Cloned Prokaryotic vs. Eukaryotic
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Target Summary Statistics
Success of soluble targe ts: Prokaryotic vs. Eukaryotic
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Selected Cloned Expressed Soluble Purified X-ray or NMR data collection In PDB
• 4,418 targets cloned• 141 structures• 3.4% successful targets
GO, Cellular Localization, and SignalP
• Search for targets that have • any of the three GO ontologies defined• no GO ontologies defined at all
116 NESG structures do not have Molecular Function defined
LOCTarget
• Secretory proteins require formation of disulfide bonds• Oxidative Folding needed for proper native folding
• 2,132 “Extracellular” NESG targets
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.
SignalP
• 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
Lodish et al. Molecular Cell Biology 4th edition, Figure 7.1 (2000)
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
• 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
Homology Modeling Automatically (HOMA)
Bad alignment Bad model
Poor quality template Poor quality model
Quality scores of 3-D structuresQuality Z-scores - Homology Models vs. Experimentally Determined
Structures
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Homology ModelsExperimentally Determined Structures
Search
• Search for C. elegans proteins in local database.
• Keyword: “Ubiquitin” in any field
Results:72 C. elegans proteins2 Experimentally determined structures1 Homology model11 Potential models
Results:152 C. elegans proteins2 Experimentally determined structures1 Homology model19 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 individual groups• Structure information is entered into SPiNE manually• Manually run PSVS and MolScript
• 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.
• 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 theProtein NMR lab and NESG!
Aneerban BhattacharyaJohn Everett
All the scientists who solved the structures!