What is Structural Genomics Is the process of high throughtput determination of 3D structures of Biological macromolecules What is the Goal of Structural Genomics Provision of enough structural templates to facilitate homology modeling of most proteins ID: 926682
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Slide1
Çağdaş DAĞ
STRUCTURAL GENOMICS
Slide2What is Structural Genomics ?Is the process of high-throughtput determination of 3-D structures of Biological macromolecules
What is the Goal of Structural Genomics ?
Provision of enough structural templates to facilitate homology modeling of most proteins.
Structural elucidation of complete biological pathway
To determine new protein folds
To determine the functions of unknown proteins
to develop improved methods that will result in
high-throughput biology and protein structure determination
Slide3What can we learn from structure ?The structure will reveal the fold of the protein
The structure will reveal the active site
The structure may reveal evolutionary links
between proteins lacking sequence similarity
The structure may reveal the function of the protein
Slide4Overview Structural Genomics
Slide5Target SelectionComplete organisms;thermophilic, mesophilic
or halophiliceukaryotic or prokaryoticHUMAN DISEASETargets in this area of structural genomics are G-protein coupled receptors, ion channels and kinases etc.
The development of techniques to allow over-expression, purification and crystallization of these targets is required and in progress
Slide6Cloning, Expression and PurificationDevelop technologies necessary for large-scale initiatives develop high-throughput (HTP) cloning
develop high-throughput expressiondevelop high-throughput purification
Slide7Slide8NMR SpectroscopyProtein<20
kDaN15 C13
Label
NMR
Aggregated, Unfolded
Folded
Structure
Protein-Protein
Interactions
Co-Expression
Stable Domain
Insoluble
Protein-Protein
Interactions
Limited
Proteolysis
Co-Expression
Soluble
Expression
Purification
Crystal Trials
Protein (>20kDa)
CRYSTALLOGRAPHY
STRUCTURE DETERMINATION
Slide9STRUCTURAL GENOMIC CENTERS
BIGS - Bacterial Targets at IGS-CNRS, FranceBSGC - Berkeley Structural Genomics Center, USACESG - Center for Eukaryotic Structural Genomics, USAISPC - Israel Structural Proteomics Center, IsrealJCSG - Joint Center for Structural Genomics, USAMCSG - The Midwest Center for Structural Genomics, USA, UK, Canada
NESG - Northeast Structural Genomics Consortium, USANYSGRC - New York SGXRC - New York Structural Genomics Research Consortium, USA
OPPF - Oxford Protein Production Facility, UK
PSF - Protein Structure Factory, Germany
RIKEN - RIKEN Structural Genomics Initiative, Japan
S2F - Structure 2 Function Project
SECSG - SouthEast Collaboratory for Structural Genomics, USA
SGPP - Structural Genomics of Pathogenic Protozoa Consortium, USA
SPEX Db - (BSGI) - Montreal-Kingston Bacterial Structural Genomics Initiative, Canada
SPINE - Structural Proteomics in Europe, EU
TB - Mycobacterium tuberculosis (TB) Structural Genomics Consortium, 70 labs from 12 countries
XMTB - Mycobacterium Tuberculosis Structural Proteomics Project, Germany
The first phase of the Protein Structure Initiative (PSI-1) lasted from June 2000 until September 2005, and had a budget
of $270 million
funded primarily by NIGMS
The second phase of the Protein Structure Initiative (PSI-2) lasted from July 2005 to June 2010
PSI-2 had a five-year budget of
$325 million
provided by NIGMS
Slide10PSI grant period LSC ALL-PSI PSI-2 grant year 2005 390 427 PSI-2 grant year 2006 620 700 PSI-2 grant year 2007 682 718 PSI-2 grant year 2008 796 818 PSI-2 grant year 2009 822 879 PSI-2 grant extension 217 244 PSI-2 total depositions 3527 3786 PSI-3 grant year 2010 280 283 PSI-3 total depositions 377 381 PSI-1 + PSI-2 + PSI-3 4804 5583
Determinated Protein Structures
Slide11The Northeast Structural Genomics (NESG) consortiumProduction stage NESG targets cloned 23,695 Expression tested 22,159 Expressed (E > 0) 16,888 Expressed-Soluble (S > 0) 12,453Expressed-Soluble (ES >= 9) 9,946 Fermented 7,271 Purified (>= 0.5 mg yield) 4,848 HSQC spectra recorded 2,597 "Good" HSQC spectra 1,353 HTP crystal screening 2,522 Crystal hit 1,295 X-Ray structures 547 NMR structures 452
Total structures 958 Human proteins Production stage NESGtargets cloned 5,479Expression tested 5,046Expressed (E > 0) 3,986Expressed-Soluble (S > 0) 2,599 Expressed-Soluble (ES >= 9) 2,051
Fermented 1,097 Purified (>= 0.5 mg yield) 813 HSQC spectra recorded 422
"Good" HSQC spectra 235HTP crystal screening 320Crystal hit 130
X-Ray structures 35
NMR structures 66
Total structures 93
Slide12The Midwest
Center for Structural Genomics (MCSG)
Slide13The Center for Eukaryotic Structural
Genomics-National Magnetic Resonance Facility-Madison
University of Wisconsin-Madison