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STRUCTURAL GENOMICS

What 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

What 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

Overview Structural Genomics

Target Selection

Complete organisms;thermophilic, mesophilic or halophiliceukaryotic or prokaryotic

HUMAN 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

Cloning, Expression and Purification

Develop technologies necessary for large-scale initiatives

develop high-throughput (HTP) cloning

develop high-throughput expression

develop high-throughput purification

NMR SpectroscopyProtein<20 kDa

N15 C13 Label NMR

Aggregated, Unfolded

Folded

Structure

Protein-ProteinInteractions

Co-Expression

Stable Domain

Insoluble

Protein-ProteinInteractions

Limited Proteolysis

Co-Expression

Soluble

Expression Purification

Crystal Trials

Protein (>20kDa)

CRYSTALLOGRAPHYSTRUCTURE DETERMINATION

STRUCTURAL 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, CanadaNESG - Northeast Structural Genomics Consortium, USANYSGRC - New York SGXRC - New York Structural Genomics Research Consortium, USAOPPF - Oxford Protein Production Facility, UKPSF - Protein Structure Factory, GermanyRIKEN - RIKEN Structural Genomics Initiative, JapanS2F - Structure 2 Function ProjectSECSG - SouthEast Collaboratory for Structural Genomics, USASGPP - Structural Genomics of Pathogenic Protozoa Consortium, USASPEX Db - (BSGI) - Montreal-Kingston Bacterial Structural Genomics Initiative, CanadaSPINE - Structural Proteomics in Europe, EUTB - Mycobacterium tuberculosis (TB) Structural Genomics Consortium, 70 labs from 12 countriesXMTB - 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 2010PSI-2 had a five-year budget of $325 million provided by NIGMS

PSI grant period LSC ALL-PSI

PSI-2 grant year 2005 390427

PSI-2 grant year 2006 620700

PSI-2 grant year 2007 682718

PSI-2 grant year 2008 796818

PSI-2 grant year 2009 822879

PSI-2 grant extension 217244

PSI-2 total depositions 3527 3786

PSI-3 grant year 2010 280283

PSI-3 total depositions 377381

PSI-1 + PSI-2 + PSI-3 4804 5583

Determinated Protein Structures

The Northeast Structural Genomics (NESG) consortium

Production stage NESG targets

cloned 23,695Expression tested 22,159Expressed (E > 0) 16,888Expressed-Soluble (S > 0) 12,453Expressed-Soluble (ES >= 9) 9,946Fermented 7,271Purified (>= 0.5 mg yield) 4,848HSQC spectra recorded 2,597"Good" HSQC spectra 1,353HTP crystal screening 2,522Crystal hit 1,295X-Ray structures 547

NMR structures 452Total structures 958

Human proteins Production stage NESGtargets

cloned 5,479

Expression tested5,046

Expressed (E > 0)3,986

Expressed-Soluble (S > 0) 2,599

Expressed-Soluble (ES >= 9) 2,051Fermented

1,097Purified (>= 0.5 mg yield) 813

HSQC spectra recorded 422"Good" HSQC spectra 235HTP crystal screening 320Crystal hit

130X-Ray structures

35NMR structures

66Total structures

93

The Midwest Center for Structural Genomics (MCSG)

The Center for Eukaryotic Structural Genomics-National Magnetic Resonance Facility-Madison

University of Wisconsin-Madison