Accelerated Technologies Center for Gene to 3D Structure

1
Accelerated Technologies Center for Gene to 3D
Structure
ATCG3D is a PSI-2 Specialized Center Funded by
the NIGMS and NCRR, Grant U54-GM074961

• ATCG3D Mission Accelerate the development,
  integration, and deployment of three emerging
  technologies which have high potential to improve
  the economics of protein structure determination
  by X-ray crystallographic methods.

• Tunable laboratory Synchrotron X-ray source
• Nanovolume microfluidic crystallization labcard
• Computer-aided construct engineering and
  synthetic gene design

PI, Lance Stewart
Co-PIs, Peter Kuhn Raymond Stevens

Collaborating PI, Rustem Ismagilov
Collaborating PI, Ron Ruth
Slide prepared by Lance Stewart
2
Improving the Economics of the Gene-to-Structure
Transformation Process
PDB Deposition
Transformation Process(components)
Biological Interest

• Goal to develop new technologies and integrate
  them with off the shelf technologies to arrive at
  user friendly, high impact tools that make the
  gene-to-structure transformation process more
  economical
• Dissemination of technologies through commercial
  partners

Slide prepared by Lance Stewart
3
Downloadable Gene Composer Software

• deCODE has made Gene Composer Software available
  via free clickthrough license download.
• Feedback will help drive feature development in
  Gene Composer.
• Gene Composer is also commercially available
  through Emerald BioSystems.
• Growing user base for Gene Composer Software
  since Jan. 2006.
• On-line synthetic gene design workshops.

www.GeneComposer.net
Slide prepared by Lance Stewart
4
Simple 4-Microsyringe Pump System and
Microplugger Control Software and Labcard
Prototype
Emerald BioSystems is offering commercial systems
as of July 2007
pH Gradient Test, 10nl Plugs
Microplugger Control Software
In Situ X-ray Diffraction of Protein Crystals in
Labcards
Micro-Syringe Pump System
Labcard Prototype
Slide prepared by Lance Stewart
5
Hybrid Method Combining Sparse Matrix and
Gradient Screening

L. Li, D. Mustafi, Q. Fu, V. Tereshko, D.L. Chen,
J.D. Tice, R.F. Ismagilov PNAS, 2006, 103, 19243.
Slide prepared by Rustem Ismagilov
6
Counterdiffusion Confined Geometry Microfluidic
Crystallization

• Topas COC plastic microfluidic crystallization
  Greiner Bio-One labcard
• Individual Lysozyme Crystals grown in
  microcapillary channels by counterdiffision
  methods
• In situ X-ray diffraction on individual crystals
  reveals different diffraction quality

Prototype
Greiner Bio-One Commercialization of Confined
Geometry Counterdiffusion Labcard
Prototype
Slide prepared by Lance Stewart from data of Joe
Ng and Peter Kuhn
7
DETECT-X Imaging of Protein Crystals in
Microfluidic Devices

• DETECT-X Imager used in conjunction with Millipol
  software
• High signal to noise imaging of crystals
• Crystal orientation imaging
• Potential to Enable Efficient Complete in situ
  X-ray diffraction Data Set Collection

Emerald BioSystems, Commercial Launch of
DETECT-X, Q2 2007
W. Kaminski, Millipol Software Norgren Systems
LLC Hardware Engineering
Slide prepared by Lance Stewart with data from
Peter Nollert
8
A Conceptual Picture of the Compact Light Source
Slide prepared by Lance Stewart
9
The Compact Light Source Prototype and X-ray
Optics
ATCG3D Overview August 2007, www.atcg3d.org
Compact Light Source
X-ray Optics
Slide prepared by Lance Stewart, data provided by
Ron Ruth
10
C-ME for Efficient Structure Annotation

• Efficient, interactive, database driven structure
  annotation software
• Wikipedia-like continuous community based
  annotation
• Knowledge saved, grown, useful, and built over
  time

Slide prepared by Lance Stewart, data provided by
Peter Kuhn
11
Technologies for Improving the Economics of the
Gene-to-Structure
Structure Grade Protein
Diffraction Quality Crystals
X-ray Structure Solved
Target Gene Cloned
Biological Interest
Codon Re-Engineering By Gene Synthesis
www.GeneComposer.net
Crystal Orientation Imaging with DETECT-X
Micro-Pump System and Plastic Crystallization
Labcards for in situ X-ray Diffraction
Tunable Laboratory X-Rays
Annotation with C-ME
Slide prepared by Lance Stewart