STRUCTURAL GENOMICS OF EUKARYOTIC MODEL ORGANISMS

Project Details

Description

DESCRIPTION (Taken from the Application): The development of a Northeast
Structural Genomics Consortium for evaluating the feasibility, costs, economies
of scale, and value of structural genomics is proposed. The primary goal of the
pilot project is to develop integrated technologies for high-throughput (HTP)
protein production and 3D structure determination. These would form key
components of the scientific infrastructure required for the next stage of the
genome project. The principal components of the project include the design,
development, and testing of: i) bioinformatics methods for clustering and
prioritizing candidate proteins for biophysical analysis; ii) biotechnologies
and robotic methods for htp expression plasmid construction, expression
screening, and protein production; iii) htp methods for analysis of
"foldedness" of expressed proteins by biophysical techniques including NMR and
circular dichroism spectroscopies; iv) cost efficient production of 13C, 15N,
2H, and/or SeMet enriched protein samples suitable for NMR or crystallographic
analysis; v) experimental and theoretical methods for parsing large multidomain
proteins into domain encoding segments; vi) robotic methods for htp protein
crystallization screening, solubility screening, and crystal manipulation, vii)
new NMR pulse sequences providing rapid collection of data suitable for
high-resolution 3D structure determination; viii) automated computational
methods for determining 3D protein structures from raw diffraction and/or NMR
data; ix) methods for analyzing 3D protein structures in order to develop
testable hypotheses regarding biochemical functions; x) development of
integrated project databases to keep track of the reagents and information
generated in a large-scale structural genomics effort; and xi) organized
dissemination of the resulting expression plasmids, protein reagents, software,
resonance assignments, functional annotations, and 3D structures. A unique
feature of this project will be the combination of strong efforts in both X-ray
crystallography and solution-state NMR spectroscopy, allowing a rigorous and
parallel evaluation of the complementary values of these methods for
genomic-scale structure analysis. The primary genome targets for this
methodology development will be eukaryotic model organisms which are subjects
of extensive functional genomics research, including S. cerevisiae, C. elegans,
D. melanogaster, and homologous human proteins. It is likely that genes that
are conserved across this set of genomes are biologically and/or biomedically
important. It will also be valuable to correlate the structural and biochemical
function analysis of these proteins with the extensive biological data emerging
from large-scale functional genomics efforts. Within these genomes, the pilot
project will focus on proposed open reading frames (ORFs) encoding
phylogenetically conserved polypeptide chains of less than 340 amino acids with
no predicted 3D structures.
StatusFinished
Effective start/end date9/30/008/31/06

Funding

  • National Institute of General Medical Sciences: $4,290,231.00

ASJC

  • Biochemistry

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