modelling, comparison, and analysis of proteomes ram samudrala university of washington
TRANSCRIPT
Modelling, comparison, and analysis of proteomesRam Samudrala
University of Washington
What is a “proteome”?
All proteins of a particular system(organelle, cell, organism)
What does it mean to “model a proteome”?
For any protein, we wish to:
- figure out what it looks like (structure or form)
- understand what it does (function)
Repeat for all proteins in a system
Understand the relationships between all of them
ANNOTATION{EXPRESSION
+INTERACTION
}
Pragmatic reasons:
- rational drug design and treatment of disease- protein and genetic engineering- build networks to model cellular pathways- study organismal function and evolution
?
Why should we model proteomes?
Intellectual challenge:Because it’s there!
Computational aspects of functional genomics
structure based methodsmicroenvironment analysis
zinc binding site?
structure comparison
homology function?
sequence based methods
sequence comparisonmotif searches
phylogenetic profilesdomain fusion analyses
+
experimental datasingle molecule + genomic/proteomic
+
*
**
*Bioverse
*
*
assign function toentire protein space
Bioverse – explore relationships among molecules and systems
Jason McDermott
http://bioverse.compbio.washington.edu
Bioverse – explore relationships among molecules and systems
Jason Mcdermott
Bioverse – prediction of protein interaction networks
Jason Mcdermott
Interacting protein database
protein α
protein β
experimentallydeterminedinteraction
Target proteome
protein A85%
predictedinteraction
protein B90%
Assign confidence based on similarity and strength of interaction
Bioverse – M. tuberculosis predicted protein interaction network
Jason McDermott
Bioverse – E. coli predicted protein interaction network
Jason McDermott
Bioverse – V. cholerae predicted protein interaction network
Jason McDermott
Bioverse – C. elegans predicted protein interaction network
Jason McDermott
Bioverse – H. sapiens predicted protein interaction network
Jason McDermott
Bioverse – organisation of the interaction networks
Jason McDermottCi = 2n/ki(ki-1)
Bioverse – viewer
Aaron Chang
Take home message
Prediction of protein structure and function can be used to model whole genomes to understand
organismal function and evolution
Acknowledgements
Aaron ChangAshley LamEkachai JenwitheesukGong ChengJason McDermottKai WangLing-Hong Hung
Lynne TownsendMarissa LaMadridMike InouyeStewart MoughonShing-Chung NganYi-Ling ChengZach Frazier