[Colloquium] TTIC Talk: Yan Yuan Tseng, University of Chicago

[Julia MacGlashan]

*REMINDER*

When:             *Friday, May 28 @ 11:00am
*

Where:           * TTIC Conference Room #526*, 6045 S Kenwood Ave, 5th Floor


Who:              * **Yan Yuan Tseng*, University of Chicago, Department of
Ecology and Evolution


 Title:          *      **A geometric approach to protein structure,
function and evolution*******



 The function of a protein is often fulfilled via molecular interactions on
its surfaces, so identifying functionally important protein surfaces and
locating key residues are critical for understanding protein functions. I
use a geometric approach to extract site-specific spatial information from
coordinates of structures. To reduce the search space and expedite the
process of surface partitioning, probe radii are designed according to the
physicochemical textures of molecules. For each putative surface, I obtain
its geometric measurements such as residue composition (spatial pattern),
solvent-accessible area, and molecular volume. In a large-scale shape
analysis, I develop an exact algorithm, SplitPocket, and conduct accurate
computations to identify ~38,900 protein functional surfaces from ~19,000
crystal structures for the prediction of unbound binding sites and the
inference of molecular functions. However, inferring protein functions from
structures is a challenging task, as an increasing number of orphan protein
structures from structural genomics project are now solved without their
biochemical functions characterized. For proteins binding to similar ligands
and carrying out similar functions, their binding surfaces are under similar
physicochemical constraints, and hence the sets of allowed and forbidden
residue substitutions are similar. In this presentation, I present my
methods for predicting protein functions by incorporating evolutionary
information specific to an individual binding region and by rapidly matching
local surfaces. I also discuss these predictions, biological implications
and medically important applications such as human disease-associated SNPs
(Single-Nucleotide Polymorphisms). Finally, I show that the methods
demonstrate the power of geometric and evolutionary matching for studying
structural evolution on the basis of protein functional surfaces.

Host:              Jinbo Xu, j3xu at ttic.edu
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