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Transcript
PROTEINS AS MATRICES Gevorg Grigoryan, PhD Background: Cells Nano-Machines Cells are tiny machines: sense environment, respond, make decisions move, search for food (example) synthesize chemicals make copies of themselves Cellular macromolecules: e.g. proteins workhorses of the cell responsible for many of these tasks Background: Proteins Primary structure: chains of amino acids 20 amino acids: aka “residues” different in side-chain polar/hydrophobic acidic/basic large/small Background: Protein Structure Amino-acid sequence defines the full molecular structure of the protein and ultimately its function: …AKWLMENI… folding function Background: Protein Structure Secondary structure: common -helices local structural motifs -sheets Background: Protein Structure Tertiary and Quaternary structure: Nowadays, much more data… Protein Data Bank (PDB): www.pdb.org – available to anyone for free as of Jan 25, 2011 at 4 PM there are 70,813 Structures Protein Structural Universe Protein Structural Universe Questions about the Universe of Protein Structure: What is the universe? Where are the building blocks? Are there functions specific to certain fragments? Can we design new structure/functions from building blocks? Need: convenient representation of structure efficient search and classification methods Representation: Distance Maps A good representation of structure is key: Search Search Method Mapping of Distances for the Characterization of Topology (MaDCaT) Search Method Mapping of Distances for the Characterization of Topology (MaDCaT) 1 2 3 1 1 2 3 2 3 Search Method Mapping of Distances for the Characterization of Topology (MaDCaT) Search Method: branch and bound Mapping of Distances for the Characterization of Topology (MaDCaT) Search Method: branch and bound Mapping of Distances for the Characterization of Topology (MaDCaT) Search Method: branch and bound Mapping of Distances for the Characterization of Topology (MaDCaT) Search Method: branch and bound Mapping of Distances for the Characterization of Topology (MaDCaT) Search Method: Result Mapping of Distances for the Characterization of Topology (MaDCaT) Conclusions/Future Distance maps are a feasible way of representing and classifying protein structure Searches for tertiary structural elements, with multiple fragments are possible Future questions: given any structure, decompose it into common blocks splice common fragments together to engineer new structure at some point efficiency is an issue, need better search approaches