Biotech 2012 spring-6_protein_interactions_0
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Transcript of Biotech 2012 spring-6_protein_interactions_0
Protein-protein Interactions
Outline Introduction The Study of Protein-protein
Interaction by Mass Spectrometry Yeast-Two-Hybrid Phage Display Protein-protein Interaction on the
Web Information Extraction (IE)
Introduction The Study of Protein-protein
Interaction by Mass Spectrometry Yeast-Two-Hybrid Phage Display Protein-protein Interaction on the
Web Information Extraction (IE)
Introduction
Nature, 2000, 405:837-846.
Introduction Intrinsic to every cellular process Form the basis of phenomena -DNA replication and transcription -metabolism -signal transduction -cell cycle control
Introduction The Study of Protein-protein
Interaction by Mass Spectrometry
Yeast-Two-Hybrid Phage Display Protein-Protein Interaction on the
Web Information Extraction (IE)
The Study of Protein-protein Interaction by Mass Spectrometry
A key question about a protein,in addition to when and where it is expressed, is with which other proteins does it interact. Interaction partners are an immediate lead into biological function and can potentially be exploited for therapeutic purposes. Creation of a protein–protein interaction map of the cell would be of immense value to understanding the biology of the cell. Purification of protein complex
bait
The study of Protein-protein Interaction by Mass Spectrometry
Nature Biotechnology, 1999, 17, 676-682.
The Study of Protein-protein Interaction by Mass Spectrometry
Nature Biotechnology, 1999, 17, 676-682.
Generic Strategy to Analyze the Spatial Organization of Multi-protein Complexes by Cross-linking and Mass Spectrometry (1/2)
Anal. Chem., 2000,72, 267-275.
Generic Strategy to Analyze the Spatial Organization of Multi-Protein Complexes by Cross-Linking and Mass Spectrometry (2/2)
Anal. Chem., 2000,72, 267-275.
Introduction The Study of Protein-protein
Interaction by Mass Spectrometry Yeast-Two-Hybrid Phage Display Protein-Protein Interaction on the
Web Information Extraction (IE)
Yeast Two-hybrid
Researchers insert a gene in yeast for a "bait" protein alongside DNA for half of an "activator" protein. The other half of the activator DNA is then inserted alongside DNA for random "prey" proteins. The yeast cells are then grown up and the proteins are allowed to interact. If bait and prey proteins bind, the two halves of the activator protein be close enough to work together to turn on another yeast gene that turns the cell blue, signaling a match.ILLUSTRATION: C. SLAYDEN
Yeast Two-Hybrid System Useful in the study of various interactions The technology was originally developed
during the late 1980's in the laboratory Dr. Stanley Fields (see Fields and Song, 1989, Nature).
Yeast Two-Hybrid Assay
Hybrid proteins
DNA-binding domain
Bait domain Activation domainFish domain
Hybrid 1 Hybrid 2
Transcriptional Activation by Hybrid Protein in Yeast
UAS HIS geneTransfect yeast cells with genes encoding hybrid 1 and hybrid 2
Transcription-initiation complex
//
HIS mRNA
Fishing for Proteins that Interaction with Ras
ras gene
TRP
cDNA from library
LEU
Bait plasmid Fish plasmid
Transfect into trp, leu, his mutant yeast cells
Select for cells that grow in absence of tryptophan and leucine
Plate selected cells on medium lacking histidine
Fishing for Proteins that Interaction with Ras
HIS
Ras hybridBait
Fish
Ras-interacting hybrid
Fishing for Proteins that Interaction with Ras
Colony Formation
Fishing for Proteins that Interaction with Ras
Ras hybridBait
Fish
Noninteracting hybrid
HIS
Fishing for Proteins that Interaction with Ras
No Colony Formation
Introduction The Study of Protein-protein
Interaction by Mass Spectrometry Yeast-Two-Hybrid Phage Display Protein-Protein Interaction on the
Web Information Extraction (IE)
Phage Display A method where bacteriophage
particles are made to express either a peptide or protein of interest fused to a capsid or coat protein.
It can be used for peptide epitopes, peptide ligands, enzyme substrates or single-chain antibody fragments.
Phage DisplayBacterially expressed GST-fusion proteins or domains
Immobilize individually into wells
Wash unbound phage particles
Amplify phage particles
Sequence the cDNA insert
Introduction The Study of Protein-protein
Interaction by Mass Spectrometry Yeast-Two-Hybrid Phage Display Protein-Protein Interaction on
the Web Information Extraction (IE)
Protein-protein Interaction on the Web DIP Suiseki Useful database
http://dip.doe-mbi.ucla.edu
DIP NEWSJanuary 24th, 2002 Another release of the complete dataset.
It contains more than 11,000 individual protein-protein interactions described in 1,800 research papers. Please, note that this is, most probably, the last dataset released in the old format as we anticipate the next one (to be released witin ~3-4 months; we'll try to prepare at least 3 updates a year) will be XML formatted.
Database of Interacting Proteins
Suiseki(1/3)
•DNA replication •The Immune system •The E2F transcription factor •The talin/viniculin/actin system
is a system for the extraction of protein-protein interactions from large collections of scientific text
http://www.pdg.cnb.uam.es/suiseki/
Suiseki (2/3)
Suiseki (3/3)
Regulate Activate
Introduction The Study of Protein-protein
Interaction by Mass Spectrometry Yeast-Two-Hybrid Phage Display Protein-protein Interaction on the
Web Information Extraction (IE)
Information Extraction (IE) A vast amount of data on protein-
protein interactions residues in the published literature, which never been entered into databases.
IE have been applied to gaining information on protein-protein interactions.
Mining Literature for Protein-protein Interactions
Mining Literature for Protein-protein Interactions
Mining Literature for Protein-protein Interactions
Detection of Protein Names Protein Names are not
standardized and are often used in different forms in free text style.
Creation of the Protein Name List
Comp Funct Genom 2001, 2, 196-206
Extraction of the interactions The nouns and verbs are taken
from a hand constructed list containing nouns such as activation, phosphorylation or interaction, and verbs such as activates, binds or phosphorylates. Rules are applied directly to the text by string comparison.
Comp Funct Genom 2001, 2, 196-206
Extraction of the Interactions The sentence “The expressed p53
protein showed nuclear localization and its expression was associated with an induction of p21 and bax expression” relates p53 with p21 and bax but does not imply a physical interaction between them.
Comp Funct Genom 2001, 2, 196-206
Distribution of the Protein Interaction Universe
Comp Funct Genom 2001, 2, 196-206