Proteindomainsvs.structuredomains-anexample.pptVIP

Protein domains vs. structure domains - an example. Genome of the week Nanoarchaeum equitans - archaea Hyperthermophile Diverged early in evolution from other archaea New kingdom of archaea? Obligate symbiont with Ignicoccus Smallest completely sequenced genome 500kB Genome reduction observed in symbionts (Schmidt) Is N. equitans a “primitive” archaea or is the genome undergoing reductive evolution? N. equitans lacks genes necessary for many aspects of central metabolism. Can’t make lipids, vitamins, amino acids, etc. Parasite, not symbiont? First archaea Genome is quite compact. 95% of genome codes for genes. 552. Not primitive. Has complete set of information pathway and cell cycle genes found in archaea. No longer undergoing reductive evolution. Normally would find pseudogenes - not found. Protein complexes - why? Proteins often function as large, multi-subunit complexes. ribosomes Can get clues about the function of a protein by knowing what other proteins it contacts. Protein:protein interactions Genetic approach Yeast 2-hybrid Biochemical approach Co-immunoprecipitation Fusion protein affinity chromatography Cell-biology FRET - fluorescence resonance energy transfer Computational Rosetta Stone Co-regulation Phylogenetic analysis Yeast 2-hybrid approach Based on the fact some transcriptional activators have separable DNA binding (BD) and transcriptional activation domains (AD). GAL4, LexA Protein you are studying = Bait Fused to the DNA binding domain of GAL4 Protein(s) you are screening = Fish or Prey Fused to the activation domain of GAL4 Transform Bait and Fish plasmids into yeast, measure the expression of a reporter gene. Usually a gene can be selected for when expressed. Yeast 2-hybrid on a genome wide scale Clone every gene in your genome into both the “bait” and “fish” vectors. Systematically screen each gene for interactions. Mate individual yeast strains. Many false positives. Interactome Term to define all of the protein interactions that ta