Note_ProteinChaperones – ProteinChaperones

Name
WID Note_ProteinChaperones
Name ProteinChaperones
 
Comments
Comments The specific chaperone requirements for the folding of each protein were compiled for other bacteria (see sources below), and mapped to M. genitalium by homology. Tig – may interact with all nascent peptides at the ribosome polypeptide exit site (L23) [PUB_0005, PUB_0009, PUB_0014, PUB_0388, PUB_0644] and assist in early folding. Highly epxressed protein. Binds vacant ribosomes with half-life of 11 s [PUB_0005]; binds ribosome-peptide complexes with half-life of 15-50 s [PUB_0005]; remains associated with the peptide for a up to 35 more seconds after peptide release from the ribosome [PUB_0005]. Trigger factor-50S ribosome affinity: KD=1 µM [PUB_0005] and kon=200 × 103 M-1s-1. We model trigger as required for the proper folding of all proteins. DnaK – Deuerling et al performed a proteome-scale search for DnaK substrates in E. coli [PUB_0388]. Functions as a monomer and binds short, linear, unfolded peptide segments [PUB_0014, PUB_0644]. Interacts with peptide backbone [PUB_0014, PUB_0644]. Regulated by co-chaperones (eg DnaJ) [PUB_0014, PUB_0644]. GrpE co-chaperone catalyzes ATP hydrolysis and peptide release [PUB_0014, PUB_0644]. DnaK folds 5-18% of proteins. DnaK substrates are generally > 30 kDa in size. DnaK binds proteins with half life < 2 min. DnaJ - Co-chaperone for DnaK and a chaperone itself [PUB_0014, PUB_0644]. Recognizes hydrophobic and aromatic residues and interacts with peptide side chains [PUB_0014, PUB_0644]. GroEL – Kerner et al performed a proteome-scale search for GroEL substrates in E. coli [PUB_0389] and Endo and Kurusu performed a proteome-scale search for GroEL substrates in B. subtilis [PUB_0391]. Kener et al found that 250 of 2400 cytosolic proteins interact with GroEL and that 85 of these require GroEL for folding. GroEL Functions as two heptameric rings [PUB_0014, PUB_0644]. GroEL folds 10-15% of proteins. GroEL substrates are 20-60 kDa in size. GroEL binds proteins with half life 30 s - 10 min. FtsH – may act as molecule chaperone for membrane proteins [PUB_0014]. Several other functions have also been associated with FtsH. To date no proteome-scale studies of FtsH activity has been performed, and FtsH's chaperone substrates are not well characterized. Conequently we chose not to model FtsH as a molecular chaperone, but rather a protease. Substrates of SecB, a molecular chaperone not present in M. genitalium, have also been identified on proteome-scale in E. coli [PUB_0390].
References
  1. Eds Lund P. Molecular Chaperones in the Cell. Oxford University Press, New York (2001). WholeCell: PUB_0014, ISBN: 9780199638673

  2. Eds Pain R. Mechanisms of protein folding. Oxford University Press: USA (2000). WholeCell: PUB_0644, ISBN: 9780199637881

  3. Baars L, Ytterberg AJ, Drew D, Wagner S, Thilo C, van Wijk KJ, de Gier JW. Defining the role of the Escherichia coli chaperone SecB using comparative proteomics. J Biol Chem 281, 10024-34 (2006). WholeCell: PUB_0390, PubMed: 16352602

  4. Deuerling E, Patzelt H, Vorderwülbecke S, Rauch T, Kramer G, Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Mol Microbiol 47, 1317-28 (2003). WholeCell: PUB_0388, PubMed: 12603737

  5. Endo A, Kurusu Y. Identification of in vivo substrates of the chaperonin GroEL from Bacillus subtilis. Biosci Biotechnol Biochem 71, 1073-7 (2007). WholeCell: PUB_0391, PubMed: 17420574

  6. ... 3 more

  7. Kaiser CM, Chang HC, Agashe VR, Lakshmipathy SK, Etchells SA, Hayer-Hartl M, Hartl FU, Barral JM. Real-time observation of trigger factor function on translating ribosomes. Nature 444, 455-60 (2006). WholeCell: PUB_0005, PubMed: 17051157

  8. Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, Stines AP, Georgopoulos C, Frishman D, Hayer-Hartl M, Mann M, Hartl FU. Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122, 209-20 (2005). WholeCell: PUB_0389, PubMed: 16051146

  9. Raine A, Ivanova N, Wikberg JE, Ehrenberg M. Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome. Biochimie 86, 495-500 (2004). WholeCell: PUB_0009, PubMed: 15308339

 
Metadata
Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:58