Process_ProteinDecay – Protein decay

Name
WID Process_ProteinDecay
Name Protein decay
 
Implementation
Initialization order 1 View in model
 
Reactions
Chemical reactions View in model
 
Parameters
Parameters View in model
 
Comments
Comments Protein degradation occurs by an enzyme dependent process similar to RNA degradation. First, in an energy-dependent fashion peptides are hydrolytically cleaved into 10-20 amino acid fragments by xsDNA the lon protease, or if the ribosome stalled during the synthesis of the peptide, by the FtsH protease. Second, 8 peptidases together hydrolytically degrade the peptide fragments produced by the lon protease, producing individual amino acids. Protein degradation is modeled as a Poisson process, similar to RNA degradation. Poisson simulation of protein damage, repair, and decay mediated by chaperone: clpB chaperone disaggregates proteins by an energy-dependent mechanism proteases: lon, ftsH; each is believed to processively cleave peptideas in smaller peptides of approximately 20 amino acids ftsH: cleaves peptides with tmRNA stalled translation proteolysis tag; parameterized by fragment length (aa) kinetic rate (cleaves/s) energy per cleavage (ATP/cleavage) lon: cleaves all other peptides; parameterized by fragment length (aa) kinetic rate (cleaves/s) energy per cleavage (ATP/cleavage) several peptidases: the specific functions and kinetics of the individual peptidases are unknown and not modelled; decay proceeds as long as at least one of each peptidase is present Misfold/aggregate proteins Protein misfolding/aggregatation is modeled as a poisson process with a small rate constant Fold/disaggregate cytosolic proteins Occurs if clpB is present Decay macromolecular complexes Model decay is poisson process with rate paramter given by the inverse weighted average half life of the complex's subunits Salvage bound prosthetic groups Mark subunits as damaged to be degraded by xsDNA the protease/peptidase or ribonuclease machinery Decay protein monomers Model selection of monomers that decay as poission process with rate parameters equal to the decay rates (ln(2)/half life as computed by the N-end rule) of the monomers. Execute decay reactions as long as the following are available Lon/FtsH protease for normal / ribosome-stalled peptides Complete peptidase complement Water for hydrolysis of peptide bonds Simulate metabolic conversion of transferred amino acids back to precursors: fMet --> Met Gln --> Glu
 
Metadata
Created 2012-10-01 15:07:35
Last updated 2012-10-01 15:14:00