title: Slippery substrates impair ATP-dependent protease function by slowing unfolding.
abstract: ATP-dependent proteases are responsible for most energy-dependent protein degradation across all species. Proteases initially bind an unstructured region on a substrate and then translocate along the polypeptide chain, unfolding and degrading protein domains as they are encountered. Although this process is normally processive, resulting in the complete degradation of substrate proteins to small peptides, some substrates are released prematurely. Regions of low sequence complexity within the substrate such as the glycine-rich region (GRR) from p105 or glycine-alanine repeats (GAr) from the EBNA1 (Epstein-Barr virus nuclear antigen-1) protein, can trigger partial degradation and fragment release. Loss of processivity could be due to inability to hold on to the substrate (faster release) or inability to unfold and degrade a substrate domain (slower unfolding). I previously showed that the GRR slows domain unfolding by the proteasome (Kraut, D. A., Israeli, E., Schrader, E. K., Patil, A., Nakai, K., Nanavati, D., Inobe, T., and Matouschek, A. (2012) ACS Chem. Biol. 7, 1444-1453). In contrast, a recently published study concluded that GArs increase the rate of substrate release from ClpXP, a bacterial ATP-dependent protease (Too, P. H., Erales, J., Simen, J. D., Marjanovic, A., and Coffino, P. (2013) J. Biol. Chem. 288, 13243-13257). Here, I show that these apparently contradictory results can be reconciled through a reanalysis of the ClpXP GAr data. This reanalysis shows that, as with the proteasome, low complexity sequences in substrates slow their unfolding and degradation by ClpXP, with little effect on release rates. Thus, despite their evolutionary distance and limited sequence identity, both ClpXP and the proteasome share a common mechanism by which substrate sequences regulate the processivity of degradation.
authors.affiliation: From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Kraut
mesh_terms: D049069:ATP-Dependent Proteases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D000409:Alanine / Q000235:genetics*; D000595:Amino Acid Sequence / Q000235:genetics; D049071:Endopeptidase Clp / Q000737:chemistry / Q000235:genetics; D019309:Epstein-Barr Virus Nuclear Antigens / Q000737:chemistry / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics; D005998:Glycine / Q000235:genetics*; D007700:Kinetics; D008962:Models, Theoretical; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary; D058767:Protein Unfolding; D059748:Proteolysis; D020449:Repetitive Sequences, Amino Acid / Q000235:genetics
chemical_list: D019309:Epstein-Barr Virus Nuclear Antigens; D029968:Escherichia coli Proteins; D049069:ATP-Dependent Proteases; C483573:ClpXP protease, E coli; D049071:Endopeptidase Clp; D046988:Proteasome Endopeptidase Complex; C417029:EBV-encoded nuclear antigen 1; D000409:Alanine; D005998:Glycine
keywords: ATP-dependent Protease; Enzyme Kinetics; Pre-steady-state Kinetics; Proteasome; Protein Degradation; Protein Denaturation; Protein Evolution; Protein Translocation; Protein Unfolding