Fig 1.
USP14-bound 26S proteasome in substrate degradation.
(A) The structure of USP14-bound proteasome. (B) Conformations of the human 26S proteasome and their transitions known from experiments [3,9,27]. (
,
,
,
) are for proteasomal conformations free of substrate (in the presence of substrate), with subscripts A, B, C, D (and the numbers) representing conformational (and sub-conformational) differences. The EA-like, ED-like, and SD-like conformations shown in dashed boxes are for USP14-bound proteasome, with structures similar to EA, ED, and SD. The superscript UBL (or USP14) denotes that the proteasome is bound with the UBL domain (or with both UBL and USP domains of USP14). The thin arrows (or thick gray arrows) are for experimentally certain (or less certain) conformation transitions. (C) The reaction network for USP14-regulated proteasomal substrate degradation reformulated from (B). Constituents of the proteasomal complex are denoted with P (for 26S proteasome), D (for USP14), and S (for substrates), respectively.
Fig 2.
Time evolution for the reactions in
Fig 1C for USP14-regulated proteasomal substrate degradation. The results are obtained by numerical simulations of Equations A in S1 Text. Detailed information of calculation is given in Method. The parameters used in simulation are listed in Supporting information (Table A in S1 Text).
Fig 3.
Dynamics of the USP14-bound proteasome.
(A) Time evolution of the proportions of EA-like, ED-like, and SD-like categories of conformation, as well as the concentration of residual substrate () relative to the initial amount over time. (B) Temporal changes in the proportions of
,
, and
conformations within the EA-like conformation. (C) Temporal changes in the proportions of
,
,
,
,
, and
conformations within the ED-like conformation. (D) Temporal changes in the proportions of
,
,
, and
conformations within the SD-like conformation. Solid lines represent simulation results, and dots are from the experimental data [27].
Fig 4.
Simplified model and the influence of substrate and ATP on substrate degradation.
(A) Simplification of the reaction network in Fig 1C for USP14-regulated proteasomal substrate degradation. Pink and green arrows represent the reaction loop for USP14-mediated deubiquitination and the loop for substrate degradation, respectively. (B) A simple reaction network of proteasomal substrate degradation free of USP14. Blue arrows indicate the loop of substrate degradation. (C) The experimentally observed substrate translocation rates (dots) [30] fitted with the formula of Eq. 5 (curve). (D) The dependence of substrate degradation rate on the concentrations of substrate and ATP predicted by Eqs. 3, 5 and 6. The black dashed line denotes the half-maximal effective concentration (EC50) of the substrate under various ATP concentrations. The parameter values used are listed in Table B in S1 Text.
Fig 5.
Effects of USP14 on substrate preference in proteasomal degradation.
The preference ratio η in Eq. 8 is illustrated in the relative rate space versus
(A), and in
versus
space (B). The black dashed line indicates
where the degradation preferences of substrate S to T in USP14-bound and USP14-free proteasomes are equal. Parameters:
for (A), and
for (B).