Each monomer model contains 4 beads, each of which represents a subdomain.
The TM JM dimer was simulated with elastic network model (ENM) restraints within each monomer where a harmonic potential was applied to all pairs of backbone particles within a cut-off distance of 7 Å to maintain the secondary structure of the protein [29].
The TMS of the E. coli homology model were fitted individually to each monomer complex of the equivalent unsymmetrized maps determined with and without the preprotein peptide.
Helix 2 of each monomer is modeled as a coiled-coil extension of the C-terminal "leucine zipper". Helix 1 does not interact with helix 1 from its partner in the dimer but with the hydrophobic surface created when the helix 2 regions of the dimer interact with each other as a coiled-coil.
In rigid body modeling, a Uch37 monomer model (PDB ID 3IHR) and the NMR structure of Rpn13C were modeled together using MASSHA (Konarev et al., 2001) (Fig. 5B).
With the 3D homology models for the Rvb1 and Rvb2 monomers, we generated the hetero-hexameric Rvb1/2 model in PyMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC) by computationally aligning each monomer to the corresponding homolog in the crystal structure of the truncated human Rvb1/2 hexameric ring (2XSZ, [ Gorynia et al., 2011 ]).
Briefly, for the "model-free" analysis, an aggregation model with monomer, dimer, trimer, tetramer, pentamer, hexamer, septamer, and octamer was assumed, where the fraction of each oligomeric species was variable and allowed to float in the fitting of the pbICS curves.
The phase problem was solved by molecular replacement with the program PHASER (McCoy et al, 2005) using as search model one monomer of the structure of the OBP from A. gambiae, AgamOBP1 (PDB 2ERB; [20]), edited with the chainsaw program [36].
Raman spectra of a model PBTTT monomer were calculated at the B3LYP/Def-2SV d) level of theory using the ORCA computational suite.
In DLA, higher-order structures emerge through the stepwise accretion of monomers onto a growing assembly; this model assumes that monomer concentrations are sufficiently low that diffusion is the limiting factor in assembly kinetics.
