Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. Residues α1-12, β1-2, and those from the C termini, including the epitope-tag peptides, were not detected in the electron density maps, probably because of disordering.Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Side chains of residues β139-145 exhibited weak electron density and B factors around 70 Å 2. All non-glycine φ and ψ angles lie in the allowed regions of the Ramachandran plot, with 90% in the most favorable regions. The final model contained residues α13-199 and β3-192, 198 water molecules, and three monosaccharides ( Table 1). Four subsequent cycles of minimization and rebuilding allowed identification of water molecules from electron density > 2σ in 2F o-F o maps. No saccharides could be modeled at the other expected glycosylation sites, α165Asn and β92Asn.
Continuous electron density was also seen for two N-acetylglucosamine and one mannose moiety at one of the N-linked carbohydrate sites, Asn α15. After four rounds of rebuilding and refinement, the 3F o-2F o and F o-F o omit maps, in which helical regions or individual domains of DM were omitted, revealed clear, bias-free electron density for the omitted regions. The minimization included a bulk-solvent correction coupled with simulated annealing and individual B factor refinement.
#The chaperone catalyst free
At all stages, data from 34.0 to 2.5 Å, with | F obs | > 0, were included, with 10% of omitted reflections for R free calculation. Experimental Procedures Purification and Crystallization Mutations at DR His β81 or in the putative DM/DR interface or the structure of DM/DR complex could test this model or, in the latter case, may suggest another mode of destabilizing the peptide/DR interface. Such a DM/DR interaction could lower the free energy barrier to peptide dissociation and have the properties of an open transition state conformer of DR favoring faster peptide association as well. In such a hypothetical interaction, a polar residue like Asp α61 (Glu in mouse) of DM might contact His β81 of DR, distorting a third conserved peptide-to-MHC hydrogen bond (P1 in Figure 3). A testable although speculative model for DM catalytic activity would be for a nonpolar residue like Trp α62 on this lateral face of DM to contact Phe α51 of DR, which projects off the surface of DR at the N-terminal end of the extended strand characteristic of the “left” end of the peptide-binding sites of class II molecules, and to move neighboring Ser α53, breaking two conserved peptide-to-MHC hydrogen bonds (P-2 and P-1 in Figure 3).
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