Distribution and solvent-exposure of Hsp70 chaperone binding sites
across the E. coli proteome
Abstract
Many proteins must interact with molecular chaperones to achieve their
native folded state in the cell. Yet, how chaperone binding and
binding-site characteristics affect the folding process is poorly
understood. The ubiquitous Hsp70 chaperone system prevents
client-protein aggregation by holding unfolded conformations or by
unfolding misfolded states. Hsp70 binding sites of client proteins
comprise a nonpolar core surrounded by positively charged residues.
However, a detailed analysis of Hsp70 binding sites on a proteome-wide
scale is still lacking. Further, it is not known whether proteins
undergo some degree of folding while chaperone bound. Here, we begin to
address the above questions by identifying Hsp70 binding sites in 2,258
E. coli proteins. We find that most proteins bear at least one
Hsp70 binding site and that the number of Hsp70 binding sites is
directly proportional to protein size. Aggregation propensity upon
release from the ribosome correlates with number of Hsp70 binding sites
only in the case of large proteins. Interestingly, Hsp70 binding sites
are more solvent-exposed than other nonpolar sites, in protein native
states. Our findings show that the majority of E. coli proteins
are systematically enabled to interact with Hsp70 even if this
interaction only takes place during a fraction of the protein lifetime.
In addition, our data suggest that some conformational sampling may take
place within Hsp70-bound states, due to the solvent exposure of some
chaperone binding sites in native proteins. In all, we propose that
Hsp70-chaperone-binding traits have evolved to favor Hsp70-assisted
protein folding devoid of aggregation.