Elucidating the mechanisms of the molecular sieving phenomenon created by comb-shaped polymers grafted to a protein – a simulation study

Advances in polymer chemistry now allow the creation of protein–polymer conjugates of great complexity. These advances equally enable the fine-tuning of their structure (and hence properties) to address specific challenges they face as therapeutics. Some of these challenges faced by non-human proteins include their rapid degradation, elimination or immunogenicity in vivo, and one of the most recognized solutions for this is to mask their surface with chains of linear poly(ethylene glycol). This, however, generally reduces bioactivity. Several experimental studies have shown that switching from linear to architecturally complex polymers (comb-shaped, branched, dendronized) partially resolves this issue for a subset of proteins whose bioactivity involves small molecules, by creating a “molecular sieving” effect. The mechanisms underlying molecular sieving, however, have never been entirely elucidated. This study presents a coarse-grained model of α-chymotrypsin modified with multiple chains of the comb-shaped polymer poly(oligo(ethylene glycol) methyl ether methacrylate) to study molecular sieving. Results demonstrate the steric nature of the phenomenon (i.e., creation of gaps in the polymer coating), though steric considerations alone could not reconcile all of the experimental trends. The simulations rather suggest that these gaps enable the selective accumulation of small (substrate) molecules near the surface of the protein (in a favourable microenvironment created by the polymer), which exacerbates the “molecular sieving” phenomenon (i.e., difference in the ability of small vs. large substrates to reach the protein).