The Surface of Protein λ_6–85 Can Act as a Template for Recurring Poly(ethylene glycol) Structure

PEGylated proteins play an increasingly important role in pharmaceutical drug delivery. We recently showed that short poly­(ethylene glycol) (PEG) chains can affect protein structure, even when they are not making extensive contact with the protein surface. In contrast, PEG is generally thought to form a relatively unstructured coil, and its compactness depends on solvent conditions. Here we test whether a host protein could allow PEG to form recurrent structural motifs while the PEG chain is in contact with the protein surface. We link a PEG oligomer (<i>n</i> = 45) to one of two nearly opposite locations on the small α-helical protein λ_6–85 to investigate this question. We first demonstrate experimentally that in these particular positions, PEG does not significantly affect the thermodynamic stability or folding kinetics of λ_6–85. We then use several all-atom molecular dynamics (MD) simulations 1 μs in duration to show how PEG equilibrates between states extending into the solvent and states packed onto the protein surface. The packing reveals recurring structures, including persistent hydrogen bond and hydrophobic contact patterns that appear multiple times. Some interactions of PEG with surface lysines are best described as an “intermittent slithering” motion of the PEG around the side chain, as seen in short MD movies. Thus, PEG achieves a variety of metastable organized structures on the protein surface, somewhere between a random globule and true folding. We also investigated the PEG–protein interaction in the unfolded state of the protein. We find that PEG has a propensity to stabilize certain helices of λ_6–85, no matter which of the two positions it was attached to. Thus, sufficiently long PEG chains are organized by the protein surface and in turn interact with certain elements of protein structure more than others, even when PEG is attached to very different sites