All-Atom Molecular Dynamics Simulations of Polyethylene Glycol (PEG) and LIMP‑2 Reveal That PEG Penetrates Deep into the Proposed CD36 Cholesterol-Transport Tunnel

Polyethylene glycol
(PEG) is the most prominent clinically administered
synthetic polymer. For example, over 300 million people have been
administered PEGylated liposome vaccines for SARS-CoV-2. PEG is used
in mammals because it has low affinity for most proteins and vice
versa. However, this makes it difficult to study the few interactions
with proteins that PEG has. On the atomistic level, there are two
PEG-protein structures: (1) PEG-LIMP-2 and (2) PEG-αPEG. In
the first structure, two monomers of a 1.5 kDa PEG polymer (PEG2)
had electron density deep in the postulated cholesterol transport
tunnel of LIMP-2, a lysosomal cholesterol transport protein and member
of the CD36 super family of proteins. It is unclear how PEG entered
this tunnel. In the second structure, PEG wrapped around a surface-exposed
tryptophan on its antibody. Since tryptophan is a rare residue, it
is unclear if this PEG-Trp interaction is ubiquitous. To gain deeper
mechanistic insight into PEG–protein interactions, we surrounded
the LIMP-2 apo structure with 13 PEG chains of 10 monomers each (PEG10),
water, and KCl and simulated the system using NAMD. One of the 13
chains penetrated LIMP-2 and came within 3 Å of PEG2. This was
possible because of the strong hydrogen bonding between multiple oxygens
along PEG10 and Arg192 but, most importantly, the clamping of the
tertiary structure on PEG10. Clamping stabilized the movements of
PEG10, and the leading oxygen of PEG10 was able to penetrate LIMP-2
and head toward to the position occupied by PEG2. Phe383 appears to
act as a gate for objects to move through this cavity, which continues
to the basal/membrane side of LIMP-2. Of all residues, PEG10 molecules
had the most sustained interactions with lysine and arginine because
of their strong hydrogen-bonding capabilities. These results show
that the oxygens of PEG bind residues with high hydrogen bonding capabilities.
However, the PEG–protein interaction is likely to be transient
unless groups of resides can clamp down on PEG or a cavity that at
least part of the PEG chain can enter is in close proximity to lower
PEG’s entropy.