Microsecond Simulations of the Diphtheria Toxin Translocation
Domain in Association with Anionic Lipid Bilayers
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Abstract
Diphtheria toxin
translocation (T) domain undergoes conformational
changes in acidic solution and associates with the lipid membranes,
followed by refolding and transmembrane insertion of two nonpolar
helices. This process is an essential step in delivery of the toxic
catalytic domain of the diphtheria toxin to the infected cell, yet
its molecular determinants are poorly characterized and understood.
Therefore, an atomistic model of the T-domain–membrane interaction
is needed to help characterize factors responsible for such association.
In this work, we present atomistic model structures of T-domain membrane-bound
conformations and investigate structural factors responsible for T-domain
affinity with the lipid bilayer in acidic solution using all-atom
molecular dynamics (MD) simulations. The initial models of the protein
conformations and protein–membrane association that serve as
starting points in the present work were developed using atomistic
simulations of partial unfolding of the T-domain in acidic solution
(Kurnikov, I. V.; et al. <i>J. Mol. Biol.</i> <b>2013</b>, <i>425</i>, 2752–2764), and coarse-grained simulations
of the T-domain association with the membranes of various compositions
(Flores-Canales, J. C.; et al. <i>J. Membr. Biol.</i> <b>2015</b>, <i>248</i>, 529–543). In this work
we present atomistic level modeling of two distinct configurations
of the T-domain in association with the anionic lipid bilayer. In
microsecond-long MD simulations both conformations retain their compact
structure and gradually penetrate deeper into the bilayer interface.
One membrane-bound conformation is stabilized by the protein contacts
with the lipid hydrophobic core. The second modeled conformation is
initially inserted less deeply and forms multiple contacts with the
lipid at the interface (headgroup) region. Such contacts are formed
by the charged and hydrophilic groups of partially unfolded terminal
helixes and loops. Neutralization of the acidic residues at the membrane
interface allows for deeper insertion of the protein and reorientation
of the protein at the membrane interface, which corroborates that
acidic residue protonation as well as presence of the anionic lipids
may play a role in the membrane association and further membrane insertion
of the T-domain as implicated in experiments. All simulations reported
in this work were performed using AMBER force-field on Anton supercomputer.
To perform these reported simulations, we developed and carefully
tested a force-field for the anionic 1-palmitoyl-2-oleoyl-phosphatidyl-glycerol
(POPG) lipid, compatible with the Amber 99SB force-field and stable
in microsecond-long MD simulations in isothermal–isobaric ensemble