Antimicrobial resistance stimulates the search for antimicrobial
forms that may be less subject to acquired resistance. Here we report
a conceptual design of protein pseudocapsids exhibiting a broad spectrum
of antimicrobial activities. Unlike conventional antibiotics, these
agents are effective against phenotypic bacterial variants, while
clearing “superbugs” in vivo without
toxicity. The design adopts an icosahedral architecture that is polymorphic
in size, but not in shape, and that is available in both l and d epimeric forms. Using a combination of nanoscale
and single-cell imaging we demonstrate that such pseudocapsids inflict
rapid and irreparable damage to bacterial cells. In phospholipid membranes
they rapidly convert into nanopores, which remain confined to the
binding positions of individual pseudocapsids. This mechanism ensures
precisely delivered influxes of high antimicrobial doses, rendering
the design a versatile platform for engineering structurally diverse
and functionally persistent antimicrobial agents.
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
The pressing need of new antimicrobial products is growing stronger, particularly because of widespread antimicrobial resistance, endangering our ability to treat common infections.The recent coronavirus pandemic has dramatically highlighted the...
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