Biomimetic Design of Affinity Peptide Ligand for Capsomere
of Virus-Like Particle
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Abstract
Virus-like particle (VLP) of murine
polyomavirus (MPV) is a <i>T</i> = 7d icosahedral capsid
that self-assembles from 72 capsomeres
(Caps), each of which is a pentamer of major coat protein VP1. VLP
has great potential in vaccinology, gene therapy, drug delivery, and
materials science. However, its application is hindered by high cost
downstream processes, leading to an urgent demand of a highly efficient
affinity ligand for the separation and purification of Cap by affinity
chromatography. Herein a biomimetic design strategy of an affinity
peptide ligand of Cap has been developed on the basis of the binding
structure of the C-terminus of minor coat protein (VP2-C) on the inner
surface of Cap. The molecular interactions between VP2-C and Cap were
first examined using all-atom molecular dynamics (MD) simulations
coupled with the molecular mechanics/Poisson–Boltzmann surface
area (MM/PBSA) method, where V283, P285, D286, W287, L289, and Y296
of VP2-C were identified as the hot spots. An affinity peptide library
(DWXLXLXY, X denotes arbitrary amino acids except cysteine) was then
constructed for virtual screening sequently by docking with AUTODOCK
VINA, binding structure comparison, and final docking with ROSETTA
FlexPepDock. Ten peptide candidates were selected and further confirmed
by MD simulations and MM/PBSA, where DWDLRLLY was found to have the
highest affinity to Cap. In DWDLRLLY, six residues are favorable for
the binding, including W2, L4, L6 and Y8 inheriting from VP2-C, and
R5 and L7 selected in the virtual screening. This confirms the high
efficiency and accuracy of the biomimetic design strategy. DWDLRLLY
was then experimentally validated by a one-step purification of Cap
from crude cell lysate using affinity chromatography with the octapeptide
immobilized on Sepharose gel. The purified Caps were observed to self-assemble
into VLP with consistent structure of authentic MPV