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114. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodiesMiguel Soler, Ario De Marco, Sara Fortuna, 2016, original scientific article Abstract: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular
recognition. Their small size represents a precious advantage for rational mutagenesis based on
modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate
mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule
docking. The method was tested on two sets of nanobodies characterized experimentally
for their biophysical features. One set contained point mutations introduced to humanize a wild type
sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae
and human hallmarks. The method resulted in accurate scoring approaches to predict experimental
yields and enabled to identify the structural modifications induced by mutations. This work is a
promising tool for the in silico development of single-domain antibodies and opens the opportunity to
customize single functional domains of larger macromolecules
Keywords: nanobodies, molecular dynamics, modeling, antibody solubility
Published in RUNG: 11.10.2016; Views: 4689; Downloads: 244
 Full text (1,95 MB) |
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117. NaLi-H1: A universal synthetic library of humanized nanobodies providing highly functional antibodies and intrabodiesSandrine Moutel, Nicolas Bery, Virginie Bernard, Laura Keller, Emilie Lemesre, Ario De Marco, Laetitia Ligat, Jean-Christophe Rain, Gilles Fevre, Aurelien Olichon, Franck Perez, 2016, original scientific article Abstract: In vitro selection of antibodies allows to obtain highly functional binders, rapidly and at
lower cost. Here, we describe the first fully synthetic phage display library of humanized llama
single domain antibody (NaLi-H1: Nanobody Library Humanized 1). Based on a humanized synthetic
single domain antibody (hs2dAb) scaffold optimized for intracellular stability, the highly diverse
library provides high affinity binders without animal immunization. NaLi-H1 was screened following
several selection schemes against various targets (Fluorescent proteins, actin, tubulin, p53, HP1).
Conformation antibodies against active RHO GTPase were also obtained. Selected hs2dAb were
used in various immunoassays and were often found to be functional intrabodies, enabling tracking
or inhibition of endogenous targets. Functionalization of intrabodies allowed specific protein
knockdown in living cells. Finally, direct selection against the surface of tumor cells produced
hs2dAb directed against tumor-specific antigens further highlighting the potential use of this
library for therapeutic applications.
Keywords: nanobodies, synthetic phage display library, in vitro panning
Published in RUNG: 17.08.2016; Views: 5207; Downloads: 243
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120. An intrabody specific for the nucleophosmin carboxy-terminal mutant and fused to a nuclear localization sequence binds its antigen but fails to relocate it in the nucleusArio De Marco, Chiara Martinelli, Emanuela Colombo, Daniele Piccini, Cristina Sironi, Pier Giuseppe Pelicci, 2014, original scientific article Keywords: intrabody, leukemia, protein shuttling, recombinant fusion protein, single-chain antibody
Published in RUNG: 16.06.2016; Views: 4135; Downloads: 24
 Link to full text |
