Conventional and In Silico-Based Approaches for the Optimization of Nanobody Biophysical Characteristics

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: 15 July 2024 | Viewed by 594

Special Issue Editor


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Guest Editor
Lab of Environmental and Life Sciences, University of Nova Gorica, 5000 Rožna Dolina, Nova Gorica, Slovenia
Interests: nanobodies; protein functionalization; protein quality control; pre-immune libraries; alternative scaffolds

Special Issue Information

Dear Colleagues,

Nanobodies have become a particularly appreciated class of reagents to be used in many different fields of basic research, diagnostics, and therapy. A clear advantage of these recombinant antibodies is the simplicity with which they can be engineered into improved versions of the binders originally recovered by panning. Apart from random mutagenesis, their short sequences make them particularly suitable for rational design and the resulting variants can easily be tested and compared in terms of their biophysical characteristics. This opportunity has been exploited, in combination with improvements relative to their expression (e.g., purification and combination in different formats and fusions), to produce high amounts of nanobodies and nanobody-fusion proteins with desiderable features and functions suitable for final applications. Nanobodies are indeed now a sort of model for testing new approaches, both related to conventional chemical and biochemical methodologies and driven by in silico algorithms, that aim at the more rapid and safer optimization of pre-existing binders. This collection wishes to gather innovative ideas conceived for the achievement of new paradigms in the field of nanobody technology (rational design, innovative functionalization strategies, selection procedures, expression and purification optimization, methods to improve selectivity, epitope recognition, or specific antigen conformations).

Prof. Dr. Ario de Marco
Guest Editor

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Keywords

  • nanobodies
  • modeling
  • screening strategies
  • random mutagenesis
  • rational engineering
  • expression conditions

Published Papers (1 paper)

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10 pages, 1246 KiB  
Article
A Practical Guide for the Quality Evaluation of Fluobodies/Chromobodies
by Urša Štrancar, Claudia D’Ercole, Lucia Cikatricisová, Mirna Nakić, Matteo De March and Ario de Marco
Biomolecules 2024, 14(5), 587; https://doi.org/10.3390/biom14050587 - 15 May 2024
Viewed by 433
Abstract
Background: Fluorescent proteins (FPs) are pivotal reagents for flow cytometry analysis or fluorescent microscopy. A new generation of immunoreagents (fluobodies/chromobodies) has been developed by fusing recombinant nanobodies to FPs. Methods: We analyzed the quality of such biomolecules by a combination of gel filtration [...] Read more.
Background: Fluorescent proteins (FPs) are pivotal reagents for flow cytometry analysis or fluorescent microscopy. A new generation of immunoreagents (fluobodies/chromobodies) has been developed by fusing recombinant nanobodies to FPs. Methods: We analyzed the quality of such biomolecules by a combination of gel filtration and SDS-PAGE to identify artefacts due to aggregation or material degradation. Results: In the SDS-PAGE run, unexpected bands corresponding to separate fluobodies were evidenced and characterized as either degradation products or artefacts that systematically resulted in the presence of specific FPs and some experimental conditions. The elimination of N-terminal methionine from FPs did not impair the appearance of FP fragments, whereas the stability and migration characteristics of some FP constructs were strongly affected by heating in loading buffer, which is a step samples undergo before electrophoretic separation. Conclusions: In this work, we provide explanations for some odd results observed during the quality control of fluobodies and summarize practical suggestions for the choice of the most convenient FPs to fuse to antibody fragments. Full article
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