title: Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies.
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 whole-molecule 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.
authors.affiliation: MOlecular NAnotechnology for LIfe Science Applications (MoNaLiSA) Theory Group, Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Soler
authors.affiliation: Center for biomedical sciences and engineering, University of Nova Gorica, Glavni Trg 8, 5271 Vipava, Slovenia.
authors.forename: Ario
authors.initials: A
authors.lastname: de Marco
authors.affiliation: MOlecular NAnotechnology for LIfe Science Applications (MoNaLiSA) Theory Group, Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy.|Center for biomedical sciences and engineering, University of Nova Gorica, Glavni Trg 8, 5271 Vipava, Slovenia.
authors.forename: Sara
authors.initials: S
authors.lastname: Fortuna
mesh_terms: D055592:Biophysical Phenomena; D000071194:Camelidae / Q000235:genetics; D003102:Colloids / Q000737:chemistry; D003198:Computer Simulation; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011487:Protein Conformation; D061905:Single-Domain Antibodies / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012995:Solubility; D013816:Thermodynamics
chemical_list: D003102:Colloids; D061905:Single-Domain Antibodies