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Title:Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies
Authors:Soler, Miguel (Author)
de Marco, Ario (Author)
Fortuna, Sara (Author)
Files:.pdf Soler_et_al-2016-Scientific_Reports.pdf (1,95 MB)
 
Language:English
Work type:Not categorized (r6)
Tipology:1.01 - Original Scientific Article
Organization:UNG - University of Nova Gorica
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
Year of publishing:2016
Number of pages:11
Numbering:6:34869 |
COBISS_ID:4531707 Link is opened in a new window
URN:URN:SI:UNG:REP:LFCPDQKV
DOI:10.1038/srep34869 Link is opened in a new window
License:CC BY 4.0
This work is available under this license: Creative Commons Attribution 4.0 International
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Record is a part of a journal

Title:Scientific Reports
Publisher:Springer Nature Publishing
Year of publishing:2016

Document is financed by a project

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Funding Programme:Sofinanciranje znanstvenoraziskovalnega sodelovanja med RS in Belgijo
Project no.:N4-0046
Name:
Acronym:
Project ID:info:eu-repo/grantAgreement/ARRS/Sofinanciranje%20znanstvenoraziskovalnega%20sodelovanja%20med%20RS%20in%20Belgijo/N4-0046

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