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Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays

The non-covalent biological bonds that constitute protein–protein or protein–ligand interactions play crucial roles in many cellular functions, including mitosis, motility, and cell–cell adhesion. The effect of external force ([Formula: see text] ) on the unbinding rate ([Formula: see text] ) of mac...

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Autores principales: Paul, Apurba, Alper, Joshua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8741823/
https://www.ncbi.nlm.nih.gov/pubmed/34996945
http://dx.doi.org/10.1038/s41598-021-03690-1
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author Paul, Apurba
Alper, Joshua
author_facet Paul, Apurba
Alper, Joshua
author_sort Paul, Apurba
collection PubMed
description The non-covalent biological bonds that constitute protein–protein or protein–ligand interactions play crucial roles in many cellular functions, including mitosis, motility, and cell–cell adhesion. The effect of external force ([Formula: see text] ) on the unbinding rate ([Formula: see text] ) of macromolecular interactions is a crucial parameter to understanding the mechanisms behind these functions. Optical tweezer-based single-molecule force spectroscopy is frequently used to obtain quantitative force-dependent dissociation data on slip, catch, and ideal bonds. However, analyses of this data using dissociation time or dissociation force histograms often quantitatively compare bonds without fully characterizing their underlying biophysical properties. Additionally, the results of histogram-based analyses can depend on the rate at which force was applied during the experiment and the experiment’s sensitivity. Here, we present an analytically derived cumulative distribution function-like approach to analyzing force-dependent dissociation force spectroscopy data. We demonstrate the benefits and limitations of the technique using stochastic simulations of various bond types. We show that it can be used to obtain the detachment rate and force sensitivity of biological macromolecular bonds from force spectroscopy experiments by explicitly accounting for loading rate and noisy data. We also discuss the implications of our results on using optical tweezers to collect force-dependent dissociation data.
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spelling pubmed-87418232022-01-10 Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays Paul, Apurba Alper, Joshua Sci Rep Article The non-covalent biological bonds that constitute protein–protein or protein–ligand interactions play crucial roles in many cellular functions, including mitosis, motility, and cell–cell adhesion. The effect of external force ([Formula: see text] ) on the unbinding rate ([Formula: see text] ) of macromolecular interactions is a crucial parameter to understanding the mechanisms behind these functions. Optical tweezer-based single-molecule force spectroscopy is frequently used to obtain quantitative force-dependent dissociation data on slip, catch, and ideal bonds. However, analyses of this data using dissociation time or dissociation force histograms often quantitatively compare bonds without fully characterizing their underlying biophysical properties. Additionally, the results of histogram-based analyses can depend on the rate at which force was applied during the experiment and the experiment’s sensitivity. Here, we present an analytically derived cumulative distribution function-like approach to analyzing force-dependent dissociation force spectroscopy data. We demonstrate the benefits and limitations of the technique using stochastic simulations of various bond types. We show that it can be used to obtain the detachment rate and force sensitivity of biological macromolecular bonds from force spectroscopy experiments by explicitly accounting for loading rate and noisy data. We also discuss the implications of our results on using optical tweezers to collect force-dependent dissociation data. Nature Publishing Group UK 2022-01-07 /pmc/articles/PMC8741823/ /pubmed/34996945 http://dx.doi.org/10.1038/s41598-021-03690-1 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Paul, Apurba
Alper, Joshua
Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays
title Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays
title_full Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays
title_fullStr Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays
title_full_unstemmed Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays
title_short Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays
title_sort calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8741823/
https://www.ncbi.nlm.nih.gov/pubmed/34996945
http://dx.doi.org/10.1038/s41598-021-03690-1
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