Using persistent homology and dynamical distances to analyze protein binding

Statistical Applications in Genetics and Molecular Biology
Violeta Kovacev-NikolicGiseon Heo

Abstract

Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic, the persistence landscape, was recently introduced by Bubenik. It is a functional summary, so it is easy to calculate sample means and variances, and it is straightforward to construct various test statistics. Implementing a permutation test we detect conformational changes between closed and open forms of the maltose-binding protein, a large biomolecule consisting of 370 amino acid residues. Furthermore, persistence landscapes can be applied to machine learning methods. A hyperplane from a support vector machine shows the clear separation between the closed and open proteins conformations. Moreover, because our approach captures dynamical properties of the protein our results may help in identifying residues susceptible to ligand binding; we show that the majority of active site residues and allosteric pathway residues are located in the vicinity of the most persistent loop in the corresponding filtered Vietoris-Rips complex. This finding was not observed in the classical anisotropic network ...Continue Reading

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Citations

Jul 12, 2019·Journal of Cheminformatics·Lee SteinbergJeremy Frey
Mar 30, 2018·Scientific Reports·Francisco BelchiJacek Brodzki
Apr 5, 2020·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Erik J AmézquitaDaniel H Chitwood
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Sep 18, 2021·Journal of Theoretical Biology·Jakob Stenseke
Oct 10, 2021·Proceedings of the National Academy of Sciences of the United States of America·Oliver VipondHeather A Harrington
Jan 1, 2020·Computational and Mathematical Biophysics·David Bramer, Guo-Wei Wei
May 4, 2020··Akash RupelaBalaji Krishnamurthy

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Methods Mentioned

BETA
X-ray
MDS
biosensors
NMR

Software Mentioned

KH
DRISM
ISOMAP
Matlab
R Development Core Team
FactoMineR
Discovery Studio
AlloPathFinder
javaPlex
Anisotropic Network Model

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