Proteins across scales through graph partitioning: application to the major peanut allergen Ara h 1
File(s)
Published version
Author(s)
Zhang, H
Salazar, JD
Yaliraki, SN
Type
Journal Article
Abstract
The analysis of community structure in complex networks has been given much attention recently, as it is hoped that the communities at various scales can affect or explain the global behaviour of the system. A plethora of community detection algorithms have been proposed, insightful yet often restricted by certain inherent resolutions. Proteins are multi-scale biomolecular machines with coupled structural organization across scales, which is linked to their function. To reveal this organization, we applied a recently developed multi-resolution method, Markov Stability, which is based on atomistic graph partitioning, along with theoretical mutagenesis that further allows for hot spot identification using Gaussian process regression. The methodology finds partitions of a graph without imposing a particular scale a priori and analyses the network in a computationally efficient way. Here, we show an application on peanut allergenicity, which despite extensive experimental studies that focus on epitopes, groups of atoms associated with allergenic reactions, remains poorly understood. We compare our results against available experiment data, and we further predict distal regulatory sites that may significantly alter protein dynamics.
Date Issued
2018-10-01
Date Acceptance
2017-10-13
Citation
Journal of Complex Networks, 2018, 6 (5), pp.679-692
ISSN
2051-1310
Publisher
Oxford University Press (OUP)
Start Page
679
End Page
692
Journal / Book Title
Journal of Complex Networks
Volume
6
Issue
5
Copyright Statement
© The Author(s) 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Sponsor
Engineering & Physical Science Research Council (E
Commission of the European Communities
Engineering & Physical Science Research Council (EPSRC)
Grant Number
EP/I037180/1
607466
EP/N014529/1
Subjects
Science & Technology
Physical Sciences
Mathematics, Interdisciplinary Applications
Mathematics
peanut allergenicity
major peanut allergen Ara h 1
community detection
Markov Stability
all-scale method
protein dynamics
mutational analysis
MOLECULAR-DYNAMICS SIMULATIONS
DIGESTION-RESISTANT PEPTIDES
IN-VITRO
PREDICTION
STABILITY
NETWORKS
PATHWAYS
EPITOPES
PARALLEL
Publication Status
Published
Article Number
ARTN cnx052
Date Publish Online
2017-11-13