Transcending Markov: non-Markovian rate processes of thermosensitive TRP ion channels

The Markov state model (MSM) is a popular theoretical tool for describing the hierarchy of time scales involved in the function of many proteins especially ion channel gating. An MSM is a particular case of the general non-Markovian model, where the rate of transition from one state to another does...

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Main Authors: Ben-Abu, Y, Tucker, SJ, Contera, S
Format: Journal article
Language:English
Published: Royal Society 2023
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author Ben-Abu, Y
Tucker, SJ
Contera, S
author_facet Ben-Abu, Y
Tucker, SJ
Contera, S
author_sort Ben-Abu, Y
collection OXFORD
description The Markov state model (MSM) is a popular theoretical tool for describing the hierarchy of time scales involved in the function of many proteins especially ion channel gating. An MSM is a particular case of the general non-Markovian model, where the rate of transition from one state to another does not depend on the history of state occupancy within the system, i.e. it only includes reversible, non-dissipative processes. However, an MSM requires knowledge of the precise conformational state of the protein and is not predictive when those details are not known. In the case of ion channels, this simple description fails in real (non-equilibrium) situations, for example when local temperature changes, or when energy losses occur during channel gating. Here, we show it is possible to use non-Markovian equations (i.e. offer a general description that includes the MSM as a particular case) to develop a relatively simple analytical model that describes the non-equilibrium behaviour of the temperature-sensitive transient receptor potential (TRP) ion channels, TRPV1 and TRPM8. This model accurately predicts asymmetrical opening and closing rates, infinite processes and the creation of new states, as well as the effect of temperature changes throughout the process. This approach therefore overcomes the limitations of the MSM and allows us to go beyond a mere phenomenological description of the dynamics of ion channel gating towards a better understanding of the physics underlying these processes.
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spelling oxford-uuid:7de58e7f-e7ba-465c-afb4-9e3d2906f9732023-10-30T11:51:17ZTranscending Markov: non-Markovian rate processes of thermosensitive TRP ion channelsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:7de58e7f-e7ba-465c-afb4-9e3d2906f973EnglishSymplectic ElementsRoyal Society2023Ben-Abu, YTucker, SJContera, SThe Markov state model (MSM) is a popular theoretical tool for describing the hierarchy of time scales involved in the function of many proteins especially ion channel gating. An MSM is a particular case of the general non-Markovian model, where the rate of transition from one state to another does not depend on the history of state occupancy within the system, i.e. it only includes reversible, non-dissipative processes. However, an MSM requires knowledge of the precise conformational state of the protein and is not predictive when those details are not known. In the case of ion channels, this simple description fails in real (non-equilibrium) situations, for example when local temperature changes, or when energy losses occur during channel gating. Here, we show it is possible to use non-Markovian equations (i.e. offer a general description that includes the MSM as a particular case) to develop a relatively simple analytical model that describes the non-equilibrium behaviour of the temperature-sensitive transient receptor potential (TRP) ion channels, TRPV1 and TRPM8. This model accurately predicts asymmetrical opening and closing rates, infinite processes and the creation of new states, as well as the effect of temperature changes throughout the process. This approach therefore overcomes the limitations of the MSM and allows us to go beyond a mere phenomenological description of the dynamics of ion channel gating towards a better understanding of the physics underlying these processes.
spellingShingle Ben-Abu, Y
Tucker, SJ
Contera, S
Transcending Markov: non-Markovian rate processes of thermosensitive TRP ion channels
title Transcending Markov: non-Markovian rate processes of thermosensitive TRP ion channels
title_full Transcending Markov: non-Markovian rate processes of thermosensitive TRP ion channels
title_fullStr Transcending Markov: non-Markovian rate processes of thermosensitive TRP ion channels
title_full_unstemmed Transcending Markov: non-Markovian rate processes of thermosensitive TRP ion channels
title_short Transcending Markov: non-Markovian rate processes of thermosensitive TRP ion channels
title_sort transcending markov non markovian rate processes of thermosensitive trp ion channels
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