Excitation energy transport with noise and disorder in a model of the selectivity filter of an ion channel

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Excitation energy transport with noise and disorder in a model of the selectivity filter of an ion channel. / Jalalinejad, Amir; Bassereh, Hassan; Salari, Vahid; Ala-Nissila, Tapio; Giacometti, Achille.

In: Journal of Physics Condensed Matter, Vol. 30, No. 41, 415101, 19.09.2018, p. 1-12.

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Jalalinejad, Amir ; Bassereh, Hassan ; Salari, Vahid ; Ala-Nissila, Tapio ; Giacometti, Achille. / Excitation energy transport with noise and disorder in a model of the selectivity filter of an ion channel. In: Journal of Physics Condensed Matter. 2018 ; Vol. 30, No. 41. pp. 1-12.

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@article{64b955fbe2c04dbf9319cd078de4a232,
title = "Excitation energy transport with noise and disorder in a model of the selectivity filter of an ion channel",
abstract = "A selectivity filter is a gate in ion channels that is responsible for the selection and fast conduction of particular ions across the membrane (with high throughput rates of 108 ions s-1 and a high 1:104 discrimination rate between ions). It is made of four strands as the backbone, and each strand is composed of sequences of five amino acids connected by peptide units H-N-C=O in which the main molecules in the backbone that interact with ions in the filter are carbonyl (C=O) groups that mimic the transient interactions of ion with binding sites during ion conduction. It has been suggested that quantum coherence and possible emergence of resonances in the backbone carbonyl groups may play a role in mediating ion conduction and selectivity in the filter. Here, we investigate the influence of noise and disorder on the efficiency of excitation energy transfer (EET) in a linear harmonic chain of N = 5 sites with dipole-dipole couplings as a simple model for one P-loop strand of the selectivity filter backbone in biological ion channels. We include noise and disorder inherent in real biological systems by including spatial disorder in the chain, and random noise within a weak coupling quantum master equation approach. Our results show that disorder in the backbone considerably reduces EET, but the addition of noise helps to recover high EET for a wide range of system parameters. Our analysis may help for better understanding of the coordination of ions in the filter as well as the fast and efficient functioning of the selectivity filters in ion channels.",
keywords = "excitation energy transfer, ion channels, quantum statistical methods, selectivity filter",
author = "Amir Jalalinejad and Hassan Bassereh and Vahid Salari and Tapio Ala-Nissila and Achille Giacometti",
year = "2018",
month = "9",
day = "19",
doi = "10.1088/1361-648X/aadeab",
language = "English",
volume = "30",
pages = "1--12",
journal = "Journal of physics: Condensed matter",
issn = "0953-8984",
number = "41",

}

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TY - JOUR

T1 - Excitation energy transport with noise and disorder in a model of the selectivity filter of an ion channel

AU - Jalalinejad, Amir

AU - Bassereh, Hassan

AU - Salari, Vahid

AU - Ala-Nissila, Tapio

AU - Giacometti, Achille

PY - 2018/9/19

Y1 - 2018/9/19

N2 - A selectivity filter is a gate in ion channels that is responsible for the selection and fast conduction of particular ions across the membrane (with high throughput rates of 108 ions s-1 and a high 1:104 discrimination rate between ions). It is made of four strands as the backbone, and each strand is composed of sequences of five amino acids connected by peptide units H-N-C=O in which the main molecules in the backbone that interact with ions in the filter are carbonyl (C=O) groups that mimic the transient interactions of ion with binding sites during ion conduction. It has been suggested that quantum coherence and possible emergence of resonances in the backbone carbonyl groups may play a role in mediating ion conduction and selectivity in the filter. Here, we investigate the influence of noise and disorder on the efficiency of excitation energy transfer (EET) in a linear harmonic chain of N = 5 sites with dipole-dipole couplings as a simple model for one P-loop strand of the selectivity filter backbone in biological ion channels. We include noise and disorder inherent in real biological systems by including spatial disorder in the chain, and random noise within a weak coupling quantum master equation approach. Our results show that disorder in the backbone considerably reduces EET, but the addition of noise helps to recover high EET for a wide range of system parameters. Our analysis may help for better understanding of the coordination of ions in the filter as well as the fast and efficient functioning of the selectivity filters in ion channels.

AB - A selectivity filter is a gate in ion channels that is responsible for the selection and fast conduction of particular ions across the membrane (with high throughput rates of 108 ions s-1 and a high 1:104 discrimination rate between ions). It is made of four strands as the backbone, and each strand is composed of sequences of five amino acids connected by peptide units H-N-C=O in which the main molecules in the backbone that interact with ions in the filter are carbonyl (C=O) groups that mimic the transient interactions of ion with binding sites during ion conduction. It has been suggested that quantum coherence and possible emergence of resonances in the backbone carbonyl groups may play a role in mediating ion conduction and selectivity in the filter. Here, we investigate the influence of noise and disorder on the efficiency of excitation energy transfer (EET) in a linear harmonic chain of N = 5 sites with dipole-dipole couplings as a simple model for one P-loop strand of the selectivity filter backbone in biological ion channels. We include noise and disorder inherent in real biological systems by including spatial disorder in the chain, and random noise within a weak coupling quantum master equation approach. Our results show that disorder in the backbone considerably reduces EET, but the addition of noise helps to recover high EET for a wide range of system parameters. Our analysis may help for better understanding of the coordination of ions in the filter as well as the fast and efficient functioning of the selectivity filters in ion channels.

KW - excitation energy transfer

KW - ion channels

KW - quantum statistical methods

KW - selectivity filter

UR - http://www.scopus.com/inward/record.url?scp=85053937642&partnerID=8YFLogxK

U2 - 10.1088/1361-648X/aadeab

DO - 10.1088/1361-648X/aadeab

M3 - Article

VL - 30

SP - 1

EP - 12

JO - Journal of physics: Condensed matter

JF - Journal of physics: Condensed matter

SN - 0953-8984

IS - 41

M1 - 415101

ER -

ID: 28603993