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 10 ions s and a high 1:10 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.

2D Vibrational Exciton Nanoimaging of Domain Formation in Self-Assembled Monolayers

“…Because of the sensitivity of vibrational excitons to molecular packing and orientation, this method is generally applicable to other molecular systems with strong mid-infrared vibrational transitions or a high density of oscillators and short-range order. Beyond characterizing delocalization lengths and defects, vibrational excitons could also play a role in ion transport , in ion channels and are suggested to impact the function of ion selectivity filters, where the mechanisms are still poorly understood. Additionally, quantum information protocols have previously been suggested using vibrational excitons as a medium for quantum state transfer, being stable even at room temperature, dependent on the underlying relaxation and dephasing pathways.…”

Effective equations for reaction coordinates in polymer transport

“…Let us consider the problem of a polymer crossing the barrier of a double-well energy profile, which is related to the transport of biomolecules accross nano-scale pores [37][38][39][40][41][42]. In many practical situations channels are so narrow that the transport dynamics of biopolymers and ions occurs on a single axis, thus, as a matter of fact, it can be considered one-dimensional [43][44][45][46]. In this crude approximation, the polymer is composed by a chain of N beads (point particles), interacting via nearest-neighbors forces and subjected to a thermal noise at temperature T .…”

Singular Value Decomposition Quantum Algorithm for Quantum Biology

“…Modeling these processes exactly is frequently computationally intractable; however, they are amenable to an open quantum system treatment . Standard methods in open quantum systems, such as the Lindblad equation, − are capable of accurately describing a variety of biologically relevant dynamical processes, including excitonic energy transport in photosynthetic light-harvesting antennae, ,− radical pair mechanisms (RPMs) for avian navigation − and other physiological functions, and transport through ion channels. − An important aspect of recent quantum algorithm development has focused on the modeling of open quantum systems, which are systems that are not isolated but instead interact with their surroundings and are generally characterized by nonunitary dynamics. The challenge in developing gate-based quantum algorithms to capture these dynamical processes is that only unitary gates can be implemented on current quantum computers, but open quantum systems exhibit nonunitary time dynamics.…”