PyRhO: A Multiscale Optogenetics Simulation Platform

Evans, Benjamin D.; Jarvis, Sarah; Schultz, Simon R.; Nikolić, Konstantin

doi:10.3389/fninf.2016.00008

Cited by 24 publications

(59 citation statements)

References 68 publications

(80 reference statements)

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“…1B). 16,21 Here, the model simulates channel photocurrents characterized by two closed states (C1 and C2) and two open states (O1 and O2) using the following set of rate equations,…”

Section: Four-state Model Fittingmentioning

confidence: 99%

Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate

VanGordon

Prignano

Dempski

et al. 2019

Preprint

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Channelrhodopsins (ChR) are cation channels that can be expressed heterologously in various living tissues, including cardiac and neuronal cells. To tune spatial and temporal control of potentials across ChR-enriched cell membranes, it is essential to understand how pore hydration impacts the ChR photocycle kinetics. Here, we measure channel opening and closing rates of channelrhodopsin chimera and selected variants (C1C2 wild type, C1C2-N297D, C1C2-N297V, and C1C2-V125L) and correlate them with changes in chemical interactions among functionally important residues in both closed and open states. Kinetic results substantiate that replacement of helices I and II in ChR2 with corresponding residues from ChR1, to make the chimera C1C2, affects the kinetics of channelrhodopsin pore gating significantly, making C1C2 a unique channel. As a prerequisite for studies of ion transport, detailed understanding of the water pathway within a ChR channel is important. Our atomistic simulations confirm that opening of the channel and initial hydration of the previously dry gating regions between helices I, II, III, and VII of the channel occurs with 1) the presence of 13-cis retinal; 2) deprotonation of a glutamic acid gating residue, E129; and 3) subsequent weakening of the central gate hydrogen bond between the same glutamic acid E129 and asparagine N282 in the central region of the pore. Also, an aspartate (D292) is the unambiguous primary proton acceptor for the retinal Schiff base in the hydrated channel. SIGNIFICANCEChannelrhodopsins (ChR) are light-sensitive ion channels used in optogenetics, a technique that applies light to selectively and non-invasively control cells (e.g., neurons) that have been modified genetically to express those channels. Using electrophysiology, we measured the opening and closing rates of a ChR chimera, and several variants, and correlated those rates with changes in chemical interactions determined from atomistic simulations. Significant new insights include correlation of single-point-mutations with four factors associated with pore hydration and cation conductance. Additionally, our work unambiguously identifies the primary proton acceptor for the retinal chromophore in the channel open state. These new insights add to mechanistic understanding of lightgated membrane transport and should facilitate future efforts to control membrane potentials spatially and temporally in optogenetics.

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“…1B). 16,21 Here, the model simulates channel photocurrents characterized by two closed states (C1 and C2) and two open states (O1 and O2) using the following set of rate equations,…”

Section: Four-state Model Fittingmentioning

confidence: 99%

Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate

VanGordon

Prignano

Dempski

et al. 2019

Preprint

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“…14). The model was designed in the direct lineage of similar work, carried out over the 337 past decade [11][12][13]27], but also taking into account the more recent conclusion on the 338 actual, more complex, photocycle of channelrhodopsins [25]. Additionally, our analysis 339 is based on a set of voltage-clamp experiments on ChrimsonR-transfected HEK293 cells 340 at a holding potential of −60 mV and at physiological temperature (for direct use in Direct observation of the data revealed that there is a fast light adaptation 347 mechanism that has not been described previously.…”

Section: On Time Constants Comparison 316mentioning

confidence: 99%

“…),(9),(10),(11),(12) and(13) display the comparison between the data and 295 the simulations for six different cells. They show that the main features are in fact 296 captured by the five-state model.297Activation curve 298…”

mentioning

confidence: 99%

Modeling the Electro-chemical Properties of Microbial Opsin ChrimsonR for Application to Optogenetics-based Vision Restoration

Sabatier¹,

Joffrois²,

Gauvain³

et al. 2018

Preprint

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Optogenetic activation of neurons [1] have greatly contributed to our understanding of how neural circuits operate, and holds huge promise in the field of neural prosthetics, particularly in sensory restoration. The discovery of new channelrhodopsins, Chrimson -which is 45 nm more red-shifted than any previously discovered or engineered channelrhodopsin -and its mutant ChrimsonR with faster kinetics [2] made this technology available for medical applications. However, a detailed model that would be able to accurately reproduce the membrane potential dynamics in cells transfected with ChrimsonR under light stimulation is missing. We address this issue by developing the first model for the electrochemical behavior of ChrimsonR that predicts its conductance in response to arbitrary light stimulation. Our model captures ON and OFF dynamics of the protein for stimuli with frequencies up to 100 Hz and their relationship with the brightness, as well as its activation curve, the steady-state amplitude of the response as a function of light intensity. Additionally, we capture a slow adaptation mechanism at a Introduction 1 This paper studies the activation dynamics of ChrimsonR, a channelrhodopsin which is 2 currently the best candidate for optogenetic-based sensory restoration in human 3 patients, due to its peak spectral sensitivity in the red at 590 nm, which is 45 nm more 4 red-shifted than all previously known channelrhodopsins [3]. However, design of 5 light-stimulation protocols for optogenetics-based vision restoration would greatly 6 benefit from a model of the channel's behavior, as its dynamics will influence the 7 PLOS 1/25ChrimsonR mediated temporal dynamics of membrane potential in transfected neurons. 8To address this issue, here we introduce for the first time the relevant kinetics and the 9 expected behavior of the channel. In particular, we propose a predictive model of the 10 conductance of a population of channels expressed in a given cell in response to 11 arbitrary illumination stimuli spanning the whole dynamic range of the protein. 12Upon photostimulation, channelrhodopsins modify their conformation and form a 13 water-filled pore allowing some ions to flow through the channel. The illumination 14 signal therefore drives the conductance of the cell's membrane, which then induces a 15 current through the membrane, the subsequent modification of the membrane potential 16 and the possible triggering of action potentials. A predictive model of the 17 channelrhodopsin's conductance provides the mapping between the controlled 18 illumination and the physiologically relevant variable. 19The main features of this transformation that we capture are the ON and OFF 20 dynamics (and their relationship to the brightness value of the stimulus); the activation 21 curve, the steady-state amplitude of the response as a function of light intensity as well 22 as a slow adaptation mechanism leading to a progressive decrease in the amplitude of 23 the response. These features can be captured using a five-state Markov k...

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“…Hence, computational modeling is fundamental to understanding the light-induced ionic transport in cell membranes, not only for cell physiology but also to develop new treatments. [34][35][36][37][38][39][40] Although the photoresponse of vf-Chrimson and vf-Chrimson-expressing neurons has only been recently experimentally studied, 10 it is also important to undertake a theoretical analysis to understand and optimize the photodynamics of this ultrafast red-shifted opsin.…”

Section: Introductionmentioning

confidence: 99%

Theoretical optimization of high-frequency optogenetic spiking of red-shifted very fast-Chrimson-expressing neurons

2019

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A detailed theoretical analysis and optimization of high-fidelity, high-frequency firing of the red-shifted very-fast-Chrimson (vf-Chrimson) expressing neurons is presented. A four-state model for vf-Chrimson photocycle has been formulated and incorporated in Hodgkin-Huxley and Wang-Buzsaki spiking neuron circuit models. The effect of various parameters that include irradiance, pulse width, frequency, expression level, and membrane capacitance has been studied in detail. Theoretical simulations are in excellent agreement with recently reported experimental results. The analysis and optimization bring out additional interesting features. A minimal pulse width of 1.7 ms at 23 mW∕mm 2 induces a peak photocurrent of 1250 pA. Optimal irradiance (0.1 mW∕mm 2) and pulse width (50 μs) to trigger action potential have been determined. At frequencies beyond 200 Hz, higher values of expression level and irradiance result in spike failure. Singlet and doublet spiking fidelity can be maintained up to 400 and 150 Hz, respectively. The combination of expression level and membrane capacitance is a crucial factor to achieve high-frequency firing above 500 Hz. Its optimization enables 100% spike probability of up to 1 kHz. The study is useful in designing new high-frequency optogenetic neural spiking experiments with desired spatiotemporal resolution, by providing insights into the temporal spike coding, plasticity, and curing neurodegenerative diseases.

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PyRhO: A Multiscale Optogenetics Simulation Platform

Cited by 24 publications

References 68 publications

Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate

Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate

Modeling the Electro-chemical Properties of Microbial Opsin ChrimsonR for Application to Optogenetics-based Vision Restoration

Theoretical optimization of high-frequency optogenetic spiking of red-shifted very fast-Chrimson-expressing neurons

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