Biology subjects

Whittaker, D. G.

Publications and source records attributed to Whittaker, D. G..

5 recordsLinked to original sources

bioRxiv2024

A range of voltage-clamp protocol designs for rapid capture of hERG kinetics

We provide details of a series of short voltage-clamp protocols designed for gathering a large amount of information on hERG (Kv11.1) ion channel gating. The protocols have a limited number of steps and consist only of steps and ramps, making them easy to implement on any patch clamp setup, including automated platforms. The primary objective is to assist with parameterisation, selection and refinement of mathematical models of hERG gating. We detail a series of manual and automated model-driven designs, together with an explanation of their rationale and design criteria. Although the protocols are intended to study hERG1a currents, the approaches could be easily extended and generalised to other ion channel currents.

biophysics↗

bioRxiv2024

Optimal experimental designs for characterising ion channel gating by filling the phase-voltage space of model dynamics

Voltage-clamp waveforms are imposed in the patch-clamp electrophysiology technique to provoke ion currents, the particular waveform that is used is known as the voltage-clamp protocol. Designing protocols to probe and quantify how gating for a particular ion channel occurs has typically been done manually and results in a suite of long protocols. It is desirable to gain the same, or even more, information in a shorter time, and also to automate the process of designing these protocols. In this paper we introduce a new optimal experimental design objective for ion channel characterisation, which involves considering a 3-dimensional phase space for the channel states combined with the voltage, using room-temperature hERG/Kv11.1 currents as an example. A range of designs are proposed, the best of which visits 82% of the discretised phase-voltage space in a 9 second protocol. This new protocol design strategy results in a simulated current visiting a wide range of channel gating states, at a wide variety of voltages, and we therefore expect these designs to be very useful in characterising ion currents, parameterising models, as well as being a challenging test of assumptions made about ion channel gating.

biophysics↗

bioRxiv2023

The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk

Background and PurposeDrug-induced reduction of the rapid delayed rectifier potassium current carried by the human Ether-a-go-go-Related Gene (hERG) channel is associated with increased risk of arrhythmias. Recent updates to drug safety regulatory guidelines attempt to capture each drugs hERG binding mechanism by combining in vitro assays with in silico simulations. In this study, we investigate the impact on in silico proarrhythmic risk predictions due to uncertainty in the hERG binding mechanism and physiological hERG current model. Experimental ApproachPossible pharmacological binding models were designed for the hERG channel to account for known and postulated small molecule binding mechanisms. After selecting a subset of plausible binding models for each compound through calibration to available voltage-clamp electrophysiology data, we assessed their effects, and the effects of different physiological models, on proarrhythmic risk predictions. Key ResultsFor some compounds, multiple binding mechanisms can explain the same data produced under the safety testing guidelines, which results in different inferred binding rates. This can result in substantial uncertainty in the predicted torsade risk, which often spans more than one risk category. By comparison, we found that the effect of a different hERG physiological current model on risk classification was subtle. Conclusion and ImplicationsThe approach developed in this study assesses the impact of uncertainty in hERG binding mechanisms on predictions of drug-induced proarrhythmic risk. For some compounds, these results imply the need for additional binding data to decrease uncertainty in safety-critical applications.

biophysics↗

bioRxiv2022

Ion channel model reduction using manifold boundaries

Mathematical models of voltage-gated ion channels are used in basic research, industrial and clinical settings. These models range in complexity, but typically contain numerous variables representing the proportion of channels in a given state, and parameters describing the voltage-dependent rates of transition between states. An open problem is selecting the appropriate degree of complexity and structure for an ion channel model given data availability. Here, we simplify a model of the cardiac human Ether-a-go-go Related Gene (hERG) potassium ion channel, which carries cardiac IKr, using the manifold boundary approximation method (MBAM). The MBAM approximates high-dimensional model-output manifolds by reduced models describing their boundaries, resulting in models with fewer parameters (and often variables). We produced a series of models of reducing complexity starting from an established 5-state hERG model with 15 parameters. Models with up to 3 fewer states and 8 fewer parameters were shown to retain much of the predictive capability of the full model and were validated using experimental hERG1a data collected in HEK293 cells at 37{degrees}C. The method provides a way to simplify complex models of ion channels that improves parameter identifiability and will aid in future model development.

biophysics↗

bioRxiv2019

Accounting for variability in ion current recordings using a mathematical model of artefacts in voltage-clamp experiments

Mathematical models of ion channels, which constitute indispensable components of action potential models, are commonly constructed by fitting to whole-cell patch-clamp data. In a previous study we fitted cell-specific models to hERG1a (Kv11.1) recordings simultaneously measured using an automated high-throughput system, and studied cell-cell variability by inspecting the resulting model parameters. However, the origin of the observed variability was not identified. Here we study the source of variability by constructing a model that describes not just ion current dynamics, but the entire voltage-clamp experiment. The experimental artefact components of the model include: series resistance, membrane and pipette capacitance, voltage offsets, imperfect compensations made by the amplifier for these phenomena, and leak current. In this model, variability in the observations can be explained by either cell properties, measurement artefacts, or both. Remarkably, by assuming that variability arises exclusively from measurement artefacts, it is possible to explain a larger amount of the observed variability than when assuming cell-specific ion current kinetics. This assumption also leads to a smaller number of model parameters. This result suggests that most of the observed variability in patch-clamp data measured under the same conditions is caused by experimental artefacts, and hence can be compensated for in post-processing by using our model for the patch-clamp experiment. This study has implications for the question of the extent to which cell-cell variability in ion channel kinetics exists, and opens up routes for better correction of artefacts in patch-clamp data.

biophysics↗