Doing Charges Right: Modelling Ion-Controlled Biological Processes with the Correct Toolbox

Introduction

Electrical stimuli are essential for a plethora of biological functions. Unlike in electronics, where electrons form currents, nature rather exploits ions as charge carriers. Lack of a consistent molecular picture of the action of ions impairs progress in fundamental understanding of ion-controlled biological processes and in designing smart strategies for fixing ion-related pathological conditions.

Molecular Simulations

Molecular simulations represent a powerful tool for modelling such processes; however, they can only be as good as the underlying interaction model (force field). A major drawback of commonly used force fields is the lack of description of electronic polarization, which results in severe artifacts such as a dramatic over-binding of ions. This prevents, for example, accurate modelling of calcium signalling processes. This now well-recognized deficiency hampers faithful modelling of complex ion-involving biological processes.

Proposed Solution

We will employ machine learning techniques to build a de novo comprehensive force field for biological systems that accounts for electronic polarization in a mean field way via charge scaling. This approach will qualitatively improve modelling of ions in biological contexts without additional computational costs.

Relevant Ion-Specific Processes

This will allow us to address accurately the following highly relevant ion-specific processes of increasing complexity from molecular over cellular to organ levels:

1. Dissolution of radical anions of aromatic molecules as key intermediates in technologically and biologically important non-enzymatic and enzymatic Birch reduction processes.
2. Direct membrane translocation of cationic cell-penetrating peptides with a potential for drug delivery.
3. Circulation of calcium ions as signalling charge carriers through ion channels of hair cells in the cochlea.

Community Contribution

At the same time, the newly developed charge scaled force field will be made freely available to the community for further development and ready to be used within major simulation program packages.