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Differentiable simulation to develop molecular dynamics force fields for disordered proteins.

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Peer-reviewed

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Abstract

Implicit solvent force fields are computationally efficient but can be unsuitable for running molecular dynamics on disordered proteins. Here I improve the a99SB-disp force field and the GBNeck2 implicit solvent model to better describe disordered proteins. Differentiable molecular simulations with 5 ns trajectories are used to jointly optimise 108 parameters to better match explicit solvent trajectories. Simulations with the improved force field better reproduce the radius of gyration and secondary structure content seen in experiments, whilst showing slightly degraded performance on folded proteins and protein complexes. The force field, called GB99dms, reproduces the results of a small molecule binding study and improves agreement with experiment for the aggregation of amyloid peptides. GB99dms, which can be used in OpenMM, is available at https://github.com/greener-group/GB99dms. This work is the first to show that gradients can be obtained directly from nanosecond-length differentiable simulations of biomolecules and highlights the effectiveness of this approach to training whole force fields to match desired properties.

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Acknowledgements: I thank the Sjors Scheres group and Conny Yu for useful discussions; all contributors to Molly.jl; William Moses and Valentin Churavy for support with Enzyme.jl; Jake Grimmett, Toby Darling and Ivan Clayson for help with high-performance computing; and D. E. Shaw Research for providing data. This work was supported by the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) [MC_UP_1201/33]. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.

Keywords

34 Chemical Sciences, 3407 Theoretical and Computational Chemistry, Bioengineering

Journal Title

Chem Sci

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Journal ISSN

2041-6520
2041-6539

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Publisher

Royal Society of Chemistry (RSC)
Sponsorship
Medical Research Council (MC_UP_1201/33)