Derivative-free optimization of rate parameters of capsid assembly models from bulk in vitro data

TL;DR

This paper demonstrates that derivative-free optimization methods can efficiently and accurately infer kinetic rate parameters of virus capsid assembly models from bulk in vitro data, even with noisy and limited datasets.

Contribution

It introduces the application of derivative-free optimization techniques to improve parameter inference in capsid assembly models using experimental data.

Findings

DFO methods outperform traditional approaches in speed and accuracy

Rich data sources significantly enhance model fitting quality

DFO methods are robust to noisy and limited data

Abstract

The assembly of virus capsids from free coat proteins proceeds by a complicated cascade of association and dissociation steps, the great majority of which cannot be directly experimentally observed. This has made capsid assembly a rich field for computational models to attempt to fill the gaps in what is experimentally observable. Nonetheless, accurate simulation predictions depend on accurate models and there are substantial obstacles to model inference for such systems. Here, we describe progress in learning parameters for capsid assembly systems, particularly kinetic rate constants of coat-coat interactions, by computationally fitting simulations to experimental data. We previously developed an approach to learn rate parameters of coat-coat interactions by minimizing the deviation between real and simulated light scattering data monitoring bulk capsid assembly in vitro. This is a difficult data-fitting problem, however, because of the high computational cost of simulating assembly trajectories, the stochastic noise inherent to the models, and the limited and noisy data available for fitting. Here we show that a newer classes of methods, based on derivative-free optimization (DFO), can more quickly and precisely learn physical parameters from static light scattering data. We further explore how the advantages of the approaches might be affected by alternative data sources through simulation of a model of time-resolved mass spectrometry data, an alternative technology for monitoring bulk capsid assembly that can be expected to provide much richer data. The results show that advances in both the data and the algorithms can improve model inference, with rich data leading to high-quality fits for all methods, but DFO methods showing substantial advantages over less informative data sources better representative of the current experimental practice.