Machine Learning Coarse-Grained Potentials of Protein Thermodynamics

Abstract

A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.

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Cited by in corpus (7)

• Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
• TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations
• A perspective on protein structure prediction using quantum computers
• AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics
• Scaling Graph Neural Networks to Large Proteins
• Constraint Decoupled Latent Diffusion for Protein Backmapping
• Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model