Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins.

Abstract

Elucidating protein dynamics is crucial for deciphering fundamental biological processes, from enzyme catalysis to cellular signaling, as its dysregulation directly causes protein misfolding diseases such as Alzheimer's and Parkinson's. While artificial intelligence has revolutionized static protein structure prediction, capturing the high-dimensional dynamics of protein folding remains a formidable challenge that limits our ability to fully understand these vital biological phenomena. Here we present DA2-GRASP, a computational framework that overcomes this barrier by integrating deep learning with advanced sampling techniques to map protein folding pathways with unprecedented efficiency and accuracy. DA2-GRASP learns low-dimensional latent representations of protein conformations via a variational autoencoder and combines multidirectional generative sampling guided by local potential energy gradients to efficiently steer conformational transitions along energetically favorable paths, enabling accurate and efficient reconstruction of folding pathways. Our method achieves sublinear computational scaling with sequence length, contrasting the quadratical scaling of molecular dynamics-based conventional approaches, enabling tractable simulations. It maintains high precision in quantifying mutation-induced perturbations to folding thermodynamics, crucial for understanding disease mutations. It also enables atomistic characterization of the folding process of medium-sized proteins such as ubiquitin and small ubiquitin-like modifier (SUMO, ∼80 residues) on standard workstations, a task typically requiring specialized supercomputing platforms such as Anton. Analysis of these proteins provides new mechanistic insights into how structurally similar folds with low sequence identity navigate divergent folding pathways. DA2-GRASP thus establishes a versatile and powerful framework for exploring protein-folding dynamics and their functional consequences.