Prediction of Sub-Monomer A2 Domain Dynamics of the von Willebrand Factor by Machine Learning Algorithm and Coarse-Grained Molecular Dynamics Simulation

• Published in: Scientific reports Vol. 9; no. 1; pp. 9037 - 11
• Main Authors: Morabito, Michael J., Usta, Mustafa, Cheng, Xuanhong, Zhang, Xiaohui F., Oztekin, Alparslan, Webb, Edmund B.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21.06.2019; Nature Publishing Group
• Subjects: 631/57/2266; 631/57/2272/2273; Algorithms; Artificial intelligence; Biopolymers; Conformation; Humanities and Social Sciences; Humans; Learning algorithms; Machine Learning; Macromolecules; Molecular dynamics; Molecular Dynamics Simulation; multidisciplinary; Polymers; Protein Conformation; Science; Science (multidisciplinary); Von Willebrand factor; von Willebrand Factor - chemistry
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-44044-2

We develop a machine learning tool useful for predicting the instantaneous dynamical state of sub-monomer features within long linear polymer chains, as well as extracting the dominant macromolecular motions associated with sub-monomer behaviors of interest. We employ the tool to better understand and predict sub-monomer A2 domain unfolding dynamics occurring amidst the dominant large-scale macromolecular motions of the biopolymer von Willebrand Factor (vWF) immersed in flow. Results of coarse-grained Molecular Dynamics (MD) simulations of non-grafted vWF multimers subject to a shearing flow were used as input variables to a Random Forest Algorithm (RFA). Twenty unique features characterizing macromolecular conformation information of vWF multimers were used for training the RFA. The corresponding responses classify instantaneous A2 domain state as either folded or unfolded, and were directly taken from coarse-grained MD simulations. Three separate RFAs were trained using feature/response data of varying resolution, which provided deep insights into the highly correlated macromolecular dynamics occurring in concert with A2 domain unfolding events. The algorithm is used to analyze results of simulation, but has been developed for use with experimental data as well.