Comparison Between All-Atom and Coarse-Grained Dynamics Simulations for Predicting Mechanical Properties of Proteins
Year: 2025
Type: article
Abstract: In this work, we perform all-atom and coarse-grained dynamics simulations to predict the mechanical properties of a typical synthetic protein system. Previous experiments showed that proteins with a larger molecular weight exhibit better mechanical performance. Our steered molecular dynamics (SMD) simulations at the all-atom level only capture intermolecular interactions and fail to reproduce this tendency. The results of the dissipative particle dynamics (DPD) simulations at the coarse-grained level are consistent with experiments. The comparison between two levels of resolution highlights the importance of simulation scales in predicting mechanical properties of complex systems. We also reveal some underlying factors correlated with the mechanical properties of synthetic proteins, such as molecular weights, fabrication processes, the ratio of hydrophobic to hydrophilic segments and their order in the amino acid sequences.
Authors: Zihan He, Liangxu Xie, Binbin Xie, Lin Shen
Institutions: Beijing Normal University, Jiangsu University of Technology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: diamond
OpenAlex ID: W4413279758