TY - JOUR
T1 - Comparison Between All-Atom and Coarse-Grained Dynamics Simulations for Predicting Mechanical Properties of Proteins
AU - He , Zihan
AU - Xie , Liangxu
AU - Xie , Binbin
AU - Shen , Lin
JO - Communications in Computational Chemistry
VL - 3
SP - 243
EP - 248
PY - 2025
DA - 2025/09
SN - 7
DO - http://doi.org/10.4208/cicc.2025.217.01
UR - https://global-sci.org/intro/article_detail/cicc/24345.html
KW - steered molecular dynamics, dissipative particle dynamics, mechanical property, silk protein, multiscale simulation.
AB - <p style="text-align: justify;">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.</p>