As {Simple} {As} {Possible}, but {Not} {Simpler}: {Exploring} the {Fidelity} of {Coarse}-{Grained} {Protein} {Models} for {Simulated} {Force} {Spectroscopy}

Publication Type
Journal Article
Year of Publication
Habibi, Mona
Rottler, Jörg
Plotkin, Steven S.
Name of Publication
PLOS Computational Biology
Biochemical simulations, Melting, Protein structure, Protein structure comparison, Protein structure prediction, Relaxation (physics), Simulation and modeling, Superoxide dismutase

Author Summary Although experimentalists can now unfold single proteins in the lab by pulling them apart and measuring the force and extension, a clear idea of how the protein changes shape and loses structure during this process is currently missing. Molecular dynamics simulations can offer insight as to what is actually happening structurally when you pull a protein apart. However, typical simulations of processes that happen nearly instantaneously in the lab take weeks to perform, when every atom must be accounted for. Researchers have thus resorted to much faster “coarse-grained models”, where the system is simplified by removing select atoms and the remaining interactions rescaled, but the accuracy of such simulations are known to suffer as a result. How accurate or inaccurate are the current coarse-grained models in capturing the unfolding mechanisms of proteins? Our findings upon investigating this question suggest that, while coarse-grained models successfully capture early unfolding events of nearly-folded proteins, they suffer when trying to describe the late stages of unfolding in mostly-disordered proteins. By showing how coarse-grained models may fail to capture the accuracy of their more sophisticated but cumbersome counterparts, we can shed light on how to improve their reliability, increase their speed, and enhance their relevance in capturing biologically-relevant phenomena.