Piecewise All-Atom SMD Simulations Reveal Key Secondary Structures in Luciferase Unfolding Pathway.
Journal Article (Journal Article)
Although the folding of single-domain proteins is well characterized theoretically and experimentally, the folding of large multidomain proteins is less well known. Firefly luciferase, a 550 residue three-domain protein, has been commonly used as a substrate to study chaperone reactions and as a model system for the study of folding of long polypeptide chains, including related phenomena such as cotranslational folding. Despite being characterized by various experimental techniques, the atomic-level contributions of various secondary structures of luciferase to its fold's mechanical stability remain unknown. Here, we developed a piecewise approach for all-atom steered molecular dynamics simulations to examine specific secondary structures that resist mechanical unfolding while minimizing the amount of computational resources required by the large water box of standard all-atom steered molecular dynamics simulations. We validated the robustness of this approach with a small NI3C protein and used our approach to elucidate the specific secondary structures that provide the largest contributions to luciferase mechanostability. In doing so, we show that piecewise all-atom steered molecular dynamics simulations can provide novel atomic resolution details regarding mechanostability and can serve as a platform for novel mutagenesis studies as well as a point for comparison with high-resolution force spectroscopy experiments.
Full Text
Duke Authors
Cited Authors
- Zhang, P; Wang, D; Yang, W; Marszalek, PE
Published Date
- December 2020
Published In
Volume / Issue
- 119 / 11
Start / End Page
- 2251 - 2261
PubMed ID
- 33130123
Pubmed Central ID
- PMC7732773
Electronic International Standard Serial Number (EISSN)
- 1542-0086
International Standard Serial Number (ISSN)
- 0006-3495
Digital Object Identifier (DOI)
- 10.1016/j.bpj.2020.10.023
Language
- eng