Untangling the molecular mechanism of SpCas9 catalytic activation

Mar 4, 2025·
Shaoyong Lu
,
Xinyi Li
,
Jiacheng Wei
Feiying Chen
Feiying Chen
,
Mingyu Li
,
Ning Liu
,
Jian Zhang
· 1 min read
SpCas9 activation and allosteric mechanism overview.
Abstract
This manuscript combines 160 microseconds of unbiased molecular dynamics simulations with Markov state modeling, in-vitro cleavage assays, and a cellular fluorescence reporter system to explain SpCas9 catalytic activation. It proposes a gear-and-wedge model in which L1 linker folding and L2 linker unfolding drive HNH domain relocation, while REC2 stabilizes activation intermediates.
Type
Publication
Under review
Status
Open access
publications

Citation. Shaoyong Lu, Xinyi Li, Jiacheng Wei, Feiying Chen, Mingyu Li, Ning Liu, and Jian Zhang. Untangling the molecular mechanism of SpCas9 catalytic activation: A gear-and-wedge fitting model. Under review.

This manuscript links atomistic simulation to biochemical and cellular validation, showing how linker remodeling and REC2-domain motion coordinate the large HNH-domain displacement required for SpCas9 activation.

CRISPR-Cas9 Molecular Dynamics Protein Engineering
Feiying Chen
Authors
Feiying Chen
PhD Student in Biology
Feiying Chen is a PhD student in Biology at Tsinghua University. His research interests include perturbation biology, AI virtual cell modeling, single-cell transcriptomics, AI-driven drug discovery, and phenotype-based drug design.