2019
DOI: 10.1021/acs.jcim.8b00988
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Structure and Dynamics of the CRISPR–Cas9 Catalytic Complex

Abstract: CRISPR−Cas9 is a bacterial immune system with exciting applications for genome editing. In spite of extensive experimental characterization, the active site chemistry of the RuvC domainwhich performs DNA cleavageshas remained elusive. Its knowledge is key for structure-based engineering aimed at improving DNA cleavages. Here, we deliver an in-depth characterization by using quantum-classical (QM/MM) molecular dynamics (MD) simulations and a Gaussian accelerated MD method, coupled with bioinformatics analysis… Show more

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Cited by 67 publications
(124 citation statements)
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“…Understanding the catalytic mechanism involved in accurate editing by CRISPR/Cas9 is particularly important, but it has been poorly addressed so far, due to uncertainties in the available Figure 8b) (40). This agrees well with the requirements for the catalysis, as it favors an in-line SN2-like nucleophilic attack.…”
Section: Simulations Of Crispr/cas9 Complexessupporting
confidence: 53%
See 1 more Smart Citation
“…Understanding the catalytic mechanism involved in accurate editing by CRISPR/Cas9 is particularly important, but it has been poorly addressed so far, due to uncertainties in the available Figure 8b) (40). This agrees well with the requirements for the catalysis, as it favors an in-line SN2-like nucleophilic attack.…”
Section: Simulations Of Crispr/cas9 Complexessupporting
confidence: 53%
“…This has been a difficulty in obtaining the mechanistic details of how the catalytic Mg 2+ ions meditate the concerted DNA strand cleavage by two domains of Cas9. However, this issue has been overcome by employing density functional theory (DFT) based quantum-mechanics/molecular-mechanics (QM/MM) hybrid quantum/classical simulations (40), which are presented later in this review. However, the authors also pointed out that the conclusions from MD trajectories could be affected by the limitations of available simulation techniques.…”
Section: Molecular Mechanism Of Crispr/cas9mentioning
confidence: 99%
“…A GaMD method has been employed (Miao et al, 2015), adding a boost potential to the simulation that accelerates transitions between low-energy states (see section "Materials and Methods"). The method has been shown to enhance a broad sampling of the conformational space in large biomolecular systems McCammon, 2016, 2018;Wang and Chan, 2017;Liao and Wang, 2018;Sibener et al, 2018), including CRISPR-Cas9 as apo form and in complex with nucleic acids (Palermo et al, 2017;Palermo, 2019b), or bound to off-target DNAs (Ricci et al, 2019). Recently, GaMD has shown to sample long time scale motions in agreement with NMR relaxation experiments, showing that the method can efficiently capture the dynamics of large protein/nucleic acid complexes (East et al, 2020).…”
Section: Resultsmentioning
confidence: 96%
“…Based on extensive tests on the CRISPR-Cas9 system, 14,[39][40] the system threshold energy is = ,"-for all GaMD simulations. The boost potential was applied in a dual-boost scheme, in which two acceleration potentials are applied simultaneously to the system: (i) the torsional terms only and (ii) across the entire potential.…”
Section: Molecular Dynamics (Md) Simulationsmentioning
confidence: 99%