BEGIN:VCALENDAR VERSION:2.0 PRODID:-//jEvents 2.0 for Joomla//EN CALSCALE:GREGORIAN METHOD:PUBLISH BEGIN:VEVENT UID:f4008e526f1a075388ae267b9ae26c03 CATEGORIES:Physical Chemistry Seminar CREATED:20210226T181052 SUMMARY:Prof. Giulia Palermo, UC Riverside DESCRIPTION:Multi-scaling the CRISPR-Cas Revolution from Gene Editing to Viral Detectio n\n \nIn recent years, CRISPR has become synonymous with a transformative g enome editing technology that is innovating life science with cutting-edge impact in basic and applied sciences. By enabling the correction of DNA mut ations, the CRISPR technology promises to treat a myriad of human genetic d iseases, impacting also pharmaceutics, biofuel production, and agriculture with the development of drought-resistant crops. I will report about the us e of computational approaches to clarify the molecular basis underlying the genome editing function of CRISPR-Cas9 and newly discovered CRISPR systems that are emerging as powerful tools for viral detection, including the SAR S-CoV-2 coronavirus that has posed the current pandemic. We have implemente d a multiscale approach, which revealed the mechanistic basis of nucleic ac id binding, catalysis, selectivity, and allostery in CRISPR systems. We com bined classical molecular dynamics (MD) and enhanced simulation methods to characterize the dynamics of the Cas9 endonuclease and its interplay with n ucleic acids over long timescales. Using a Gaussian accelerated MD method, which enables routine access to millisecond timescales, and the Anton-2 sup ercluster we determined the formation of a catalytically active state, whic h is prone to DNA cleavages. These computational predictions have been conf irmed by single-molecule FRET experiments and by the recent determination t hrough cryo-EM of the activated structure, which remarkably overlaps our mo del. By applying network models derived from graph theory, we have characte rized a mechanism of allosteric regulation, transferring the information of DNA binding to the catalytic sites for cleavages. This mechanism is now be ing probed in novel Anti-CRISPR proteins, forming multi-mega Dalton complex es with the CRISPR enzyme and used for gene regulation and control. A mixed Quantum Mechanics/Molecular Mechanics (QM/MM) approach is being used to es tablish the catalytic mechanism of DNA cleavage and the critical role of me tal ions, with the ultimate goal of providing information for improving the catalytic efficiency and the specificity of CRISPR-Cas9. Finally, by using multi-microsecond MD simulations we have recently probed a mechanism of DN A-induced of activation in the Cas12a enzyme, which underlies the detection of viral genetic elements, including the SARS-CoV-2 coronavirus. Overall, our outcomes contribute to addressing the mechanistic function of the CRISP R system, providing information that is critical for novel engineering and that could impact the development of improved genome editing tools for biom edical applications.\nHosted by Professor Richard Remsing\n \nFor Webex mee ting information, please contact Loretta Lupo @ (mailto:lal275@chem.rutger s.edu)This email address is being protected from spambots. You need JavaScr ipt enabled to view it.\n X-ALT-DESC;FMTTYPE=text/html:
Multi-scaling the CRISPR-Cas Revolution from Gene Editing to Viral Det ection
In recent y ears, CRISPR has become synonymous with a transformative genome editing tec hnology that is innovating life science with cutting-edge impact in basic a nd applied sciences. By enabling the correction of DNA mutations, the CRISP R technology promises to treat a myriad of human genetic diseases, impactin g also pharmaceutics, biofuel production, and agriculture with the developm ent of drought-resistant crops. I will report about the use of computa tional approaches to clarify the molecular basis underlying the genome edit ing function of CRISPR-Cas9 and newly discovered CRISPR systems that are em erging as powerful tools for viral detection, including the SARS-CoV-2 coro navirus that has posed the current pandemic. We have implemented a multisca le approach, which revealed the mechanistic basis of nucleic acid binding, catalysis, selectivity, and allostery in CRISPR systems. We combined classi cal molecular dynamics (MD) and enhanced simulation methods to characterize the dynamics of the Cas9 endonuclease and its interplay with nucleic acids over long timescales. Using a Gaussian accelerated MD method, which enable s routine access to millisecond timescales, and the Anton-2 supercluster we determined the formation of a catalytically active state, which is prone t o DNA cleavages. These computational predictions have been confirmed by sin gle-molecule FRET experiments and by the recent determination through cryo- EM of the activated structure, which remarkably overlaps our model. By appl ying network models derived from graph theory, we have characterized a mech anism of allosteric regulation, transferring the information of DNA binding to the catalytic sites for cleavages. This mechanism is now being probed i n novel Anti-CRISPR proteins, forming multi-mega Dalton complexes with the CRISPR enzyme and used for gene regulation and control. A mixed Quantum Mec hanics/Molecular Mechanics (QM/MM) approach is being used to establish the catalytic mechanism of DNA cleavage and the critical role of metal ions, wi th the ultimate goal of providing information for improving the catalytic e fficiency and the specificity of CRISPR-Cas9. Finally, by using multi-micro second MD simulations we have recently probed a mechanism of DNA-induced of activation in the Cas12a enzyme, which underlies the detection of viral ge netic elements, including the SARS-CoV-2 coronavirus. Overall, our outcomes contribute to addressing the mechanistic function of the CRISPR syste m, providing information that is critical for novel engineering and th at could impact the development of improved genome editing tools for b iomedical applications.
Hosted by Professor Richard Remsing strong>
For Webex meeting information, please contact Lo
retta Lupo @