Display options
Cite
Palermo G, Chen JS, Ricci CG, et al. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys. 2018;51doi: 10.1017/S0033583518000070.
Palermo, G., Chen, J. S., Ricci, C. G., Rivalta, I., Jinek, M., Batista, V. S., Doudna, J. A., & McCammon, J. A. (2018). Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Quarterly reviews of biophysics, 51. https://doi.org/10.1017/S0033583518000070
Palermo, Giulia, et al. "Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain." Quarterly reviews of biophysics vol. 51 (2018). doi: https://doi.org/10.1017/S0033583518000070
Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys. 2018;51. doi: 10.1017/S0033583518000070. Epub 2018 Aug 03. PMID: 30555184; PMCID: PMC6292676.
Copy Download .nbib Format: NLM
Share it on

Q Rev Biophys. 2018;51. doi: 10.1017/S0033583518000070. Epub 2018 Aug 03.

Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.

Quarterly reviews of biophysics

Giulia Palermo, Janice S Chen, Clarisse G Ricci, Ivan Rivalta, Martin Jinek, Victor S Batista, Jennifer A Doudna, J Andrew McCammon

Affiliations

  1. Department of Bioengineering, University of California, Riverside, CA 92507.
  2. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
  3. Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
  4. Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
  5. Université de Lyon, École Normale Supérieure (ENS) de Lyon, CNRS, Lyon 1, France.
  6. Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
  7. Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107, USA.
  8. Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.
  9. Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
  10. Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA.
  11. National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA.
  12. San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.

PMID: 30555184 PMCID: PMC6292676 DOI: 10.1017/S0033583518000070

Abstract

Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 - a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution - reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1-3 regions 'sense' nucleic acids, 'regulate' the HNH conformational transition, and ultimately 'lock' the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1-3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.

Keywords: CRISPR–Cas9; genome editing; molecular dynamics; protein/nucleic acid interactions

Conflict of interest statement

Conflict of interest. None.

References

  1. EMBO J. 2018 May 15;37(10): - PubMed
  2. J Chem Theory Comput. 2015 Aug 11;11(8):3584-3595 - PubMed
  3. Nat Commun. 2017 Nov 9;8(1):1375 - PubMed
  4. Nat Commun. 2016 Sep 14;7:12778 - PubMed
  5. Sci Rep. 2016 Jan 29;6:19940 - PubMed
  6. Cell. 2014 Feb 27;156(5):935-49 - PubMed
  7. Science. 2014 Mar 14;343(6176):1247997 - PubMed
  8. Nat Commun. 2017 Nov 10;8(1):1430 - PubMed
  9. Curr Opin Struct Biol. 2017 Apr;43:68-78 - PubMed
  10. Science. 2016 Jan 1;351(6268):84-8 - PubMed
  11. J Chem Phys. 2013 Oct 28;139(16):164106 - PubMed
  12. ACS Cent Sci. 2016 Oct 26;2(10):756-763 - PubMed
  13. Nat Commun. 2017 Oct 23;8(1):1095 - PubMed
  14. Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3036-3041 - PubMed
  15. Nature. 2016 Jan 28;529(7587):490-5 - PubMed
  16. Mol Simul. 2016;42(13):1046-1055 - PubMed
  17. J Chem Theory Comput. 2017 Aug 8;13(8):3927-3935 - PubMed
  18. Nature. 2014 Sep 25;513(7519):569-73 - PubMed
  19. J Phys Chem B. 2016 Aug 25;120(33):8313-20 - PubMed
  20. Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6584-6589 - PubMed
  21. Nature. 2015 Nov 5;527(7576):110-3 - PubMed
  22. J Am Chem Soc. 2016 Aug 24;138(33):10374-7 - PubMed
  23. Biophys J. 2007 Jun 1;92(11):3817-29 - PubMed
  24. Chem Rev. 2018 Apr 25;118(8):4177-4338 - PubMed
  25. Proteins. 1993 Dec;17(4):412-25 - PubMed
  26. J Chem Theory Comput. 2011 Sep 13;7(9):2886-2902 - PubMed
  27. Nat Biotechnol. 2018 Mar;36(3):265-271 - PubMed
  28. Science. 2016 Feb 19;351(6275):867-71 - PubMed
  29. J Am Chem Soc. 2018 Feb 28;140(8):2971-2984 - PubMed
  30. Annu Rev Biophys. 2017 May 22;46:505-529 - PubMed
  31. J Chem Theory Comput. 2013 Sep 10;9(9):3878-88 - PubMed
  32. J Chem Phys. 2005 Feb 1;122(5):54101 - PubMed
  33. Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):E516-25 - PubMed
  34. J Chem Theory Comput. 2017 Jan 10;13(1):340-352 - PubMed
  35. Sci Adv. 2017 Aug 04;3(8):eaao0027 - PubMed
  36. Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12162-12167 - PubMed
  37. J Am Chem Soc. 2018 Jun 27;140(25):7778-7781 - PubMed
  38. Science. 2015 Jun 26;348(6242):1477-81 - PubMed
  39. Nat Methods. 2016 Jan;13(1):24-7 - PubMed
  40. Science. 2012 Aug 17;337(6096):816-21 - PubMed
  41. Nature. 2017 Oct 19;550(7676):407-410 - PubMed
  42. Sci Rep. 2017 Dec 8;7(1):17271 - PubMed
  43. Science. 2014 Nov 28;346(6213):1258096 - PubMed
  44. Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7260-7265 - PubMed
  45. Acc Chem Res. 2015 Feb 17;48(2):220-8 - PubMed
  46. J Chem Theory Comput. 2013 Feb 12;9(2):857-62 - PubMed
  47. Proteins. 2006 Mar 1;62(4):1053-61 - PubMed
  48. J Am Chem Soc. 2017 Nov 15;139(45):16028-16031 - PubMed

Substances

MeSH terms

Publication Types

Grant support