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Skeens E, East KW, Lisi GP. 1H, 13C, 15 N backbone resonance assignment of the recognition lobe subdomain 3 (Rec3) from Streptococcus pyogenes CRISPR-Cas9. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:25-28. [PMID: 32935194 PMCID: PMC8635283 DOI: 10.1007/s12104-020-09977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
Rec3 is a subdomain of the recognition (Rec) lobe within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated protein Cas9 that is involved in nucleic acid binding and is critical to HNH endonuclease activation. Here, we report the backbone resonance assignments of an engineered construct of the Rec3 subdomain from Streptococcus pyogenes Cas9. We also analyze backbone chemical shift data to predict secondary structure and an overall fold that is consistent with that of Rec3 from the full-length S. pyogenes Cas9 protein.
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Kyle W East
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA
| | - George P Lisi
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA.
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Backbone-independent NMR resonance assignments of methyl probes in large proteins. Nat Commun 2021; 12:691. [PMID: 33514730 PMCID: PMC7846771 DOI: 10.1038/s41467-021-20984-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/09/2020] [Indexed: 11/08/2022] Open
Abstract
Methyl-specific isotope labeling is a powerful tool to study the structure, dynamics and interactions of large proteins and protein complexes by solution-state NMR. However, widespread applications of this methodology have been limited by challenges in obtaining confident resonance assignments. Here, we present Methyl Assignments Using Satisfiability (MAUS), leveraging Nuclear Overhauser Effect cross-peak data, peak residue type classification and a known 3D structure or structural model to provide robust resonance assignments consistent with all the experimental inputs. Using data recorded for targets with known assignments in the 10-45 kDa size range, MAUS outperforms existing methods by up to 25,000 times in speed while maintaining 100% accuracy. We derive de novo assignments for multiple Cas9 nuclease domains, demonstrating that the methyl resonances of multi-domain proteins can be assigned accurately in a matter of days, while reducing biases introduced by manual pre-processing of the raw NOE data. MAUS is available through an online web-server.
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East KW, Newton JC, Morzan UN, Narkhede Y, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP. Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. J Am Chem Soc 2020; 142:1348-1358. [PMID: 31885264 PMCID: PMC7497131 DOI: 10.1021/jacs.9b10521] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian-accelerated molecular dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond time scale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome-editing capability.
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Affiliation(s)
- Kyle W. East
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Jocelyn C. Newton
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Yogesh Narkhede
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Erin Skeens
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
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NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes. Biophys Rev 2019; 12:155-174. [PMID: 31838649 DOI: 10.1007/s12551-019-00609-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022] Open
Abstract
Allostery is a ubiquitous biological mechanism in which a distant binding site is coupled to and drastically alters the function of a catalytic site in a protein. Allostery provides a high level of spatial and temporal control of the integrity and activity of biomolecular assembles composed of proteins, nucleic acids, or small molecules. Understanding the physical forces that drive allosteric coupling is critical to harnessing this process for use in bioengineering, de novo protein design, and drug discovery. Current microscopic models of allostery highlight the importance of energetics, structural rearrangements, and conformational fluctuations, and in this review, we discuss the synergistic use of solution NMR spectroscopy and computational methods to probe these phenomena in allosteric systems, particularly protein-nucleic acid complexes. This combination of experimental and theoretical techniques facilitates an unparalleled detection of subtle changes to structural and dynamic equilibria in biomolecules with atomic resolution, and we provide a detailed discussion of specialized NMR experiments as well as the complementary methods that provide valuable insight into allosteric pathways in silico. Lastly, we highlight two case studies to demonstrate the adaptability of this approach to enzymes of varying size and mechanistic complexity.
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