51
|
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.
Collapse
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
| |
Collapse
|
52
|
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y. Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States. Mol Cell 2019; 76:938-952.e5. [PMID: 31668930 PMCID: PMC6934045 DOI: 10.1016/j.molcel.2019.09.025] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/13/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022]
Abstract
High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.
Collapse
Affiliation(s)
- Wei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Zhi Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Chao Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangkang Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Raed Ibraheim
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Xue Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Min Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiuyu Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Sheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.
| |
Collapse
|
53
|
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.
Collapse
|
54
|
Zewde NT. Multiscale Solutions to Quantitative Systems Biology Models. Front Mol Biosci 2019; 6:119. [PMID: 31737643 PMCID: PMC6831518 DOI: 10.3389/fmolb.2019.00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/14/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nehemiah T Zewde
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| |
Collapse
|
55
|
Borišek J, Saltalamacchia A, Gallì A, Palermo G, Molteni E, Malcovati L, Magistrato A. Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations. Biomolecules 2019; 9:E633. [PMID: 31640290 PMCID: PMC6843770 DOI: 10.3390/biom9100633] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
The spliceosome accurately promotes precursor messenger-RNA splicing by recognizing specific noncoding intronic tracts including the branch point sequence (BPS) and the 3'-splice-site (3'SS). Mutations of Hsh155 (yeast)/SF3B1 (human), which is a protein of the SF3b factor involved in BPS recognition and induces altered BPS binding and 3'SS selection, lead to mis-spliced mRNA transcripts. Although these mutations recur in hematologic malignancies, the mechanism by which they change gene expression remains unclear. In this study, multi-microsecond-long molecular-dynamics simulations of eighth distinct ∼700,000 atom models of the spliceosome Bact complex, and gene sequencing of SF3B1, disclose that these carcinogenic isoforms destabilize intron binding and/or affect the functional dynamics of Hsh155/SF3B1 only when binding non-consensus BPSs, as opposed to the non-pathogenic variants newly annotated here. This pinpoints a cross-talk between the distal Hsh155 mutation and BPS recognition sites. Our outcomes unprecedentedly contribute to elucidating the principles of pre-mRNA recognition, which provides critical insights on the mechanism underlying constitutive/alternative/aberrant splicing.
Collapse
Affiliation(s)
- Jure Borišek
- CNR-IOM-Democritos National Simulation Center c/o SISSA, 34136 Trieste, Italy.
- National Institute of Chemistry, 1000 Ljubljana, Slovenia.
| | | | - Anna Gallì
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy.
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside CA 92521, USA.
| | - Elisabetta Molteni
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | - Luca Malcovati
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy.
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | | |
Collapse
|
56
|
Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q. Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. PLoS Biol 2019; 17:e3000496. [PMID: 31603896 PMCID: PMC6808508 DOI: 10.1371/journal.pbio.3000496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/23/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have been harnessed as powerful genome editing tools in diverse organisms. However, the off-target effects and the protospacer adjacent motif (PAM) compatibility restrict the therapeutic applications of these systems. Recently, a Streptococcus pyogenes Cas9 (SpCas9) variant, xCas9, was evolved to possess both broad PAM compatibility and high DNA fidelity. Through determination of multiple xCas9 structures, which are all in complex with single-guide RNA (sgRNA) and double-stranded DNA containing different PAM sequences (TGG, CGG, TGA, and TGC), we decipher the molecular mechanisms of the PAM expansion and fidelity enhancement of xCas9. xCas9 follows a unique two-mode PAM recognition mechanism. For non-NGG PAM recognition, xCas9 triggers a notable structural rearrangement in the DNA recognition domains and a rotation in the key PAM-interacting residue R1335; such mechanism has not been observed in the wild-type (WT) SpCas9. For NGG PAM recognition, xCas9 applies a strategy similar to WT SpCas9. Moreover, biochemical and cell-based genome editing experiments pinpointed the critical roles of the E1219V mutation for PAM expansion and the R324L, S409I, and M694I mutations for fidelity enhancement. The molecular-level characterizations of the xCas9 nuclease provide critical insights into the mechanisms of the PAM expansion and fidelity enhancement of xCas9 and could further facilitate the engineering of SpCas9 and other Cas9 orthologs.
Collapse
MESH Headings
- Amino Acid Substitution
- CRISPR-Associated Protein 9/chemistry
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Cloning, Molecular
- Clustered Regularly Interspaced Short Palindromic Repeats
- Crystallography, X-Ray
- DNA/chemistry
- DNA/genetics
- DNA/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Editing
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Isoenzymes/chemistry
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Klebsiella pneumoniae/genetics
- Klebsiella pneumoniae/metabolism
- Models, Molecular
- Mutagenesis, Site-Directed/methods
- Mutation
- Nucleotide Motifs
- Protein Binding
- Protein Engineering/methods
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Streptococcus pyogenes/genetics
- Streptococcus pyogenes/metabolism
Collapse
Affiliation(s)
- Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hongyuan Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yifei Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yu Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, Shanghai, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| |
Collapse
|
57
|
Borišek J, Saltalamacchia A, Spinello A, Magistrato A. Exploiting Cryo-EM Structural Information and All-Atom Simulations To Decrypt the Molecular Mechanism of Splicing Modulators. J Chem Inf Model 2019; 60:2510-2521. [DOI: 10.1021/acs.jcim.9b00635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jure Borišek
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrea Saltalamacchia
- International School for Advanced studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Spinello
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
58
|
Zuo Z, Zolekar A, Babu K, Lin VJT, Hayatshahi HS, Rajan R, Wang YC, Liu J. Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. eLife 2019; 8:e46500. [PMID: 31361218 PMCID: PMC6706240 DOI: 10.7554/elife.46500] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/21/2019] [Indexed: 12/21/2022] Open
Abstract
The CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (SpyCas9), along with a programmable single-guide RNA (sgRNA), has been exploited as a significant genome-editing tool. Despite the recent advances in determining the SpyCas9 structures and DNA cleavage mechanism, the cleavage-competent conformation of the catalytic HNH nuclease domain of SpyCas9 remains largely elusive and debatable. By integrating computational and experimental approaches, we unveiled and validated the activated Cas9-sgRNA-DNA ternary complex in which the HNH domain is neatly poised for cleaving the target DNA strand. In this catalysis model, the HNH employs the catalytic triad of D839-H840-N863 for cleavage catalysis, rather than previously implicated D839-H840-D861, D837-D839-H840, or D839-H840-D861-N863. Our study contributes critical information to defining the catalytic conformation of the HNH domain and advances the knowledge about the conformational activation underlying Cas9-mediated DNA cleavage.
Collapse
Affiliation(s)
- Zhicheng Zuo
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
- College of Chemistry and Chemical EngineeringShanghai University of Engineering ScienceShanghaiChina
| | - Ashwini Zolekar
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research CenterUniversity of OklahomaNormanUnited States
| | - Victor JT Lin
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Hamed S Hayatshahi
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research CenterUniversity of OklahomaNormanUnited States
| | - Yu-Chieh Wang
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Jin Liu
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| |
Collapse
|
59
|
Palermo G, Casalino L, Magistrato A, Andrew McCammon J. Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations. J Struct Biol 2019; 206:267-279. [PMID: 30880083 PMCID: PMC6637970 DOI: 10.1016/j.jsb.2019.03.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
Noncoding RNA (ncRNA) has a key role in regulating gene expression, mediating fundamental processes and diseases via a variety of yet unknown mechanisms. Here, we review recent applications of conventional and enhanced Molecular Dynamics (MD) simulations methods to address the mechanistic function of large biomolecular systems that are tightly involved in the ncRNA function and that are of key importance in life sciences. This compendium focuses of three biomolecular systems, namely the CRISPR-Cas9 genome editing machinery, group II intron ribozyme and the ribonucleoprotein complex of the spliceosome, which edit and process ncRNA. We show how the application of a novel accelerated MD simulations method has been key in disclosing the conformational transitions underlying RNA binding in the CRISPR-Cas9 complex, suggesting a mechanism for RNA recruitment and clarifying the conformational changes required for attaining genome editing. As well, we discuss the use of mixed quantum-classical MD simulations in deciphering the catalytic mechanism of RNA splicing as operated by group II intron ribozyme, one of the largest ncRNA structures crystallized so far. Finally, we debate the future challenges and opportunities in the field, discussing the recent application of MD simulations for unraveling the functional biophysics of the spliceosome, a multi-mega Dalton complex of proteins and small nuclear RNAs that performs RNA splicing in humans. This showcase of applications highlights the current talent of MD simulations to dissect atomic-level details of complex biomolecular systems instrumental for the design of finely engineered genome editing machines. As well, this review aims at inspiring future investigations of several other ncRNA regulatory systems, such as micro and small interfering RNAs, which achieve their function and specificity using RNA-based recognition and targeting strategies.
Collapse
Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, Bourns College of Engineering, University of California Riverside, 900 University Avenue, Riverside, CA 92521, United States.
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali, Democritos National Simulation Center c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States; Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, United States; National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093, United States
| |
Collapse
|
60
|
|
61
|
Ricci C, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS CENTRAL SCIENCE 2019; 5:651-662. [PMID: 31041385 PMCID: PMC6487449 DOI: 10.1021/acscentsci.9b00020] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Indexed: 05/02/2023]
Abstract
CRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its applicability. Here, all-atom enhanced molecular dynamics (MD) simulations-using Gaussian accelerated MD (GaMD)-are used to decipher the mechanism of off-target binding at the molecular level. GaMD reveals that base pair mismatches in the target DNA at distal sites with respect to the protospacer adjacent motif (PAM) can induce an extended opening of the RNA:DNA heteroduplex, which leads to newly formed interactions between the unwound DNA and the L2 loop of the catalytic HNH domain. These conserved interactions constitute a "lock" effectively decreasing the conformational freedom of the HNH domain and hampering its activation for cleavage. Remarkably, depending on their positions at PAM distal sites, DNA mismatches responsible for off-target cleavages are unable to "lock" the HNH domain, thereby leading to the unselective cleavage of DNA sequences. In consistency with the available experimental data, the ability to "lock" the catalytic HNH domain in an inactive "conformational checkpoint" is shown to be a key determinant in the onset of off-target effects. This mechanistic rationale contributes in clarifying a long lasting open issue in the CRISPR-Cas9 function and poses the foundation for designing novel and more specific Cas9 variants, which could be obtained by magnifying the "locking" interactions between HNH and the target DNA in the presence of any incorrect off-target sequence, thus preventing undesired cleavages.
Collapse
Affiliation(s)
- Clarisse
G. Ricci
- Department
of Pharmacology, Department of Chemistry and Biochemistry, and National Biomedical
Computation Resource, University of California
San Diego, La Jolla, California 92093, United States
| | - Janice S. Chen
- Department of Molecular
and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, Innovative Genomics
Institute, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, University
of California Berkeley, Berkeley, California 94720, United States
| | - Yinglong Miao
- Center
for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Martin Jinek
- Department
of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jennifer A. Doudna
- Department of Molecular
and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, Innovative Genomics
Institute, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, University
of California Berkeley, Berkeley, California 94720, United States
| | - J. Andrew McCammon
- Department
of Pharmacology, Department of Chemistry and Biochemistry, and National Biomedical
Computation Resource, University of California
San Diego, La Jolla, California 92093, United States
| | - Giulia Palermo
- Department
of Bioengineering, Bourns College of Engineering, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| |
Collapse
|
62
|
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. Allostery in Its Many Disguises: From Theory to Applications. Structure 2019; 27:566-578. [PMID: 30744993 PMCID: PMC6688844 DOI: 10.1016/j.str.2019.01.003] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/29/2018] [Accepted: 01/02/2019] [Indexed: 12/19/2022]
Abstract
Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
Collapse
Affiliation(s)
| | | | - Nikolay V Dokholyan
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Departments of Pharmacology and Biochemistry & Molecular Biology, Penn State Medical Center, Hershey, PA, USA
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A(∗)STAR), and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jing Li
- Departments of Biology and T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, USA
| | - Vincent J Hilser
- Departments of Biology and T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, USA
| | - Ivet Bahar
- School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | | | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg, Germany
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Jerome Eberhardt
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177 CNRS & Université de Strasbourg, Strasbourg, France
| | | | - Peter G Bolhuis
- van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam, Netherlands
| | - Jocelyne Vreede
- van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Amsterdam, Netherlands
| | - Pietro Faccioli
- Physics Department, Università di Trento and INFN-TIFPA, Trento, Italy
| | - Simone Orioli
- Physics Department, Università di Trento and INFN-TIFPA, Trento, Italy
| | - Riccardo Ravasio
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Le Yan
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Carolina Brito
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Matthieu Wyart
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Paraskevi Gkeka
- Structure Design and Informatics, Sanofi R&D, Chilly-Mazarin, France
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Giulia Palermo
- Department of Chemistry and Biochemistry, University of California, San Diego, USA; Department of Bioengineering, University of California Riverside, CA 92507, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, USA
| | - Joanna Panecka-Hofman
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS) and Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Munich, Germany
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, Robert H Smith Faculty of Agriculture Food and Environment, The Hebrew University, Jerusalem, Israel
| | - Ruth Nussinov
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA
| | - Hyunbum Jang
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tom McLeish
- Department of Physics, University of York, York, UK
| |
Collapse
|
63
|
Can multiscale simulations unravel the function of metallo-enzymes to improve knowledge-based drug discovery? Future Med Chem 2019; 11:771-791. [DOI: 10.4155/fmc-2018-0495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Metallo-enzymes are a large class of biomolecules promoting specialized chemical reactions. Quantum-classical quantum mechanics/molecular mechanics molecular dynamics, describing the metal site at quantum mechanics level, while accounting for the rest of system at molecular mechanics level, has an accessible time-scale limited by its computational cost. Hence, it must be integrated with classical molecular dynamics and enhanced sampling simulations to disentangle the functions of metallo-enzymes. In this review, we provide an overview of these computational methods and their capabilities. In particular, we will focus on some systems such as CYP19A1 a Fe-dependent enzyme involved in estrogen biosynthesis, and on Mg2+-dependent DNA/RNA processing enzymes/ribozymes and the spliceosome, a protein-directed ribozyme. This information may guide the discovery of drug-like molecules and genetic manipulation tools.
Collapse
|
64
|
Palermo G, Ricci CG, McCammon JA. The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution. PHYSICS TODAY 2019; 72:30-36. [PMID: 31511751 PMCID: PMC6738945 DOI: 10.1063/pt.3.4182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since the discovery of the DNA double helix, the main molecular repository of genetic information, scientists have been struggling to find ways to efficiently manipulate genes. The ability to mark, modify, or regulate specific sequences of DNA in a controlled fashion is of key importance because of the ways that gene editing could be used to improve human life. For example, genetic therapies are being developed to permanently cure cancer and other life-threatening diseases.
Collapse
|
65
|
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. We disclose a two-metal aided architecture in the RuvC active site, which is poised to operate DNA cleavages, in analogy with other DNA/RNA processing enzymes. The conformational dynamics of the RuvC domain further reveals that an "arginine finger" stably contacts the scissile phosphate, with the function of stabilizing the active complex. Remarkably, the formation of a catalytically competent state of the RuvC domain is only observed upon the conformational activation of the other nuclease domain of CRISPR-Cas9-i.e., the HNH domain-such allowing concerted cleavages of double stranded DNA. This structure is in agreement with the available experimental data and remarkably differs from previous models based on classical mechanics, demonstrating also that only quantum mechanical simulations can accurately describe the metal-aided active site in CRISPR-Cas9. This fully catalytic structure-in which both the HNH and RuvC domains are prone to perform DNA cleavages-constitutes a stepping-stone for understanding DNA cleavage and specificity. It calls for novel experimental verifications and offers the structural foundations for engineering efforts aimed at improving the genome editing capability of CRISPR-Cas9.
Collapse
Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, Bourns College of Engineering , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States
| |
Collapse
|
66
|
Yoon H, Zhao LN, Warshel A. Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII. ACS Catal 2019; 9:1329-1336. [PMID: 34046245 PMCID: PMC8153514 DOI: 10.1021/acscatal.8b04324] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating the nature of the gene editing mechanism of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is an important task in view of the role of this breakthrough to the advancement of human medicine. In particular, it is crucial to understand the catalytic mechanism of Cas9 (one of the CRISPR associated proteins) and its role in confirming accurate editing. Thus, we focus in this work on an attempt to analyze the catalytic mechanism of Cas9. Considering the absence of detailed structural information on the active form of Cas9, we use an empirical valence bond (EVB) which is calibrated on the closely related mechanism of T4 endonuclease VII. The calibrated EVB is then used in studying the reaction of Cas9, while trying several structural models. It is found that the catalytic activation requires a large conformational change, where K848 or other positively charged group moves from a relatively large distance toward the scissile phosphate. This conformational change leads to the change in position of the Mg2+ ion and to a major reduction in the activation barrier for the catalytic reaction. Our finding provides an important clue on the nature of the catalytic activation of CAS9 and thus should help in elucidating a key aspect of the gene editing process. For example, the approach used here should be effective in exploring the nature of off target activation and its relationship to the energetics of the unwinding process. This strategy may offer ways to improve the selectivity of Cas9.
Collapse
Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Li Na Zhao
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| |
Collapse
|
67
|
Negre CFA, Morzan UN, Hendrickson HP, Pal R, Lisi GP, Loria JP, Rivalta I, Ho J, Batista VS. Eigenvector centrality for characterization of protein allosteric pathways. Proc Natl Acad Sci U S A 2018; 115:E12201-E12208. [PMID: 30530700 PMCID: PMC6310864 DOI: 10.1073/pnas.1810452115] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Determining the principal energy-transfer pathways responsible for allosteric communication in biomolecules remains challenging, partially due to the intrinsic complexity of the systems and the lack of effective characterization methods. In this work, we introduce the eigenvector centrality metric based on mutual information to elucidate allosteric mechanisms that regulate enzymatic activity. Moreover, we propose a strategy to characterize the range of correlations that underlie the allosteric processes. We use the V-type allosteric enzyme imidazole glycerol phosphate synthase (IGPS) to test the proposed methodology. The eigenvector centrality method identifies key amino acid residues of IGPS with high susceptibility to effector binding. The findings are validated by solution NMR measurements yielding important biological insights, including direct experimental evidence for interdomain motion, the central role played by helix h[Formula: see text], and the short-range nature of correlations responsible for the allosteric mechanism. Beyond insights on IGPS allosteric pathways and the nature of residues that could be targeted by therapeutic drugs or site-directed mutagenesis, the reported findings demonstrate the eigenvector centrality analysis as a general cost-effective methodology to gain fundamental understanding of allosteric mechanisms at the molecular level.
Collapse
Affiliation(s)
- Christian F A Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545;
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
| | - Uriel N Morzan
- Department of Chemistry, Yale University, New Haven, CT 06520-8107;
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
| | - Heidi P Hendrickson
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
- Department of Chemistry, Lafayette College, Easton, PA 18042
| | - Rhitankar Pal
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
| | - George P Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, Lyon, France;
- Dipartimento di Chimica Industriale "Toso Montanari," Università degli Studi di Bologna, Viale del Risorgimento, 4I-40136 Bologna, Italy
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney NSW 2052, Australia
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520-8107;
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
| |
Collapse
|