1
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Zhao S, Liu J, Zuo Z. Secondary Conformational Checkpoint in CRISPR-Cas9. J Chem Theory Comput 2024; 20:3440-3448. [PMID: 38625092 DOI: 10.1021/acs.jctc.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
A specific checkpoint between target DNA binding and cleavage primarily governs the precision of Cas9 gene editing. Although various CRISPR-Cas9 variants have been developed to improve DNA cleavage accuracy, we still lack a comprehensive understanding of how they work at the molecular level. Herein, we have focused on studying the late-stage conformational transitions of Cas9 and an evolved Cas9 mutant (evoCas9) that start from the precleavage state. Our submilliseconds of dynamic simulations reveal that the presence of base mismatches leads the HNH nuclease domain of Cas9 to alter its principal functional modes of motion, thereby impairing its conformational activation. This observation suggests the existence of a secondary conformational checkpoint that fine-tunes the final DNA cleavage activation. Remarkably, evoCas9 is prone to deviating from the normal activation pathway with base mismatches. This is characterized by a noticeable shift in the positioning of the HNH domain and a significantly perturbed allosteric communication network within the enzyme. Therefore, the mutations evolved in evoCas9 also reinforce the secondary checkpoint in addition to the previously identified primary checkpoint, collectively ensuring this variant's high gene-editing accuracy. This mechanism should also apply to other Cas9-guide RNA variants with enhanced fidelity.
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Affiliation(s)
- Shuxin Zhao
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai 201620, China
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2
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Yu T, Liu T, Wang Y, Zhao X, Zhang W. Effect of Cas9 Protein on the Seed-Target Base Pair of the sgRNA/DNA Hybrid Duplex. J Phys Chem B 2023. [PMID: 37243666 DOI: 10.1021/acs.jpcb.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-associated protein (Cas9) has been widely used for gene editing. Not all guide RNAs can cleave the DNA efficiently remains a major challenge to CRISPR/Cas9-mediated genome engineering. Therefore, understanding how the Cas9 complex successfully and efficiently identifies specific functional targets through base-pairing has great implications for such applications. The 10-nt seed sequence at the 3' end of the guide RNA is critical to target recognition and cleavage. Here, through stretching molecular dynamics simulation, we studied the thermodynamics and kinetics of the binding-dissociation process of the seed base and the target DNA base with the Cas9 protein. The results showed that in the presence of Cas9 protein, the enthalpy change and entropy change in binding-dissociation of the seed base with the target are smaller than those without the Cas9 protein. The reduction of entropy penalty upon association with the protein resulted from the pre-organization of the seed base in an A-form helix, and the reduction of enthalpy change was due to the electrostatic attraction of the positively charged channel with the negative target DNA. The binding barrier coming from the entropy loss and the dissociation barrier resulting from the destruction of the base pair in the presence of Cas9 protein were lower than those without protein, which indicates that the seed region is crucial for efficiently searching the correct target by accelerating the binding rate and dissociating fast from the wrong target.
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Affiliation(s)
- Ting Yu
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Taigang Liu
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou, Henan 466000, PR China
| | - Xuanlin Zhao
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
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3
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Vora DS, Yadav S, Sundar D. Hybrid Multitask Learning Reveals Sequence Features Driving Specificity in the CRISPR/Cas9 System. Biomolecules 2023; 13:biom13040641. [PMID: 37189388 DOI: 10.3390/biom13040641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
CRISPR/Cas9 technology is capable of precisely editing genomes and is at the heart of various scientific and medical advances in recent times. The advances in biomedical research are hindered because of the inadvertent burden on the genome when genome editors are employed—the off-target effects. Although experimental screens to detect off-targets have allowed understanding the activity of Cas9, that knowledge remains incomplete as the rules do not extrapolate well to new target sequences. Off-target prediction tools developed recently have increasingly relied on machine learning and deep learning techniques to reliably understand the complete threat of likely off-targets because the rules that drive Cas9 activity are not fully understood. In this study, we present a count-based as well as deep-learning-based approach to derive sequence features that are important in deciding on Cas9 activity at a sequence. There are two major challenges in off-target determination—the identification of a likely site of Cas9 activity and the prediction of the extent of Cas9 activity at that site. The hybrid multitask CNN–biLSTM model developed, named CRISP–RCNN, simultaneously predicts off-targets and the extent of activity on off-targets. Employing methods of integrated gradients and weighting kernels for feature importance approximation, analysis of nucleotide and position preference, and mismatch tolerance have been performed.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Yadav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
- Yardi School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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4
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Platani M, Sokefun O, Bassil E, Apidianakis Y. Genetic engineering and genome editing in plants, animals and humans: Facts and myths. Gene 2023; 856:147141. [PMID: 36574935 DOI: 10.1016/j.gene.2022.147141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Human history is inextricably linked to the introduction of desirable heritable traits in plants and animals. Selective breeding (SB) predates our historical period and has been practiced since the advent of agriculture and farming more than ten thousand years ago. Since the 1970s, methods of direct plant and animal genome manipulation are constantly being developed. These are collectively described as "genetic engineering" (GE). Plant GE aims to improve nutritional value, insect resistance and weed control. Animal GE has focused on livestock improvement and disease control. GE applications also involve medical improvements intended to treat human disease. The scientific consensus built around marketed products of GE organisms (GEOs) is usually well established, noting significant benefits and low risks. GEOs are exhaustively scrutinized in the EU and many non-EU countries for their effects on human health and the environment, but scrutiny should be equally applied to all previously untested organisms derived directly from nature or through selective breeding. In fact, there is no evidence to suggest that natural or selectively bred plants and animals are in principle safer to humans than GEOs. Natural and selectively bred strains evolve over time via genetic mutations that can be as risky to humans and the environment as the mutations found in GEOs. Thus, previously untested plant and animal strains aimed for marketing should be proven useful or harmful to humans only upon comparative testing, regardless of their origin. Highlighting the scientific consensus declaring significant benefits and rather manageable risks provided by equitably accessed GEOs, can mitigate negative predispositions by policy makers and the public. Accordingly, we provide an overview of the underlying technologies and the scientific consensus to help resolve popular myths about the safety and usefulness of GEOs.
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Affiliation(s)
- Maria Platani
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Owolabi Sokefun
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Elias Bassil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
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5
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Nierzwicki Ł, Ahsan M, Palermo G. The Electronic Structure of Genome Editors from the First Principles. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2023; 5:014003. [PMID: 36926635 PMCID: PMC10016068 DOI: 10.1088/2516-1075/acb410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to characterize the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods - i.e., thermodynamic integration and metadynamics - to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues' protonation states. Overall, first-principles methods are shown to unravel the electronic structure of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
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6
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Bhattacharya S, Satpati P. Insights into the Mechanism of CRISPR/Cas9-Based Genome Editing from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:1817-1837. [PMID: 36687047 PMCID: PMC9850488 DOI: 10.1021/acsomega.2c05583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The CRISPR/Cas9 system is a popular genome-editing tool with immense therapeutic potential. It is a simple two-component system (Cas9 protein and RNA) that recognizes the DNA sequence on the basis of RNA:DNA complementarity, and the Cas9 protein catalyzes the double-stranded break in the DNA. In the past decade, near-atomic resolution structures at various stages of the CRISPR/Cas9 DNA editing pathway have been reported along with numerous experimental and computational studies. Such studies have boosted knowledge of the genome-editing mechanism. Despite such advancements, the application of CRISPR/Cas9 in therapeutics is still limited, primarily due to off-target effects. Several studies aim at engineering high-fidelity Cas9 to minimize the off-target effects. Molecular Dynamics (MD) simulations have been an excellent complement to the experimental studies for investigating the mechanism of CRISPR/Cas9 editing in terms of structure, thermodynamics, and kinetics. MD-based studies have uncovered several important molecular aspects of Cas9, such as nucleotide binding, catalytic mechanism, and off-target effects. In this Review, the contribution of MD simulation to understand the CRISPR/Cas9 mechanism has been discussed, preceded by an overview of the history, mechanism, and structural aspects of the CRISPR/Cas9 system. These studies are important for the rational design of highly specific Cas9 and will also be extremely promising for achieving more accurate genome editing in the future.
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7
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Chiappori F, Mollica L. Editorial: RNAs at the crossroads between effectors and targets; discovery and development of new drugs. Front Mol Biosci 2023; 10:1157440. [PMID: 36923644 PMCID: PMC10010567 DOI: 10.3389/fmolb.2023.1157440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Affiliation(s)
- Federica Chiappori
- National Research Council-Institute for Biomedical Technologies, Milan, Italy
| | - Luca Mollica
- L.I.T.A, Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
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8
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Prokhorova DV, Vokhtantsev IP, Tolstova PO, Zhuravlev ES, Kulishova LM, Zharkov DO, Stepanov GA. Natural Nucleoside Modifications in Guide RNAs Can Modulate the Activity of the CRISPR-Cas9 System In Vitro. CRISPR J 2022; 5:799-812. [PMID: 36350691 DOI: 10.1089/crispr.2022.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
At the present time, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has been widely adopted as an efficient genomic editing tool. However, there are some actual problems such as the off-target effects, cytotoxicity, and immunogenicity. The incorporation of modifications into guide RNAs permits enhancing both the efficiency and the specificity of the CRISPR-Cas9 system. In this study, we demonstrate that the inclusion of N6-methyladenosine, 5-methylcytidine, and pseudouridine in trans-activating RNA (tracrRNA) or in single guide RNA (sgRNA) enables efficient gene editing in vitro. We found that the complexes of modified guide RNAs with Cas9 protein promoted cleavage of the target short/long duplexes and plasmid substrates. In addition, the modified monomers in guide RNAs allow increasing the specificity of CRISPR-Cas9 system in vitro and promote diminishing both the immunostimulating and the cytotoxic effects of sgRNAs.
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Affiliation(s)
- Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ivan P Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Polina O Tolstova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lilia M Kulishova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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9
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Mollica L, Cupaioli FA, Rossetti G, Chiappori F. An overview of structural approaches to study therapeutic RNAs. Front Mol Biosci 2022; 9:1044126. [PMID: 36387283 PMCID: PMC9649582 DOI: 10.3389/fmolb.2022.1044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2023] Open
Abstract
RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.
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Affiliation(s)
- Luca Mollica
- Department of Medical Biotechnologies and Translational Medicine, L.I.T.A/University of Milan, Milan, Italy
| | | | | | - Federica Chiappori
- National Research Council—Institute for Biomedical Technologies, Milan, Italy
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10
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Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FHT, Palermo G, Cameron P, Donohoue PD, Jinek M. Structural basis for Cas9 off-target activity. Cell 2022; 185:4067-4081.e21. [PMID: 36306733 PMCID: PMC10103147 DOI: 10.1016/j.cell.2022.09.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/01/2022] [Accepted: 09/15/2022] [Indexed: 11/06/2022]
Abstract
The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, Cas9 can bind and cleave partially complementary off-target sequences, which raises safety concerns for its use in clinical applications. Here, we report crystallographic structures of Cas9 bound to bona fide off-target substrates, revealing that off-target binding is enabled by a range of noncanonical base-pairing interactions within the guide:off-target heteroduplex. Off-target substrates containing single-nucleotide deletions relative to the guide RNA are accommodated by base skipping or multiple noncanonical base pairs rather than RNA bulge formation. Finally, PAM-distal mismatches result in duplex unpairing and induce a conformational change in the Cas9 REC lobe that perturbs its conformational activation. Together, these insights provide a structural rationale for the off-target activity of Cas9 and contribute to the improved rational design of guide RNAs and off-target prediction algorithms.
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Affiliation(s)
- Martin Pacesa
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Chun-Han Lin
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Antoine Cléry
- Institute of Biochemistry, ETH Zurich, Hönggerbergring 64, 8093 Zurich, Switzerland
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthew J Irby
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Frédéric H-T Allain
- Institute of Biochemistry, ETH Zurich, Hönggerbergring 64, 8093 Zurich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Peter Cameron
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Paul D Donohoue
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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11
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Daskalakis V. Deciphering the QR Code of the CRISPR-Cas9 System: Synergy between Gln768 (Q) and Arg976 (R). ACS PHYSICAL CHEMISTRY AU 2022; 2:496-505. [PMID: 36855610 PMCID: PMC9955204 DOI: 10.1021/acsphyschemau.2c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 10/14/2022]
Abstract
Markov state models (MSMs) and machine learning (ML) algorithms can extrapolate the long-time-scale behavior of large biomolecules from molecular dynamics (MD) trajectories. In this study, an MD-MSM-ML scheme has been applied to probe the large endonuclease (Cas9) in the bacterial adaptive immunity CRISPR-Cas9 system. CRISPR has become a programmable and state-of-the-art powerful genome editing tool that has already revolutionized life sciences. CRISPR-Cas9 is programmed to process specific DNA sequences in the genome. However, human/biomedical applications are compromised by off-target DNA damage. Characterization of Cas9 at the structural and biophysical levels is a prerequisite for the development of efficient and high-fidelity Cas9 variants. The Cas9 wild type and two variants (R63A-R66A-R70A, R69A-R71A-R74A-R78A) are studied herein. The configurational space of Cas9 is provided with a focus on the conformations of the side chains of two residues (Gln768 and Arg976). A model for the synergy between those two residues is proposed. The results are discussed within the context of experimental literature. The results and methodology can be exploited for the study of large biomolecules in general and for the engineering of more efficient and safer Cas9 variants for applications.
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12
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Vora DS, Verma Y, Sundar D. A Machine Learning Approach to Identify the Importance of Novel Features for CRISPR/Cas9 Activity Prediction. Biomolecules 2022; 12:1123. [PMID: 36009017 PMCID: PMC9405635 DOI: 10.3390/biom12081123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
The reprogrammable CRISPR/Cas9 genome editing tool's growing popularity is hindered by unwanted off-target effects. Efforts have been directed toward designing efficient guide RNAs as well as identifying potential off-target threats, yet factors that determine efficiency and off-target activity remain obscure. Based on sequence features, previous machine learning models performed poorly on new datasets, thus there is a need for the incorporation of novel features. The binding energy estimation of the gRNA-DNA hybrid as well as the Cas9-gRNA-DNA hybrid allowed generating better performing machine learning models for the prediction of Cas9 activity. The analysis of feature contribution towards the model output on a limited dataset indicated that energy features played a determining role along with the sequence features. The binding energy features proved essential for the prediction of on-target activity and off-target sites. The plateau, in the performance on unseen datasets, of current machine learning models could be overcome by incorporating novel features, such as binding energy, among others. The models are provided on GitHub (GitHub Inc., San Francisco, CA, USA).
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Yugesh Verma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
- Yardi School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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13
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Vora DS, Jaiswal AK, Sundar D. Implementing accelerated dynamics to unravel the effects of high-fidelity Cas9 mutants on target DNA and guide RNA hybrid stability. J Biomol Struct Dyn 2022:1-13. [PMID: 35882048 DOI: 10.1080/07391102.2022.2103032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The clustered regularly interspersed short palindromic repeats (CRISPR) and its associated nuclease (Cas9) offers a unique and easily reprogrammable system for editing eukaryotic genomes. Cas9 is guided to the target by an RNA strand, and precise edits are created by introducing double-stranded breaks. However, nuclease activity of Cas9 is also triggered at other sites other than the target sit, which is a major limitation for various applications. Cas9 variants have been designed to improve the efficacy of the tool by introducing certain mutations. However, the on-target activity of such Cas9 variants is often seen as compromised. Hence, understanding the sub-molecular differences in the variants is essential to elucidate the factors that contribute to efficiency. The study reveals distortions in the PAM-distal regions of the nucleic hybrids as well as changes in the interactions between the Cas9 variants and RNA-DNA hybrid, contributing to the explanation for differences in on-target activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India
| | - Atul Kumar Jaiswal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India.,Yardi School of Artificial Intelligence, Indian Institute of Technology (IIT) Delhi, New Delhi, India
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14
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Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
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Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
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15
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Chen Q, Chuai G, Zhang C, Zhang Q, Liu Q. Toward a molecular mechanism-based prediction of CRISPR-Cas9 targeting effects. Sci Bull (Beijing) 2022; 67:1201-1204. [PMID: 36546144 DOI: 10.1016/j.scib.2022.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Qinchang Chen
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201210, China
| | - Guohui Chuai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201210, China
| | - Chao Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Qing Zhang
- Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Shanghai, Roche R&D Center (China) Ltd., Shanghai 201203, China.
| | - Qi Liu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201210, China.
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16
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Saha A, Arantes PR, Palermo G. Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods. Curr Opin Struct Biol 2022; 75:102400. [PMID: 35689914 DOI: 10.1016/j.sbi.2022.102400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/25/2022] [Accepted: 05/07/2022] [Indexed: 12/24/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) genome-editing revolution established the beginning of a new era in life sciences. Here, we review the role of state-of-the-art computations in the CRISPR-Cas9 revolution, from the early refinement of cryo-EM data to enhanced simulations of large-scale conformational transitions. Molecular simulations reported a mechanism for RNA binding and the formation of a catalytically competent Cas9 enzyme, in agreement with subsequent structural studies. Inspired by single-molecule experiments, molecular dynamics offered a rationale for the onset of off-target effects, while graph theory unveiled the allosteric regulation. Finally, the use of a mixed quantum-classical approach established the catalytic mechanism of DNA cleavage. Overall, molecular simulations have been instrumental in understanding the dynamics and mechanism of CRISPR-Cas9, contributing to understanding function, catalysis, allostery, and specificity.
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Affiliation(s)
- Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States. https://twitter.com/@aakashsahha
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States. https://twitter.com/@pablitoarantes
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States; Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States.
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17
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Esmaeeli R, Andal B, Perez A. Searching for Low Probability Opening Events in a DNA Sliding Clamp. Life (Basel) 2022; 12:life12020261. [PMID: 35207548 PMCID: PMC8876151 DOI: 10.3390/life12020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022] Open
Abstract
The β subunit of E. coli DNA polymererase III is a DNA sliding clamp associated with increasing the processivity of DNA synthesis. In its free form, it is a circular homodimer structure that can accomodate double-stranded DNA in a nonspecific manner. An open state of the clamp must be accessible before loading the DNA. The opening mechanism is still a matter of debate, as is the effect of bound DNA on opening/closing kinetics. We use a combination of atomistic, coarse-grained, and enhanced sampling strategies in both explicit and implicit solvents to identify opening events in the sliding clamp. Such simulations of large nucleic acid and their complexes are becoming available and are being driven by improvements in force fields and the creation of faster computers. Different models support alternative opening mechanisms, either through an in-plane or out-of-plane opening event. We further note some of the current limitations, despite advances, in modeling these highly charged systems with implicit solvent.
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18
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Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Front Mol Biosci 2022; 9:1072733. [PMID: 36699705 PMCID: PMC9868570 DOI: 10.3389/fmolb.2022.1072733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide RNA (gRNA) that serves as a binding scaffold to guide it to the target DNA duplex via a RecA-like strand-displacement mechanism but without ATP binding or hydrolysis. The target search begins with the protospacer adjacent motif or PAM-interacting domain, recognizing it at the major groove of the duplex and melting its downstream duplex where an RNA-DNA heteroduplex is formed at nanomolar affinity. The rate-limiting step is the formation of an R-loop structure where the HNH domain inserts between the target heteroduplex and the displaced non-target DNA strand. Once the R-loop structure is formed, the non-target strand is rapidly cleaved by RuvC and ejected from the active site. This event is immediately followed by cleavage of the target DNA strand by the HNH domain and product release. Within CRISPR-associated protein 9, the HNH domain is inserted into the RuvC domain near the RuvC active site via two linker loops that provide allosteric communication between the two active sites. Due to the high flexibility of these loops and active sites, biophysical techniques have been instrumental in characterizing the dynamics and mechanism of the CRISPR-associated protein 9 nucleases, aiding structural studies in the visualization of the complete active sites and relevant linker structures. Here, we review biochemical, structural, and biophysical studies on the underlying mechanism with emphasis on how CRISPR-associated protein 9 selects the target DNA duplex and rejects non-target sequences.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Mohd Ahsan
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Souvik Sinha
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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19
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Abstract
:
Clustered regularly interspaced short palindromic repeats along with CRISPR-associated protein
mechanisms preserve the memory of previous experiences with DNA invaders, in particular spacers
that are embedded in CRISPR arrays between coordinate repeats. There has been a fast progression in
the comprehension of this immune system and its implementations; however, there are numerous points
of view that anticipate explanations to make the field an energetic research zone. The efficiency of
CRISPR-Cas depends upon well-considered single guide RNA; for this purpose, many bioinformatics
methods and tools are created to support the design of greatly active and precise single guide RNA. Insilico
single guide RNA architecture is a crucial point for effective gene editing by means of the
CRISPR technique. Persistent attempts have been made to improve in-silico single guide RNA formulation
having great on-target effectiveness and decreased off-target effects. This review offers a summary
of the CRISPR computational tools to help different researchers pick a specific tool for their work according
to pros and cons, along with new thoughts to make new computational tools to overcome all existing
limitations.
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Affiliation(s)
- Mohsin Ali Nasir
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Samia Nawaz
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
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20
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Nierzwicki L, East KW, Morzan UN, Arantes PR, Batista VS, Lisi GP, Palermo G. Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9. eLife 2021; 10:e73601. [PMID: 34908530 PMCID: PMC8741213 DOI: 10.7554/elife.73601] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat and associated Cas9 protein) is a molecular tool with transformative genome editing capabilities. At the molecular level, an intricate allosteric signaling is critical for DNA cleavage, but its role in the specificity enhancement of the Cas9 endonuclease is poorly understood. Here, multi-microsecond molecular dynamics is combined with solution NMR and graph theory-derived models to probe the allosteric role of key specificity-enhancing mutations. We show that mutations responsible for increasing the specificity of Cas9 alter the allosteric structure of the catalytic HNH domain, impacting the signal transmission from the DNA recognition region to the catalytic sites for cleavage. Specifically, the K855A mutation strongly disrupts the allosteric connectivity of the HNH domain, exerting the highest perturbation on the signaling transfer, while K810A and K848A result in more moderate effects on the allosteric communication. This differential perturbation of the allosteric signal correlates to the order of specificity enhancement (K855A > K848A ~ K810A) observed in biochemical studies, with the mutation achieving the highest specificity most strongly perturbing the signaling transfer. These findings suggest that alterations of the allosteric communication from DNA recognition to cleavage are critical to increasing the specificity of Cas9 and that allosteric hotspots can be targeted through mutational studies for improving the system's function.
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Affiliation(s)
- Lukasz Nierzwicki
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
| | - Kyle W East
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Uriel N Morzan
- International Centre for Theoretical PhysicsTriesteItaly
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
| | | | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
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21
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Wang J, Arantes PR, Bhattarai A, Hsu RV, Pawnikar S, Huang YMM, Palermo G, Miao Y. Gaussian accelerated molecular dynamics (GaMD): principles and applications. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1521. [PMID: 34899998 PMCID: PMC8658739 DOI: 10.1002/wcms.1521] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/28/2021] [Indexed: 12/20/2022]
Abstract
Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined reaction coordinates or collective variables, GaMD provides unconstrained enhanced sampling and is advantageous for simulating complex biological processes. The GaMD boost potential exhibits a Gaussian distribution, thereby allowing for energetic reweighting via cumulant expansion to the second order (i.e., "Gaussian approximation"). This leads to accurate reconstruction of free energy landscapes of biomolecules. Hybrid schemes with other enhanced sampling methods, such as the replica exchange GaMD (rex-GaMD) and replica exchange umbrella sampling GaMD (GaREUS), have also been introduced, further improving sampling and free energy calculations. Recently, new "selective GaMD" algorithms including the ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD) enabled microsecond simulations to capture repetitive dissociation and binding of small-molecule ligands and highly flexible peptides. The simulations then allowed highly efficient quantitative characterization of the ligand/peptide binding thermodynamics and kinetics. Taken together, GaMD and its innovative variants are applicable to simulate a wide variety of biomolecular dynamics, including protein folding, conformational changes and allostery, ligand binding, peptide binding, protein-protein/nucleic acid/carbohydrate interactions, and carbohydrate/nucleic acid interactions. In this review, we present principles of the GaMD algorithms and recent applications in biomolecular simulations and drug design.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, United States
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr, Lawrence, KS, 66047, United States
| | - Rohaine V Hsu
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, United States
| | - Yu-Ming M Huang
- Department of Physics & Astronomy, Wayne State University, 666 W Hancock St, Detroit, MI 48207, USA
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, Kansas 66047, United States
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22
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Nierzwicki Ł, Arantes PR, Saha A, Palermo G. Establishing the allosteric mechanism in CRISPR-Cas9. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1503. [PMID: 34322166 PMCID: PMC8315640 DOI: 10.1002/wcms.1503] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR-Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three steps of the CRISPR-Cas9 function: affecting DNA recognition, mediating the cleavage and interfering with the off-target activity. An allosteric communication that activates concerted DNA cleavages was found to led through the L1/L2 loops, which connect the HNH and RuvC catalytic domains. The identification of these "allosteric transducers" inspired the development of novel variants of the Cas9 protein with improved specificity, opening a new avenue for controlling the CRISPR-Cas9 activity. Discussed studies also highlight the critical role of the recognition lobe in the conformational activation of the catalytic HNH domain. Specifically, the REC3 region was found to modulate the dynamics of HNH by sensing the formation of the RNA:DNA hybrid. The role of REC3 was revealed to be particularly relevant in the presence of DNA mismatches. Indeed, interference of REC3 with the RNA:DNA hybrid containing mismatched pairs at specific positions resulted in locking HNH in an inactive "conformational checkpoint" conformation, thereby hampering off-target cleavages. Overall, MD simulations established the fundamental mechanisms underlying the allosterism of CRISPR-Cas9, aiding engineering strategies to develop new CRISPR-Cas9 variants for improved genome editing.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Pablo Ricardo Arantes
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California
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23
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Nierzwicki Ł, Palermo G. Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules. Front Mol Biosci 2021; 8:641208. [PMID: 33884260 PMCID: PMC8053777 DOI: 10.3389/fmolb.2021.641208] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today's cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution density maps obtained for protein flexible domains, as well as the ensemble of coexisting conformational states arising from cryo-EM, poses new challenges and opportunities for Molecular Dynamics (MD) simulations. With the ability to describe the biomolecular dynamics at the atomic level, MD can extend the capabilities of cryo-EM, capturing the conformational variability and predicting biologically relevant short-lived conformational states. Here, we report about the state-of-the-art MD procedures that are currently used to refine, reconstruct and interpret cryo-EM maps. We show the capability of MD to predict short-lived conformational states, finding remarkable confirmation by cryo-EM structures subsequently solved. This has been the case of the CRISPR-Cas9 genome editing machinery, whose catalytically active structure has been predicted through both long-time scale MD and enhanced sampling techniques 2 years earlier than cryo-EM. In summary, this contribution remarks the ability of MD to complement cryo-EM, describing conformational landscapes and relating structural transitions to function, ultimately discerning relevant short-lived conformational states and providing mechanistic knowledge of biological function.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California, Riverside, CA, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, CA, United States
- Department of Chemistry, University of California, Riverside, CA, United States
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24
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Modrzejewski D, Hartung F, Lehnert H, Sprink T, Kohl C, Keilwagen J, Wilhelm R. Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:574959. [PMID: 33329634 PMCID: PMC7719684 DOI: 10.3389/fpls.2020.574959] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/30/2020] [Indexed: 05/03/2023]
Abstract
CRISPR/Cas enables a targeted modification of DNA sequences. Despite their ease and efficient use, one limitation is the potential occurrence of associated off-target effects. This systematic review aims to answer the following research question: Which factors affect the occurrence of off-target effects caused by the use of CRISPR/Cas in plants? Literature published until March 2019 was considered for this review. Articles were screened for relevance based on pre-defined inclusion criteria. Relevant studies were subject to critical appraisal. All studies included in the systematic review were synthesized in a narrative report, but studies rated as high and medium/high validity were reported separately from studies rated as low and medium/low or unclear validity. In addition, we ran a binary logistic regression analysis to verify five factors that may affect the occurrence of off-target effects: (1) Number of mismatches (2) Position of mismatches (3) GC-content of the targeting sequence (4) Altered nuclease variants (5) Delivery methods. In total, 180 relevant articles were included in this review containing 468 studies therein. Seventy nine percentage of these studies were rated as having high or medium/high validity. Within these studies, 6,416 potential off-target sequences were assessed for the occurrence of off-target effects. Results clearly indicate that an increased number of mismatches between the on-target and potential off-target sequence steeply decreases the likelihood of off-target effects. The observed rate of off-target effects decreased from 59% when there is one mismatch between the on-target and off-target sequences toward 0% when four or more mismatches exist. In addition, mismatch/es located within the first eight nucleotides proximal to the PAM significantly decreased the occurrence of off-target effects. There is no evidence that the GC-content significantly affects off-target effects. The database regarding the impact of the nuclease variant and the delivery method is very poor as the majority of studies applied the standard nuclease SpCas9 and the CRISPR/Cas system was stably delivered in the genome. Hence, a general significant impact of these two factors on the occurrence of off-target effects cannot be proved. This identified evidence gap needs to be filled by systematic studies exploring these individual factors in sufficient numbers.
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Affiliation(s)
- Dominik Modrzejewski
- Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institute, Quedlinburg, Germany
| | - Frank Hartung
- Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institute, Quedlinburg, Germany
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25
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Casalino L, Nierzwicki Ł, Jinek M, Palermo G. Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics. ACS Catal 2020; 10:13596-13605. [PMID: 33520346 PMCID: PMC7842700 DOI: 10.1021/acscatal.0c03566] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum-classical molecular dynamics (MD) and free energy methods are used to disclose the two-metal-dependent mechanism of phosphodiester bond cleavage in CRISPR-Cas9. Ab initio MD reveals a conformational rearrangement of the Mg2+-bound RuvC active site, which entails the relocation of H983 to act as a general base. Then, the DNA cleavage proceeds through a concerted associative pathway fundamentally assisted by the joint dynamics of the two Mg2+ ions. This clarifies previous controversial experimental evidence, which could not fully establish the catalytic role of the conserved H983 and the metal cluster conformation. The comparison with other two-metal-dependent enzymes supports the identified mechanism and suggests a common catalytic strategy for genome editing and recombination. Overall, the non-target DNA cleavage catalysis described here resolves a fundamental open question in the CRISPR-Cas9 biology and provides valuable insights for improving the catalytic efficiency and the metal-dependent function of the Cas9 enzyme, which are at the basis of the development of genome editing tools.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
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