1
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Islas P, Platnich CM, Gidi Y, Karimi R, Ginot L, Saliba D, Luo X, Cosa G, Sleiman HF. Automated Synthesis of DNA Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2403477. [PMID: 39049795 DOI: 10.1002/adma.202403477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/10/2024] [Indexed: 07/27/2024]
Abstract
DNA nanotechnology has revolutionized the ability to position matter at the nanoscale, but the preparation of DNA-based architectures remains laborious. To facilitate the formation of custom structures, a fully automated method is reported to produce sequence- and size-defined DNA nanotubes. By programming the sequential addition of desired building blocks, rigid DX-tile-based DNA nanotubes and flexible wireframe DNA structures are attained, where the total number of possible constructs increases as a power function of the number of different units available. Using single-molecule fluorescence imaging, the kinetics and yield of each synthetic step can be quantitatively determined, revealing differences in self-assembly dynamics as the nanotube is built up from the solid support and providing new insights into DNA self-assembly. The exploitation of automation for both assembly and analysis (through an ad-hoc developed K-means clustering algorithm) facilitates a workflow wherein the synthesis parameters may be iteratively improved upon, demonstrating how a single-molecule "assembly-analysis-optimization" sequence can be used to generate complex, noncovalent materials in good yield. The presented synthetic strategy is generalizable, making use of equipment already available in most standard laboratories and represents the first fully automated supramolecular assembly on a solid support.
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Affiliation(s)
- Patricia Islas
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Yasser Gidi
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Ryan Karimi
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Lorianne Ginot
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
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2
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Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase. Nucleic Acids Res 2024; 52:7447-7464. [PMID: 38884215 PMCID: PMC11260461 DOI: 10.1093/nar/gkae500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/11/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The Orthoflavivirus NS3 helicase (NS3h) is crucial in virus replication, representing a potential drug target for pathogenesis. NS3h utilizes nucleotide triphosphate (ATP) for hydrolysis energy to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. Intermediate states along the ATP hydrolysis cycle and conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. Extensive molecular dynamics simulations of West Nile virus NS3h+ssRNA in the apo, ATP, ADP+Pi and ADP bound states were used to model the conformational ensembles along this cycle. Energetic and structural clustering analyses depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). Based on these results, MVIL mutants (D471L, D471N and D471E) were found to have a substantial reduction in ATPase activity and RNA replication compared to the wild-type. Simulations of the mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.
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Affiliation(s)
- Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
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3
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Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401150. [PMID: 38582512 PMCID: PMC11220639 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325011China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Haihong Li
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan430072China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
| | - Ximiao Hou
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
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4
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Nolte DD. Coherent light scattering from cellular dynamics in living tissues. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:036601. [PMID: 38433567 DOI: 10.1088/1361-6633/ad2229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
This review examines the biological physics of intracellular transport probed by the coherent optics of dynamic light scattering from optically thick living tissues. Cells and their constituents are in constant motion, composed of a broad range of speeds spanning many orders of magnitude that reflect the wide array of functions and mechanisms that maintain cellular health. From the organelle scale of tens of nanometers and upward in size, the motion inside living tissue is actively driven rather than thermal, propelled by the hydrolysis of bioenergetic molecules and the forces of molecular motors. Active transport can mimic the random walks of thermal Brownian motion, but mean-squared displacements are far from thermal equilibrium and can display anomalous diffusion through Lévy or fractional Brownian walks. Despite the average isotropic three-dimensional environment of cells and tissues, active cellular or intracellular transport of single light-scattering objects is often pseudo-one-dimensional, for instance as organelle displacement persists along cytoskeletal tracks or as membranes displace along the normal to cell surfaces, albeit isotropically oriented in three dimensions. Coherent light scattering is a natural tool to characterize such tissue dynamics because persistent directed transport induces Doppler shifts in the scattered light. The many frequency-shifted partial waves from the complex and dynamic media interfere to produce dynamic speckle that reveals tissue-scale processes through speckle contrast imaging and fluctuation spectroscopy. Low-coherence interferometry, dynamic optical coherence tomography, diffusing-wave spectroscopy, diffuse-correlation spectroscopy, differential dynamic microscopy and digital holography offer coherent detection methods that shed light on intracellular processes. In health-care applications, altered states of cellular health and disease display altered cellular motions that imprint on the statistical fluctuations of the scattered light. For instance, the efficacy of medical therapeutics can be monitored by measuring the changes they induce in the Doppler spectra of livingex vivocancer biopsies.
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Affiliation(s)
- David D Nolte
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, United States of America
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5
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Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569434. [PMID: 38077049 PMCID: PMC10705498 DOI: 10.1101/2023.11.30.569434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The flavivirus NS3 helicase (NS3h), a highly conserved protein, plays a pivotal role in virus replication and thus represents a potential drug target for flavivirus pathogenesis. NS3h utilizes nucleotide triphosphate, such as ATP, for hydrolysis energy (ATPase) to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. The intermediate states along the ATP binding and hydrolysis cycle, as well as the conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. We use extensive molecular dynamics simulations of apo, ATP, ADP+Pi, and ADP bound to WNV NS3h+ssRNA to model the conformational ensembles along this cycle. Energetic and structural clustering analyses on these trajectories depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). These findings were experimentally corroborated using viral replicons encoding three mutations at the D471 position. Replication assays using these mutants demonstrated a substantial reduction in viral replication compared to the wild-type. Molecular simulations of the D471 mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.
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Affiliation(s)
- Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
| | - Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
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6
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García-Martínez A, Zinovjev K, Ruiz-Pernía JJ, Tuñón I. Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations. J Am Chem Soc 2023; 145:24809-24819. [PMID: 37921592 PMCID: PMC10852352 DOI: 10.1021/jacs.3c09015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/30/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
We computationally study the Zika NS3 helicase, a biological motor, using ATP hydrolysis energy for nucleic acid remodeling. Through molecular mechanics and hybrid quantum mechanics/molecular mechanics simulations, we explore the conformational landscape of motif V, a conserved loop connecting the active sites for ATP hydrolysis and nucleic acid binding. ATP hydrolysis, initiated by a meta-phosphate group formation, involves the nucleophilic attack of a water molecule activated by Glu286 proton abstraction. Motif V hydrogen bonds to this water via the Gly415 backbone NH group, assisting hydrolysis. Posthydrolysis, free energy is released when the inorganic phosphate moves away from the coordination shell of the magnesium ion, inducing a significant shift in the conformational landscape of motif V to establish a hydrogen bond between the Gly415 NH group and Glu285. According to our simulations, the Zika NS3 helicase acts as a ratchet biological motor with motif V transitions steered by Gly415's γ-phosphate sensing in the ATPase site.
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Affiliation(s)
| | - Kirill Zinovjev
- Departamento de Química Física, Universidad de Valencia, 46100 Bujassot, Spain
| | | | - Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia, 46100 Bujassot, Spain
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7
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Le ST, Choi S, Lee SW, Kim H, Ahn B. ssDNA reeling is an intermediate step in the reiterative DNA unwinding activity of the WRN-1 helicase. J Biol Chem 2023; 299:105081. [PMID: 37495105 PMCID: PMC10480542 DOI: 10.1016/j.jbc.2023.105081] [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: 01/26/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
RecQ helicases are highly conserved between bacteria and humans. These helicases unwind various DNA structures in the 3' to 5'. Defective helicase activity elevates genomic instability and is associated with predisposition to cancer and/or premature aging. Recent single-molecule analyses have revealed the repetitive unwinding behavior of RecQ helicases from Escherichia coli to humans. However, the detailed mechanisms underlying this behavior are unclear. Here, we performed single-molecule studies of WRN-1 Caenorhabditis elegans RecQ helicase on various DNA constructs and characterized WRN-1 unwinding dynamics. We showed that WRN-1 persistently repeated cycles of DNA unwinding and rewinding with an unwinding limit of 25 to 31 bp per cycle. Furthermore, by monitoring the ends of the displaced strand during DNA unwinding we demonstrated that WRN-1 reels in the ssDNA overhang in an ATP-dependent manner. While WRN-1 reeling activity was inhibited by a C. elegans homolog of human replication protein A, we found that C. elegans replication protein A actually switched the reiterative unwinding activity of WRN-1 to unidirectional unwinding. These results reveal that reeling-in ssDNA is an intermediate step in the reiterative unwinding process for WRN-1 (i.e., the process proceeds via unwinding-reeling-rewinding). We propose that the reiterative unwinding activity of WRN-1 may prevent extensive unwinding, allow time for partner proteins to assemble on the active region, and permit additional modulation in vivo.
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Affiliation(s)
- Son Truong Le
- Department of Life Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Seoyun Choi
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington DC, USA
| | - Seung-Won Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hajin Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.
| | - Byungchan Ahn
- Department of Life Sciences, University of Ulsan, Ulsan, Republic of Korea.
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8
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Harden TT, Vincent BJ, DePace AH. Transcriptional activators in the early Drosophila embryo perform different kinetic roles. Cell Syst 2023; 14:258-272.e4. [PMID: 37080162 PMCID: PMC10473017 DOI: 10.1016/j.cels.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/26/2022] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Combinatorial regulation of gene expression by transcription factors (TFs) may in part arise from kinetic synergy-wherein TFs regulate different steps in the transcription cycle. Kinetic synergy requires that TFs play distinguishable kinetic roles. Here, we used live imaging to determine the kinetic roles of three TFs that activate transcription in the Drosophila embryo-Zelda, Bicoid, and Stat92E-by introducing their binding sites into the even-skipped stripe 2 enhancer. These TFs influence different sets of kinetic parameters, and their influence can change over time. All three TFs increased the fraction of transcriptionally active nuclei; Zelda also shortened the first-passage time into transcription and regulated the interval between transcription events. Stat92E also increased the lifetimes of active transcription. Different TFs can therefore play distinct kinetic roles in activating the transcription. This has consequences for understanding the composition and flexibility of regulatory DNA sequences and the biochemical function of TFs. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Timothy T Harden
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ben J Vincent
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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9
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Jia X, Li Y, Wang T, Bi L, Guo L, Chen Z, Zhang X, Ye S, Chen J, Yang B, Sun B. Discrete RNA-DNA hybrid cleavage by the EXD2 exonuclease pinpoints two rate-limiting steps. EMBO J 2023; 42:e111703. [PMID: 36326837 PMCID: PMC9811613 DOI: 10.15252/embj.2022111703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
EXD2 is a recently identified exonuclease that cleaves RNA and DNA in double-stranded (ds) forms. It thus serves as a model system for investigating the similarities and discrepancies between exoribonuclease and exodeoxyribonuclease activities and for understanding the nucleic acid (NA) unwinding-degradation coordination of an exonuclease. Here, using a single-molecule fluorescence resonance energy transfer (smFRET) approach, we show that despite stable binding to both substrates, EXD2 barely cleaves dsDNA and yet displays both exoribonuclease and exodeoxyribonuclease activities toward RNA-DNA hybrids with a cleavage preference for RNA. Unexpectedly, EXD2-mediated hybrid cleavage proceeds in a discrete stepwise pattern, wherein a sudden 4-bp duplex unwinding increment and the subsequent dwell constitute a complete hydrolysis cycle. The relatively weak exodeoxyribonuclease activity of EXD2 partially originates from frequent hybrid rewinding. Importantly, kinetic analysis and comparison of the dwell times under varied conditions reveal two rate-limiting steps of hybrid unwinding and nucleotide excision. Overall, our findings help better understand the cellular functions of EXD2, and the cyclic coupling between duplex unwinding and exonucleolytic degradation may be generalizable to other exonucleases.
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Affiliation(s)
- Xinshuo Jia
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yanan Li
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Teng Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Ziting Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Shasha Ye
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Present address:
ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Jia Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Bei Yang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghaiChina
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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10
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Cao X, Liu K, Yan S, Li S, Li Y, Jin T, Liu S. Mechanical regulation of the helicase activity of Zika virus NS3. Biophys J 2022; 121:4900-4908. [PMID: 35923103 PMCID: PMC9808545 DOI: 10.1016/j.bpj.2022.07.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/15/2022] [Accepted: 07/25/2022] [Indexed: 01/07/2023] Open
Abstract
Zika virus (ZIKV) is a positive-sense single-stranded RNA virus that infects humans and can cause birth defects and neurological disorders. Its non-structural protein 3 (NS3) contains a protease domain and a helicase domain, both of which play essential roles during the viral life cycle. However, it has been shown that ZIKV NS3 has an inherently weak helicase activity, making it unable to unwind long RNA duplexes alone. How this activity is stimulated to process the viral genome and whether the two domains of NS3 are functionally coupled remain unclear. Here, we used optical tweezers to characterize the RNA-unwinding properties of ZIKV NS3-including its processivity, velocity, and step size-at the single-molecule level. We found that external forces that weaken the stability of the duplex RNA substrate significantly enhance the helicase activity of ZIKV NS3. On the other hand, we showed that the protease domain increases the binding affinity of NS3 to RNA but has only a minor effect on unwinding per se. Our findings suggest that the ZIKV NS3 helicase is activated on demand in the context of viral replication, a paradigm that may be generalizable to other flaviviruses.
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Affiliation(s)
- Xiaocong Cao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Kaixian Liu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shannon Yan
- Institute of Quantitative Biosciences (QB3), University of California-Berkeley, Berkeley, California
| | - Sai Li
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York
| | - Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York.
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11
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Spatiotemporally controlled generation of NTPs for single-molecule studies. Nat Chem Biol 2022; 18:1144-1151. [PMID: 36131148 PMCID: PMC9512701 DOI: 10.1038/s41589-022-01100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 12/22/2022]
Abstract
Many essential processes in the cell depend on proteins that use nucleoside triphosphates (NTPs). Methods that directly monitor the often-complex dynamics of these proteins at the single-molecule level have helped to uncover their mechanisms of action. However, the measurement throughput is typically limited for NTP-utilizing reactions, and the quantitative dissection of complex dynamics over multiple sequential turnovers remains challenging. Here we present a method for controlling NTP-driven reactions in single-molecule experiments via the local generation of NTPs (LAGOON) that markedly increases the measurement throughput and enables single-turnover observations. We demonstrate the effectiveness of LAGOON in single-molecule fluorescence and force spectroscopy assays by monitoring DNA unwinding, nucleosome sliding and RNA polymerase elongation. LAGOON can be readily integrated with many single-molecule techniques, and we anticipate that it will facilitate studies of a wide range of crucial NTP-driven processes. ![]()
A new method for controlling NTP-driven reactions in single-molecule experiments via the local generation of NTPs (LAGOON) markedly increases the measurement throughput and enables single-turnover observations.
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12
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Li J, Ma J, Kumar V, Fu H, Xu C, Wang S, Jia Q, Fan Q, Xi X, Li M, Liu H, Lu Y. Identification of flexible Pif1-DNA interactions and their impacts on enzymatic activities. Nucleic Acids Res 2022; 50:7002-7012. [PMID: 35748877 PMCID: PMC9262596 DOI: 10.1093/nar/gkac529] [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: 12/12/2021] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Flexible regions in biomolecular complexes, although crucial to understanding structure-function relationships, are often unclear in high-resolution crystal structures. In this study, we showed that single-molecule techniques, in combination with computational modeling, can characterize dynamic conformations not resolved by high-resolution structure determination methods. Taking two Pif1 helicases (ScPif1 and BsPif1) as model systems, we found that, besides a few tightly bound nucleotides, adjacent solvent-exposed nucleotides interact dynamically with the helicase surfaces. The whole nucleotide segment possessed curved conformations and covered the two RecA-like domains of the helicases, which are essential for the inch-worm mechanism. The synergetic approach reveals that the interactions between the exposed nucleotides and the helicases could be reduced by large stretching forces or electrostatically shielded with high-concentration salt, subsequently resulting in reduced translocation rates of the helicases. The dynamic interactions between the exposed nucleotides and the helicases underlay the force- and salt-dependences of their enzymatic activities. The present single-molecule based approach complements high-resolution structural methods in deciphering the molecular mechanisms of the helicases.
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Affiliation(s)
| | | | | | - Hang Fu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China,School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Qinkai Fan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China,School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuguang Xi
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette F-91190, France
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China,School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiguang Liu
- Correspondence may also be addressed to Haiguang Liu. Tel: +86 10 56981816;
| | - Ying Lu
- To whom correspondence should be addressed. Tel: +86 10 82648122;
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13
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Xue C, Salunkhe SJ, Tomimatsu N, Kawale AS, Kwon Y, Burma S, Sung P, Greene EC. Bloom helicase mediates formation of large single-stranded DNA loops during DNA end processing. Nat Commun 2022; 13:2248. [PMID: 35473934 PMCID: PMC9042962 DOI: 10.1038/s41467-022-29937-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
Bloom syndrome (BS) is associated with a profoundly increased cancer risk and is caused by mutations in the Bloom helicase (BLM). BLM is involved in the nucleolytic processing of the ends of DNA double-strand breaks (DSBs), to yield long 3' ssDNA tails that serve as the substrate for break repair by homologous recombination (HR). Here, we use single-molecule imaging to demonstrate that BLM mediates formation of large ssDNA loops during DNA end processing. A BLM mutant lacking the N-terminal domain (NTD) retains vigorous in vitro end processing activity but fails to generate ssDNA loops. This same mutant supports DSB end processing in cells, however, these cells do not form RAD51 DNA repair foci and the processed DSBs are channeled into synthesis-dependent strand annealing (SSA) instead of HR-mediated repair, consistent with a defect in RAD51 filament formation. Together, our results provide insights into BLM functions during homologous recombination.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Sameer J Salunkhe
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Nozomi Tomimatsu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ajinkya S Kawale
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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14
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Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1688. [PMID: 34472205 PMCID: PMC8888775 DOI: 10.1002/wrna.1688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Flaviviruses are a major health concern because over half of the world population is at risk of infection and there are very few antiviral therapeutics to treat diseases resulting from infection. Replication is an essential part of the flavivirus survival. One of the viral proteins, NS3 helicase, is critical for unwinding the double stranded RNA intermediate during flaviviral replication. The helicase performs the unwinding of the viral RNA intermediate structure in an ATP-dependent manner. NS3 helicase is a member of the Viral/DEAH-like subfamily of the superfamily 2 helicase containing eight highly conserved structural motifs (I, Ia, II, III, IV, IVa, V, and VI) localized between the ATP-binding and RNA-binding pockets. Of these structural motifs only three are well characterized for function in flaviviruses (I, II, and VI). The roles of the other structural motifs are not well understood for NS3 helicase function, but comparison of NS3 with other superfamily 2 helicases within the viral/DEAH-like, DEAH/RHA, and DEAD-box subfamilies can be used to elucidate the roles of these structural motifs in the flavivirus NS3 helicase. This review aims to summarize the role of each conserved structural motif within flavivirus NS3 in RNA helicase function. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Kelly E. Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
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15
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Yue K, Yao B, Shi Y, Yang Y, Qian Z, Ci Y, Shi L. The stalk domain of SARS-CoV-2 NSP13 is essential for its helicase activity. Biochem Biophys Res Commun 2022; 601:129-136. [PMID: 35245742 PMCID: PMC8864812 DOI: 10.1016/j.bbrc.2022.02.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/11/2022]
Abstract
COVID-19, caused by SARS-CoV-2, has been spreading worldwide for more than two years and has led to immense challenges to human health. Despite the great efforts that have been made, our understanding of SARS-CoV-2 is still limited. The viral helicase, NSP13 is an important enzyme involved in SARS-CoV-2 replication and transcription. Here we highlight the important role of the stalk domain in the enzymatic activity of NSP13. Without the stalk domain, NSP13 loses its dsRNA unwinding ability due to the lack of ATPase activity. The stalk domain of NSP13 also provides a rigid connection between the ZBD and helicase domain. We found that the tight connection between the stalk and helicase is necessary for NSP13-mediated dsRNA unwinding. When a short flexible linker was inserted between the stalk and helicase domains, the helicase activity of NSP13 was impaired, although its ATPase activity remained intact. Further study demonstrated that linker insertion between the stalk and helicase domains attenuated the RNA binding ability and affected the thermal stability of NSP13. In summary, our results suggest the crucial role of the stalk domain in NSP13 enzymatic activity and provide mechanistic insight into dsRNA unwinding by SARS-CoV-2 NSP13.
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Affiliation(s)
- Kun Yue
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Bin Yao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yingchao Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhaohui Qian
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, 100176, China
| | - Yali Ci
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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16
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Evans GW, Craggs T, Kapanidis AN. The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation. J Mol Biol 2022; 434:167410. [PMID: 34929202 PMCID: PMC8783057 DOI: 10.1016/j.jmb.2021.167410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 12/12/2021] [Indexed: 12/03/2022]
Abstract
DNA polymerases maintain genomic integrity by copying DNA with high fidelity, part of which relies on the polymerase fingers opening-closing transition, a series of conformational changes during the DNA synthesis reaction cycle. Fingers opening and closing has been challenging to study, mainly due to the need to synchronise molecular ensembles. We previously studied fingers opening-closing on single polymerase-DNA complexes using single-molecule FRET; however, our work was limited to pre-chemistry reaction steps. Here, we advance our analysis to extensible substrates, and observe DNA polymerase (Pol) conformational changes across the entire DNA polymerisation reaction in real-time, gaining direct access to an elusive post-chemistry step rate-limiting for DNA synthesis. Our results showed that Pol adopts the fingers-closed conformation during polymerisation, and that the post-chemistry rate-limiting step occurs in the fingers-closed conformation. We found that fingers-opening in the Pol-DNA binary complex in the absence of polymerisation is slow (∼5.3 s-1), and comparable to the rate of fingers-opening after polymerisation (3.4 s-1); this indicates that the fingers-opening step itself could be largely responsible for the slow post-chemistry step, with the residual rate potentially accounted for by pyrophosphase release. We also observed that DNA chain-termination of the 3' end of the primer increases substantially the rate of fingers-opening in the Pol-DNA binary complex (5.3 → 29 s-1), demonstrating that the 3'-OH residue is important for the kinetics of fingers conformational changes. Our observations offer mechanistic insight and tools to offer mechanistic insight for all nucleic acid polymerases.
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Affiliation(s)
- Geraint W Evans
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom. https://twitter.com/geraintwe
| | - Timothy Craggs
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom; Sheffield Institute for Nucleic Acids, Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom. https://twitter.com/Craggs_Lab
| | - Achillefs N Kapanidis
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom.
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17
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RQC helical hairpin in Bloom's syndrome helicase regulates DNA unwinding by dynamically intercepting nascent nucleotides. iScience 2022; 25:103606. [PMID: 35005551 PMCID: PMC8718986 DOI: 10.1016/j.isci.2021.103606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/03/2021] [Accepted: 12/08/2021] [Indexed: 11/24/2022] Open
Abstract
The RecQ family of helicases are important for maintenance of genomic integrity. Although functions of constructive subdomains of this family of helicases have been extensively studied, the helical hairpin (HH) in the RecQ-C-terminal domain (RQC) has been underappreciated and remains poorly understood. Here by using single-molecule fluorescence resonance energy transfer, we found that HH in the human BLM transiently intercepts different numbers of nucleotides when it is unwinding a double-stranded DNA. Single-site mutations in HH that disrupt hydrogen bonds and/or salt bridges between DNA and HH change the DNA binding conformations and the unwinding features significantly. Our results, together with recent clinical tests that correlate single-site mutations in HH of human BLM with the phenotype of cancer-predisposing syndrome or Bloom's syndrome, implicate pivotal roles of HH in BLM's DNA unwinding activity. Similar mechanisms might also apply to other RecQ family helicases, calling for more attention to the RQC helical hairpin.
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18
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Thompson MD, Malone EG, Byrd AK. Monitoring helicase-catalyzed unwinding of multiple duplexes simultaneously. Methods Enzymol 2022; 672:1-27. [PMID: 35934470 PMCID: PMC9397138 DOI: 10.1016/bs.mie.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Helicases catalyze the unwinding of duplex nucleic acids to aid a variety of cellular processes. Although helicases unwind duplex DNA in the same direction that they translocate on single-stranded DNA, forked duplexes provide opportunities to monitor unwinding by helicase monomers bound to each arm of the fork. The activity of the helicase bound to the displaced strand can be discerned alongside the helicase bound to the translocase strand using a forked substrate with accessible duplexes on both strands labeled with different fluorophores. In order to quantify the effect of protein-protein interactions on the activity of multiple monomers of the Bacteroides fragilis Pif1 helicase bound to separate strands of a forked DNA junction, an ensemble gel-based assay for monitoring simultaneous duplex unwinding was developed (Su et al., 2019). Here, the use of that assay is described for measuring the total product formation and rate constants of product formation of multiple duplexes on a single nucleic acid substrate. Use of this assay may aid characterization of protein-protein interactions between multiple helicase monomers at forked nucleic acid junctions and can assist with the characterization of helicase action on the displaced strand of forked duplexes.
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Affiliation(s)
- Matthew D Thompson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Emory G Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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19
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Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase. Nat Commun 2021; 12:7015. [PMID: 34853304 PMCID: PMC8636605 DOI: 10.1038/s41467-021-27304-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
UvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. Previous estimates of its step size have been indirect, and a consensus on its stepping mechanism is lacking. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hexameric helicases.
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20
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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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21
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Yoo J, Lee D, Im H, Ji S, Oh S, Shin M, Park D, Lee G. The mechanism of gap creation by a multifunctional nuclease during base excision repair. SCIENCE ADVANCES 2021; 7:7/29/eabg0076. [PMID: 34261654 PMCID: PMC8279506 DOI: 10.1126/sciadv.abg0076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/28/2021] [Indexed: 05/30/2023]
Abstract
During base excision repair, a transient single-stranded DNA (ssDNA) gap is produced at the apurinic/apyrimidinic (AP) site. Exonuclease III, capable of performing both AP endonuclease and exonuclease activity, are responsible for gap creation in bacteria. We used single-molecule fluorescence resonance energy transfer to examine the mechanism of gap creation. We found an AP site anchor-based mechanism by which the intrinsically distributive enzyme binds strongly to the AP site and becomes a processive enzyme, rapidly creating a gap and an associated transient ssDNA loop. The gap size is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA and is limited to a few nucleotides to maintain genomic stability. When the 3' end is released from the AP endonuclease, polymerase I quickly initiates DNA synthesis and fills the gap. Our work provides previously unidentified insights into how a signal of DNA damage changes the enzymatic functions.
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Affiliation(s)
- Jungmin Yoo
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Donghun Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Hyeryeon Im
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sangmi Ji
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sanghoon Oh
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-Ro, Jung-gu, Daegu 41944, Korea
| | - Daeho Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea.
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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22
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Fairlamb MS, Whitaker AM, Bain FE, Spies M, Freudenthal BD. Construction of a Three-Color Prism-Based TIRF Microscope to Study the Interactions and Dynamics of Macromolecules. BIOLOGY 2021; 10:biology10070571. [PMID: 34201434 PMCID: PMC8301196 DOI: 10.3390/biology10070571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/05/2023]
Abstract
Simple Summary Prism-based single-molecule total internal reflection fluorescence (prismTIRF) microscopes are excellent tools for studying macromolecular dynamics and interactions. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope using commercially available components with the hope of assisting those who aim to implement TIRF imaging techniques in their laboratory. Abstract Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for the real-time visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. While building a prismTIRF microscope without expert assistance can pose a significant challenge, the components needed to build a prismTIRF microscope are relatively affordable and, with some guidance, the assembly can be completed by a determined novice. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope which can be utilized for the study of macromolecular complexes, including the multi-component protein–DNA complexes responsible for DNA repair, replication, and transcription. Our hope is that this article can assist laboratories that aspire to implement single-molecule TIRF techniques, and consequently expand the application of this technology.
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Affiliation(s)
- Max S. Fairlamb
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Amy M. Whitaker
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Fletcher E. Bain
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
- Correspondence:
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23
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Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA. Proc Natl Acad Sci U S A 2021; 118:2102621118. [PMID: 34074787 PMCID: PMC8201915 DOI: 10.1073/pnas.2102621118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In transcription factors’ search for target genes, one-dimensional diffusion of the protein along DNA is essential. Experimentally, it remains challenging to resolve the individual diffusional steps of protein on DNA. Here, we report mainly all-atom equilibrium simulations of a WRKY domain protein in association with and diffusion along DNA. We demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic motions. Processive protein diffusions on DNA have been further sampled in a coarse-grained model. We have also found preferential DNA-strand association of the domain protein, which becomes most prominent at specific DNA binding, and it can be common for small-domain proteins to balance movements on the DNA with the sequence recognition. Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to one strand of DNA with significant energetic bias compared with the other, or nonpreferred strand. The preferential DNA-strand binding becomes most prominent in the static process, from nonspecific to specific DNA binding, but less distinct during diffusive movements of the domain protein on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base-pair stepping cycle of the protein tracking along major groove of DNA with a homogeneous poly-adenosine sequence, as individual hydrogen bonds break and reform at the protein–DNA binding interface. Further DNA-groove tracking motions of the protein forward or backward, with occasional sliding as well as strand crossing to minor groove of DNA, were also captured. The processive diffusion of WRKY along DNA has been further sampled via coarse-grained MD simulations. The study thus provides structural dynamics details on diffusion of a small TF domain protein, suggests how the protein approaches a specific recognition site on DNA, and supports further high-precision experimental detection. The stochastic movements revealed in the TF diffusion also provide general clues about how other protein walkers step and slide along DNA.
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Loeff L, Kerssemakers JWJ, Joo C, Dekker C. AutoStepfinder: A fast and automated step detection method for single-molecule analysis. PATTERNS 2021; 2:100256. [PMID: 34036291 PMCID: PMC8134948 DOI: 10.1016/j.patter.2021.100256] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 01/05/2023]
Abstract
Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step detection method, AutoStepfinder, that determines steps in large datasets without requiring prior knowledge on the noise contributions and location of steps. The analysis is based on a series of partition events that minimize the difference between the data and the fit. A dual-pass strategy determines the optimal fit and allows AutoStepfinder to detect steps of a wide variety of sizes. We demonstrate step detection for a broad variety of experimental traces. The user-friendly interface and the automated detection of AutoStepfinder provides a robust analysis procedure that enables anyone without programming knowledge to generate step fits and informative plots in less than an hour. Fast, automated, and bias-free detection of steps within single-molecule trajectories Robust step detection without any prior knowledge on the data A dual-pass strategy for the detection of steps over a wide variety of scales A user-friendly interface for a simplified step fitting procedure
Single-molecule techniques have made it possible to track individual protein complexes in real time with a nanometer spatial resolution and a millisecond timescale. Accurate determination of the dynamic states within single-molecule time traces provides valuable kinetic information that underlie the function of biological macromolecules. Here, we present a new automated step detection method called AutoStepfinder, a versatile, robust, and easy-to-use algorithm that allows researchers to determine the kinetic states within single-molecule time trajectories without any bias.
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Affiliation(s)
- Luuk Loeff
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
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25
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Ge M, Molt RW, Jenkins HT, Blackburn GM, Jin Y, Antson AA. Octahedral Trifluoromagnesate, an Anomalous Metal Fluoride Species, Stabilizes the Transition State in a Biological Motor. ACS Catal 2021; 11:2769-2773. [PMID: 33717640 PMCID: PMC7944477 DOI: 10.1021/acscatal.0c04500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/26/2020] [Indexed: 01/11/2023]
Abstract
![]()
Isoelectronic metal
fluoride transition state analogue (TSA) complexes,
MgF3– and AlF4–, have proven to be immensely useful in understanding mechanisms
of biological motors utilizing phosphoryl transfer. Here we report
a previously unobserved octahedral TSA complex, MgF3(H2O)−, in a 1.5 Å resolution Zika virus
NS3 helicase crystal structure. 19F NMR provided independent
validation and also the direct observation of conformational tightening
resulting from ssRNA binding in solution. The TSA stabilizes the two
conformations of motif V of the helicase that link ATP hydrolysis
with mechanical work. DFT analysis further validated the MgF3(H2O)− species, indicating the significance
of this TSA for studies of biological motors.
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Affiliation(s)
- Mengyu Ge
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - Robert W. Molt
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940, United States
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Yi Jin
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
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26
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Cho J, Oh S, Lee D, Han JW, Yoo J, Park D, Lee G. Spectroscopic sensing and quantification of AP-endonucleases using fluorescence-enhancement by cis– trans isomerization of cyanine dyes. RSC Adv 2021; 11:11380-11386. [PMID: 35423644 PMCID: PMC8695990 DOI: 10.1039/d0ra08051a] [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: 09/21/2020] [Accepted: 03/08/2021] [Indexed: 11/21/2022] Open
Abstract
Apurinic/apyrimidinic (AP) endonucleases are vital DNA repair enzymes, and proposed to be a prognostic biomarker for various types of cancer in humans. Numerous DNA sensors have been developed to evaluate the extent of nuclease activity but their DNA termini are not protected against other nucleases, hampering accurate quantification. Here we developed a new fluorescence enhancement (FE)-based method as an enzyme-specific DNA biosensor with nuclease-protection by three functional units (an AP-site, Cy3 and termini that are protected from exonucleolytic cleavage). A robust FE signal arises from the fluorescent cis–trans isomerization of a cyanine dye (e.g., Cy3) upon the enzyme-triggered structural change from double-stranded (ds)DNA to single-stranded (ss)DNA that carries Cy3. The FE-based assay reveals a linear dependency on sub-nanomolar concentrations as low as 10−11 M for the target enzyme and can be also utilized as a sensitive readout of other nuclease activities. Apurinic/apyrimidinic (AP) endonucleases are vital DNA repair enzymes, and proposed to be a prognostic biomarker for various types of cancer in humans.![]()
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Affiliation(s)
- JunHo Cho
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Sanghoon Oh
- Department of Biomedical Science and Engineering
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - DongHun Lee
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Jae Won Han
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Jungmin Yoo
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Daeho Park
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
- Cell Mechanobiology Research Center
| | - Gwangrog Lee
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
- Department of Biomedical Science and Engineering
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27
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Mickolajczyk KJ, Shelton PMM, Grasso M, Cao X, Warrington SE, Aher A, Liu S, Kapoor TM. Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase. Biophys J 2020; 120:1020-1030. [PMID: 33340543 PMCID: PMC7837305 DOI: 10.1016/j.bpj.2020.11.2276] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/26/2020] [Accepted: 11/10/2020] [Indexed: 12/21/2022] Open
Abstract
The superfamily 1 helicase nonstructural protein 13 (nsp13) is required for SARS-CoV-2 replication. The mechanism and regulation of nsp13 has not been explored at the single-molecule level. Specifically, force-dependent unwinding experiments have yet to be performed for any coronavirus helicase. Here, using optical tweezers, we find that nsp13 unwinding frequency, processivity, and velocity increase substantially when a destabilizing force is applied to the RNA substrate. These results, along with bulk assays, depict nsp13 as an intrinsically weak helicase that can be activated >50-fold by piconewton forces. Such force-dependent behavior contrasts the known behavior of other viral monomeric helicases, such as hepatitis C virus NS3, and instead draws stronger parallels to ring-shaped helicases. Our findings suggest that mechanoregulation, which may be provided by a directly bound RNA-dependent RNA polymerase, enables on-demand helicase activity on the relevant polynucleotide substrate during viral replication.
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Affiliation(s)
- Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Patrick M M Shelton
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Michael Grasso
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Xiaocong Cao
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York; Laboratory of Structural Immunology, University of Science and Technology of China, Hefei, Anhui, China
| | - Sara E Warrington
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Amol Aher
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York.
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York.
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28
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Jungblut A, Hopfner KP, Eustermann S. Megadalton chromatin remodelers: common principles for versatile functions. Curr Opin Struct Biol 2020; 64:134-144. [PMID: 32771531 DOI: 10.1016/j.sbi.2020.06.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023]
Abstract
ATP-dependent chromatin remodelers are enigmatic macromolecular machines that govern the arrangement and composition of nucleosomes across eukaryotic genomes. Here, we review the recent breakthrough provided by cryo-electron microscopy that reveal the first high-resolution insights into all four families of remodelers. We highlight the emerging structural and mechanistic principles with a particular focus on multi-subunit SWI/SNF and INO80/SWR1 complexes. A conserved architecture comprising a motor, rotor, stator and grip suggests a unifying mechanism for how stepwise DNA translocation enables large scale reconfigurations of nucleosomes. A molecular circuitry involving the nuclear actin containing module establishes a framework for understanding allosteric regulation. Remodelers emerge as programable hubs that enable differential processing of genetic and epigenetic information in response to the physiological state of a cell.
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Affiliation(s)
- Anna Jungblut
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany; Candidate for joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.
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29
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Du Pont KE, Davidson RB, McCullagh M, Geiss BJ. Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft. J Biol Chem 2020; 295:1551-1564. [PMID: 31914411 PMCID: PMC7008374 DOI: 10.1074/jbc.ra119.011922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/22/2019] [Indexed: 01/01/2023] Open
Abstract
The unwinding of dsRNA intermediates is critical for the replication of flavivirus RNA genomes. This activity is provided by the C-terminal helicase domain of viral nonstructural protein 3 (NS3). As a member of the superfamily 2 (SF2) helicases, NS3 requires the binding and hydrolysis of ATP/NTP to translocate along and unwind double-stranded nucleic acids. However, the mechanism of energy transduction between the ATP- and RNA-binding pockets is not well-understood. Previous molecular dynamics simulations conducted by our group have identified Motif V as a potential "communication hub" for this energy transduction pathway. To investigate the role of Motif V in this process, here we combined molecular dynamics, biochemistry, and virology approaches. We tested Motif V mutations in both the replicon and recombinant protein systems to investigate viral genome replication, RNA-binding affinity, ATP hydrolysis activity, and helicase-mediated unwinding activity. We found that the T407A and S411A substitutions in NS3 reduce viral replication and increase the helicase-unwinding turnover rates by 1.7- and 3.5-fold, respectively, suggesting that flaviviruses may use suboptimal NS3 helicase activity for optimal genome replication. Additionally, we used simulations of each mutant to probe structural changes within NS3 caused by each mutation. These simulations indicate that Motif V controls communication between the ATP-binding pocket and the helical gate. These results help define the linkage between ATP hydrolysis and helicase activities within NS3 and provide insight into the biophysical mechanisms for ATPase-driven NS3 helicase function.
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Affiliation(s)
- Kelly E Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523; Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Russell B Davidson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Martin McCullagh
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523.
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523; School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523.
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30
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Ablenas CJ, Gidi Y, Powdrill MH, Ahmed N, Shaw TA, Mesko M, Götte M, Cosa G, Pezacki JP. Hepatitis C Virus Helicase Binding Activity Monitored through Site-Specific Labeling Using an Expanded Genetic Code. ACS Infect Dis 2019; 5:2118-2126. [PMID: 31640339 DOI: 10.1021/acsinfecdis.9b00220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of unwinding catalyzed by the hepatitis C virus nonstructural protein 3 helicase (NS3h) has been a subject of considerable interest, with NS3h serving as a prototypical enzyme in the study of helicase function. Recent studies support an ATP-fueled, inchworm-like stepping of NS3h on the nucleic acid that would result in the displacement of the complementary strand of the duplex during unwinding. Here, we describe the screening of a site of incorporation of an unnatural amino acid in NS3h for fluorescent labeling of the enzyme to be used in single-molecule Förster resonance energy transfer (FRET) experiments. From the nine potential sites identified in NS3h for incorporation of the unnatural amino acid, only one allowed for expression and fluorescent labeling of the recombinant protein. Incorporation of the unnatural amino acid was confirmed via bulk assays to not interfere with unwinding activity of the helicase. Binding to four different dsDNA sequences bearing a ssDNA overhang segment of varying length (either minimal 6 or 7 base length overhang to ensure binding or a long 24 base overhang) and sequence was recorded with the new NS3h construct at the single-molecule level. Single-molecule fluorescence displayed time intervals with anticorrelated donor and acceptor emission fluctuations associated with protein binding to the substrates. An apparent FRET value was estimated from the binding events showing a single FRET value of ∼0.8 for the 6-7 base overhangs. A smaller mean value and a broad distribution was in turn recorded for the long ssDNA overhang, consistent with NS3h exploring a larger physical space while bound to the DNA construct. Notably, intervals where NS3h binding was recorded were exhibited at time periods where the acceptor dye reversibly bleached. Protein induced fluorescence intensity enhancement in the donor channel became apparent at these intervals. Overall, the site-specific fluorescent labeling of NS3h reported here provides a powerful tool for future studies to monitor the dynamics of enzyme translocation during unwinding by single-molecule FRET.
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Affiliation(s)
- Christopher J. Ablenas
- Department of Biochemistry, McGill University, Montreal, Quebec H3G1Y6, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Yasser Gidi
- Department of Chemistry, McGill University, Montreal, Quebec H3A0B8, Canada
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Noreen Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Mihai Mesko
- Department of Chemistry, McGill University, Montreal, Quebec H3A0B8, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G2R7, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, Montreal, Quebec H3A0B8, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
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31
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Shin S, Hyun K, Kim J, Hohng S. ATP Binding to Rad5 Initiates Replication Fork Reversal by Inducing the Unwinding of the Leading Arm and the Formation of the Holliday Junction. Cell Rep 2019; 23:1831-1839. [PMID: 29742437 DOI: 10.1016/j.celrep.2018.04.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 02/20/2018] [Accepted: 04/05/2018] [Indexed: 11/30/2022] Open
Abstract
Replication fork reversal is one of the major pathways for reactivating stalled DNA replication. Many enzymes with replication fork reversal activity have DNA-unwinding activity as well, but none of the fork reversal enzymes in the SWI/SNF family shows a separate DNA-unwinding activity, raising the question of how they initiate the remodeling process. Here, we found ATP binding to Rad5 induces the unwinding of the leading arm of the replication fork and proximally positions the leading and lagging arms. This facilitates the spontaneous remodeling of the replication fork into a four-way junction. Once the four-way junction is formed, Rad5 migrates the four-way junction at a speed of 7.1 ± 0.14 nt/s. The 3' end anchoring of the leading arm by Rad5's HIRAN domain is critical for both branch migration and the recovery of the three-way junction, but not for the structural transition to the four-way junction.
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Affiliation(s)
- Soochul Shin
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul 08826, Republic of Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul 08826, Republic of Korea.
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32
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Hamann F, Enders M, Ficner R. Structural basis for RNA translocation by DEAH-box ATPases. Nucleic Acids Res 2019; 47:4349-4362. [PMID: 30828714 PMCID: PMC6486627 DOI: 10.1093/nar/gkz150] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/28/2019] [Accepted: 02/22/2019] [Indexed: 12/15/2022] Open
Abstract
DEAH-box adenosine triphosphatases (ATPases) play a crucial role in the spliceosome-mediated excision of pre-mRNA introns. Recent spliceosomal cryo-EM structures suggest that these proteins utilize translocation to apply forces on ssRNAs rather than direct RNA duplex unwinding to ensure global rearrangements. By solving the crystal structure of Prp22 in different adenosine nucleotide-free states, we identified two missing conformational snapshots of genuine DEAH-box ATPases that help to unravel the molecular mechanism of translocation for this protein family. The intrinsic mobility of the RecA2 domain in the absence of adenosine di- or triphosphate (ADP/ATP) and RNA enables DEAH-box ATPases to adopt different open conformations of the helicase core. The presence of RNA suppresses this mobility and stabilizes one defined open conformation when no adenosine nucleotide is bound. A comparison of this novel conformation with the ATP-bound state of Prp43 reveals that these ATPases cycle between closed and open conformations of the helicase core, which accommodate either a four- or five-nucleotide stack in the RNA-binding tunnel, respectively. The continuous repetition of these states enables these proteins to translocate in 3′-5′ direction along an ssRNA with a step-size of one RNA nucleotide per hydrolyzed ATP. This ATP-driven motor function is maintained by a serine in the conserved motif V that senses the catalytic state and accordingly positions the RecA2 domain.
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Affiliation(s)
- Florian Hamann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Marieke Enders
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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33
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Branched unwinding mechanism of the Pif1 family of DNA helicases. Proc Natl Acad Sci U S A 2019; 116:24533-24541. [PMID: 31744872 DOI: 10.1073/pnas.1915654116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Members of the Pif1 family of helicases function in multiple pathways that involve DNA synthesis: DNA replication across G-quadruplexes; break-induced replication; and processing of long flaps during Okazaki fragment maturation. Furthermore, Pif1 increases strand-displacement DNA synthesis by DNA polymerase δ and allows DNA replication across arrays of proteins tightly bound to DNA. This is a surprising feat since DNA rewinding or annealing activities limit the amount of single-stranded DNA product that Pif1 can generate, leading to an apparently poorly processive helicase. In this work, using single-molecule Förster resonance energy transfer approaches, we show that 2 members of the Pif1 family of helicases, Pif1 from Saccharomyces cerevisiae and Pfh1 from Schizosaccharomyces pombe, unwind double-stranded DNA by a branched mechanism with 2 modes of activity. In the dominant mode, only short stretches of DNA can be processively and repetitively opened, with reclosure of the DNA occurring by mechanisms other than strand-switching. In the other less frequent mode, longer stretches of DNA are unwound via a path that is separate from the one leading to repetitive unwinding. Analysis of the kinetic partitioning between the 2 different modes suggests that the branching point in the mechanism is established by conformational selection, controlled by the interaction of the helicase with the 3' nontranslocating strand. The data suggest that the dominant and repetitive mode of DNA opening of the helicase can be used to allow efficient DNA replication, with DNA synthesis on the nontranslocating strand rectifying the DNA unwinding activity.
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34
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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35
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Xu S, Ci Y, Wang L, Yang Y, Zhang L, Xu C, Qin C, Shi L. Zika virus NS3 is a canonical RNA helicase stimulated by NS5 RNA polymerase. Nucleic Acids Res 2019; 47:8693-8707. [PMID: 31361901 PMCID: PMC6895266 DOI: 10.1093/nar/gkz650] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 01/19/2023] Open
Abstract
Zika virus is a positive single-strand RNA virus whose replication involved RNA unwinding and synthesis. ZIKV NS3 contains a helicase domain, but its enzymatic activity is not fully characterized. Here, we established a dsRNA unwinding assay based on the FRET effect to study the helicase activity of ZIKV NS3, which provided kinetic information in real time. We found that ZIKV NS3 specifically unwound dsRNA/dsDNA with a 3' overhang in the 3' to 5' direction. The RNA unwinding ability of NS3 significantly decreased when the duplex was longer than 18 base pairs. The helicase activity of NS3 depends on ATP hydrolysis and binding to RNA. Mutations in the ATP binding region or the RNA binding region of NS3 impair its helicase activity, thus blocking viral replication in the cell. Furthermore, we showed that ZIKV NS5 interacted with NS3 and stimulated its helicase activity. Disrupting NS3-NS5 interaction resulted in a defect in viral replication, revealing the tight coupling of RNA unwinding and synthesis. We suggest that NS3 helicase activity is stimulated by NS5; thus, viral replication can be carried out efficiently. Our work provides a molecular mechanism of ZIKV NS3 unwinding and novel insights into ZIKV replication.
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MESH Headings
- Adenosine Triphosphate/chemistry
- Adenosine Triphosphate/metabolism
- Animals
- Binding Sites
- Chlorocebus aethiops
- Cloning, Molecular
- Cricetulus
- Epithelial Cells/virology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Gene Expression Regulation, Viral
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Kinetics
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Structure, Tertiary
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/metabolism
- Substrate Specificity
- Vero Cells
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
- Zika Virus/genetics
- Zika Virus/metabolism
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Affiliation(s)
- Shan Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Yali Ci
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Leijie Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Leiliang Zhang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
| | - Caimin Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Chengfeng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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36
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Seol Y, Harami GM, Kovács M, Neuman KC. Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase. eLife 2019; 8:e45909. [PMID: 31464683 PMCID: PMC6773442 DOI: 10.7554/elife.45909] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
RecQ helicases promote genomic stability through their unique ability to suppress illegitimate recombination and resolve recombination intermediates. These DNA structure-specific activities of RecQ helicases are mediated by the helicase-and-RNAseD like C-terminal (HRDC) domain, via unknown mechanisms. Here, employing single-molecule magnetic tweezers and rapid kinetic approaches we establish that the HRDC domain stabilizes intrinsic, sequence-dependent, pauses of the core helicase (lacking the HRDC) in a DNA geometry-dependent manner. We elucidate the core unwinding mechanism in which the unwinding rate depends on the stability of the duplex DNA leading to transient sequence-dependent pauses. We further demonstrate a non-linear amplification of these transient pauses by the controlled binding of the HRDC domain. The resulting DNA sequence- and geometry-dependent pausing may underlie a homology sensing mechanism that allows rapid disruption of unstable (illegitimate) and stabilization of stable (legitimate) DNA strand invasions, which suggests an intrinsic mechanism of recombination quality control by RecQ helicases.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule BiophysicsNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaUnited States
| | - Gábor M Harami
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research GroupEötvös Loránd UniversityBudapestHungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research GroupEötvös Loránd UniversityBudapestHungary
- Department of Biochemistry, MTA-ELTE Motor Pharmacology Research GroupEötvös Loránd UniversityBudapestHungary
| | - Keir C Neuman
- Laboratory of Single Molecule BiophysicsNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaUnited States
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37
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Abstract
While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold.
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Affiliation(s)
- Holger Flechsig
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan
| | - Alexander S Mikhailov
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan.,2 Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin , Germany
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38
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Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase. Proc Natl Acad Sci U S A 2019; 116:9558-9567. [PMID: 31000599 PMCID: PMC6511008 DOI: 10.1073/pnas.1900656116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Here, we report the crystal structure of the nsP2h bound to the conserved 3'-end 14 nucleotides of the CHIKV genome and the nonhydrolyzable transition-state nucleotide analog ADP-AlF4 Overall, the structural analysis revealed that nsP2h adopts a uniquely folded N-terminal domain followed by a superfamily 1 RNA helicase fold. The conserved helicase motifs establish polar contacts with the RNA backbone. There are three hydrophobic residues (Y161, F164, and F287) which form stacking interactions with RNA bases and thereby bend the RNA backbone. An F287A substitution that disrupted these stacking interactions increased the basal ATPase activity but decreased the RNA binding affinity. Furthermore, the F287A substitution reduced viral infectivity by attenuating subgenomic RNA synthesis. Replication of the mutant virus was restored by pseudoreversion (A287V) or adaptive mutations in the RecA2 helicase domain (T358S or V410I). Y161A and/or F164A substitutions, which were designed to disrupt the interactions with the RNA molecule, did not affect the ATPase activity but completely abolished the replication and transcription of viral RNA and the infectivity of CHIKV. Our study sheds light on the roles of the RNA helicase region in viral replication and provides insights that might be applicable to alphaviruses and other RNA viruses in general.
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39
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Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling. Nat Commun 2019; 10:1720. [PMID: 30979890 PMCID: PMC6461674 DOI: 10.1038/s41467-019-09657-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/20/2019] [Indexed: 11/11/2022] Open
Abstract
ATP-dependent chromatin remodelling enzymes (remodellers) regulate DNA accessibility in eukaryotic genomes. Many remodellers reposition (slide) nucleosomes, however, how DNA is propagated around the histone octamer during this process is unclear. Here we examine the real-time coordination of remodeller-induced DNA movements on both sides of the nucleosome using three-colour single-molecule FRET. During sliding by Chd1 and SNF2h remodellers, DNA is shifted discontinuously, with movement of entry-side DNA preceding that of exit-side DNA. The temporal delay between these movements implies a single rate-limiting step dependent on ATP binding and transient absorption or buffering of at least one base pair. High-resolution cross-linking experiments show that sliding can be achieved by buffering as few as 3 bp between entry and exit sides of the nucleosome. We propose that DNA buffering ensures nucleosome stability during ATP-dependent remodelling, and provides a means for communication between remodellers acting on opposite sides of the nucleosome. Chromatin remodelling enzymes (remodellers) regulate DNA accessibility of eukaryotic genomes, which rely in large part on an ability to reposition nucleosomes. Here the authors use three-colour single-molecule FRET to simultaneously monitor remodeller-induced DNA movements on both sides of the nucleosome in real-time.
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40
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Crickard JB, Greene EC. Helicase Mechanisms During Homologous Recombination in Saccharomyces cerevisiae. Annu Rev Biophys 2019; 48:255-273. [PMID: 30857400 DOI: 10.1146/annurev-biophys-052118-115418] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Helicases are enzymes that move, manage, and manipulate nucleic acids. They can be subdivided into six super families and are required for all aspects of nucleic acid metabolism. In general, all helicases function by converting the chemical energy stored in the bond between the gamma and beta phosphates of adenosine triphosphate into mechanical work, which results in the unidirectional movement of the helicase protein along one strand of a nucleic acid. The results of this translocation activity can range from separation of strands within duplex nucleic acids to the physical remodeling or removal of nucleoprotein complexes. In this review, we focus on describing key helicases from the model organism Saccharomyces cerevisiae that contribute to the regulation of homologous recombination, which is an essential DNA repair pathway for fixing damaged chromosomes.
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Affiliation(s)
- J Brooks Crickard
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; ,
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; ,
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41
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Schlierf M, Wang G, Chen XS, Ha T. Hexameric helicase G40P unwinds DNA in single base pair steps. eLife 2019; 8:42001. [PMID: 30688211 PMCID: PMC6370340 DOI: 10.7554/elife.42001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023] Open
Abstract
Most replicative helicases are hexameric, ring-shaped motor proteins that translocate on and unwind DNA. Despite extensive biochemical and structural investigations, how their translocation activity is utilized chemo-mechanically in DNA unwinding is poorly understood. We examined DNA unwinding by G40P, a DnaB-family helicase, using a single-molecule fluorescence assay with a single base pair resolution. The high-resolution assay revealed that G40P by itself is a very weak helicase that stalls at barriers as small as a single GC base pair and unwinds DNA with the step size of a single base pair. Binding of a single ATPγS could stall unwinding, demonstrating highly coordinated ATP hydrolysis between six identical subunits. We observed frequent slippage of the helicase, which is fully suppressed by the primase DnaG. We anticipate that these findings allow a better understanding on the fine balance of thermal fluctuation activation and energy derived from hydrolysis. Living cells store their genetic code written in molecules of DNA, with two strands of DNA twisted together to form the familiar double helix. When a cell prepares to divide, it must unwind its DNA so that the individual strands can be copied. Enzymes known as DNA helicases play a vital role in this unwinding process; yet, it is not completely clear how these enzymes move along the DNA. Schlierf et al. have now developed a new approach to see how an individual DNA helicase called G40P unwinds the DNA double helix. The experiments used a molecular ruler to measure the DNA unwinding and showed that the helicase opened the double helix one letter of genetic code at a time. Also, specific sequence of letters within the DNA molecules could slow down and stop G40P or even cause it to move backwards. DNA helicases work closely with other proteins inside cells to perform their task. DNA primases, for example, are enzymes that create the starting points for making new strands of DNA. Schlierf et al. found that the primase DnaG could also prevent G40P from moving backwards on the DNA, a new and unexpected function of DnaG. These findings contribute to an ongoing debate among researchers with partially contradictory models for how DNA helicases unwind the DNA double helix. Although originally from a virus, G40P is similar to a helicase enzyme found in bacteria. Therefore, a better understanding of this helicase may lead to new ways to stop bacteria copying their DNA, which might one day become new antibiotics to treat bacterial infections.
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Affiliation(s)
- Michael Schlierf
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Illinois, United States.,B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Ganggang Wang
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Taekjip Ha
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Illinois, United States.,Howard Hughes Medical Institute, Baltimore, United States.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States.,Department of Biophysics, Johns Hopkins University, Baltimore, United States
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42
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Togashi Y, Flechsig H. Coarse-Grained Protein Dynamics Studies Using Elastic Network Models. Int J Mol Sci 2018; 19:ijms19123899. [PMID: 30563146 PMCID: PMC6320916 DOI: 10.3390/ijms19123899] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/28/2018] [Accepted: 12/03/2018] [Indexed: 01/03/2023] Open
Abstract
Elastic networks have been used as simple models of proteins to study their slow structural dynamics. They consist of point-like particles connected by linear Hookean springs and hence are convenient for linear normal mode analysis around a given reference structure. Furthermore, dynamic simulations using these models can provide new insights. As the computational cost associated with these models is considerably lower compared to that of all-atom models, they are also convenient for comparative studies between multiple protein structures. In this review, we introduce examples of coarse-grained molecular dynamics studies using elastic network models and their derivatives, focusing on the nonlinear phenomena, and discuss their applicability to large-scale macromolecular assemblies.
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Affiliation(s)
- Yuichi Togashi
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
- RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
- Cybermedia Center, Osaka University, 5-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
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43
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Wang X, Park S, Zeng L, Jain A, Ha T. Toward Single-Cell Single-Molecule Pull-Down. Biophys J 2018; 115:283-288. [PMID: 29804751 DOI: 10.1016/j.bpj.2018.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/04/2018] [Accepted: 05/10/2018] [Indexed: 11/19/2022] Open
Abstract
Single-molecule pull-down (SiMPull) can capture native protein complexes directly from cell lysates for analysis of complex composition and activities at the single-molecule level. Although SiMPull requires many fewer cells compared to conventional pull-down assays, all studies so far have been performed using lysates from many cells. In principle, extending SiMPull to the single-cell level will allow the investigation of cell-to-cell variations on the stoichiometry and activities of biomolecular complexes. We developed a protocol to lyse bacterial cells in situ and capture the released proteins on the imaging surface using antibodies. The use of lysozymes delayed the protein release until after the flow has ceased, and the use of a 10-μm spacer reduces the capture radius within which ∼70% of target proteins can be captured to below 30 μm. Proteins thus captured can be unambiguously assigned to the originating cell. The developed platform should be compatible with high-throughput protein analysis and protein-protein interaction analysis at the single-cell level through single-molecule imaging.
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Affiliation(s)
- Xuefeng Wang
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa; Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Seongjin Park
- Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Lanying Zeng
- Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, Texas
| | - Ankur Jain
- Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Taekjip Ha
- Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Howard Hughes Medical Institute, Baltimore, Maryland; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland.
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44
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Single-Molecule FRET Analysis of Replicative Helicases. Methods Mol Biol 2018. [PMID: 29971721 DOI: 10.1007/978-1-4939-8556-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Over the recent years single-molecule fluorescence resonance energy transfer (smFRET) technique has proven to be one of the most powerful tools for revealing mechanistic insights into helicase activities. Here we describe details of single-molecule FRET assays for probing DNA unwinding activities as well as functional dynamics by replicative helicases in real time. The ability of smFRET to measure the behavior of biomolecules at a nanometer scale enabled us to address how the leading and lagging strand synthesis are coordinated during DNA replication, to resolve DNA unwinding steps of Bacteriophage T7 helicase, and to observe heterogeneous unwinding patterns modulated by the DNA binding domain of E1 helicase. These single-molecule FRET assays are generally applicable to other replicative and nonreplicative hexameric helicases.
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45
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Banerjee S, Maurya S, Roy R. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018; 43:519-540. [PMID: 30002270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise. This article highlights some of the methods and recent applications of single-molecule fluorescence in the field of virology. Here, we have focused on new findings in virus-cell interaction, virus cell entry and transport, viral membrane fusion, genome release, replication, translation, assembly, genome packaging, egress and interaction with host immune proteins that underline the advantage of single-molecule approach to the question at hand. Finally, we discuss the challenges, outlook and potential areas for improvement and future use of single-molecule fluorescence that could further aid our understanding of viruses.
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Affiliation(s)
- Sunaina Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
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46
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Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018. [DOI: 10.1007/s12038-018-9769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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47
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Wang W, Shen H, Moringo NA, Carrejo NC, Ye F, Robinson JT, Landes CF. Super-Temporal-Resolved Microscopy Reveals Multistep Desorption Kinetics of α-Lactalbumin from Nylon. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6697-6702. [PMID: 29763567 DOI: 10.1021/acs.langmuir.8b00686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Insight into the mechanisms driving protein-polymer interactions is constantly improving due to advances in experimental and computational methods. In this study, we used super-temporal-resolved microscopy (STReM) to study the interfacial kinetics of a globular protein, α-lactalbumin (α-LA), adsorbing at the water-nylon 6,6 interface. The improved temporal resolution of STReM revealed that residence time distributions involve an additional step in the desorption process. Increasing the ionic strength in the bulk solution accelerated the desorption rate of α-LA, attributed to adsorption-induced conformational changes. Ensemble circular dichroism measurements were used to support a consecutive reaction mechanism. Without the improved temporal resolution of STReM, the desorption intermediate was not resolvable, highlighting both STReM's potential to uncover new kinetic mechanisms and the continuing need to push for better time and space resolution.
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Affiliation(s)
- Wenxiao Wang
- Department of Electrical and Computer Engineering , Rice University , MS 366 , Houston , Texas 77251-1892 , United States
| | - Hao Shen
- Department of Chemistry , Rice University , MS 60 , Houston , Texas 77251-1892 , United States
| | - Nicholas A Moringo
- Department of Chemistry , Rice University , MS 60 , Houston , Texas 77251-1892 , United States
| | - Nicole C Carrejo
- Department of Chemistry , Rice University , MS 60 , Houston , Texas 77251-1892 , United States
| | - Fan Ye
- Department of Electrical and Computer Engineering , Rice University , MS 366 , Houston , Texas 77251-1892 , United States
| | - Jacob T Robinson
- Department of Electrical and Computer Engineering , Rice University , MS 366 , Houston , Texas 77251-1892 , United States
- Department of Bioengineering , Rice University , MS 142 , Houston , Texas 77251-1892 , United States
| | - Christy F Landes
- Department of Electrical and Computer Engineering , Rice University , MS 366 , Houston , Texas 77251-1892 , United States
- Department of Chemistry , Rice University , MS 60 , Houston , Texas 77251-1892 , United States
- Smalley-Curl Institute , Rice University , Houston , Texas 77251 , United States
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48
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Ma JB, Jia Q, Xu CH, Li JH, Huang XY, Ma DF, Li M, Xi XG, Lu Y. Asynchrony of Base-Pair Breaking and Nucleotide Releasing of Helicases in DNA Unwinding. J Phys Chem B 2018; 122:5790-5796. [PMID: 29733603 DOI: 10.1021/acs.jpcb.8b01470] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Helicases harness the energy of nucleotide triphosphate hydrolysis to unwind double-stranded DNA (dsDNA) in discrete steps. In spite of intensive studies, the mechanism of stepping is still poorly understood. Here, we applied single-molecule fluorescent resonant energy transfer to characterize the stepping of two nonring helicases, Escherichia coli RecQ ( E. coli RecQ) and Saccharomyces cerevisiae Pif1 (ScPif1). Our data showed that when forked dsDNA with free overhangs are used as substrates, both E. coli RecQ and ScPif1 unwind the dsDNA in nonuniform steps that distribute over broad ranges. When tension is exerted on the overhangs, the overall profile of the step-size distribution of ScPif1 is narrowed, whereas that of E. coli RecQ remains unchanged. Moreover, the measured step sizes of the both helicases concentrate on integral multiples of a half base pair. We propose a universal stepping mechanism, in which a helicase breaks one base pair at a time and sequesters the nascent nucleotides and then releases them after a random number of base-pair breaking events. The mechanism can interpret the observed unwinding patterns quantitatively and provides a general view of the helicase activity.
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Affiliation(s)
- Jian-Bing Ma
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chun-Hua Xu
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China
| | - Jing-Hua Li
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China
| | - Xing-Yuan Huang
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dong-Fei Ma
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xu-Guang Xi
- College of Life Sciences , Northwest A&F University , Yangling 712100 , Shaanxi , China.,LBPA, ENS de Cachan , CNRS, Université Paris-Saclay , Cachan F-94235 , France
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China
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49
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LeGresley SE, Briggs K, Fischer CJ. Molecular motor translocation kinetics: Application of Monte Carlo computer simulations to determine microscopic kinetic parameters. Biosystems 2018; 168:8-25. [PMID: 29733888 DOI: 10.1016/j.biosystems.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 10/17/2022]
Abstract
Methods for studying the translocation of motor proteins along a filament (e.g., nucleic acid and polypeptide) typically monitor the total production of ADP, the arrival/departure of the motor protein at/from a particular location (often one end of the filament), or the dissociation of the motor protein from the filament. The associated kinetic time courses are often analyzed using a simple sequential uniform n-step mechanism to estimate the macroscopic kinetic parameters (e.g., translocation rate and processivity) and the microscopic kinetic parameters (e.g., kinetic step-size and the rate constant for the rate-limiting step). These sequential uniform n-step mechanisms assume repetition of uniform and irreversible rate-limiting steps of forward motion along the filament. In order to determine how the presence of non-uniform motion (e.g., backward motion, random pauses, or jumping) affects the estimates of parameters obtained from such analyses, we evaluated computer simulated translocation time courses containing non-uniform motion using a simple sequential uniform n-step model. By comparing the kinetic parameters estimated from the analysis of the data generated by these simulations with the input parameters of the simulations, we were able to determine which of the kinetic parameters were likely to be over/under estimated due to non-uniform motion of the motor protein.
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Affiliation(s)
- Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA
| | - Koan Briggs
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA
| | - Christopher J Fischer
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA.
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Loeff L, Brouns SJJ, Joo C. Repetitive DNA Reeling by the Cascade-Cas3 Complex in Nucleotide Unwinding Steps. Mol Cell 2018; 70:385-394.e3. [PMID: 29706536 DOI: 10.1016/j.molcel.2018.03.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/23/2018] [Accepted: 03/24/2018] [Indexed: 01/12/2023]
Abstract
CRISPR-Cas provides RNA-guided adaptive immunity against invading genetic elements. Interference in type I systems relies on the RNA-guided Cascade complex for target DNA recognition and the Cas3 helicase/nuclease protein for target degradation. Even though the biochemistry of CRISPR interference has been largely covered, the biophysics of DNA unwinding and coupling of the helicase and nuclease domains of Cas3 remains elusive. Here, we employed single-molecule Förster resonance energy transfer (FRET) to probe the helicase activity with high spatiotemporal resolution. We show that Cas3 remains tightly associated with the target-bound Cascade complex while reeling the DNA using a spring-loaded mechanism. This spring-loaded reeling occurs in distinct bursts of 3 bp, which underlie three successive 1-nt unwinding events. Reeling is highly repetitive, allowing Cas3 to repeatedly present its inefficient nuclease domain with single-strand DNA (ssDNA) substrate. Our study reveals that the discontinuous helicase properties of Cas3 and its tight interaction with Cascade ensure controlled degradation of target DNA only.
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Affiliation(s)
- Luuk Loeff
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, the Netherlands
| | - Stan J J Brouns
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, the Netherlands; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708WE, the Netherlands.
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, the Netherlands.
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