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de Jager M, Kolbeck PJ, Vanderlinden W, Lipfert J, Filion L. Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning. Biophys J 2024; 123:3231-3241. [PMID: 39044429 DOI: 10.1016/j.bpj.2024.07.023] [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: 03/28/2024] [Revised: 06/18/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here, we present a simple and generic coarse-grained model for DNA-protein and protein-protein interactions and investigate the role of the latter in the protein-induced compaction of DNA. Our approach models the DNA as a discrete worm-like chain. The proteins are treated in the grand canonical ensemble, and the protein-DNA binding strength is taken from experimental measurements. Protein-DNA interactions are modeled as an isotropic binding potential with an imposed binding valency without specific assumptions about the binding geometry. To systematically and quantitatively classify DNA-protein complexes, we present an unsupervised machine learning pipeline that receives a large set of structural order parameters as input, reduces the dimensionality via principal-component analysis, and groups the results using a Gaussian mixture model. We apply our method to recent data on the compaction of viral genome-length DNA by HIV integrase and find that protein-protein interactions are critical to the formation of looped intermediate structures seen experimentally. Our methodology is broadly applicable to DNA-binding proteins and protein-induced DNA compaction and provides a systematic and semi-quantitative approach for analyzing their mesoscale complexes.
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Affiliation(s)
- Marjolein de Jager
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands.
| | - Pauline J Kolbeck
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands; Department of Physics and Center for NanoScience, LMU, Munich, Germany
| | - Willem Vanderlinden
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands; Department of Physics and Center for NanoScience, LMU, Munich, Germany; School of Physics and Astronomy, University of Edinburgh, Scotland, United Kingdom
| | - Jan Lipfert
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands; Department of Physics and Center for NanoScience, LMU, Munich, Germany
| | - Laura Filion
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
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2
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Chua GNL, Liu S. When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. Annu Rev Biophys 2024; 53:169-191. [PMID: 38237015 DOI: 10.1146/annurev-biophys-030822-032904] [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] [Indexed: 06/26/2024]
Abstract
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.
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Affiliation(s)
- Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
- Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
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3
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Gien H, Morse M, McCauley MJ, Rouzina I, Gorelick RJ, Williams MC. Cationic Residues of the HIV-1 Nucleocapsid Protein Enable DNA Condensation to Maintain Viral Core Particle Stability during Reverse Transcription. Viruses 2024; 16:872. [PMID: 38932164 PMCID: PMC11209390 DOI: 10.3390/v16060872] [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: 03/29/2024] [Revised: 04/30/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a multifunctional viral protein necessary for HIV-1 replication. Recent studies have demonstrated that reverse transcription (RT) completes in the intact viral capsid, and the timing of RT and uncoating are correlated. How the small viral core stably contains the ~10 kbp double stranded (ds) DNA product of RT, and the role of NC in this process, are not well understood. We showed previously that NC binds and saturates dsDNA in a non-specific electrostatic binding mode that triggers uniform DNA self-attraction, condensing dsDNA into a tight globule against extending forces up to 10 pN. In this study, we use optical tweezers and atomic force microscopy to characterize the role of NC's basic residues in dsDNA condensation. Basic residue mutations of NC lead to defective interaction with the dsDNA substrate, with the constant force plateau condensation observed with wild-type (WT) NC missing or diminished. These results suggest that NC's high positive charge is essential to its dsDNA condensing activity, and electrostatic interactions involving NC's basic residues are responsible in large part for the conformation, size, and stability of the dsDNA-protein complex inside the viral core. We observe DNA re-solubilization and charge reversal in the presence of excess NC, consistent with the electrostatic nature of NC-induced DNA condensation. Previous studies of HIV-1 replication in the presence of the same cationic residue mutations in NC showed significant defects in both single- and multiple-round viral infectivity. Although NC participates in many stages of viral replication, our results are consistent with the hypothesis that cationic residue mutations inhibit genomic DNA condensation, resulting in increased premature capsid uncoating and contributing to viral replication defects.
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Affiliation(s)
- Helena Gien
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
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4
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Burdick RC, Morse M, Rouzina I, Williams MC, Hu WS, Pathak VK. HIV-1 uncoating requires long double-stranded reverse transcription products. SCIENCE ADVANCES 2024; 10:eadn7033. [PMID: 38657061 PMCID: PMC11042746 DOI: 10.1126/sciadv.adn7033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
HIV-1 cores, which contain the viral genome and replication machinery, must disassemble (uncoat) during viral replication. However, the viral and host factors that trigger uncoating remain unidentified. Recent studies show that infectious cores enter the nucleus and uncoat near the site of integration. Here, we show that efficient uncoating of nuclear cores requires synthesis of a double-stranded DNA (dsDNA) genome >3.5 kb and that the efficiency of uncoating correlates with genome size. Core disruption by capsid inhibitors releases viral DNA, some of which integrates. However, most of the viral DNA is degraded, indicating that the intact core safeguards viral DNA. Atomic force microscopy and core content estimation reveal that synthesis of full-length genomic dsDNA induces substantial internal strain on the core to promote uncoating. We conclude that HIV-1 cores protect viral DNA from degradation by host factors and that synthesis of long double-stranded reverse transcription products is required to trigger efficient HIV-1 uncoating.
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Affiliation(s)
- Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
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Joshi J, McCauley MJ, Morse M, Muccio MR, Kanlong JG, Rocha MS, Rouzina I, Musier-Forsyth K, Williams MC. Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity. Int J Mol Sci 2024; 25:1410. [PMID: 38338688 PMCID: PMC10855526 DOI: 10.3390/ijms25031410] [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: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.
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Affiliation(s)
- Joha Joshi
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael R. Muccio
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Joseph G. Kanlong
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Márcio S. Rocha
- Department of Physics, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil;
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
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6
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McMillan RB, Bediako H, Devenica LM, Velasquez A, Hardy IP, Ma YE, Roscoe DM, Carter AR. Protamine folds DNA into flowers and loop stacks. Biophys J 2023; 122:4288-4302. [PMID: 37803830 PMCID: PMC10645571 DOI: 10.1016/j.bpj.2023.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023] Open
Abstract
DNA in sperm undergoes an extreme compaction to almost crystalline packing levels. To produce this dense packing, DNA is dramatically reorganized in minutes by protamine proteins. Protamines are positively charged proteins that coat negatively charged DNA and fold it into a series of toroids. The exact mechanism for forming these ∼50-kbp toroids is unknown. Our goal is to study toroid formation by starting at the "bottom" with folding of short lengths of DNA that form loops and working "up" to more folded structures that occur on longer length scales. We previously measured folding of 200-300 bp of DNA into a loop. Here, we look at folding of intermediate DNA lengths (L = 639-3003 bp) that are 2-10 loops long. We observe two folded structures besides loops that we hypothesize are early intermediates in the toroid formation pathway. At low protamine concentrations (∼0.2 μM), we see that the DNA folds into flowers (structures with multiple loops that are positioned so they look like the petals of a flower). Folding at these concentrations condenses the DNA to 25% of its original length, takes seconds, and is made up of many small bending steps. At higher protamine concentrations (≥2 μM), we observe a second folded structure-the loop stack-where loops are stacked vertically one on top of another. These results lead us to propose a two-step process for folding at this length scale: 1) protamine binds to DNA, bending it into loops and flowers, and 2) flowers collapse into loop stacks. These results highlight how protamine uses a bind-and-bend mechanism to rapidly fold DNA, which may be why protamine can fold the entire sperm genome in minutes.
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Affiliation(s)
- Ryan B McMillan
- Department of Physics, Amherst College, Amherst, Massachusetts
| | - Hilary Bediako
- Department of Physics, Amherst College, Amherst, Massachusetts
| | - Luka M Devenica
- Department of Physics, Amherst College, Amherst, Massachusetts
| | | | - Isabel P Hardy
- Department of Physics, Amherst College, Amherst, Massachusetts
| | - Yuxing E Ma
- Department of Physics, Amherst College, Amherst, Massachusetts
| | - Donna M Roscoe
- Department of Physics, Amherst College, Amherst, Massachusetts
| | - Ashley R Carter
- Department of Physics, Amherst College, Amherst, Massachusetts.
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7
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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8
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Morse M, Sefcikova J, Rouzina I, Beuning PJ, Williams M. Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates. Nucleic Acids Res 2022; 51:290-303. [PMID: 36533523 PMCID: PMC9841419 DOI: 10.1093/nar/gkac1179] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein performs several functions including binding, compacting, and packaging the ∼30 kb viral genome into the viral particle. N protein consists of two ordered domains, with the N terminal domain (NTD) primarily associated with RNA binding and the C terminal domain (CTD) primarily associated with dimerization/oligomerization, and three intrinsically disordered regions, an N-arm, a C-tail, and a linker that connects the NTD and CTD. We utilize an optical tweezers system to isolate a long single-stranded nucleic acid substrate to measure directly the binding and packaging function of N protein at a single molecule level in real time. We find that N protein binds the nucleic acid substrate with high affinity before oligomerizing and forming a highly compact structure. By comparing the activities of truncated protein variants missing the NTD, CTD, and/or linker, we attribute specific steps in this process to the structural domains of N protein, with the NTD driving initial binding to the substrate and ensuring high localized protein density that triggers interprotein interactions mediated by the CTD, which forms a compact and stable protein-nucleic acid complex suitable for packaging into the virion.
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Affiliation(s)
- Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mark C Williams
- To whom correspondence should be addressed. Tel: +1 617 373 5705;
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9
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Zhang B, Xie Y, Lan Z, Li D, Tian J, Zhang Q, Tian H, Yang J, Zhou X, Qiu S, Lu K, Liu Y. SARS-CoV-2 Nucleocapsid Protein Has DNA-Melting and Strand-Annealing Activities With Different Properties From SARS-CoV-2 Nsp13. Front Microbiol 2022; 13:851202. [PMID: 35935242 PMCID: PMC9354549 DOI: 10.3389/fmicb.2022.851202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the world and has had a devastating impact on health and economy. The biochemical characterization of SARS-CoV-2 proteins is important for drug design and development. In this study, we discovered that the SARS-CoV-2 nucleocapsid protein can melt double-stranded DNA (dsDNA) in the 5′-3′ direction, similar to SARS-CoV-2 nonstructural protein 13. However, the unwinding activity of SARS-CoV-2 nucleocapsid protein was found to be more than 22 times weaker than that of SARS-CoV-2 nonstructural protein 13, and the melting process was independent of nucleoside triphosphates and Mg2+. Interestingly, at low concentrations, the SARS-CoV-2 nucleocapsid protein exhibited a stronger annealing activity than SARS-CoV-2 nonstructural protein 13; however, at high concentrations, it promoted the melting of dsDNA. These findings have deepened our understanding of the SARS-CoV-2 nucleocapsid protein and will help provide novel insights into antiviral drug development.
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Affiliation(s)
- Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- Bo Zhang,
| | - Yan Xie
- School of Public Health, Zunyi Medical University, Zunyi, China
| | - Zhaoling Lan
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Dayu Li
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Junjie Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Qintao Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Hongji Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Jiali Yang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Xinnan Zhou
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Keyu Lu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- Keyu Lu,
| | - Yang Liu
- School of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Yang Liu,
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