1
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Kim H, Pak Y. Three-State Diffusion Model of DNA Glycosylase Translocation along Stretched DNA as Revealed by Free Energy Landscapes at the All-Atom Level. J Chem Theory Comput 2024; 20:2666-2675. [PMID: 38451471 DOI: 10.1021/acs.jctc.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
DNA glycosylases play key roles in the maintenance of genomic integrity. These enzymes effectively find rare damaged sites in DNA and participate in subsequent base excision repair. Single-molecule and ensemble experiments have revealed key aspects of this damage-site searching mechanism and the involvement of facilitated diffusion. In this study, we describe free energy landscapes of enzyme translocation along nonspecific DNA obtained using a fully atomistic molecular dynamics (MD) simulation of a well-known DNA glycosylase, human 8-oxoguanine DNA glycosylase 1 (hOGG1). Based on an analysis of simulated free energy profiles, we propose a three-state model for the damage-site searching mechanism. In the three states, named the L1, L2, and L3 states, the L1 state is a helical sliding mode in close contact with DNA, whereas the L2 state is a major- or minor-groove tracking mode in loose contact with DNA and the L3 state is a two-dimensional freely diffusing mode during which hOGG1 is somewhat removed from the DNA surface (∼24 Å away from the surface). This three-state model well describes key experimental findings obtained from single-molecule and ensemble experiments and provides a unified molecular picture of the DNA lesion-searching mechanism of hOGG1.
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Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
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2
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Cintori L, Di Guilmi AM, Canitrot Y, Huet S, Campalans A. Spatio-temporal dynamics of the DNA glycosylase OGG1 in finding and processing 8-oxoguanine. DNA Repair (Amst) 2023; 129:103550. [PMID: 37542751 DOI: 10.1016/j.dnarep.2023.103550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
OGG1 is the DNA glycosylase responsible for the removal of the oxidative lesion 8-oxoguanine (8-oxoG) from DNA. The recognition of this lesion by OGG1 is a complex process that involves scanning the DNA for the presence of 8-oxoG, followed by recognition and lesion removal. Structural data have shown that OGG1 evolves through different stages of conformation onto the DNA, corresponding to elementary steps of the 8-oxoG recognition and extrusion from the double helix. Single-molecule studies of OGG1 on naked DNA have shown that OGG1 slides in persistent contact with the DNA, displaying different binding states probably corresponding to the different conformation stages. However, in cells, the DNA is not naked and OGG1 has to navigate into a complex and highly crowded environment within the nucleus. To ensure rapid detection of 8-oxoG, OGG1 alternates between 3D diffusion and sliding along the DNA. This process is regulated by the local chromatin state but also by protein co-factors that could facilitate the detection of oxidized lesions. We will review here the different methods that have been used over the last years to better understand how OGG1 detects and process 8-oxoG lesions.
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Affiliation(s)
- Luana Cintori
- Molecular, Cellular and Developmental Biology unit, Centre de Biologie Integrative, University of Toulouse, CNRS, F-31062 Toulouse, France
| | - Anne-Marie Di Guilmi
- Université de Paris-Cite, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France; Université Paris-Saclay, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Yvan Canitrot
- Molecular, Cellular and Developmental Biology unit, Centre de Biologie Integrative, University of Toulouse, CNRS, F-31062 Toulouse, France
| | - Sebastien Huet
- Université Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, ´ Sante, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France; Institut Universitaire de France, Paris, France
| | - Anna Campalans
- Université de Paris-Cite, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France; Université Paris-Saclay, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France.
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3
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D’Augustin O, Gaudon V, Siberchicot C, Smith R, Chapuis C, Depagne J, Veaute X, Busso D, Di Guilmi AM, Castaing B, Radicella JP, Campalans A, Huet S. Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells. Nucleic Acids Res 2023; 51:4942-4958. [PMID: 37021552 PMCID: PMC10250219 DOI: 10.1093/nar/gkad243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 02/28/2023] [Accepted: 03/24/2023] [Indexed: 04/07/2023] Open
Abstract
The DNA-glycosylase OGG1 oversees the detection and clearance of the 7,8-dihydro-8-oxoguanine (8-oxoG), which is the most frequent form of oxidized base in the genome. This lesion is deeply buried within the double-helix and its detection requires careful inspection of the bases by OGG1 via a mechanism that remains only partially understood. By analyzing OGG1 dynamics in the nucleus of living human cells, we demonstrate that the glycosylase constantly samples the DNA by rapidly alternating between diffusion within the nucleoplasm and short transits on the DNA. This sampling process, that we find to be tightly regulated by the conserved residue G245, is crucial for the rapid recruitment of OGG1 at oxidative lesions induced by laser micro-irradiation. Furthermore, we show that residues Y203, N149 and N150, while being all involved in early stages of 8-oxoG probing by OGG1 based on previous structural data, differentially regulate the sampling of the DNA and recruitment to oxidative lesions.
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Affiliation(s)
- Ostiane D’Augustin
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | | | - Capucine Siberchicot
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
| | - Jordane Depagne
- Université de Paris-Cité, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
| | - Xavier Veaute
- Université de Paris-Cité, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
| | - Didier Busso
- Université de Paris-Cité, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
| | - Anne-Marie Di Guilmi
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | | | - J Pablo Radicella
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Anna Campalans
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
- Institut Universitaire de France, Paris, France
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4
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Moncho-Jordá A, Göth N, Dzubiella J. Liquid structure of bistable responsive macromolecules using mean-field density-functional theory. SOFT MATTER 2023; 19:2832-2846. [PMID: 37000605 DOI: 10.1039/d2sm01523d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Macromolecular crowding typically applies to biomolecular and polymer-based systems in which the individual particles often feature a two-state folded/unfolded or coil-to-globule transition, such as found for proteins and peptides, DNA and RNA, or supramolecular polymers. Here, we employ a mean-field density functional theory (DFT) of a model of soft and bistable responsive colloids (RCs) in which the size of the macromolecule is explicitly resolved as a degree of freedom living in a bimodal 'Landau' energy landscape (exhibiting big and small states), thus directly responding to the crowding environment. Using this RC-DFT we study the effects of self-crowding on the liquid bulk structure and thermodynamics for different energy barriers and softnesses of the bimodal energy landscape, in conditions close to the coil-to-globule transition. We find substantial crowding effects on the internal distributions, a complex polydispersity behavior, and quasi-universal compression curves for increasing (generalized) packing fractions. Moreover, we uncover distinct signatures of bimodal versus unimodal behavior in the particle compression. Finally, the analysis of the pair structure - derived from the test particle route - reveals that the microstructure of the liquid is quite inhomogeneous due to local depletion effects, tuneable by particle softness.
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Affiliation(s)
- Arturo Moncho-Jordá
- Institute Carlos I for Theoretical and Computational Physics, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva S/N, 18071 Granada, Spain.
- Departamento de Física Aplicada, Universidad de Granada, Campus Fuentenueva S/N, 18071 Granada, Spain
| | - Nils Göth
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Straße 3, D-79104 Freiburg, Germany.
| | - Joachim Dzubiella
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Straße 3, D-79104 Freiburg, Germany.
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5
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Carcamo CC, Poyton MF, Ranjan A, Park G, Louder RK, Feng XA, Kim JM, Dzu T, Wu C, Ha T. ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA. eLife 2022; 11:e77352. [PMID: 35876491 PMCID: PMC9365391 DOI: 10.7554/elife.77352] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022] Open
Abstract
One-dimensional (1D) target search is a well-characterized phenomenon for many DNA-binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA-binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.
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Affiliation(s)
- Claudia C Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
| | - Matthew F Poyton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
| | - Anand Ranjan
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Giho Park
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Robert K Louder
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xinyu A Feng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
| | - Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Thuc Dzu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
- Howard Hughes Medical InstituteBaltimoreUnited States
- Johns Hopkins University, Department of Biomedical EngineeringBaltimoreUnited States
- Johns Hopkins University, Department of BiophysicsBaltimoreUnited States
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6
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Resolving the subtle details of human DNA alkyltransferase lesion search and repair mechanism by single-molecule studies. Proc Natl Acad Sci U S A 2022; 119:e2116218119. [PMID: 35259021 PMCID: PMC8931253 DOI: 10.1073/pnas.2116218119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We directly visualize DNA translocation and lesion recognition by the O6-alkylguanine DNA alkyltransferase (AGT). Our data show bidirectional movement of AGT monomers and clusters on undamaged DNA that depended on Zn2+ occupancy of AGT. A role of cooperative AGT clusters in enhancing lesion search efficiencies by AGT has previously been proposed. Surprisingly, our data show no enhancement of DNA translocation speed by AGT cluster formation, suggesting that AGT clusters may serve a different role in AGT function. Our data support preferential cluster formation by AGT at alkyl lesions, suggesting a role of these clusters in stabilizing lesion-bound complexes. From our data, we derive a new model for the lesion search and repair mechanism of AGT. The O6-alkylguanine DNA alkyltransferase (AGT) is an important DNA repair protein. AGT repairs highly mutagenic and cytotoxic alkylguanine lesions that result from metabolic products but are also deliberately introduced during chemotherapy, making a better understanding of the working mechanism of AGT essential. To investigate lesion interactions by AGT, we present a protocol to insert a single alkylguanine lesion at a well-defined position in long DNA substrates for single-molecule fluorescence microscopy coupled with dual-trap optical tweezers. Our studies address the longstanding enigma in the field of how monomeric AGT complexes at alkyl lesions seen in crystal structures can be reconciled with AGT clusters on DNA at high protein concentrations that have been observed from atomic force microscopy (AFM) and biochemical studies. A role of AGT clusters in enhancing lesion search efficiencies by AGT has previously been proposed. Surprisingly, our data show no enhancement of DNA translocation speed by AGT cluster formation, suggesting that AGT clusters may serve a different role in AGT function. Interestingly, a possible role of these clusters is indicated by preferential cluster formation at alkyl lesions in our studies. From our data, we derive a model for the lesion search and repair mechanism of AGT.
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7
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Tan CJ, Basak R, Yadav I, van Kan JA, Arluison V, van der Maarel JRC. Mobility of Bacterial Protein Hfq on dsDNA: Role of C-Terminus-Mediated Transient Binding. J Phys Chem B 2022; 126:1477-1482. [PMID: 35166115 DOI: 10.1021/acs.jpcb.1c10234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mobility of protein is fundamental in the machinery of life. Here, we have investigated the effect of DNA binding in conjunction with DNA segmental fluctuation (internal motion) of the bacterial Hfq master regulator devoid of its amyloid C-terminus domain. Hfq is one of the most abundant nucleoid associated proteins that shape the bacterial chromosome and is involved in several aspects of nucleic acid metabolism. Fluorescence microscopy has been used to track a C-terminus domain lacking mutant form of Hfq on double-stranded DNA, which is stretched by confinement to a rectangular nanofluidic channel. The mobility of the mutant is strongly accelerated with respect to the wild-type variant. Furthermore, it shows a reverse dependence on the internal motion of DNA, in that slower motion results in slower protein diffusion. The results demonstrate the subtle role of DNA internal motion in controlling the mobility of a nucleoid associated protein, and, in particular, the importance of transient binding and moving DNA strands out of the way.
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Affiliation(s)
- Chuan Jie Tan
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Rajib Basak
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Indresh Yadav
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Véronique Arluison
- Université de Paris, UFR SDV, Paris 75006, France.,Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette 91191, France
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8
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Basak R, Yadav I, Arluison V, van Kan JA, van der Maarel JRC. Probing Amyloid-DNA Interaction with Nanofluidics. Methods Mol Biol 2022; 2538:305-317. [PMID: 35951308 DOI: 10.1007/978-1-0716-2529-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanofluidics is an emerging methodology to investigate single biomacromolecules without functionalization and/or attachment of the molecules to a substrate. In conjunction with fluorescence microscopy, it can be used to investigate structural and dynamical aspects of amyloid-DNA interaction. Here, we summarize the methodology for fabricating lab-on-chip devices in relatively cheap polymer resins and featuring quasi one-dimensional nanochannels with a cross-sectional diameter of tens to a few hundred nanometers. Site-specific staining of amyloid-forming protein Hfq with a fluorescence dye is also described. The methodology is illustrated with two application studies. The first study involves assembling bacterial amyloid proteins such as Hfq on double-stranded DNA and monitoring the folding and compaction of DNA in a condensed state. The second study is about the concerted motion of Hfq on DNA and how this is related to DNA's internal motion. Explicit details of procedures and workflows are given throughout.
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Affiliation(s)
- Rajib Basak
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Indresh Yadav
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France
- Université de Paris, Paris, France
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore, Singapore
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9
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Schaich MA, Van Houten B. Searching for DNA Damage: Insights From Single Molecule Analysis. Front Mol Biosci 2021; 8:772877. [PMID: 34805281 PMCID: PMC8602339 DOI: 10.3389/fmolb.2021.772877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/18/2021] [Indexed: 01/26/2023] Open
Abstract
DNA is under constant threat of damage from a variety of chemical and physical insults, such as ultraviolet rays produced by sunlight and reactive oxygen species produced during respiration or inflammation. Because damaged DNA, if not repaired, can lead to mutations or cell death, multiple DNA repair pathways have evolved to maintain genome stability. Two repair pathways, nucleotide excision repair (NER) and base excision repair (BER), must sift through large segments of nondamaged nucleotides to detect and remove rare base modifications. Many BER and NER proteins share a common base-flipping mechanism for the detection of modified bases. However, the exact mechanisms by which these repair proteins detect their damaged substrates in the context of cellular chromatin remains unclear. The latest generation of single-molecule techniques, including the DNA tightrope assay, atomic force microscopy, and real-time imaging in cells, now allows for nearly direct visualization of the damage search and detection processes. This review describes several mechanistic commonalities for damage detection that were discovered with these techniques, including a combination of 3-dimensional and linear diffusion for surveying damaged sites within long stretches of DNA. We also discuss important findings that DNA repair proteins within and between pathways cooperate to detect damage. Finally, future technical developments and single-molecule studies are described which will contribute to the growing mechanistic understanding of DNA damage detection.
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Affiliation(s)
- Matthew A Schaich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, Pittsburgh, PA, United States
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10
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Kamagata K, Itoh Y, Tan C, Mano E, Wu Y, Mandali S, Takada S, Johnson RC. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo. Nucleic Acids Res 2021; 49:8642-8664. [PMID: 34352099 PMCID: PMC8421229 DOI: 10.1093/nar/gkab658] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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11
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Larsen JB, Taebnia N, Dolatshahi-Pirouz A, Eriksen AZ, Hjørringgaard C, Kristensen K, Larsen NW, Larsen NB, Marie R, Mündler AK, Parhamifar L, Urquhart AJ, Weller A, Mortensen KI, Flyvbjerg H, Andresen TL. Imaging therapeutic peptide transport across intestinal barriers. RSC Chem Biol 2021; 2:1115-1143. [PMID: 34458827 PMCID: PMC8341777 DOI: 10.1039/d1cb00024a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Oral delivery is a highly preferred method for drug administration due to high patient compliance. However, oral administration is intrinsically challenging for pharmacologically interesting drug classes, in particular pharmaceutical peptides, due to the biological barriers associated with the gastrointestinal tract. In this review, we start by summarizing the pharmacological performance of several clinically relevant orally administrated therapeutic peptides, highlighting their low bioavailabilities. Thus, there is a strong need to increase the transport of peptide drugs across the intestinal barrier to realize future treatment needs and further development in the field. Currently, progress is hampered by a lack of understanding of transport mechanisms that govern intestinal absorption and transport of peptide drugs, including the effects of the permeability enhancers commonly used to mediate uptake. We describe how, for the past decades, mechanistic insights have predominantly been gained using functional assays with end-point read-out capabilities, which only allow indirect study of peptide transport mechanisms. We then focus on fluorescence imaging that, on the other hand, provides opportunities to directly visualize and thus follow peptide transport at high spatiotemporal resolution. Consequently, it may provide new and detailed mechanistic understanding of the interplay between the physicochemical properties of peptides and cellular processes; an interplay that determines the efficiency of transport. We review current methodology and state of the art in the field of fluorescence imaging to study intestinal barrier transport of peptides, and provide a comprehensive overview of the imaging-compatible in vitro, ex vivo, and in vivo platforms that currently are being developed to accelerate this emerging field of research.
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Affiliation(s)
- Jannik Bruun Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nayere Taebnia
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Alireza Dolatshahi-Pirouz
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Anne Zebitz Eriksen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Claudia Hjørringgaard
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kasper Kristensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nanna Wichmann Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Niels Bent Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Rodolphe Marie
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ann-Kathrin Mündler
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ladan Parhamifar
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Andrew James Urquhart
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Arjen Weller
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kim I Mortensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Henrik Flyvbjerg
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Thomas Lars Andresen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
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12
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Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome? Int J Mol Sci 2020; 21:ijms21218360. [PMID: 33171795 PMCID: PMC7664663 DOI: 10.3390/ijms21218360] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
The most frequent DNA lesion resulting from an oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoG). 8-oxoG is a premutagenic base modification due to its capacity to pair with adenine. Thus, the repair of 8-oxoG is critical for the preservation of the genetic information. Nowadays, 8-oxoG is also considered as an oxidative stress-sensor with a putative role in transcription regulation. In mammalian cells, the modified base is excised by the 8-oxoguanine DNA glycosylase (OGG1), initiating the base excision repair (BER) pathway. OGG1 confronts the massive challenge that is finding rare occurrences of 8-oxoG among a million-fold excess of normal guanines. Here, we review the current knowledge on the search and discrimination mechanisms employed by OGG1 to find its substrate in the genome. While there is considerable data from in vitro experiments, much less is known on how OGG1 is recruited to chromatin and scans the genome within the cellular nucleus. Based on what is known of the strategies used by proteins searching for rare genomic targets, we discuss the possible scenarios allowing the efficient detection of 8-oxoG by OGG1.
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13
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Yadav I, Basak R, Yan P, van Kan JA, Arluison V, van der Maarel JRC. Role of Internal DNA Motion on the Mobility of a Nucleoid-Associated Protein. J Phys Chem Lett 2020; 11:8424-8429. [PMID: 32930601 DOI: 10.1021/acs.jpclett.0c02251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein transport on DNA is at the core of the machinery of life. Here we investigated the influence of DNA internal motion on the mobility of Hfq, which is involved in several aspects of nucleic acid metabolism and is one of the nucleoid-associated proteins that shape the bacterial chromosome. Fluorescence microscopy was used to follow Hfq on double-stranded DNA that was stretched by confinement to a channel with a diameter of 125 nm. The protein mobility shows a strong dependence on the internal motion of DNA in that slower motion results in faster protein diffusion. A model of released diffusion is proposed that is based on three-dimensional diffusion through the interior of the DNA coil interspersed by periods in which the protein is immobilized in a bound state. We surmise that the coupling between DNA internal motion and protein mobility has important implications for DNA metabolism and protein-binding-related regulation of gene expression.
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Affiliation(s)
- Indresh Yadav
- Department of Physics, National University of Singapore, Singapore 117542
| | - Rajib Basak
- Department of Physics, National University of Singapore, Singapore 117542
| | - Peiyan Yan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Véronique Arluison
- Université de Paris, UFR SDV, 75006 Paris, France
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France
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14
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Serov AS, Laurent F, Floderer C, Perronet K, Favard C, Muriaux D, Westbrook N, Vestergaard CL, Masson JB. Statistical Tests for Force Inference in Heterogeneous Environments. Sci Rep 2020; 10:3783. [PMID: 32123194 PMCID: PMC7052274 DOI: 10.1038/s41598-020-60220-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 02/05/2020] [Indexed: 01/22/2023] Open
Abstract
We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed drift includes a "spurious” force term when the diffusivity varies in space. We show how Bayesian inference can be leveraged to reliably infer forces by taking into account such spurious forces of unknown amplitude as well as experimental sources of error. The method is based on marginalizing the force posterior over all possible spurious force contributions. The approach is combined with a Bayes factor statistical test for the presence of forces. The performance of our method is investigated analytically, numerically and tested on experimental data sets. The main results are obtained in a closed form allowing for direct exploration of their properties and fast computation. The method is incorporated into TRamWAy, an open-source software platform for automated analysis of biomolecule trajectories.
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Affiliation(s)
- Alexander S Serov
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France.
| | - François Laurent
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France
| | - Charlotte Floderer
- Infectious Disease Research Institute of Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Karen Perronet
- Laboratoire Charles Fabry, Université Paris-Saclay, Institut d'Optique Graduate School, CNRS UMR8501, 91127, Palaiseau Cedex, France
| | - Cyril Favard
- Infectious Disease Research Institute of Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Delphine Muriaux
- Infectious Disease Research Institute of Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Nathalie Westbrook
- Laboratoire Charles Fabry, Université Paris-Saclay, Institut d'Optique Graduate School, CNRS UMR8501, 91127, Palaiseau Cedex, France
| | - Christian L Vestergaard
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France.
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France.
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15
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Falcao RC, Coombs D. Diffusion analysis of single particle trajectories in a Bayesian nonparametrics framework. Phys Biol 2020; 17:025001. [DOI: 10.1088/1478-3975/ab64b3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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16
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Dey P, Bhattacherjee A. Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu. Biophys J 2020; 118:505-517. [PMID: 31862109 PMCID: PMC6976804 DOI: 10.1016/j.bpj.2019.11.3388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/03/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.
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Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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17
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Dey P, Bhattacherjee A. Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase. J Phys Chem B 2019; 123:10354-10364. [DOI: 10.1021/acs.jpcb.9b07342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
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18
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Shin J, Kolomeisky AB. Facilitation of DNA loop formation by protein-DNA non-specific interactions. SOFT MATTER 2019; 15:5255-5263. [PMID: 31204761 DOI: 10.1039/c9sm00671k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these systems remain not well understood. Existing theoretical studies focus only on specific interactions between protein and DNA molecules at target sequences. However, the electrostatic origin of primary protein-DNA interactions suggests that interactions of proteins with all DNA segments should be considered. Here we theoretically investigate the role of non-specific interactions between protein and DNA molecules on the dynamics of loop formation. Our approach is based on analyzing a discrete-state stochastic model via a method of first-passage probabilities supplemented by Monte Carlo computer simulations. It is found that depending on a protein sliding length during the non-specific binding event three different dynamic regimes of the DNA loop formation might be observed. In addition, the loop formation time might be optimized by varying the protein sliding length, the size of the DNA molecule, and the position of the specific target sequences on DNA. Our results demonstrate the importance of non-specific protein-DNA interactions in the dynamics of DNA loop formations.
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Affiliation(s)
- Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA.
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas 77005, USA. and Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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19
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Shin J, Kolomeisky AB. Molecular search with conformational change: One-dimensional discrete-state stochastic model. J Chem Phys 2018; 149:174104. [PMID: 30409016 DOI: 10.1063/1.5051035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search, the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic modes. To understand the mechanisms of molecular search with alternating dynamics, we investigate the search dynamics with stochastic transitions between two conformations in a one-dimensional discrete-state stochastic model. It is explicitly analyzed using the first-passage time probability method to obtain a full dynamic description of the search process. A general dynamic phase diagram is developed. It is found that there are several dynamic regimes in the molecular search with conformational transitions, and they are determined by the relative values of the relevant length scales in the system. Theoretical predictions are fully supported by Monte Carlo computer simulations.
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Affiliation(s)
- Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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20
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Esadze A, Stivers JT. Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation. Chem Rev 2018; 118:11298-11323. [PMID: 30379068 DOI: 10.1021/acs.chemrev.8b00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Preservation of the coding potential of the genome and highly regulated gene expression over the life span of a human are two fundamental requirements of life. These processes require the action of repair enzymes or transcription factors that efficiently recognize specific sites of DNA damage or transcriptional regulation within a restricted time frame of the cell cycle or metabolism. A failure of these systems to act results in accumulated mutations, metabolic dysfunction, and disease. Despite the multifactorial complexity of cellular DNA repair and transcriptional regulation, both processes share a fundamental physical requirement that the proteins must rapidly diffuse to their specific DNA-binding sites that are embedded within the context of a vastly greater number of nonspecific DNA-binding sites. Superimposed on the needle-in-the-haystack problem is the complex nature of the cellular environment, which contains such high concentrations of macromolecules that the time frame for diffusion is expected to be severely extended as compared to dilute solution. Here we critically review the mechanisms for how these proteins solve the needle-in-the-haystack problem and how the effects of cellular macromolecular crowding can enhance facilitated diffusion processes. We restrict the review to human proteins that use stochastic, thermally driven site-recognition mechanisms, and we specifically exclude systems involving energy cofactors or circular DNA clamps. Our scope includes ensemble and single-molecule studies of the past decade or so, with an emphasis on connecting experimental observations to biological function.
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Affiliation(s)
- Alexandre Esadze
- Department of Pharmacology and Molecular Sciences , Johns Hopkins University School of Medicine , 725 North Wolfe Street , WBSB 314, Baltimore , Maryland 21205 , United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences , Johns Hopkins University School of Medicine , 725 North Wolfe Street , WBSB 314, Baltimore , Maryland 21205 , United States
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