Sub-cellular biochemistry/Subcellular biochemistry, Год журнала: 2024, Номер unknown, С. 359 - 399
Опубликована: Янв. 1, 2024
Язык: Английский
Science Advances, Год журнала: 2024, Номер 10(17)
Опубликована: Апрель 24, 2024
HIV-1 cores, which contain the viral genome and replication machinery, must disassemble (uncoat) during replication. However, host factors that trigger uncoating remain unidentified. Recent studies show infectious cores enter nucleus uncoat near site of integration. Here, we efficient nuclear requires synthesis a double-stranded DNA (dsDNA) >3.5 kb efficiency correlates with size. Core disruption by capsid inhibitors releases DNA, some integrates. most is degraded, indicating intact core safeguards DNA. Atomic force microscopy content estimation reveal full-length genomic dsDNA induces substantial internal strain on to promote uncoating. We conclude protect from degradation long reverse transcription products required
Язык: Английский
Процитировано
16
Nucleic Acids Research, Год журнала: 2022, Номер 51(1), С. 290 - 303
Опубликована: Дек. 19, 2022
The SARS-CoV-2 nucleocapsid (N) protein performs several functions including binding, compacting, and packaging the ∼30 kb viral genome into particle. N consists of two ordered domains, with terminal domain (NTD) primarily associated RNA binding C (CTD) dimerization/oligomerization, three intrinsically disordered regions, an N-arm, a C-tail, linker that connects NTD CTD. We utilize optical tweezers system to isolate long single-stranded nucleic acid substrate measure directly function at single molecule level in real time. find binds high affinity before oligomerizing forming highly compact structure. By comparing activities truncated variants missing NTD, CTD, and/or linker, we attribute specific steps this process structural domains protein, driving initial ensuring localized density triggers interprotein interactions mediated by which forms stable protein-nucleic complex suitable for virion.
Язык: Английский
Процитировано
36
Journal of Molecular Biology, Год журнала: 2023, Номер 435(16), С. 167988 - 167988
Опубликована: Янв. 26, 2023
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body work provided new insights into role played by membraneless organelles. These rapid advancements have been made possible increasing awareness peculiar physical properties that give rise to such bodies and complex biology enables their function. Viral infections are not extraneous this. Indeed, host cells, viruses can harness existing compartments or, even, induce formation ones. By hijacking machinery, these intracellular assist replication, assembly, packaging viral genome as well escape immune response. Here, we provide perspective on fundamental polymer physics concepts may help connect interpret different observed phenomena, ranging from condensation genomes phase separation multicomponent solutions. We complement discussion basis with description biophysical methods quantitative for testing developing theoretical computational models.
Язык: Английский
Процитировано
16
Annual Review of Biophysics, Год журнала: 2024, Номер 53(1), С. 169 - 191
Опубликована: Янв. 18, 2024
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of substrate to control its metabolism. It is now possible directly observe these activities-often central protein function-thanks advent single-molecule fluorescence- force-based techniques. In particular, integration fluorescence detection force manipulation has unlocked multidimensional measurements protein-DNA interactions yielded unprecedented mechanistic insights into biomolecular processes that orchestrate cellular life. this review, we first introduce different experimental geometries developed for correlative microscopy, with a focus optical tweezers as technique. We then describe utility integrative platforms imaging dynamics chromatin, well their unique capabilities in generating complex configurations uncovering force-dependent behaviors. Finally, give perspective future directions emerging research field.
Язык: Английский
Процитировано
6
International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(3), С. 1410 - 1410
Опубликована: Янв. 24, 2024
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 four complementary approaches, including optical tweezers, atomic force microscopy, duplex melting measurements, isothermal titration calorimetry. We show that intercalates into double stranded (dsDNA) KD ~ 200 µM, this entropically driven. propose chloroquine-induced dsDNA intercalation, which happens in same concentration range its observed toxic effects on cells, responsible for drug’s cytotoxicity.
Язык: Английский
Процитировано
4
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Март 30, 2024
ABSTRACT Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved bending, bridging, looping, (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations natural approach. Here we present simple generic model for the DNA-protein protein-protein interactions, investigate role latter protein-induced DNA. Our approach models as discrete worm-like chain. proteins treated grand-canonical ensemble protein-DNA binding strength is taken from experimental measurements. modeled an isotropic potential with imposed valency, without specific assumptions about geometry. To systematically quantitatively classify complexes, unsupervised machine learning pipeline that receives large set structural order parameters input, reduces dimensionality via principal component analysis, groups results using Gaussian mixture model. We apply our method recent data on viral genome-length HIV integrase find critical formation looped intermediate structures seen experimentally. methodology broadly applicable DNA-binding provides systematic quantitative analyzing their mesoscale complexes. SIGNIFICANCE central storage transmission genetic information frequently compacted condensed proteins. Their size dynamic nature make resulting complexes difficult probe simulations. explore ∼kbp interacting defined valency concentration. analysis uses define conformational states pathways between them. integrase. account observed intermediates simulated good agreement observations.
Язык: Английский
Процитировано
3
Опубликована: Окт. 15, 2024
The human immunodeficiency virus (HIV) infects non-dividing cells and its genome must be compacted to enter the cell nucleus. Here, we show that viral enzyme integrase (IN) compacts HIV DNA mimetics in vitro . Under physiological conditions, IN-compacted genomes are consistent size with those found for pre-integration complexes infected cells. Compaction occurs two stages: first IN tetramers bridge strands assemble into “rosette” structures consist of a nucleo-protein core extruding bare DNA. In second stage, loops condense onto rosette form disordered viscoelastic outer layer. Notably, complex is susceptible towards inhibitors, whereas diffuse layer not. Together, our data suggest has structural role compaction raise possibility develop inhibitors target IN-DNA interactions condensates.
Язык: Английский
Процитировано
3
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown
Опубликована: Янв. 30, 2025
Abstract Protein-DNA condensates mediate transcription and regulate gene expression DNA replication repair. The intermolecular bridging forces stabilizing have direct roles in these processes. Here we use optical tweezers to measure forces. In the presence of protamine, a single condensate is observed on 20.5-knt single-stranded (ssDNA) tethered between two microbeads. Stretching produces force curves with sawtooth pattern, suggesting that dissembled by sequential rupture individual protamine-ssDNA bridges. are 11.3 ± 4.6 pN, unfolding lengths 1.3 0.8 µm for contrast, double-stranded (dsDNA) forms protamine-bridged tangles can withstand high enough (∼55 pN) strand separation. ssDNA tracks unpeeled at nicks dsDNA overstretching seed tangle formation upon retraction, but initial sufficient ssDNA-to-dsDNA ratio appear liquid-like, as indicated pattern subsequent stretching. raises 34 8 which revert ∼10 pN adding external ssDNA. line single-molecule results, protamine-dsDNA mixtures form solid-like aggregates require addition become liquid droplets. Conversely, slows fusion This work demonstrates first measurements shows tune their magnitude protein-DNA condensates.
Язык: Английский
Процитировано
0
Biophysical Journal, Год журнала: 2023, Номер 122(21), С. 4288 - 4302
Опубликована: Окт. 6, 2023
Язык: Английский
Процитировано
7
Journal of Chemical Theory and Computation, Год журнала: 2023, Номер 19(15), С. 4822 - 4827
Опубликована: Июнь 30, 2023
The recent random batch Ewald algorithm, originating from a stochastic approximation, performs 1 order of magnitude faster than the mainstream algorithms such as particle-particle particle-mesh method for handling long-range electrostatics in large-scale simulations. However, this algorithm fails to fully capture electrostatic correlations. Here, we demonstrate that, when incorporating known screening condition could be simply amended without loss any efficiency.
Язык: Английский
Процитировано
6