Single Molecule
Recently Published Documents


TOTAL DOCUMENTS

19246
(FIVE YEARS 7904)

H-INDEX

257
(FIVE YEARS 83)

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lance T. Denes ◽  
Chase P. Kelley ◽  
Eric T. Wang

AbstractWhile the importance of RNA localization in highly differentiated cells is well appreciated, basic principles of RNA localization in skeletal muscle remain poorly characterized. Here, we develop a method to detect and quantify single molecule RNA localization patterns in skeletal myofibers, and uncover a critical role for directed transport of RNPs in muscle. We find that RNAs localize and are translated along sarcomere Z-disks, dispersing tens of microns from progenitor nuclei, regardless of encoded protein function. We find that directed transport along the lattice-like microtubule network of myofibers becomes essential to achieve this localization pattern as muscle development progresses; disruption of this network leads to extreme accumulation of RNPs and nascent protein around myonuclei. Our observations suggest that global active RNP transport may be required to distribute RNAs in highly differentiated cells and reveal fundamental mechanisms of gene regulation, with consequences for myopathies caused by perturbations to RNPs or microtubules.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Irene Carlon-Andres ◽  
Tomas Malinauskas ◽  
Sergi Padilla-Parra

AbstractThe HIV-1 envelope glycoprotein (Env) mediates viral entry into the host cell. Although the highly dynamic nature of Env intramolecular conformations has been shown with single molecule spectroscopy in vitro, the bona fide Env intra- and intermolecular mechanics when engaged with live T cells remains unknown. We used two photon fast fluorescence lifetime imaging detection of single-molecule Förster Resonance Energy Transfer occurring between fluorescent labels on HIV-1 Env on native virions. Our observations reveal Env dynamics at two levels: transitions between different intramolecular conformations and intermolecular interactions between Env within the viral membrane. Furthermore, we show that three broad neutralizing anti-Env antibodies directed to different epitopes restrict Env intramolecular dynamics and interactions between adjacent Env molecules when engaged with living T cells. Importantly, our results show that Env-Env interactions depend on efficient virus maturation, and that is disrupted upon binding of Env to CD4 or by neutralizing antibodies. Thus, this study illuminates how different intramolecular conformations and distribution of Env molecules mediate HIV-1 Env–T cell interactions in real time and therefore might control immune evasion.


Author(s):  
Christoph Manz ◽  
Andrei Yu Kobitski ◽  
Ayan Samanta ◽  
Karin Nienhaus ◽  
Andres Jäschke ◽  
...  

AbstractSAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg2+ and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-l-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg2+ concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. Our data show pronounced and specific effects of the SAM and SAH ligands on the RNA conformational energy landscape. Interestingly, both SAM and SAH shifted the fractional populations toward terminator folds, but only gradually, so the effect cannot explain the switching action. Instead, we propose that the noticeably accelerated dynamics of interconversion between terminator and antiterminator states upon SAM binding may be essential for control of transcription.


2021 ◽  
Author(s):  
Takahiro K. Fujiwara ◽  
Shinji Takeuchi ◽  
Ziya Kalay ◽  
Yosuke Nagai ◽  
Taka A. Tsunoyama ◽  
...  

Using the ultrafast camera system and new theories for hop diffusion described in the companion paper, we for the first time demonstrated that membrane molecules undergo hop diffusion among the compartments in the bulk basal plasma membrane (PM), with virtually the same compartment sizes (108 nm) as those in the bulk apical PM and the same dwell lifetimes within a compartment (10 and 24 ms for the phospholipid and transferrin receptor [TfR], respectively), suggesting that the basic structures and molecular dynamics are very similar in the bulk regions of the apical and basal PMs. Ultrafast PALM and single-molecule imaging revealed that the focal adhesion (FA) is mostly a fluid membrane, partitioned into ~74-nm compartments where TfR and β3 integrin undergo hop diffusion, and that the FA membrane is sparsely dotted with 51-nm diameter paxillin islands, where many other FA proteins probably assemble (compartmentalized archipelago model). β3 integrin intermittently associates with the paxillin islands, dynamically linking them to the extracellular matrix.


2021 ◽  
Author(s):  
Takahiro K. Fujiwara ◽  
Shinji Takeuchi ◽  
Ziya Kalay ◽  
Yosuke Nagai ◽  
Taka A. Tsunoyama ◽  
...  

The spatial resolution of fluorescence microscopy has recently been greatly improved. However, its temporal resolution has not been improved much, despite its importance for examining living cells. Here, by developing an ultrafast camera system, we achieved the world′s highest time resolutions for single fluorescent-molecule imaging of 33 (100) µs (multiple single molecules simultaneously) with a single-molecule localization precision of 34 (20) nm for Cy3 (best dye found), and for PALM data acquisition of a view-field of 640x640 pixels at 1 kHz with a single-molecule localization precision of 29 nm for mEos3.2. Both are considered the ultimate rates with available probes. This camera system (1) successfully detected fast hop diffusion of membrane molecules in the plasma membrane, detectable previously only by using less preferable 40-nm gold probes and bright-field microscopy, and (2) enabled PALM imaging of the entire live cell, while revealing meso-scale dynamics and structures, caveolae and paxillin islands in the focal adhesion, proving its usefulness for cell biology research.


2021 ◽  
Author(s):  
Dávid P. Jelenfi ◽  
Attila Tajti ◽  
Péter G. Szalay

The electron transport through the single-molecule junction of 1,4-Diaminobenzene (BDA) is modeled using ab initio quantum-classical molecular dynamics of electron attached states. Observations on the nature of the process are made by time-resolved analysis of energy differences, non-adiabatic transition probabilities and the spatial distribution of the excess electron. The role of molecular vibrations that facilitate the transport by being responsible for the periodic behaviour of these quantities is shown using normal mode analysis. The results support a mechanism involving the electron's direct hopping between the electrodes, without its presence on the molecule, with the prime importance of the bending vibrations that periodically alter the molecule{electrode interactions. No relevant differences are found between results provided by the ADC(2) and SOS-ADC(2) excited state models. Our approach provides an alternative insight into the role of nuclear motions in the electron transport process, one which is more expressive from the chemical perspective.


Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1579
Author(s):  
Yuanlei Cheng ◽  
Yashuo Zhang ◽  
Huijuan You

G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force–spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.


Sign in / Sign up

Export Citation Format

Share Document