Cytoplasmic dyneins drive microtubule-based, minus-end directed transport in eukaryotic cells. Whereas cytoplasmic dynein 1 has been widely studied, IFT dynein has received far less attention. Here, we use fluorescence microscopy of labelled motors in living Caenorhabditis elegans to investigate IFT-dynein motility at the ensemble and single-molecule level. We find that while the kinesin composition of motor ensembles varies along the track, the amount of dynein remains relatively constant. Remarkably, this does not result in directionality changes of cargo along the track, as has been reported for other opposite-polarity, tug-of-war motility systems. At the single-molecule level, IFT-dynein trajectories reveal unexpected dynamics, including diffusion at the base, and pausing and directional switches along the cilium. Stochastic simulations show that the ensemble IFT-dynein distribution depends upon the probability of single-motor directional switches. Our results provide quantitative insight into IFT-dynein dynamics in vivo, shedding light on the complex functioning of dynein motors in general.
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http://dx.doi.org/10.1038/ncomms14591 | DOI Listing |
JACS Au
December 2024
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facilitate a systematic investigation of these sequence-ensemble relationships, we selected a set of 16 naturally occurring intrinsically disordered regions of identical length but with large differences in amino acid composition, hydrophobicity, and charge patterning. We probed their conformational ensembles with single-molecule Förster resonance energy transfer (FRET), complemented by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as small-angle X-ray scattering (SAXS).
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Physics, Stockholm University, AlbaNova University Center, SE-10691 Stockholm, Sweden.
Vibrational polaritons are formed by strong coupling of molecular vibrations and photon modes in an optical cavity. Experiments have demonstrated that vibrational strong coupling can change molecular properties and even affect chemical reactivity. However, the interactions in a molecular ensemble are complex, and the exact mechanisms that lead to modifications are not fully understood yet.
View Article and Find Full Text PDFACS Nano
December 2024
Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States.
Two or more protein ligands may compete against each other to interact transiently with a protein receptor. While this is a ubiquitous phenomenon in cell signaling, existing technologies cannot identify its kinetic complexity because specific subpopulations of binding events of different ligands are hidden in the averaging process in an ensemble. In addition, the limited time resolution of prevailing methods makes detecting and discriminating binding events among diverse interacting partners challenging.
View Article and Find Full Text PDFNanoscale
December 2024
Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface, LRS, F-75005 Paris, France.
This paper addresses the complementarity and potential disparities between single-molecule and ensemble-average approaches to probe the binding mechanism of oligopeptides on inorganic solids. Specifically, we explore the peptide/gold interface owing to its significance in various topics and its suitability to perform experiments both in model and real conditions. Experimental results show that the studied peptide adopts a lying configuration upon adsorption on the gold surface and interacts through its peptidic links and deprotonated thiolate extremities, in agreement with theoretical predictions.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
A major challenge in epigenetics is uncovering the dynamic distribution of nucleosomes and other DNA-binding proteins, which plays a crucial role in regulating cellular functions. Established approaches such as ATAC-seq, ChIP-seq, and CUT&RUN provide valuable insights but are limited by the ensemble nature of their data, masking the cellular and molecular heterogeneity that is often functionally significant. Recently, long-read sequencing technologies, particularly Single Molecule, Real-Time (SMRT/PacBio) sequencing, have introduced transformative capabilities, such as N-methyladenine (6mA) footprinting.
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