Aug 02, 2022

Volume 121Issue 15p2827-2994
Cover picture: Simultaneous determination of mechanical strain and turnover of individual actin stress fibers.

New and Notable

  • New and Notable

    Sensing a little friction

    • Elizabeth G. Kelley,
    • Frederick A. Heberle
    Lipid membranes are central to the architecture of living cells, providing protection from the external environment as well as internal compartmentalization necessary for the biochemical reactions that sustain life. Their primary role as a simple barrier belies the chemical complexity of these multifunctional materials. Modern lipidomics techniques have uncovered a remarkably rich set of lipid building blocks that endow cells with precise control over the properties of their membranes (1,2) and the ability to change these properties in space and time.

Computational Tools

  • Computational Tool

    POTATO: Automated pipeline for batch analysis of optical tweezers data

    • Stefan Buck,
    • Lukas Pekarek,
    • Neva Caliskan
    Optical tweezers are a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein-nucleic acid interactions, and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (practical optical tweezers analysis tool).
  • Computational Tool

    DeepTracer-ID: De novo protein identification from cryo-EM maps

    • Luca Chang,
    • Fengbin Wang,
    • Kiernan Connolly,
    • Hanze Meng,
    • Zhangli Su,
    • Virginija Cvirkaite-Krupovic,
    • Mart Krupovic,
    • Edward H. Egelman,
    • Dong Si
    The recent revolution in cryo-electron microscopy (cryo-EM) has made it possible to determine macromolecular structures directly from cell extracts. However, identifying the correct protein from the cryo-EM map is still challenging and often needs additional sequence information from other techniques, such as tandem mass spectrometry and/or bioinformatics. Here, we present DeepTracer-ID, a server-based approach to identify the candidate protein in a user-provided organism de novo from a cryo-EM map, without the need for additional information.


  • Article

    Oligomerization processes limit photoactivation and recovery of the orange carotenoid protein

    • Elena A. Andreeva,
    • Stanisław Niziński,
    • Adjélé Wilson,
    • Matteo Levantino,
    • Elke De Zitter,
    • Rory Munro,
    • Fernando Muzzopappa,
    • Aurélien Thureau,
    • Ninon Zala,
    • Gotard Burdzinski,
    • Michel Sliwa,
    • Diana Kirilovsky,
    • Giorgio Schirò,
    • Jacques-Philippe Colletier
    Open Access
    The orange carotenoid protein (OCP) is a photoactive protein involved in cyanobacterial photoprotection by quenching of the excess of light-harvested energy. The photoactivation mechanism remains elusive, in part due to absence of data pertaining to the timescales over which protein structural changes take place. It also remains unclear whether or not oligomerization of the dark-adapted and light-adapted OCP could play a role in the regulation of its energy-quenching activity. Here, we probed photoinduced structural changes in OCP by a combination of static and time-resolved X-ray scattering and steady-state and transient optical spectroscopy in the visible range.
  • Article

    Evaluation of weak interactions of proteins and organic cations with DNA duplex structures

    • Ryuta Morimoto,
    • Masao Horita,
    • Daisuke Yamaguchi,
    • Hiroki Nakai,
    • Shu-ichi Nakano
    Molecular interactions and reactions in living cells occur with high background concentrations of organic compounds including proteins. Uncharged water-soluble polymers are commonly used cosolutes in studies on molecular crowding, and most studies argue about the effects of intracellular crowding based on results obtained using polymer cosolutes. Further investigations using protein crowders and organic cations are important in understanding the effects of cellular environments on nucleic acids with negatively charged surfaces.
  • Article

    An NMR look at an engineered PET depolymerase

    • Cyril Charlier,
    • Sabine Gavalda,
    • Vinciane Borsenberger,
    • Sophie Duquesne,
    • Alain Marty,
    • Vincent Tournier,
    • Guy Lippens
    Plastic environmental pollution is a major issue that our generation must face to protect our planet. Plastic recycling has the potential not only to reduce the pollution but also to limit the need for fossil-fuel-based production of new plastics. Enzymes capable of breaking down plastic could thereby support such a circular economy. Polyethylene terephthalate (PET) degrading enzymes have recently attracted considerable interest and have been subjected to intensive enzyme engineering to improve their characteristics.
  • Article

    Chromatin dynamics controls epigenetic domain formation

    • Marina Katava,
    • Guang Shi,
    • D. Thirumalai
    In multicellular organisms, nucleosomes carry epigenetic information that defines distinct patterns of gene expression, which are inherited over multiple generations. The enhanced capacity for information storage arises by nucleosome modifications, which are triggered by enzymes. Modified nucleosomes can transfer the mark to others that are in proximity by a positive-feedback (modification begets modification) mechanism. We created a generic polymer model, referred to as 3DSpreader, in which each bead, representing a nucleosome, stochastically switches between unmodified (U) and modified (M) states depending on the states of the neighbors.
  • Article

    Estimating the localization spread function of static single-molecule localization microscopy images

    • Thomas R. Shaw,
    • Frank J. Fazekas,
    • Sumin Kim,
    • Jennifer C. Flanagan-Natoli,
    • Emily R. Sumrall,
    • Sarah L. Veatch
    Single-molecule localization microscopy (SMLM) permits the visualization of cellular structures an order of magnitude smaller than the diffraction limit of visible light, and an accurate, objective evaluation of the resolution of an SMLM data set is an essential aspect of the image processing and analysis pipeline. Here, we present a simple method to estimate the localization spread function (LSF) of a static SMLM data set directly from acquired localizations, exploiting the correlated dynamics of individual emitters and properties of the pair autocorrelation function evaluated in both time and space.
  • Article

    Analysis of chemomechanical behavior of stress fibers by continuum mechanics-based FRAP

    • Takumi Saito,
    • Daiki Matsunaga,
    • Shinji Deguchi
    Fluorescence recovery after photobleaching (FRAP) is a common technique to analyze the turnover of molecules in living cells. Numerous physicochemical models have been developed to quantitatively evaluate the rate of turnover driven by chemical reaction and diffusion that occurs in a few seconds to minutes. On the other hand, they have limitations in interpreting long-term FRAP responses where intracellular active movement inevitably provides target molecular architectures with additional effects other than chemical reaction and diffusion, namely directed transport and structural deformation.
  • Article

    Conformational entropy limits the transition from nucleation to elongation in amyloid aggregation

    • Tien M. Phan,
    • Jeremy D. Schmit
    The formation of β-sheet-rich amyloid fibrils in Alzheimer’s disease and other neurodegenerative disorders is limited by a slow nucleation event. To understand the initial formation of β-sheets from disordered peptides, we used all-atom simulations to parameterize a lattice model that treats each amino acid as a binary variable with β- and non-β-sheet states. We show that translational and conformational entropy give the nascent β-sheet an anisotropic surface tension that can be used to describe the nucleus with 2D classical nucleation theory.
  • Article

    Interplay between traveling wave propagation and amplification at the apex of the mouse cochlea

    • Amir Nankali,
    • Christopher A. Shera,
    • Brian E. Applegate,
    • John S. Oghalai
    Sounds entering the mammalian ear produce waves that travel from the base to the apex of the cochlea. An electromechanical active process amplifies traveling wave motions and enables sound processing over a broad range of frequencies and intensities. The cochlear amplifier requires combining the global traveling wave with the local cellular processes that change along the length of the cochlea given the gradual changes in hair cell and supporting cell anatomy and physiology. Thus, we measured basilar membrane (BM) traveling waves in vivo along the apical turn of the mouse cochlea using volumetric optical coherence tomography and vibrometry.
  • Article

    How torque on formins is relaxed strongly affects cellular swirling

    • Xi Li,
    • Bin Chen
    Chirality is a common and essential characteristic at varied scales of living organisms. By adapting the rotational clutch-filament model we previously developed, we investigate the effect of torque relaxation of a formin on cellular chiral swirling. Since it is still unclear how the torque on a formin is exactly relaxed, we probe three types of torque relaxation, as suggested in the literature. Our analysis indicates that, when a formin periodically undergoes positive and negative rotation during processive capping to relax the torque, cells hardly rotate.
  • Article

    DNA-RNA hybrid G-quadruplex tends to form near the 3′ end of telomere overhang

    • Bok-Eum Choi,
    • Hui-Ting Lee
    Telomeric repeat-containing RNA (TERRA) has been suggested to participate in telomere maintenance. TERRA consisting of UUAGGG repeats is capable of forming an intermolecular G-quadruplex (GQ) with single-stranded TTAGGG-repeat DNA in the telomere 3′ overhang. To explore the structural features and potential functions of this DNA-RNA hybrid GQ (HGQ), we used single-molecule FRET to study the folding patterns of DNA with four to seven telomeric tandem repeats annealed with a short RNA consisting of two or five telomeric repeats.
  • Article

    Systematic measurements of interleaflet friction in supported bilayers

    • Autumn A. Anthony,
    • Osman Sahin,
    • Murat Kaya Yapici,
    • Daniel Rogers,
    • Aurelia R. Honerkamp-Smith
    Open Access
    When lipid membranes curve or are subjected to strong shear forces, the two apposed leaflets of the bilayer slide past each other. The drag that one leaflet creates on the other is quantified by the coefficient of interleaflet friction, b. Existing measurements of this coefficient range over several orders of magnitude, so we used a recently developed microfluidic technique to measure it systematically in supported lipid membranes. Fluid shear stress was used to force the top leaflet of a supported membrane to slide over the stationary lower leaflet.