Biophysics articles within Nature Communications

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  • Article
    | Open Access

    The human Asc-1-4F2hc complex plays an important role in the neural development and stability. Here, authors determine the cryo-EM structures of Asc-1-4F2hc complex in three states, revealing its substrate recognition and transport mechanism.

    • Yaning Li
    • , Yingying Guo
    •  & Renhong Yan

  • Article
    | Open Access

    Catch bonds are unique protein-protein interactions where the bond lifetime increases under external pulling forces. Here, the authors engineer an artificial catch bond based on a non-catch bonding human gut bacterial adhesion protein complex.

    • Zhaowei Liu
    • , Haipei Liu
    •  & Michael A. Nash

  • Article
    | Open Access

    Electrical stimulation of hollow, 3D kidney tissues causes these tissues to inflate and change shape. The authors call this process electro-inflation and connect it to electricity driving ions into the center of the tissues, causing water to follow by osmosis.

    • Gawoon Shim
    • , Isaac B. Breinyn
    •  & Daniel J. Cohen

  • Article
    | Open Access

    CaV1.2 is crucial in cardiac, vascular and neuronal function, serving as a target for many drugs. Here, authors identify the binding site of herb-derived drug tetrandrine, and explore inhibitory mechanism of L/T-type selective DHP drug benidipine.

    • Yiqing Wei
    • , Zhuoya Yu
    •  & Yan Zhao

  • Article
    | Open Access

    Amyloid fibrils are ordered protein assemblies implicated in neurodegenerative disease. Here the authors show that hairpin trimers can be transition states of fibril nucleation, explaining how different fibril isoforms may arise from alternative nucleation sites.

    • Levent Sari
    • , Sofia Bali
    •  & Milo M. Lin

  • Article
    | Open Access

    Many bacterial toxins and viruses deform membranes prior to entering cells via clathrin independent endocytosis. Here the authors show that multivalent lipid binding by globular particles can exceed a threshold adhesion energy required for membrane deformation and that this is sufficient for internalization.

    • Raluca Groza
    • , Kita Valerie Schmidt
    •  & Helge Ewers

  • Article
    | Open Access

    It is hard to correlate force, torque and localization information. The authors report Combined Optical and Magnetic BIomolecule TWEEZers, COMBI-Tweez, that integrates optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy: they demonstrate visualisation of higher order structural motifs in DNA.

    • Jack W. Shepherd
    • , Sebastien Guilbaud
    •  & Mark C. Leake

  • Article
    | Open Access

    Studying RNA decay remains a challenging task. Here, the authors present a technology that enables inducible rapid degradation of targeted mRNAs. Visualizing mRNA decay dynamics unveils insights into P-body function in RNA metabolism.

    • Lauren A. Blake
    • , Leslie Watkins
    •  & Bin Wu

  • Article
    | Open Access

    High-resolution cryo-EM study of human muscle phosphorylase kinase reveals its complex structure and how calcium ions activate it, offering insights into glycogen metabolism and kinase regulation.

    • Xiaoke Yang
    • , Mingqi Zhu
    •  & Junyu Xiao

  • Article
    | Open Access

    Due to the focus of vaccination on the SARS CoV-2 spike protein, spike has been associated with high levels of viral mutation and subsequent immune escape. Here the authors study a conserved epitope in SARS CoV-2 sub-domain-1 and characterise the neutralising antibody response and evasion in contemporary SARS COV-2 viral strains.

    • Daming Zhou
    • , Piyada Supasa
    •  & Gavin R. Screaton

  • Article
    | Open Access

    Photoreceptor proteins utilise biological chromophores to regulate a large range of cellular processes in response to light. Here the authors identify and characterise a sub-family of multi-centre photoreceptors, termed photocobilins, that not only utilise B12 but also contain biliverdin (BV) as an additional chromophore.

    • Shaowei Zhang
    • , Laura N. Jeffreys
    •  & Nigel S. Scrutton

  • Article
    | Open Access

    Protein dynamics, crucial for life, are difficult and expensive to predict. This study shows that AI-based structure prediction methods can be modified for rapidly predicting the conformational landscapes of proteins, with strong correlations with experimentally-measured relative state populations.

    • Gabriel Monteiro da Silva
    • , Jennifer Y. Cui
    •  & Brenda M. Rubenstein

  • Article
    | Open Access

    The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Here, authors present the high-resolution cryo-EM structure of its intact tail machine, and identify multiple hydrolytic and binding modules.

    • Rong-Cheng Yu
    • , Feng Yang
    •  & Cong-Zhao Zhou

  • Article
    | Open Access

    Single molecule investigations are often performed in fluidic environments, but molecular diffusion and limited photon counts can compromise studies of processes with fast or slow dynamics. The authors introduce a planar optofluidic antenna which enhances the fluorescence signal from molecules, applicable to a diverse range of studies.

    • Luis Morales-Inostroza
    • , Julian Folz
    •  & Vahid Sandoghdar

  • Article
    | Open Access

    To promote the development of effective small molecule modulators that may help treat diverse neuropsychiatric disorders, this study elucidates the mechanism of a specific positive modulator of neuronal potassium channels at near-atomic resolution.

    • Qiansheng Liang
    • , Gamma Chi
    •  & Manuel Covarrubias

  • Article
    | Open Access

    The Epidermal Growth Factor Receptor (EGFR) is frequently found to be mutated in non-small cell lung cancer. Here, the authors show that EGFR lung cancer mutations promote the assembly of kinase-active dimers within ligand-free EGFR oligomers. These dimers bind ligand with high affinity and promote tumor growth.

    • R. Sumanth Iyer
    • , Sarah R. Needham
    •  & Marisa L. Martin-Fernandez

  • Article
    | Open Access

    Yeast cadmium factor 1 (Ycf1), a heavy metal and glutathione transporter, is regulated by an intrinsically disordered region called the regulatory domain. In this work, the authors show that this domain controls activity through autoinhibition of the glutathione cavity when it is dephosphorylated.

    • Nitesh Kumar Khandelwal
    •  & Thomas M. Tomasiak

  • Article
    | Open Access

    ERGIC-53 engages in the ER-to-Golgi transport of secretory and membrane proteins by unknown mechanisms. Here authors report a long flexible tetrameric structure of full-length ERGIC-53 complexed with its functional partner MCFD2 by cryo-EM.

    • Satoshi Watanabe
    • , Yoshiaki Kise
    •  & Kenji Inaba

  • Article
    | Open Access

    Contractile rings are formed from cytoskeletal filaments, specific crosslinkers and motor proteins during cell division. Here, authors form micron-scale contractile DNA rings from DNA nanotubes and synthetic crosslinkers, with both simulations and experiments showing ring contraction without motor proteins, offering a potential first step towards synthetic cell division machinery.

    • Maja Illig
    • , Kevin Jahnke
    •  & Kerstin Göpfrich

  • Article
    | Open Access

    The Chloride Intracellular Channel (CLIC) protein family is highly conserved, yet their function remains a matter of ongoing research. Here, authors reveal their ability to facilitate membrane fusion, shedding light on their physiological role.

    • Bar Manori
    • , Alisa Vaknin
    •  & Yoni Haitin

  • Article
    | Open Access

    Small RNAs (sRNAs) turn bacterial genes on or off by base pairing with mRNAs. Here the authors employ single molecule fluorescence to show how sRNAs and their chaperone Hfq quickly locate the proper target by repeatedly scanning an mRNA until a stable match is found.

    • Ewelina M. Małecka
    •  & Sarah A. Woodson

  • Article
    | Open Access

    I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single stranded, cytosine-rich genomic region, but the specific contributions of several factors involved in their formation are unknown. Using in-cell NMR, the authors examined DNA i-motif formation in human cells at body temperature, suggesting i-M occur in a small portion (<1%) of genomic sites predisposed to its formation.

    • Pavlína Víšková
    • , Eva Ištvánková
    •  & Lukáš Trantírek

  • Article
    | Open Access

    The ABC transporter MRP2/ABCC2 is a polyspecific efflux transporter of organic anions expressed in hepatocyte canalicular membranes. Dysfunction leads to Dubin-Johnson syndrome. Here the authors provide structural and biochemical evidence on the modulation of MRP2 by intracellular kinases and inhibition by therapeutic drugs.

    • Tiziano Mazza
    • , Theodoros I. Roumeliotis
    •  & Konstantinos Beis

  • Article
    | Open Access

    Current approaches for volumetric super-resolution microscopy can yield large and complex PSF spatial footprints. Here, the authors show a super-resolution microscopy approach using a hexagonal microlens array, which offers speed improvements in volumetric imaging compared to other single-molecule methods.

    • Sam Daly
    • , João Ferreira Fernandes
    •  & Steven F. Lee

  • Article
    | Open Access

    Artificial biomolecular condensates are valuable tools to study the design principles of phase separation. Here, the authors demonstrate and characterize a model system of artificial DNA condensates whose kinetic formation and dissolution depends on DNA inputs that activate or deactivate the phase separating DNA subunits.

    • Siddharth Agarwal
    • , Dino Osmanovic
    •  & Elisa Franco

  • Article
    | Open Access

    Two small-molecule drugs, risdiplam and branaplam, have been developed for treating spinal muscular atrophy. Here the authors develop quantitative modeling methods for the sequence-specific and concentration-dependent effects of these and other splice-modifying drugs.

    • Yuma Ishigami
    • , Mandy S. Wong
    •  & Justin B. Kinney

  • Article
    | Open Access

    Here, the authors identify a conformational switch in the amino-terminal transactivation domain of c-MYC, termed coreMYC, which cycles between a closed, inactive state and an open, active conformation. Polyphenol epigallocatechin gallate (EGCG) is used to modulate the conformational landscape of coreMYC, stabilizing the closed and inactive conformation.

    • Dilraj Lama
    • , Thibault Vosselman
    •  & Marie Arsenian Henriksson

  • Article
    | Open Access

    Membrane proteins depend on their lipid environments. Using aquaporin as a model, the authors show that the choice of lipid bilayer fundamentally affects membrane protein structure, thermodynamics, kinetic, and function, even to the point of lipid-based inhibition.

    • Anh T. P. Nguyen
    • , Austin T. Weigle
    •  & Diwakar Shukla

  • Article
    | Open Access

    Actin is critical to the survival of the parasite Toxoplasma gondii. In this study, Hvorecny and Sladewski et al. show that T. gondii actin forms intrinsically dynamic filaments in vitro due to differences in assembly contacts in the D-loop.

    • Kelli L. Hvorecny
    • , Thomas E. Sladewski
    •  & Aoife T. Heaslip

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