Molecular biophysics articles within Nature Communications

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  • Article
    | Open Access

    Here, the authors use small angle neutron scattering and coarse-grained molecular dynamics simulations to demonstrate that condensates based on the granular components of nucleoli are network fluids.

    • Furqan Dar
    • , Samuel R. Cohen
    •  & Rohit V. Pappu

  • Article
    | Open Access

    Work by Klyshko and Kim et al. lays the foundation for simulating pump-probe experiments and demonstrates how the dynamic behaviour of proteins extends to the crystal environment, emphasizing the need for an ensemble view in understanding functional motions.

    • Eugene Klyshko
    • , Justin Sung-Ho Kim
    •  & Sarah Rauscher

  • Article
    | Open Access

    Here the authors perform modelling to reveal that the timescale of actin-VASP interactions plays a critical role in actin ring formation and filament length determines droplet deformation in VASP droplets: predictions from the model were tested against VASP GAB mutant.

    • Aravind Chandrasekaran
    • , Kristin Graham
    •  & Padmini Rangamani

  • 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

    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

    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

    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

    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

  • Article
    | Open Access

    CRISPR-Cas12a is a powerful RNA-guided genome-editing system. Saha et al. show that an alpha-helical lid plays the central role in guiding the target DNA toward the single RuvC nuclease domain, resulting in a double-stranded DNA break.

    • Aakash Saha
    • , Mohd Ahsan
    •  & Giulia Palermo

  • Article
    | Open Access

    The authors show G protein subtype selectivity at the β1-adrenergic receptor is driven by the binding kinetics of ternary complex formation. Bound to G protein, the receptor adopts conformations that differ from its agonist-bound solution states.

    • Andrew J. Y. Jones
    • , Thomas H. Harman
    •  & Daniel Nietlispach

  • Article
    | Open Access

    In this work, the authors report a deep learning method, Deep DNAshape, to predict the influence of flanking regions on three-dimensional DNA structure and in structural readout mechanisms of protein-DNA binding.

    • Jinsen Li
    • , Tsu-Pei Chiu
    •  & Remo Rohs

  • Article
    | Open Access

    In this work, using a combination of Cryo-EM, in-cell experiments and biophysical analysis, the authors decoded the aggregation propensity of tau, revealing 5 central hot spots in its primary sequence and identify PAM4 as short segment that determines both the structure, as well as the cellular propagation of tau aggregates extracted from Alzheimer’s disease, corticobasal degeneration, and progressive supranuclear palsy patients.

    • Nikolaos Louros
    • , Martin Wilkinson
    •  & Joost Schymkowitz

  • Article
    | Open Access

    Cyclic AMP modulation of HCN channels underlies beta adrenergic stimulation of heart rate. Here, authors describe an intramolecular mechanism that controls cAMP affinity of the cyclic nucleotide binding domain of these channels.

    • Alessandro Porro
    • , Andrea Saponaro
    •  & Anna Moroni

  • Article
    | Open Access

    Here the authors combine 19 F NMR and femtosecond transient absorption to characterise the structural origin of the multiphasic quenching dynamics in various species of BLUF domains, highlighting the importance of the heterogeneous active-site H-bond network.

    • Yalin Zhou
    • , Siwei Tang
    •  & Dongping Zhong

  • Article
    | Open Access

    Energetic local frustration in proteins may have been positively selected by evolution when related to function such as ligand binding, allostery and other. Here the authors present a methodology to analyze local frustration patterns within protein families and superfamilies.

    • Maria I. Freiberger
    • , Victoria Ruiz-Serra
    •  & Alfonso Valencia

  • Article
    | Open Access

    Adhesive type-1 pili from Escherichia coli are filamentous protein complexes consisting of a short tip and a long rod formed by up to several thousand copies of a major subunit. Here, Giese et al. reconstitute the entire type-1 pilus rod assembly reaction in vitro, using all constituent protein subunits, and identify a subunit that acts as an irreversible assembly terminator.

    • Christoph Giese
    • , Chasper Puorger
    •  & Rudi Glockshuber

  • Article
    | Open Access

    Here the authors discover that chromatin stimulates topoisomerase II function by enabling the enzyme to achieve exceptionally high processivity and efficient supercoiling relaxation, even under low torsional stress.

    • Jaeyoon Lee
    • , Meiling Wu
    •  & Michelle D. Wang

  • Article
    | Open Access

    Dissipative structures are governed by non-equilibrium thermodynamics. Here, the authors describe a size-dependent transition from active droplets to active spherical shells—a dissipative structure that arises from reaction diffusion gradients.

    • Alexander M. Bergmann
    • , Jonathan Bauermann
    •  & Job Boekhoven

  • Article
    | Open Access

    Bcs1, a transmembrane AAA-ATPase, facilitates the translocation of folded ISP across the inner mitochondrial membrane. This study shows that the Bcs1 ATPase cycle conformational changes are highly concerted, unlike the canonical hand-over-hand mechanism.

    • Yangang Pan
    • , Jingyu Zhan
    •  & Simon Scheuring

  • Article
    | Open Access

    P2X3 activation requires tightening the inner pocket of the head domain (IP-HD) following ATP binding. Here the authors demonstrate that targeting the IP-HD with allosteric small molecules presents a potential strategy for the development of therapeutics for refractory chronic cough without taste abnormalities.

    • Chang-Run Guo
    • , Zhong-Zhe Zhang
    •  & Ye Yu

  • Article
    | Open Access

    Here, the reaction of the suicide inhibitor sulbactam with the M. tuberculosis β-lactamase (BlaC) is investigated with time-resolved crystallography. Singular Value Decomposition is implemented to extract kinetic information despite changes in unit cell parameters during the time-course of the reaction.

    • Tek Narsingh Malla
    • , Kara Zielinski
    •  & Marius Schmidt

  • Article
    | Open Access

    T-box riboswitch RNAs directly bind to specific tRNA and regulate the transcription or translation of downstream genes in bacteria. Using single-molecule FRET and ensemble biophysical analyses, here the authors uncover a Venus flytrap-like mechanism where tRNA binding to a T-box riboswitch mRNA triggers its rapid domain closure.

    • Krishna C. Suddala
    • , Janghyun Yoo
    •  & Jinwei Zhang

  • Article
    | Open Access

    Bicarbonate (HCO3−) is critical in sperm for stimulation of cAMP synthesis during fertilization, though there is dispute over how  HCO3− is transported into sperm. Here the authors use limit-of-detection LC/MS to characterize sperm protein expression and show that HCO3− is produced from CO2 diffusion into sperm rather than active transport.

    • Elena Grahn
    • , Svenja V. Kaufmann
    •  & U.Benjamin Kaupp

  • Article
    | Open Access

    CarH is a bacterial B12-binding photoreceptor involved in transcriptional regulation. Here, the authors provide insights into B12 dynamics and associated cobalt redox changes following light activation. These demonstrate the CarH response integrates light and oxygen sensing.

    • Harshwardhan Poddar
    • , Ronald Rios-Santacruz
    •  & David Leys

  • Article
    | Open Access

    Here the authors use fast kinetics, X-ray crystallography, and cryo-EM to uncover the mechanism of ribosome inhibition by amikacin and kanamycin. They find that amikacin binds near the P-site tRNA, offering new strategies to fight antibiotic resistance.

    • Savannah M. Seely
    • , Narayan P. Parajuli
    •  & Matthieu G. Gagnon

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