Molecular biophysics articles within Nature Communications

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  • Article
    | Open Access

    Studying the condensation of proteins into membraneless organelles in live cells is highly challenging. Here the authors develop a fluorescence lifetime imaging approach to monitor the condensation of proteins in nuclear organelles and report coordinated and cyclic changes in several nuclear organelles.

    • Artem Pliss
    • , Svitlana M. Levchenko
    •  & Paras N. Prasad

  • Article
    | Open Access

    The interactions of lignin with polysaccharides in plant secondary cell walls are not well understood. Here the authors employ solid-state NMR measurements to analyse intact stems of maize, Arabidopsis, switchgrass and rice and observe that lignin self-aggregates and forms highly hydrophobic microdomains that make extensive surface contacts to xylan.

    • Xue Kang
    • , Alex Kirui
    •  & Tuo Wang

  • Article
    | Open Access

    Allostery is a fundamental principle of protein regulation that remains challenging to engineer. Here authors screen human Inward Rectifier K + Channel Kir2.1 for permissibility to domain insertions and propose that differential permissibility is a metric of latent allosteric capacity in Kir2.1.

    • Willow Coyote-Maestas
    • , Yungui He
    •  & Daniel Schmidt

  • Article
    | Open Access

    Desmosomes are intercellular adhesion complexes that connect the intermediate filament cytoskeletons of neighboring cells but direct evidence for their load-bearing nature is lacking. Here the authors develop FRET-based tension sensors to measure the forces experienced by desmoplakin and infer that desmosomes become mechanically loaded when cells are exposed to external mechanical stresses.

    • Andrew J. Price
    • , Anna-Lena Cost
    •  & Carsten Grashoff

  • Article
    | Open Access

    The nucleolus is a membrane-less organelle and both Nucleophosmin (NPM1) and Surfeit locus protein 6 (SURF6) are abundant proteins within the nucleolus. Here the authors employ biophysical methods to study the properties of NPM1-S6N droplets and provide insights into the role of SURF6 in maintaining and modulating the liquid-like structure of the nucleolus.

    • Mylene C. Ferrolino
    • , Diana M. Mitrea
    •  & Richard W. Kriwacki

  • Article
    | Open Access

    The detailed folding mechanisms of membrane proteins in their natural bilayer-like environments remains poorly understood due to the lack of tools for measuring stabilities and kinetics. Here, by simulating the folding of GlpG in a bilayer, the authors provide support for the helical-hairpin hypothesis and prompt a re-evaluation of a long-standing paradigm, the two-stage hypothesis.

    • Wei Lu
    • , Nicholas P. Schafer
    •  & Peter G. Wolynes

  • Article
    | Open Access

    Phytochromes are photoreceptors that are present in plants, bacteria and fungi. Here the authors present crystal structures of the phytochrome Agp2 from Agrobacterium fabrum in the parent Pfr state as well as a functional Meta-F intermediate and discuss mechanistic implications for photoconversion.

    • Andrea Schmidt
    • , Luisa Sauthof
    •  & Patrick Scheerer

  • Article
    | Open Access

    Molecular details that underlie mechanical properties of spider silk are of great interest to material scientists. Here, the authors report a previously unknown three-state mechanism of folding and an expanded structure of a spider silk protein that may contribute to elasticity of spider silk.

    • Charlotte Rat
    • , Julia C. Heiby
    •  & Hannes Neuweiler

  • Article
    | Open Access

    Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.

    • Lukas F. Milles
    • , Eduard M. Unterauer
    •  & Hermann E. Gaub

  • Article
    | Open Access

    How interactions between binding partners form or break is hidden in the transition paths from the encounter to the formation of a stable complex. Here authors use single‐molecule spectroscopy to measure the transition path times for the association of two intrinsically disordered proteins that form a folded dimer upon binding and identify a metastable encounter complex.

    • Flurin Sturzenegger
    • , Franziska Zosel
    •  & Benjamin Schuler

  • Article
    | Open Access

    Metal ions at the active site of an enzyme act as cofactors and their dynamic fluctuations might influence enzyme activity. Here authors use single-molecule FRET to study λ-exonuclease and find that metal-ion-coordination is correlated with enzymatic reaction-steps.

    • Wonseok Hwang
    • , Jungmin Yoo
    •  & Gwangrog Lee

  • Article
    | Open Access

    How G-quadruplexes (G4s) are resolved by helicases is still a matter of investigation. Here the authors provide mechanistic insight into G4s unwinding by presenting a crystal structure of resolved G4 DNA and the G4 binding domain of RecQ helicase from the bacterium Cronobacter sakazakii.

    • Andrew F. Voter
    • , Yupeng Qiu
    •  & James L. Keck

  • Article
    | Open Access

    The E. coli MinCDE system oscillates between cell poles to position the main division protein FtsZ. Here authors use in vitro reconstitution to show that MinDE oscillations also regulate unrelated membrane proteins spatiotemporally into patterns and gradients by forming a moving physical barrier.

    • Beatrice Ramm
    • , Philipp Glock
    •  & Petra Schwille

  • Article
    | Open Access

    Generation and iterative optimization of designed enzymes can provide valuable insights for a more efficient catalysis. Here the authors have followed the iterative improvement of a designed Kemp eliminase and show that remote point mutations could remodel the designed active site via substantial conformational reorganization.

    • Nan-Sook Hong
    • , Dušan Petrović
    •  & Colin J. Jackson

  • Article
    | Open Access

    Biologically relevant weak and transient interdomain interactions within proteins are difficult to analyze. Here, the authors combine multiscale molecular dynamics simulations and high-precision FRET experiments to characterize interactions between the tandem PDZ domains of PSD-95, revealing previously hidden conformational states.

    • Inna S. Yanez Orozco
    • , Frank A. Mindlin
    •  & Hugo Sanabria

  • Article
    | Open Access

    The SNARE complex enables the fusion of synaptic vesicles with presynaptic membrane via a zippering process that is modulated by the protein complexin, though the precise mechanism remains unclear. Here, the authors used magnetic tweezers to show how complexin prepares a SNARE complex for fusion under mechanical tension.

    • Min Ju Shon
    • , Haesoo Kim
    •  & Tae-Young Yoon

  • Article
    | Open Access

    Hypoxia inducible factor (HIF)-2α transcription factor is mutated in polycythemia and various neuroendocrine tumors. Here the authors present the crystal structure of a HIF-2α peptide bound to the pVHL-elongin B-elongin C (VBC) heterotrimeric complex and propose a classification scheme for HIF-2α mutations that helps to predict disease phenotype outcome.

    • Daniel Tarade
    • , Claire M. Robinson
    •  & Michael Ohh

  • Article
    | Open Access

    How intrinsically disordered proteins (IDPs) undergo a coupled folding and binding reaction with their molecular targets remains to be understood. Here authors use single-molecule FRET to assess the contribution of cis/trans isomerization of peptidyl-prolyl bonds in regulating IDP interactions.

    • Franziska Zosel
    • , Davide Mercadante
    •  & Benjamin Schuler

  • Article
    | Open Access

    Complex assembly pathways often involve transient, partly-formed intermediates that are challenging to characterize. Here, the authors present a simple and rapid spectroscopic thermal hysteresis method for mapping the energy landscapes of supramolecular assembly.

    • Robert W. Harkness V
    • , Nicole Avakyan
    •  & Anthony K. Mittermaier

  • Article
    | Open Access

    The 3D organization of chromosomes within the nuclear space is important for biological functions. Here the authors model chromosomes as self-avoiding copolymers with distinct epigenetic states, and show that the features of experimentally generated contact maps can be reproduced and their dynamics predicted.

    • Guang Shi
    • , Lei Liu
    •  & D. Thirumalai

  • Article
    | Open Access

    Thrombin-derived C-terminal peptides (TCPs) have anti-endotoxic functions in wounds by binding to bacterial lipopolysaccharide (LPS) and Gram-negative bacteria. Here authors use a spectrum of biophysical techniques to determine the conformation of a TCP in complex with LPS and define the interaction between TCPs and CD14.

    • Rathi Saravanan
    • , Daniel A Holdbrook
    •  & Artur Schmidtchen

  • Article
    | Open Access

    Mutations in the cation channel PKD2 cause human autosomal dominant polycystic kidney disease but its channel function and gating mechanism are poorly understood. Here authors study PKD2 using electrophysiology and cryo-EM, which identifies hydrophobic gates and proposes a gating mechanism for PKD2.

    • Wang Zheng
    • , Xiaoyong Yang
    •  & Xing-Zhen Chen

  • Article
    | Open Access

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor. Here the authors provide insights into PPARγ activation by combining fluorine (19F) NMR and molecular dynamics simulations to characterize the nuclear receptor conformational ensemble in solution and the response of this ensemble to ligand and coregulatory peptide binding.

    • Ian M. Chrisman
    • , Michelle D. Nemetchek
    •  & Travis S. Hughes

  • Article
    | Open Access

    Sialic acid transporters (SiaT) are required for sialic acid uptake in a number of human pathogens and are of interest as targets for antimicrobial drug development. Here the authors present the substrate bound SiaT structure from the uropathogen Proteus mirabilis and provide insights into the mechanism of sialic acid transport.

    • Weixiao Y. Wahlgren
    • , Elin Dunevall
    •  & Rosmarie Friemann

  • Article
    | Open Access

    Evidence suggests oligomerisation of G protein-coupled receptors in membranes, but this is controversial. Here, authors use single-molecule and ensemble FRET, and spectroscopy to show that the neurotensin receptor 1 forms multiple dimer conformations that interconvert - “rolling” interfaces.

    • Patricia M. Dijkman
    • , Oliver K. Castell
    •  & Anthony Watts

  • Article
    | Open Access

    Mutations in superoxide dismutase-1 (SOD1) cause amyotrophic lateral sclerosis (ALS). Here the authors present the SOD1 crystal structure bound to the small cysteine-reactive molecule ebselen and show that ebselen is a chaperone for SOD1.

    • Michael J. Capper
    • , Gareth S. A. Wright
    •  & S. Samar Hasnain

  • Article
    | Open Access

    Cell membrane protrusions and invaginations are both driven by actin assembly but the mechanism leading to different membrane shapes is unknown. Using a minimal system and modelling the authors reconstitute the deformation modes and identify capping protein as a regulator of both deformation types.

    • Katharina Dürre
    • , Felix C. Keber
    •  & Andreas R. Bausch

  • Article
    | Open Access

    A key challenge in the field of protein design and evolution is to understand the mechanisms by which directed evolution is improving enzymes. Here the authors combine different biophysical methods and give mechanistic insights into how directed evolution increases the catalytic efficiency of human peptidyl-prolyl cis/trans isomerase CypA.

    • Renee Otten
    • , Lin Liu
    •  & James S. Fraser

  • Article
    | Open Access

    Membrane protein RodZ interacts with the actin-like protein MreB, which coordinates cell-wall insertion to maintain the typical rod-like shape of E. coli cells. Here, the authors provide evidence that RodZ modulates the biophysical properties of MreB and alters the spatial organization of cell-wall growth.

    • Alexandre Colavin
    • , Handuo Shi
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    The rational optimization of response times of protein conformational switches is a major challenge for biomolecular switch design. Here the authors present a generally applicable computational design strategy that in combination with biophysical experiments can improve response times using a Ca2+-sensor as an example.

    • Alex J. DeGrave
    • , Jeung-Hoi Ha
    •  & Lillian T. Chong

  • Article
    | Open Access

    The nucleolus is a membrane-less organelle formed through liquid–liquid phase separation (LLPS). Here the authors use biophysical methods and show that the nucleolar protein nucleophosmin (NPM1) also undergoes LLPS through homotypic, inter-NPM1 interactions and discuss implications for the ribosome biogenesis process.

    • Diana M. Mitrea
    • , Jaclyn A. Cika
    •  & Richard W. Kriwacki

  • Article
    | Open Access

    Adapter proteins assist clathrin coated pit assembly. Here, the authors combine native mass spectrometry, crystallography and SAXS measurements and show that the membrane–proximal domains of the adaptor proteins epsin and Sla2 form complexes mediated through phosphatidylinositol 4,5-bisphosphate interfaces leading to assembly formation.

    • Maria M. Garcia-Alai
    • , Johannes Heidemann
    •  & Rob Meijers

  • Article
    | Open Access

    Chromatin fibers undergo continuous structural rearrangements but their dynamic architecture is poorly understood. Here, the authors use single-molecule FRET to determine the structural states and interconversion kinetics of chromatin fibers, monitoring their effector protein-dependent dynamic motions.

    • Sinan Kilic
    • , Suren Felekyan
    •  & Beat Fierz

  • Article
    | Open Access

    An understanding of the dynamics of drug binding and unbinding processes is important for drug discovery. Here, the authors give insights into the binding mechanism of small drug-like molecules to human Hsp90 by combining thermodynamics and kinetics studies as well as molecular dynamics simulations.

    • M. Amaral
    • , D. B. Kokh
    •  & M. Frech

  • Article
    | Open Access

    Src is a prototypical signaling non-receptor protein tyrosine kinase that interconverts between distinct conformations. Here the authors use variants of the kinase-inhibitor dasatinib to define three specific conformational states of the Src kinase and shed insight on the effect of conformation-specific inhibitors on Src dynamics.

    • Michael Tong
    • , Jeff G. Pelton
    •  & Markus A. Seeliger

  • Article
    | Open Access

    The spindle checkpoint ensures the fidelity of chromosome segregation during mitosis and meiosis. Here the authors use a combination of biochemical and structural biology approaches to show how the TRIP13 ATPase and its adaptor, p31comet, catalyze the conversion of the checkpoint protein Mad2 between latent and active forms

    • Melissa L. Brulotte
    • , Byung-Cheon Jeong
    •  & Xuelian Luo

  • Article
    | Open Access

    GalNAc transferases’ (GalNAc-Ts) catalytic domains are connected to a lectin domain through a flexible linker. Here the authors present a structural analysis of GalNAc-T4 that implicates the linker region as modulator of the orientations of the lectin domain, which in turn imparts substrate specificity.

    • Matilde de las Rivas
    • , Erandi Lira-Navarrete
    •  & Ramon Hurtado-Guerrero

  • Article
    | Open Access

    Myosin VI (MVI) is known to interact with RNA Polymerase II and to play non-cytoplasmic roles in cells. Here, the authors provide evidence that the transcription co-activator NDP52 regulates MVI binding to DNA and that MVI interacts with nuclear receptors to drive gene expression.

    • Natalia Fili
    • , Yukti Hari-Gupta
    •  & Christopher P. Toseland

  • Article
    | Open Access

    KCNQ1 is a voltage-gated potassium channel that is important in cardiac and epithelial function. Here the authors present a mechanism for KCNQ1 activation and inactivation in which voltage sensor activation promotes pore opening more effectively in the intermediate open state than the fully open state, generating inactivation.

    • Panpan Hou
    • , Jodene Eldstrom
    •  & Jianmin Cui

  • Article
    | Open Access

    The vitamin B12 importer BtuCD-F is a type II ATP-binding cassette transporter. Here the authors use single-molecule fluorescence techniques to analyse ATP hydrolysis and substrate transport in individual BtuCD-F complexes embedded in liposomes, and propose a transport model.

    • Joris M. H. Goudsmits
    • , Dirk Jan Slotboom
    •  & Antoine M. van Oijen

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