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| Open AccessBiomolecular condensates form spatially inhomogeneous network fluids
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
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Article
| Open AccessThe assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili
Type 1 pili are crucial cell surface bacterial virulence factors. Here, the authors show that FimD is required to assemble the most stable quaternary pilus structure by ensuring that the resulting protein polymer is free of structural defects.
- Dawid S. Zyla
- , Thomas Wiegand
- & Rudi Glockshuber
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Article
| Open AccessComplexes of tubulin oligomers and tau form a viscoelastic intervening network cross-bridging microtubules into bundles
X-ray scattering and electron microscopy are used in concert to show that complexes of tubulin oligomers and tau are building blocks of an intervening network that cross-bridge microtubules into bundles with the same linear geometry observed in neurons.
- Phillip A. Kohl
- , Chaeyeon Song
- & Cyrus R. Safinya
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Article
| Open AccessTriggered contraction of self-assembled micron-scale DNA nanotube rings
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
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Article
| Open AccessTERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells
Here the authors show that the telomere repeat-containing RNA (TERRA) undergoes phase separation with the lysine-specific demethylase 1A (LSD1) to promote R-loop formation for homology-directed telomere DNA synthesis in the alternative lengthening of telomere (ALT) pathway.
- Meng Xu
- , Dulmi Senanayaka
- & Huaiying Zhang
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Article
| Open AccessAlternative low-populated conformations prompt phase transitions in polyalanine repeat expansions
Here, the authors show that pathogenic mutations in the polyalanine expansions of PHOX2B promote nascent structural conformations that trigger irreversible phase transitions that arrest wild-type PHOX2B, disrupting function.
- Rosa Antón
- , Miguel Á. Treviño
- & Javier Oroz
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Article
| Open AccessDynamic control of DNA condensation
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
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Article
| Open AccessHeterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex
Prion-like domains are intrinsically disordered regions found in many RNA- and DNA-binding proteins. Here, the authors show that these domains can drive sequence-specific co-phase separation of chromatin remodeling complex with FET oncofusion proteins.
- Richoo B. Davis
- , Anushka Supakar
- & Priya R. Banerjee
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Article
| Open AccessAn extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano
Sonani et al. report the cryo-EM structures of the Milano phage tail, unraveling the mechanism of its flexible-to-rigid transformation, the inter-chain disulfide network hindering tail contraction and the structural organization of receptor binding proteins.
- Ravi R. Sonani
- , Lee K. Palmer
- & Edward H. Egelman
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Article
| Open AccessConformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition
The authors use an integrative structural biology approach to elucidate molecular features of the RAS Q61 family of public tumor antigens. This information can be used to develop targeted therapeutics to combat a range of cancers.
- Andrew C. McShan
- , David Flores-Solis
- & Nikolaos G. Sgourakis
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Article
| Open AccessStochastic chain termination in bacterial pilus assembly
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
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Article
| Open AccessLiquid spherical shells are a non-equilibrium steady state of active droplets
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
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Article
| Open AccessElevated concentrations cause upright alpha-synuclein conformation at lipid interfaces
The misfolding of alpha-synuclein is associated with neurodegenerative disorders such as Parkinson’s disease. The authors report a mechanism explaining why lipid membranes catalyze the formation of harmful aggregates at elevated concentrations.
- Steven J. Roeters
- , Kris Strunge
- & Tobias Weidner
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Article
| Open AccessSpatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories
Here, the authors characterized the phase separation properties and internal structures of intracellular viral factories induced by Ebola virus and correlated these properties to important steps of viral biogenesis.
- Jingru Fang
- , Guillaume Castillon
- & Erica Ollmann Saphire
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Article
| Open AccessEarly events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering
Here the authors report time-resolved experiments showing that amyloid-β peptide molecules become partially structured even before they adhere to one another, within one millisecond. Peptide conformations change only slightly as assemblies grow in size for many minutes.
- Jaekyun Jeon
- , Wai-Ming Yau
- & Robert Tycko
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Article
| Open AccessStructural basis of HIV-1 maturation inhibitor binding and activity
HIV maturation inhibitors such as bevirimat (BVM) interfering with Gag processing are emerging as alternative anti-retroviral drug candidates. Here, the authors report structures of assemblies of HIV-1 Gag fragments spanning the CA C-terminal domain and SP1 region bound to BVM.
- Sucharita Sarkar
- , Kaneil K. Zadrozny
- & Tatyana Polenova
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Article
| Open AccessMetamorphism in TDP-43 prion-like domain determines chaperone recognition
In this work, the authors show that metamorphism in the post-translationally modified TDP-43 prion-like domain encodes determinants that command mechanisms with major relevance in disease and stress the relevance of post-translationally modified chains as the targets for disease intervention.
- Jaime Carrasco
- , Rosa Antón
- & Javier Oroz
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Article
| Open AccessUncovering the mechanism for aggregation in repeat expanded RNA reveals a reentrant transition
RNA molecules aggregate in certain conditions, but how and why remains unclear. Here the authors develop a model that quantitatively explains the conditions and mechanism of RNA aggregation, and predicts a surprising non-monotonicity in the transition.
- Ofer Kimchi
- , Ella M. King
- & Michael P. Brenner
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Article
| Open AccessThe dynamic clustering of insulin receptor underlies its signaling and is disrupted in insulin resistance
The authors find that the insulin receptor forms dynamic clusters during insulin signaling and that these clusters become dysfunctional in insulin resistance. This dysfunction is partially rescued by metformin, a drug used to treat type 2 diabetes.
- Alessandra Dall’Agnese
- , Jesse M. Platt
- & Richard A. Young
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Article
| Open AccessMagic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation
In this work the authors report the structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The study provides insights into the dynamic changes under which the neck linker goes upon binding to ADP.
- Chunting Zhang
- , Changmiao Guo
- & Tatyana Polenova
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Article
| Open AccessMacromolecular crowding and supersaturation protect hemodialysis patients from the onset of dialysis-related amyloidosis
Amyloid fibrils of β2-microglobulin (β2m) can cause dialysis-related amyloidosis. Here, the authors show that a decrease in serum albumin levels in long-term dialysis deteriorates the inhibitory effects of serum milieux on supersaturation-limited amyloid formation of β2m, suggesting that macromolecular crowding protects the onset of amyloidosis.
- Kichitaro Nakajima
- , Keiichi Yamaguchi
- & Yuji Goto
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Article
| Open AccessRubisco forms a lattice inside alpha-carboxysomes
Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment.
- Lauren Ann Metskas
- , Davi Ortega
- & Grant J. Jensen
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Article
| Open AccessIdentification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT
Ayala Mariscal et al have identified and characterized the interface of pathogenic Huntingtin and the molecular chaperone DNAJB1. Histidine-244 of the C-terminal domain of DNAJB1 is a key residues for binding to the poly-proline region of HTT. This binding site is specific for the interaction with Huntingtin.
- S. M. Ayala Mariscal
- , M. L. Pigazzini
- & J. Kirstein
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Article
| Open AccessMolecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau
Here, the authors report that α-synuclein phase-separates into liquid condensates with positively charged polypeptides such as Tau. The condensates undergo different maturation processes, including the formation of α-synuclein/Tau amyloid hetero-aggregates inside the condensates.
- Pablo Gracia
- , David Polanco
- & Nunilo Cremades
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Article
| Open AccessLight-activated mitochondrial fission through optogenetic control of mitochondria-lysosome contacts
Existing methods can lack spatiotemporal accuracy to manipulate dynamic mitochondrial behaviour in live cells. Here the authors report an optogenetic method to control mitochondria-lysosome contacts and induce mitochondrial fission; they use photoactivatable dimerizers including CRY2/CIB and SspB/iLID.
- Kangqiang Qiu
- , Weiwei Zou
- & Jiajie Diao
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Article
| Open AccessSizing up DNA nanostructure assembly with native mass spectrometry and ion mobility
Interest in oligonucleotide nanostructures has recently surged in basic and applied research. Here, the authors use native mass spectrometry and ion mobility to elucidate a prototypical hexameric DNA barrel structure as well as intermediates and byproducts of the assembly reaction.
- Jeroen F. van Dyck
- , Jonathan R. Burns
- & Frank Sobott
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Article
| Open AccesspH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils
Here the authors report the cryo-EM structure of a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembling in a pH- and concentration dependent manner into helical non-amyloid fibrils. The fibrils formation is reversible, and follows a sigmoidal kinetics. The fibrils adopt a right-handed helical superstructure composed by two protofilaments, stabilized by an outer hydrophobic ring and an inner hydrophobic centre. These findings reveal that α/β proteins can natively assemble into fibrils.
- Christin Pohl
- , Gregory Effantin
- & Pernille Harris
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Article
| Open AccessDynamic arrest and aging of biomolecular condensates are modulated by low-complexity domains, RNA and biochemical activity
Here the authors analyze material properties and aging of active phase-separated condensates by Differential Dynamic Microscopy. Arrested states are promoted by structured RNA. Low-complexity domains and biochemical reaction keep the droplets fluid-like.
- Miriam Linsenmeier
- , Maria Hondele
- & Paolo Arosio
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Article
| Open AccessNanoscale rules governing the organization of glutamate receptors in spine synapses are subunit specific
Glutamate receptors comprise two obligate subunits and two subunits that confer distinct properties and functions to the specific tetramers, which also localize to distinct synaptic spines. Here, the authors use STimulated Emission Depletion nanoscopy (STED) to provide detailed insights into the spatial organization of glutamate receptor types.
- Martin Hruska
- , Rachel E. Cain
- & Matthew B. Dalva
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Article
| Open AccessCapillary flow experiments for thermodynamic and kinetic characterization of protein liquid-liquid phase separation
Methods to quantitatively study liquid-liquid phase separation (LLPS) of proteins are lacking. Here the authors report Capillary flow experiments (Capflex) for the quantification of key LLPS parameters; they study Ddx4, the RP3 peptide and the aberrant liquid-to-solid phase transition of α-synuclein.
- Emil G. P. Stender
- , Soumik Ray
- & Alexander K. Buell
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Article
| Open AccessKinetic and structural roles for the surface in guiding SAS-6 self-assembly to direct centriole architecture
The centriole exhibits an evolutionarily conserved 9-fold radial symmetry that stems from a cartwheel containing vertically stacked ring polymers that harbor 9 homodimers of the protein SAS-6. Here the authors show how dual properties inherent to surface-guided SAS-6 self-assembly possess spatial information that dictates correct scaffolding of centriole architecture.
- Niccolò Banterle
- , Adrian P. Nievergelt
- & Pierre Gönczy
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Article
| Open AccessA multi-step nucleation process determines the kinetics of prion-like domain phase separation
The nucleation mechanisms of biological protein phase separation are poorly understood. Here, the authors perform time-resolved SAXS experiments with the low-complexity domain (LCD) of hnRNPA1 and uncover multiple kinetic regimes on the micro- to millisecond timescale. Initially, individual proteins collapse. Nucleation then occurs via two steps distinguished by their protein cluster size distributions.
- Erik W. Martin
- , Tyler S. Harmon
- & Tanja Mittag
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Article
| Open AccessCooperative stator assembly of bacterial flagellar motor mediated by rotation
Ito and co-workers unravel how bacteria such as Salmonella switch gears with their flagellar driving machinery. External load triggers the dynamic remodeling of the molecular complex sustaining the torque, and the number of stator units is adapted in a non-trivial, cooperative manner.
- Kenta I. Ito
- , Shuichi Nakamura
- & Shoichi Toyabe
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Article
| Open AccessAdeno-associated virus capsid assembly is divergent and stochastic
Adeno-associated viruses (AAVs) have emerged as promising gene therapy vectors.The AAV capsid consists of 60 subunits made up from three distinct viral proteins (VPs). Here authors record high-resolution native mass spectra of intact AAV capsids to assess the VP stoichiometries in a panel of serotypes and reveals an extremely heterogeneous population of capsids of variable composition.
- Tobias P. Wörner
- , Antonette Bennett
- & Albert J. R. Heck
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Article
| Open AccessComplete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials
Recent advances in computational methods have enabled the predictive design of self-assembling protein nanomaterials with atomic-level accuracy. Here authors investigate the assembly of two computationally designed, 120-subunit icosahedral complexes and find that assembly of each material from its two constituent protein building blocks was highly cooperative.
- Adam J. Wargacki
- , Tobias P. Wörner
- & Neil P. King
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Article
| Open AccessSequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies
Liquid ribonucleoprotein condensates typically involve a dense network of multiple proteins and RNAs. Here, the authors employ a minimal system composed of Prion-like polypeptides (PLP), Arg-rich polypeptides (RRP), and RNA to form biphasic condensates with diverse morphologies tunable via mixture stoichiometry and hierarchy of intermolecular interactions.
- Taranpreet Kaur
- , Muralikrishna Raju
- & Priya R. Banerjee
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Article
| Open AccessAsymmetrizing an icosahedral virus capsid by hierarchical assembly of subunits with designed asymmetry
Viruses have been re-engineered for many applications but the ability to build asymmetric capsids in vitro has been lacking. Here, the authors report the design of asymmetric subunits with different growth rates leading to capsids with discrete patches and potential for distinct surface chemistries.
- Zhongchao Zhao
- , Joseph Che-Yen Wang
- & Adam Zlotnick
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Article
| Open AccessCooperative function of synaptophysin and synapsin in the generation of synaptic vesicle-like clusters in non-neuronal cells
Synaptic vesicle clusters were proposed to represent phase separated condensates. Here, the authors show that only two proteins, synapsin and synaptophysin, are sufficient to make vesicle clusters in fibroblasts which are similar to those found at synapses in morphology and liquid-like properties.
- Daehun Park
- , Yumei Wu
- & Sunghoe Chang
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Article
| Open AccessStructure of native glycolipoprotein filaments in honeybee royal jelly
Female honeybee larvae develop into queens when they are fed exclusively with royal jelly (RJ) and major royal jelly protein 1 (MRJP1) is the main protein component of RJ. Here, the authors present the 3.5 Å cryo-EM structure of native RJ filament, where MRJP1 forms the outer shell surrounding apisimin tetramers with bound lipids at the core of the filament.
- Simone Mattei
- , Arvid Ban
- & Daniel Boehringer
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Article
| Open AccessConformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks
Immune cells express immunoproteasomes (i20S), which bind to specialized regulators, contain different catalytic subunits and generate immunogenic peptides. HDX-MS—based assessment of the differences between the conformational dynamics of standard and i20s reveals specific, allosteric changes in i20S and upon regulator binding.
- Jean Lesne
- , Marie Locard-Paulet
- & Julien Marcoux
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Article
| Open AccessCryo-electron microscopy structures of pyrene-labeled ADP-Pi- and ADP-actin filaments
For almost forty years, N-(1-pyrene) iodoacetamide has been used to label actin at C374, but the mechanisms of the fluorescence changes are still unknown due to the lack of structural information. Here authors provide cryo-EM structures of actin filaments with N-1-pyrene conjugated to cysteine 374 and either ADP or ADP-phosphate in the active site.
- Steven Z. Chou
- & Thomas D. Pollard
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Article
| Open AccessMolecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS
The low-complexity (LC) domain mediates liquid-liquid phase separation and fibril formation of the RNA-binding protein FUS (FUsed in Sarcoma). Here, the authors combine cryo-EM, solid-state NMR measurements and MD simulations to structurally characterise the fibrils formed by the C-terminal half of the FUS LC domain and discuss stabilizing interactions within the fibril core.
- Myungwoon Lee
- , Ujjayini Ghosh
- & Robert Tycko
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Article
| Open AccessMechanisms of microtubule dynamics and force generation examined with computational modeling and electron cryotomography
Microtubules are dynamic tubulin polymers which elongate by addition of bent guanosine triphosphate tubulin to the tips of curving protofilaments. Here authors use Brownian dynamics modeling and electron cryotomography to show that the lateral activation energy barrier in tubulin-tubulin interactions is a key parameter for this process, controlling the development of high pulling forces.
- Nikita B. Gudimchuk
- , Evgeni V. Ulyanov
- & J. Richard McIntosh
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Article
| Open AccessThe structures of two archaeal type IV pili illuminate evolutionary relationships
Archaeal type IV pili (T4P) mediate adhesion to surfaces and are receptors for hyperthermophilic archaeal viruses. Here, the authors present the cryo-EM structures of two archaeal T4P from Pyrobaculum arsenaticum and Saccharolobus solfataricus and discuss evolutionary relationships between bacterial T4P, archaeal T4P and archaeal flagellar filaments.
- Fengbin Wang
- , Diana P. Baquero
- & Edward H. Egelman
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Article
| Open AccessStructure and dynamics of the ASB9 CUL-RING E3 Ligase
Multi-subunit Cullin (CUL)-RING ligases (CRL) form the largest family of E3 ligases and are composed of a substrate receptor, a CUL, and a RING-box (RBX) protein. Here, the authors use cryo-EM and HDX-MS to characterise the ASB9 CUL-RING E3 ligase and present the structure of ASB9-ELOB/C bound to the substrate creatine kinase and the full-length CUL5 structure in complex with RBX2, and they propose a revised allosteric mechanism for CUL-E3 ligase function.
- Ryan J. Lumpkin
- , Richard W. Baker
- & Elizabeth A. Komives
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Article
| Open AccessCardiac muscle thin filament structures reveal calcium regulatory mechanism
The contraction of cardiac and skeletal muscles is regulated by Ca2+ released from the sarcoplasmic reticulum in muscle cells. Here the authors provide molecular insights into Ca2+ regulation of muscle contraction by determining the cryo-EM structures of the human cardiac muscle thin filament in the absence and presence of Ca2+.
- Yurika Yamada
- , Keiichi Namba
- & Takashi Fujii
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Article
| Open AccessStructure of the native supercoiled flagellar hook as a universal joint
The bacterial flagellar hook is a molecular universal joint that connects the rotary motor and long helical propeller of the bacterial flagellum. Here the authors present the 3.6 Å resolution cryo-EM structure of the native supercoiled Salmonella hook that provides insights into the dynamic changes of subunit conformations and intermolecular interactions of the hook protein FlgE.
- Takayuki Kato
- , Fumiaki Makino
- & Keiichi Namba
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Article
| Open AccessCycles of protein condensation and discharge in nuclear organelles studied by fluorescence lifetime imaging
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
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Article
| Open AccessLignin-polysaccharide interactions in plant secondary cell walls revealed by solid-state NMR
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