Article
|
Open Access
Featured
-
-
Article
| Open Access
Reciprocating RNA Polymerase batters through roadblocks
During transcription, RNA polymerases may encounter protein roadblocks along template DNA. Here, Qian et al. use magnetic tweezers to show that RNA polymerases can backtrack and ram into longer lived roadblocks to transit through them.
- Jin Qian
- , Allison Cartee
- & Laura Finzi
-
Article
| Open Access
Engineering an artificial catch bond using mechanical anisotropy
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
Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA
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
A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies
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
Tomosyns attenuate SNARE assembly and synaptic depression by binding to VAMP2-containing template complexes
SNARE-dependent membrane fusion underlies neurotransmission in the nervous system. Here, the authors demonstrate how, in mammalian neurons, the synaptic protein tomosyn controls secretion by increasing the energy barrier for fusion.
- Marieke Meijer
- , Miriam Öttl
- & Matthijs Verhage
-
Article
| Open Access
An optofluidic antenna for enhancing the sensitivity of single-emitter measurements
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
Dissecting the mechanism of atlastin-mediated homotypic membrane fusion at the single-molecule level
The detailed process of membrane fusion mediated by dynamin-like GTPase atlastin (ATL) remains unclear. Here, authors reveal the conformational dynamics of ATL coupled with GTP hydrolysis cycle at the single molecule level.
- Lijun Shi
- , Chenguang Yang
- & Xin Bian
-
Article
| Open Access
Drug-resistant EGFR mutations promote lung cancer by stabilizing interfaces in ligand-free kinase-active EGFR oligomers
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
RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone
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
High-density volumetric super-resolution microscopy
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
SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis
There is a lack of universal tools to analyse protein assemblies and quantify underlying structures in single-molecule localization microscopy. Here, the authors present SEMORE, a semi-automatic machine learning framework for system- and input-dependent analysis of super-resolution data.
- Steen W. B. Bender
- , Marcus W. Dreisler
- & Nikos S. Hatzakis
-
Article
| Open Access
Emergence of slip-ideal-slip behavior in tip-links serve as force filters of sound in hearing
In this work, the authors report that tetrameric tip-link complex, pivotal for force transmission, forms slip-ideal-slip bonds under tension, serving as efficient force-filters in the auditory process.
- Nisha Arora
- , Jagadish P. Hazra
- & Sabyasachi Rakshit
-
Article
| Open Access
DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2
The function of transcription factors is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains, but the lack of quantitative structural ensemble models prevents their mechanistic decoding. Here, the authors use several methods to demonstrate that DNA binding can lead to complex changes in the IDR ensemble and accessibility on the example of the C-terminal IDR of pioneer factor Sox2.
- Sveinn Bjarnason
- , Jordan A. P. McIvor
- & Pétur O. Heidarsson
-
Article
| Open Access
Molecular basis of VEGFR1 autoinhibition at the plasma membrane
Spontaneous activation of VEGFRs is a hallmark of diabetes and several cancers. Here, the authors show how in VEGFR1 a juxtamembrane segment connecting the catalytic and ligand-binding domains of the receptor can prevent its spontaneous activation.
- Manas Pratim Chakraborty
- , Diptatanu Das
- & Rahul Das
-
Article
| Open Access
Structural role for DNA Ligase IV in promoting the fidelity of non-homologous end joining
Nonhomologous end joining (NHEJ), the primary pathway of vertebrate DNA double strand-break (DSB) repair, directly re-ligates broken DNA ends with minimal errors. In this study, the authors identify structural interactions of the NHEJ-specific DNA Ligase IV (Lig4) that prioritize ligation and promote NHEJ fidelity.
- Benjamin M. Stinson
- , Sean M. Carney
- & Joseph J. Loparo
-
Article
| Open Access
Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1
Bacic et al. demonstrate that PARP1/HPF1 preferentially modify histone tails closest to the DNA break, directing ALC1-catalyzed nucleosome sliding. These findings suggest a mechanism for rendering DNA breaks more accessible to repair factors.
- Luka Bacic
- , Guillaume Gaullier
- & Sebastian Deindl
-
Article
| Open Access
A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice
Achieving genetic circuits on single DNA molecules could have varied applications. Here, authors observed proteins emerging from single DNA molecules through coupled transcription-translation complexes, and show that nascent proteins lingered on DNA, regulating cascaded reactions on the same DNA and allowing the design of a pulsatile genetic circuit.
- Ferdinand Greiss
- , Nicolas Lardon
- & Roy Bar-Ziv
-
Article
| Open Access
Folding pathway of a discontinuous two-domain protein
Here, using single molecule FRET, the unfolding and folding of a discontinuous two-domain protein was studied. The authors find that a dynamic, intermediate population entropically limits the rate of folding while the order of domain folding is kept in a slow-folding mutant.
- Ganesh Agam
- , Anders Barth
- & Don C. Lamb
-
Article
| Open Access
Cochaperones convey the energy of ATP hydrolysis for directional action of Hsp90
The precise role of cochaperones and ATP hydrolysis in driving Hsp90’s chaperone cycle is largely unclear. Here, the authors use single-molecule FRET to show that several cochaperones are necessary to establish directionality in Hsp90’s conformational cycle.
- Leonie Vollmar
- , Julia Schimpf
- & Thorsten Hugel
-
Article
| Open Access
Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP
Tripartite ATP-independent periplasmic (TRAP) transporters use an extra substrate binding protein to transport a variety of substrates in bacteria and archaea. Here the authors use a disulfide engineering approach to lock the TRAP transporter HiSiaPQM from H. influenzae in different conformational states for characterisation.
- Martin F. Peter
- , Jan A. Ruland
- & Gregor Hagelueken
-
Article
| Open Access
Dynamic stability of Sgt2 enables selective and privileged client handover in a chaperone triad
Newly synthesized tail-anchored membrane proteins (TAs) are relayed in a chaperone triad, Hsp70, Sgt2, and Get3, for delivery to the endoplasmic reticulum. Here, the authors show how the conformational dynamics of the cochaperone Sgt2 generates a decision point to enable efficient and selective TA targeting.
- Hyunju Cho
- , Yumeng Liu
- & Shu-ou Shan
-
Article
| Open Access
Force transmission by retrograde actin flow-induced dynamic molecular stretching of Talin
Focal adhesion proteins transmit intracellular forces to the extracellular matrix (ECM). Here, the authors show a force transmission by elastic transient clutch of Talin between ECM and constantly flowing F-actin at focal adhesions.
- Sawako Yamashiro
- , David M. Rutkowski
- & Naoki Watanabe
-
Article
| Open Access
Voltage sensors of a Na+ channel dissociate from the pore domain and form inter-channel dimers in the resting state
It is believed that voltage sensor domains (VSD) of voltage-gated Na+ channels are always attached to the channel. Here, authors find that VSDs detach from the channel to form inter-channel dimers.
- Ayumi Sumino
- , Takashi Sumikama
- & Katsumasa Irie
-
Article
| Open Access
Homo- and hetero-dimeric subunit interactions set affinity and efficacy in metabotropic glutamate receptors
The molecular basis of functional diversity between obligatorily dimeric mGluRs is not understood. The authors show that functional differences typically attributed to differences in the agonist binding pocket emerge from differences between homomeric and heteromeric Group II and III Gi-coupled mGluRs in dimerization interface interactions.
- Chris Habrian
- , Naomi Latorraca
- & Ehud Y. Isacoff
-
Article
| Open Access
CENP-A and CENP-B collaborate to create an open centromeric chromatin state
Centromeres are defined by the histone variant CENP-A. Using single-molecule fluorescence and cryoEM, this study shows that CENP-A and the centromeric protein CENP-B collaborate to create dynamic and open chromatin, aiding centromeric factor binding.
- Harsh Nagpal
- , Ahmad Ali-Ahmad
- & Beat Fierz
-
Article
| Open Access
A minority of final stacks yields superior amplitude in single-particle cryo-EM
Here the authors develop an iterative particle sieving method called CryoSieve, demonstrating this method outperforms other cryo-EM particle sorting algorithms to reveal that most particles are unnecessary in final stacks.
- Jianying Zhu
- , Qi Zhang
- & Chenglong Bao
-
Article
| Open Access
The separation pin distinguishes the pro– and anti–recombinogenic functions of Saccharomyces cerevisiae Srs2
Here the authors report that the main role of the protein Srs2 in homologous recombination is to remove Rad51 from single stranded DNA, rather than to drive synthesis-dependent strand annealing.
- Aviv Meir
- , Vivek B. Raina
- & Eric C. Greene
-
Article
| Open Access
Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis
Mechanistic insight into inflammasome formation is important for designing anti-inflammatory interventions. Here, the authors reveal the kinetics and distinct assembly modes of the early stages of the AIM2 inflammasome that detects pathogenic DNA.
- Meenakshi Sharma
- & Eva de Alba
-
Article
| Open Access
Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch
T-box riboswitches are RNA-based gene regulators, composed of highly structured noncoding RNAs: the T-box and a tRNA ligand. Here, the authors assess the folding of a translational T-box aptamer and dissect the role of Mg2+, intra- and intermolecular RNA-RNA interactions in modulating its folding and function.
- Xiaolin Niu
- , Zhonghe Xu
- & Xianyang Fang
-
Article
| Open Access
Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes
Fast discrimination of SARS-CoV-2 variants in clinical samples remains a challenge. Here, authors report on single molecule nanopore sensing combined with DNA molecular probes to simultaneously detect various antigens and RNA mutations of SARS-CoV-2 variants in patient samples.
- Ren Ren
- , Shenglin Cai
- & Joshua B. Edel
-
Article
| Open Access
Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation
Using single-molecule FRET, the authors discover hidden structural subpopulations of the intrinsically disordered prion-like low-complexity domain of FUS and dissect key molecular events that drive dynamic network formation during phase separation.
- Ashish Joshi
- , Anuja Walimbe
- & Samrat Mukhopadhyay
-
Article
| Open Access
DNA strand breaks and gaps target retroviral intasome binding and integration
Here the authors use biochemical assays and single molecule imaging to show that DNA breaks and single-stranded gaps modulate dynamic PFV retroviral intasome interactions with target DNA and encourage site-specific integration.
- Gayan Senavirathne
- , James London
- & Kristine E. Yoder
-
Article
| Open Access
A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint
Here the authors investigate the impact of chromatinizing origins of replication on ORC and MCM is at the single-molecule level. They find mobility of ORC reduced, but not its binding to the origin. MCM is both efficiently recruited and spatially confined to the origin.
- Humberto Sánchez
- , Zhaowei Liu
- & Nynke H. Dekker
-
Article
| Open Access
Deep-LASI: deep-learning assisted, single-molecule imaging analysis of multi-color DNA origami structures
Analysis of single-molecule experiments remains time-consuming and prone to human bias. Here, the authors propose Deep-Learning Assisted Single-molecule Imaging analysis, a tool to rapidly analyse single-, two- and three-color single-molecule FRET data.
- Simon Wanninger
- , Pooyeh Asadiatouei
- & Don C. Lamb
-
Article
| Open Access
An automated single-molecule FRET platform for high-content, multiwell plate screening of biomolecular conformations and dynamics
Single-molecule FRET (smFRET) studies often struggle with large parameter spaces. Here, the authors introduce an automated smFRET platform for multiwell plate screening of biomolecular conformations and dynamics.
- Andreas Hartmann
- , Koushik Sreenivasa
- & Michael Schlierf
-
Article
| Open Access
Chromatin organization drives the search mechanism of nuclear factors
Nuclear factors rapidly scan the genome for targets, but the role of nuclear organization in such search is uncharted. Here, by combining single molecule tracking of nuclear proteins with high resolution imaging of the nucleus, the authors investigate the search mechanism used by factors such as p53.
- Matteo Mazzocca
- , Alessia Loffreda
- & Davide Mazza
-
Article
| Open Access
Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies
Understanding the topological arrangement and transition dynamics of mesoscale assemblies is complicated by their molecular complexity. Here, the authors use DNA origami nanosprings to show that mesoscale helical handedness is dictated by backbone torque rather than achiral orientation.
- Deepak Karna
- , Eriko Mano
- & Hanbin Mao
-
Article
| Open Access
A concerted ATPase cycle of the protein transporter AAA-ATPase Bcs1
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
YTHDF2 facilitates aggresome formation via UPF1 in an m6A-independent manner
YTHDF2 has been extensively studied as an m6A-related RNA metabolism. Here, the authors show that YTHDF2 also contributes to protein homeostasis in an m6A-independent manner by promoting the formation of aggresomes through its interaction with UPF1.
- Hyun Jung Hwang
- , Tae Lim Park
- & Yoon Ki Kim
-
Article
| Open Access
Acetylation reprograms MITF target selectivity and residence time
The microphthalmia-associated transcription factor MITF is a lineage-survival oncogene that plays a crucial role in melanocyte development and melanoma. Here, the authors reveal that MITF has a very long chromatin-bound half-life, and that MITF target selectivity is regulated by K206 acetylation, a residue linked to Waardenburg syndrome.
- Pakavarin Louphrasitthiphol
- , Alessia Loffreda
- & Colin R. Goding
-
Article
| Open Access
Conserved roles for the dynein intermediate chain and Ndel1 in assembly and activation of dynein
The mechanism by which dynein-mediated cargo transport is switched on is unresolved. This study reveals insights into the roles of the human disease genes Ndel1 and LIS1 in the assembly and activation of dynein transport complexes.
- Kyoko Okada
- , Bharat R. Iyer
- & Richard J. McKenney
-
Article
| Open Access
Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature
Electron microscopy of native hydrated biological samples close to physiological temperature is challenging. Here, authors encapsulate proteins and cells as an efficient, cost-effective complement to other microscopy technique in addressing biological questions at the molecular level.
- Lingli Kong
- , Jianfang Liu
- & Gang Ren
-
Article
| Open Access
Single-molecule imaging reveals distinct elongation and frameshifting dynamics between frames of expanded RNA repeats in C9ORF72-ALS/FTD
Hexanucleotide repeat expansion in the C9ORF72 gene produces toxic dipeptide repeat (DPR) in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here the authors apply single-molecule methods to study the translation dynamics of C9ORF72 expanded repeat in different frames showing that multiple translation steps contribute to the final toxic dipeptide production.
- Malgorzata J. Latallo
- , Shaopeng Wang
- & Bin Wu
-
Article
| Open Access
Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble
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
Coordinated peptidoglycan synthases and hydrolases stabilize the bacterial cell wall
The integrity and maintenance of cell-wall peptidoglycan is essential for growth and cell shape in bacteria. Here, the authors show how the coordinated actions of a synthase, which inserts new peptidoglycan strands, and a hydrolase, which generates openings to allow the insertion, determine the integrity of bacterial cell wall.
- Huan Zhang
- , Srutha Venkatesan
- & Beiyan Nan
-
Article
| Open Access
Structural and functional insights into the modulation of T cell costimulation by monkeypox virus protein M2
The B7 family proteins B7.1 (CD80) and B7.2 (CD86) are two well-studied costimulatory ligands that play critical roles in host T cell immunity against viral infection. In this study, the authors show that oligomeric M2 protein encoded by monkeypox virus serves as a viral decoy receptor and inhibits T cell activation mediated by hB7.1/2 co-stimulation via the blockade of CD28 binding to human B7.1/2, providing molecular mechanisms of poxvirus M2 function and immune evasion.
- Shangyu Yang
- , Yong Wang
- & Haiyan Zhao
-
Article
| Open Access
Switch of cell migration modes orchestrated by changes of three-dimensional lamellipodium structure and intracellular diffusion
How do cells regulate their migration speed and direction? Here, authors discover that keratocyte cells can reversibly switch between different migration modes, by changing the 3D lamellipodium shape and intracellular diffusion.
- Chao Jiang
- , Hong-Yu Luo
- & Hui Li
-
Article
| Open Access
Control of motor landing and processivity by the CAP-Gly domain in the KIF13B tail
Intracellular transport of material along microtubules by kinesin motors is critical for cellular homeostasis. Here the authors uncover a unique role for a specialized kinesin tail domain in directing motor transport along specific microtubule tracks.
- Xiangyu Fan
- & Richard J. McKenney
-
Article
| Open Access
Energetic robustness to large scale structural fluctuations in a photosynthetic supercomplex
Robust photosynthetic light harvesting occurs in large membrane supercomplexes. Here, the authors show that supercomplexes occupy an unexpectedly large range of conformations yet maintain their efficiency due to specific, critical chlorophylls.
- Dvir Harris
- , Hila Toporik
- & Yuval Mazor
Cryo-EM structures of adenosine receptor A3AR bound to selective agonists