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Structural insights into the assembly pathway of the Helicobacter pylori CagT4SS outer membrane core complex Structure (IF 4.4) Pub Date : 2024-07-19
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Intracellular tau fragment droplets serve as seeds for tau fibrils Structure (IF 4.4) Pub Date : 2024-07-19
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Structural insights into an atypical histone binding mechanism by a PHD finger Structure (IF 4.4) Pub Date : 2024-07-18
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Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria Structure (IF 4.4) Pub Date : 2024-07-18
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Crystal structure of lipase from Pseudomonas aeruginosa reveals an unusual catalytic triad conformation Structure (IF 4.4) Pub Date : 2024-07-17
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The ribosome termination complex remodels release factor RF3 and ejects GDP Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-19 Li Li, Mariia Yu. Rybak, Jinzhong Lin, Matthieu G. Gagnon
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Structural basis of NEAT1 lncRNA maturation and menRNA instability Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-18 Ilias Skeparnias, Jinwei Zhang
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They all rock: A systematic comparison of conformational movements in LeuT-fold transporters Structure (IF 4.4) Pub Date : 2024-07-17
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Berberine analog of chloramphenicol exhibits a distinct mode of action and unveils ribosome plasticity Structure (IF 4.4) Pub Date : 2024-07-16
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Structural basis of homodimerization of the JNK scaffold protein JIP2 and its heterodimerization with JIP1 Structure (IF 4.4) Pub Date : 2024-07-15
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The power of scientific collaborations and the future of structural biology Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-15 Pedro Beltrao
The idea of a scientific discovery is often linked to the eureka moment of a lone scientist, which then transforms our thinking. However, scientific discoveries are never made by individuals in isolation. They build on the work of countless researchers, and often require interdisciplinary and collaborative teams of researchers.
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Cryo-EM structure of the R388 plasmid conjugative pilus reveals a helical polymer characterized by an unusual pilin/phospholipid binary complex Structure (IF 4.4) Pub Date : 2024-07-12 Abhinav K. Vadakkepat, Songlin Xue, Adam Redzej, Terry K. Smith, Brian T. Ho, Gabriel Waksman
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Pho pictures provide powerful perspectives of phosphate importing proteins Structure (IF 4.4) Pub Date : 2024-07-11 David Speedman, David B. Sauer
In this issue of Structure, Schneider et al.1 report multiple structures of the low-affinity inorganic-phosphate transporter Pho90 from Saccharomyces cerevisiae. With remarkable resolution of the Divalent Anion Sodium Symporter family member, their cryo-EM studies of this fungal protein reveal new modes of sodium, substrate, and lipid binding.
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The merger of two major families of proteins that regulate cellular processes Structure (IF 4.4) Pub Date : 2024-07-11 Karlett J. Parra
In this issue of Structure, Oot and Wilkens1 present new mechanistic insights to finally merge the function of V-ATPase and TLDc domain proteins. They show that TLDc proteins directly affect V-ATPase activity and assembly, expanding our understanding of how V-ATPase and TLDc proteins exert a plethora of biological functions.
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Squishy to crusty: Biophysics reveal the molecular details of FUS droplet maturation Structure (IF 4.4) Pub Date : 2024-07-11 Erich J. Sohn, David S. Libich
In a recent issue of Nature Chemical Biology, Emmanouilidis et al. (2024) investigate the maturation of biomolecular condensates of FUS1-267 and probe the molecular details of droplet aging. They observe that the liquid-to-solid transition of the droplet is mediated at the surface by FUS1–267 molecules that have adopted β-strand conformations.
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A roadmap for ribosome assembly in human mitochondria Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-11 Elena Lavdovskaia, Elisa Hanitsch, Andreas Linden, Martin Pašen, Venkatapathi Challa, Yehor Horokhovskyi, Hanna P. Roetschke, Franziska Nadler, Luisa Welp, Emely Steube, Marleen Heinrichs, Mandy Mong-Quyen Mai, Henning Urlaub, Juliane Liepe, Ricarda Richter-Dennerlein
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Resolving chaperone-assisted protein folding on the ribosome at the peptide level Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-10 Thomas E. Wales, Aleksandra Pajak, Alžběta Roeselová, Santosh Shivakumaraswamy, Steven Howell, Svend Kjær, F. Ulrich Hartl, John R. Engen, David Balchin
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Obscure DNA sequences unveil a new cancer target Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-08 Agnel Sfeir
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AlphaFold3 takes a step toward decoding molecular behavior and biological computation Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-08 Rohit Roy, Hashim M. Al-Hashimi
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VCP/p97-associated proteins are binders and debranching enzymes of K48–K63-branched ubiquitin chains Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-08 Sven M. Lange, Matthew R. McFarland, Frederic Lamoliatte, Thomas Carroll, Logesvaran Krshnan, Anna Pérez-Ràfols, Dominika Kwasna, Linnan Shen, Iona Wallace, Isobel Cole, Lee A. Armstrong, Axel Knebel, Clare Johnson, Virginia De Cesare, Yogesh Kulathu
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Molecular mechanisms of precise timing in cell lysis Biophys. J. (IF 3.2) Pub Date : 2024-07-06 Anupam Mondal, Hamid Teimouri, Anatoly B. Kolomeisky
Many biological systems exhibit precise timing of events, and one of the most known examples is cell lysis, which is a process of breaking bacterial host cells in the virus infection cycle. However, the underlying microscopic picture of precise timing remains not well understood. We present a novel theoretical approach to explain the molecular mechanisms of effectively deterministic dynamics in biological
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Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP Structure (IF 4.4) Pub Date : 2024-07-05 Antonella Costanzo, Francesca Fata, Ida Freda, Maria Laura De Sciscio, Elena Gugole, Giovanni Bulfaro, Matteo Di Renzo, Luca Barbizzi, Cécile Exertier, Giacomo Parisi, Marco D’Abramo, Beatrice Vallone, Carmelinda Savino, Linda Celeste Montemiglio
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Effects of pH on opioid receptor activation and implications for drug design Biophys. J. (IF 3.2) Pub Date : 2024-07-05 Christoph Stein
G-protein-coupled receptors are integral membrane proteins that transduce chemical signals from the extracellular matrix into the cell. Traditional drug design has considered ligand-receptor interactions only under normal conditions. However, studies on opioids indicate that such interactions are very different in diseased tissues. In such microenvironments, protons play an important role in structural
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Molecular mechanism of contactin 2 homophilic interaction Structure (IF 4.4) Pub Date : 2024-07-04 Shanghua Fan, Jianfang Liu, Nicolas Chofflet, Aaron O. Bailey, William K. Russell, Ziqi Zhang, Hideto Takahashi, Gang Ren, Gabby Rudenko
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A colloidal model for the equilibrium assembly and liquid-liquid phase separation of the reflectin A1 protein Biophys. J. (IF 3.2) Pub Date : 2024-07-04 Tse-Chiang Huang, Robert Levenson, Youli Li, Phillip Kohl, Daniel E. Morse, M. Scott Shell, Matthew E. Helgeson
Reflectin is an intrinsically disordered protein known for its ability to modulate the biophotonic camouflage of cephalopods based on its assembly-induced osmotic properties. Its reversible self-assembly into discrete, size-controlled clusters and condensed droplets are known to depend sensitively on the net protein charge, making reflectin stimuli-responsive to pH, phosphorylation, and electric fields
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Molecular insights into the initiation step of the Rcs signaling pathway Structure (IF 4.4) Pub Date : 2024-07-03 Nobuhiko Watanabe, Alexei Savchenko
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Mechanism of ceramide synthase inhibition by fumonisin B1 Structure (IF 4.4) Pub Date : 2024-07-03 Zike Zhang, Qi Fang, Tian Xie, Xin Gong
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Optical torque calculations and measurements for DNA torsional studies Biophys. J. (IF 3.2) Pub Date : 2024-07-03 Yifeng Hong, Fan Ye, Jin Qian, Xiang Gao, James T. Inman, Michelle D. Wang
The angular optical trap (AOT) is a powerful instrument for measuring the torsional and rotational properties of a biological molecule. Thus far, AOT studies of DNA torsional mechanics have been carried out using a high numerical aperture oil-immersion objective, which permits strong trapping but inevitably introduces spherical aberrations due to the glass-aqueous interface. However, the impact of
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Phalloidin-PAINT: Enhanced quantitative nanoscale imaging of F-actin Biophys. J. (IF 3.2) Pub Date : 2024-07-03 Hirushi Gunasekara, Thilini Perera, Chih-Jia Chao, Joshua Bruno, Badeia Saed, Jesse Anderson, Zongmin Zhao, Ying S. Hu
We present phalloidin-based points accumulation for imaging in nanoscale topography (phalloidin-PAINT), enabling quantitative superresolution imaging of filamentous actin (F-actin) in the cell body and delicate membrane protrusions. We demonstrate that the intrinsic phalloidin dissociation enables PAINT superresolution microscopy in an imaging buffer containing low concentrations of dye-conjugated
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Major-groove sequence-specific RNA recognition by LoaP, a paralog of transcription elongation factor NusG Structure (IF 4.4) Pub Date : 2024-07-02 Amr Elghondakly, Madison D. Jermain, Wade C. Winkler, Adrian R. Ferré-D’Amaré
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Cryo-EM structures of γ-TuRC reveal molecular insights into microtubule nucleation Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-02 Léa Mammri, Paul T. Conduit
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cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-02 Marina C. Nocente, Anida Mesihovic Karamitsos, Emilie Drouineau, Manon Soleil, Waad Albawardi, Cécile Dulary, Florence Ribierre, Hélène Picaud, Olivier Alibert, Joël Acker, Marie Kervella, Jean-Christophe Aude, Nick Gilbert, Françoise Ochsenbein, Sophie Chantalat, Matthieu Gérard
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Structural basis of MALAT1 RNA maturation and mascRNA biogenesis Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-02 Ilias Skeparnias, Charles Bou-Nader, Dimitrios G. Anastasakis, Lixin Fan, Yun-Xing Wang, Markus Hafner, Jinwei Zhang
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Proton diffusion on the surface of mixed lipid membranes highlights the role of membrane composition Biophys. J. (IF 3.2) Pub Date : 2024-07-02 Ambili Ramanthrikkovil Variyam, Mateusz Rzycki, Anna Yucknovsky, Alexei A. Stuchebrukhov, Dominik Drabik, Nadav Amdursky
Proton circuits within biological membranes, the foundation of natural bioenergetic systems, are significantly influenced by the lipid compositions of different biological membranes. In this study, we investigate the influence of mixed lipid membrane composition on the proton transfer (PT) properties on the surface of the membrane. We track the excited-state PT (ESPT) process from a tethered probe
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FimH-mannose noncovalent bonds survive minutes to hours under force Biophys. J. (IF 3.2) Pub Date : 2024-07-02 Laura A. Carlucci, Keith C. Johnson, Wendy E. Thomas
The adhesin FimH is expressed by commensal and is implicated in urinary tract infections, where it mediates adhesion to mannosylated glycoproteins on urinary and intestinal epithelial cells in the presence of a high-shear fluid environment. The FimH-mannose bond exhibits catch behavior in which bond lifetime increases with force, because tensile force induces a transition in FimH from a compact native
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Sarcomere, troponin, and myosin X-ray diffraction signals can be resolved in single cardiomyocytes Biophys. J. (IF 3.2) Pub Date : 2024-07-02 Hendrik Bruns, Titus S. Czajka, Michael Sztucki, Sören Brandenburg, Tim Salditt
Cardiac function relies on the autonomous molecular contraction mechanisms in the ventricular wall. Contraction is driven by ordered motor proteins acting in parallel to generate a macroscopic force. The averaged structure can be investigated by diffraction from model tissues such as trabecular and papillary cardiac muscle using collimated synchrotron beams, offering high resolution in reciprocal space
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Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-01 Ruth M. Saecker, Andreas U. Mueller, Brandon Malone, James Chen, William C. Budell, Venkata P. Dandey, Kashyap Maruthi, Joshua H. Mendez, Nina Molina, Edward T. Eng, Laura Y. Yen, Clinton S. Potter, Bridget Carragher, Seth A. Darst
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Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-01 Julian R. Braxton, Hao Shao, Eric Tse, Jason E. Gestwicki, Daniel R. Southworth
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Single-base tiled screen unveils design principles of PspCas13b for potent and off-target-free RNA silencing Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-07-01 Wenxin Hu, Amit Kumar, Syed Faraz Ahmed, Shijiao Qi, David K. G. Ma, Honglin Chen, Gurjeet J. Singh, Joshua M. L. Casan, Michelle Haber, Ilia Voskoboinik, Matthew R. McKay, Joseph A. Trapani, Paul G. Ekert, Mohamed Fareh
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Insight into molecular basis and dynamics of full-length CRaf kinase in cellular signaling mechanisms Biophys. J. (IF 3.2) Pub Date : 2024-06-29 Van A. Ngo
Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase
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Bioelectricity and molecular signaling Biophys. J. (IF 3.2) Pub Date : 2024-06-29 Marcel P. Goldschen-Ohm, Baron Chanda
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Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation Biophys. J. (IF 3.2) Pub Date : 2024-06-28 Maria Oranges, Chandrima Jash, Gonen Golani, Manas Seal, Sidney R. Cohen, Irit Rosenhek-Goldian, Alexey Bogdanov, Samuel Safran, Daniella Goldfarb
Protein solutions can undergo liquid-liquid phase separation (LLPS), where a dispersed phase with a low protein concentration coexists with coacervates with a high protein concentration. We focus on the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein, CPEB4, and its isoform depleted of the Exon4, CPEB4Δ4. They both exhibit LLPS, but in contrast to most systems
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Markerauto2: A fast and robust fully automatic fiducial marker-based tilt series alignment software for electron tomography Structure (IF 4.4) Pub Date : 2024-06-26 Zihe Xu, Hongjia Li, Xiaohua Wan, Jose-Jesus Fernández, Fei Sun, Fa Zhang, Renmin Han
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Conformational rigidity of cytochrome c'-α from a thermophile is associated with slow NO binding Biophys. J. (IF 3.2) Pub Date : 2024-06-26 Sotaro Fujii, Michael T. Wilson, Hannah R. Adams, Halina Mikolajek, Dimitri A. Svistunenko, Peter Smyth, Colin R. Andrew, Yoshihiro Sambongi, Michael A. Hough
Cytochromes ′-α are nitric oxide (NO)-binding heme proteins derived from bacteria that can thrive in a wide range of temperature environments. Studies of mesophilic cytochrome ′-α (AxCP-α) have revealed an unusual NO-binding mechanism involving both heme faces, in which NO first binds to form a distal hexa-coordinate Fe(II)-NO (6cNO) intermediate and then displaces the proximal His to form a proximal
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De novo design of SARS-CoV-2 main protease inhibitors with characteristic binding modes Structure (IF 4.4) Pub Date : 2024-06-25 Yan Zhu, Jiaolong Meng, Bo Feng, Yao Zhao, Yi Zang, Lingling Lu, Mingbo Su, Qi Yang, Qi Zhang, Lu Feng, Jinyi Zhao, Maolin Shao, Yuanyuan Ma, Xiuna Yang, Haitao Yang, Jia Li, Xuefeng Jiang, Zihe Rao
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The tRNA methyltransferase METTL6 requires seryl-tRNA synthetase for tRNASer targeting Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-06-25
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Structural basis of tRNA recognition by the m3C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-06-25 Philipp Throll, Luciano G. Dolce, Palma Rico-Lastres, Katharina Arnold, Laura Tengo, Shibom Basu, Stefanie Kaiser, Robert Schneider, Eva Kowalinski
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Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16 Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-06-25 Huasong Ai, Zaozhen He, Zhiheng Deng, Guo-Chao Chu, Qiang Shi, Zebin Tong, Jia-Bin Li, Man Pan, Lei Liu
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Control of mitophagy initiation and progression by the TBK1 adaptors NAP1 and SINTBAD Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-06-25 Elias Adriaenssens, Thanh Ngoc Nguyen, Justyna Sawa-Makarska, Grace Khuu, Martina Schuschnig, Stephen Shoebridge, Marvin Skulsuppaisarn, Emily Maria Watts, Kitti Dora Csalyi, Benjamin Scott Padman, Michael Lazarou, Sascha Martens
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Conformations of influenza A M2 protein in DOPC/DOPS and E. coli native lipids and proteins Biophys. J. (IF 3.2) Pub Date : 2024-06-25 Griffin Sanders, Peter P. Borbat, Elka R. Georgieva
We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IM2) protein reconstituted in 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPC/DOPS) bilayers to those in isolated () membranes, having preserved its native proteins and lipids. IM2 is a single-pass transmembrane protein known to assemble into a homo-tetrameric proton channel
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Hi-C-guided many-polymer model to decipher 3D genome organization Biophys. J. (IF 3.2) Pub Date : 2024-06-25 Chen Shi, Lei Liu, Changbong Hyeon
We propose a high-throughput chromosome conformation capture data-based many-polymer model that allows us to generate an ensemble of multi-scale genome structures. We demonstrate the efficacy of our model by validating the generated structures against experimental measurements and employ them to address key questions regarding genome organization. Our model first confirms a significant correlation
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Time-resolved fluorescence of tryptophan characterizes membrane perturbation by cyclic lipopeptides Biophys. J. (IF 3.2) Pub Date : 2024-06-22 Iulia Carabadjac, Jessica Steigenberger, Niels Geudens, Vic De Roo, Penthip Muangkaew, Annemieke Madder, José C. Martins, Heiko Heerklotz
Viscosin is a membrane-permeabilizing, cyclic lipopeptide (CLiP) produced by species. Here, we have studied four synthetic analogs (L1W, V4W, L5W, and L7W), each with one leucine (Leu; L) or valine residue exchanged for tryptophan (Trp; W) by means of time-resolved fluorescence spectroscopy of Trp. To this end, we recorded the average fluorescence lifetime, rotational correlation time and limiting
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Structural insights into the role and targeting of EGFRvIII Structure (IF 4.4) Pub Date : 2024-06-21 Atrish Bagchi, Steven E. Stayrook, Katerina T. Xenaki, Chrystal A. Starbird, Sofia Doulkeridou, Rachid el Khoulati, Rob C. Roovers, Karl R. Schmitz, Paul M.P. van Bergen en Henegouwen, Kathryn M. Ferguson
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Structural investigation of the docking domain assembly from trans-AT polyketide synthases Structure (IF 4.4) Pub Date : 2024-06-21 Se-Young Son, Da-Woon Bae, Eunji Kim, Bo-Gyeong Jeong, Myeong-Yeon Kim, So-Yeon Youn, Soojung Yi, Gyeongmin Kim, Ji-Sook Hahn, Nam Ki Lee, Yeo Joon Yoon, Sun-Shin Cha
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Modulating Ca2+ influx into adrenal chromaffin cells with short-duration nanosecond electric pulses Biophys. J. (IF 3.2) Pub Date : 2024-06-21 Sung Hae Yun, Vasilii Mansurov, Lisha Yang, Jihwan Yoon, Normand Leblanc, Gale L. Craviso, Josette Zaklit
Isolated bovine adrenal chromaffin cells exposed to single 2-, 4-, or 5-ns pulses undergo a rapid, transient rise in intracellular Ca mediated by Ca entry via voltage-gated Ca channels (VGCCs), mimicking the activation of these cells in vivo by acetylcholine. However, pulse durations 150 ns or longer elicit larger amplitude and longer-lived Ca responses due to Ca influx via both VGCCs and a yet to
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Coupling the role of lipids to the conformational dynamics of the ABC transporter P-glycoprotein Biophys. J. (IF 3.2) Pub Date : 2024-06-21 Dario De Vecchis, Lars V. Schäfer
The ATP-binding cassette transporter P-glycoprotein (P-gp) is a multidrug efflux pump that is overexpressed in a variety of cancers and associated with the drug-resistance phenomenon. P-gp structures were previously determined in detergent and in nanodiscs, in which different transmembrane helix conformations were found, “straight” and “kinked,” respectively, indicating a possible role of the lipid
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Auxin-mediated stress relaxation in pericycle and endoderm remodeling drives lateral root initiation Biophys. J. (IF 3.2) Pub Date : 2024-06-20 João R.D. Ramos, Blanca Jazmin Reyes-Hernández, Karen Alim, Alexis Maizel
Plant development relies on the precise coordination of cell growth, which is influenced by the mechanical constraints imposed by rigid cell walls. The hormone auxin plays a crucial role in regulating this growth by altering the mechanical properties of cell walls. During the postembryonic formation of lateral roots, pericycle cells deep within the main root are triggered by auxin to resume growth
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Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro Nat. Struct. Mol. Biol. (IF 12.5) Pub Date : 2024-06-19 Duc-Duy Vu, Alessio Bonucci, Manon Brenière, Metztli Cisneros-Aguirre, Philippe Pelupessy, Ziqing Wang, Ludovic Carlier, Guillaume Bouvignies, Patricia Cortes, Aneel K. Aggarwal, Martin Blackledge, Zoher Gueroui, Valérie Belle, Jeremy M. Stark, Mauro Modesti, Fabien Ferrage