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Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-27 Naho Akiyama, Kensuke Ishiguro, Takeshi Yokoyama, Kenjyo Miyauchi, Asuteka Nagao, Mikako Shirouzu, Tsutomu Suzuki
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Structures of the ribosome bound to EF-Tu–isoleucine tRNA elucidate the mechanism of AUG avoidance Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-27 Mariia Yu. Rybak, Matthieu G. Gagnon
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Molecular stripping underpins derepression of a toxin–antitoxin system Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-27 Grzegorz J. Grabe, Rachel T. Giorgio, Miłosz Wieczór, Bridget Gollan, Molly Sargen, Modesto Orozco, Stephen A. Hare, Sophie Helaine
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Structural basis of the histone ubiquitination read–write mechanism of RYBP–PRC1 Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-25 Maria Ciapponi, Elena Karlukova, Sven Schkölziger, Christian Benda, Jürg Müller
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Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase Acta Cryst. D (IF 2.2) Pub Date : 2024-03-21 Breeze, C.W., Nakano, Y., Campbell, E.C., Frkic, R.L., Lupton, D.W., Jackson, C.J.
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Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows Acta Cryst. D (IF 2.2) Pub Date : 2024-03-21 Comet, M., Dijkman, P.M., Boer Iwema, R., Franke, T., Masiulis, S., Schampers, R., Raschdorf, O., Grollios, F., Pryor, E.E., Drulyte, I.
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VitroJet: new features and case studies Acta Cryst. D (IF 2.2) Pub Date : 2024-03-15 Henderikx, R.J.M., Mann, D., Domanska, A., Dong, J., Shahzad, S., Lak, B., Filopoulou, A., Ludig, D., Grininger, M., Momoh, J., Laanto, E., Oksanen, H.M., Bisikalo, K., Williams, P.A., Butcher, S.J., Peters, P.J., Beulen, B.W.A.M.M.
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Efficient in situ screening of and data collection from microcrystals in crystallization plates Acta Cryst. D (IF 2.2) Pub Date : 2024-03-15 Thompson, A.J., Sanchez-Weatherby, J., Williams, L.J., Mikolajek, H., Sandy, J., Worrall, J.A.R., Hough, M.A.
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Musings on art and science Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-18
In addition to the usual dose of compelling science, our March issue features thoughtful reflections on the last 30 years from readers, as well as past and present editors. Perhaps influenced by these pieces or by our stunning cover — or maybe it is just the changing seasons — we are in an introspective mood this month.
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Looking back at 30 years of Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-18 Guy Riddihough, Christopher Surridge, Andreas G. Ladurner, Rosemary K. Clyne, Maria Hodges, Arianne Heinrichs, Katarzyna Marcinkiewicz, Florian Ullrich, Carolina Perdigoto, Sara Osman, Katarzyna Ciazynska, Dimitrios Typas
Over the past 30 years, Nature Structural & Molecular Biology (NSMB) has covered an enormous breadth of subjects in the broad field of molecular and structural biology. Here, some of the journal’s past and present editors recount their editorial experience at NSMB and some of the more memorable papers they worked on.
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The impact of DNA methylation on CTCF-mediated 3D genome organization Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-18 Ana Monteagudo-Sánchez, Daan Noordermeer, Maxim V. C. Greenberg
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Tipping points in epithelial-mesenchymal lineages from single cell transcriptomics data Biophys. J. (IF 3.4) Pub Date : 2024-03-19 Manuel Barcenas, Federico Bocci, Qing Nie
Understanding cell fate decision-making during complex biological processes is an open challenge that is now aided by high resolution single cell sequencing technologies. Specifically, it remains challenging to identify and characterize transition states corresponding to “tipping points” whereby cells commit to new cell states. Here, we present a computational method that takes advantage of single
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Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I Structure (IF 5.7) Pub Date : 2024-03-18 Daniel Wohlwend, Luca Mérono, Sarah Bucka, Kevin Ritter, Henning J. Jessen, Thorsten Friedrich
Wohlwend et al. determine the structure of NuoEF, the electron input module of respiratory complex I, with bound nucleotides. The adenine dinucleotides share core binding modes to the unique Rossmann-fold with the “ADP-handle” always at the same position. The ribose attached to ADP enables correct positioning of the reactive group.
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Precise and scalable self-organization in mammalian pseudo-embryos Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-15 Mélody Merle, Leah Friedman, Corinne Chureau, Armin Shoushtarizadeh, Thomas Gregor
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A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α–primase Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-15 Elwood A. Mullins, Lauren E. Salay, Clarissa L. Durie, Noah P. Bradley, Jane E. Jackman, Melanie D. Ohi, Walter J. Chazin, Brandt F. Eichman
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Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein Biophys. J. (IF 3.4) Pub Date : 2024-03-16 Pranav Garg, Shawn C.C. Hsueh, Steven S. Plotkin
The efficacy of vaccines against the SARS-CoV-2 virus significantly declines with the emergence of mutant strains, prompting investigation into the feasibility of targeting highly conserved but often cryptic regions on the S2 domain of spike protein. Using tools from molecular dynamics, we find that exposure of this conserved S2 epitope located in the central helices below the receptor binding domains
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Structure-guided drug discovery: back to the future Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-14 Cheryl H. Arrowsmith
Over the past 30 years, the field of structural biology and its associated biological insights have seen amazing progress. In this Comment, I recount several milestones in the field and how we can apply lessons from the past toward an exciting future, especially as it relates to drug discovery.
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Governing principles of transcriptional logic out of equilibrium Biophys. J. (IF 3.4) Pub Date : 2024-03-14 Smruti Dixit, Teije C. Middelkoop, Sandeep Choubey
To survive, adapt, and develop, cells respond to external and internal stimuli by tightly regulating transcription. Transcriptional regulation involves the combinatorial binding of a repertoire of transcription factors to DNA, which often results in switch-like binary outputs akin to Boolean logic gates. Recent experimental studies have demonstrated that in eukaryotes, transcription factor binding
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Bending of a lipid membrane edge by annexin A5 trimers Biophys. J. (IF 3.4) Pub Date : 2024-03-14 Mayank Prakash Pandey, Paulo Cesar Telles de Souza, Weria Pezeshkian, Himanshu Khandelia
Plasma membrane damage occurs in healthy cells and more frequently in cancer cells where high growth rates and metastasis result in frequent membrane damage. The annexin family of proteins plays a key role in membrane repair. Annexins are recruited at the membrane injury site by Ca and repair the damaged membrane in concert with several other proteins. Annexin A4 (ANXA4) and ANXA5 form trimers at the
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Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint Biophys. J. (IF 3.4) Pub Date : 2024-03-13 Ali Risheh, Alles Rebel, Paul S. Nerenberg, Negin Forouzesh
The use of fast in silico prediction methods for protein-ligand binding free energies holds significant promise for the initial phases of drug development. Numerous traditional physics-based models (e.g., implicit solvent models), however, tend to either neglect or heavily approximate entropic contributions to binding due to their computational complexity. Consequently, such methods often yield imprecise
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A hydrophobic nexus at the heart of hERG K channel gating Biophys. J. (IF 3.4) Pub Date : 2024-03-12 Matthew C. Trudeau
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Structural basis of human U5 snRNP late biogenesis and recycling Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-11 Daria Riabov Bassat, Supapat Visanpattanasin, Matthias K. Vorländer, Laura Fin, Alexander W. Phillips, Clemens Plaschka
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Structure of the human 20S U5 snRNP Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-11 Sarah Schneider, Irina Brandina, Daniel Peter, Sonal Lagad, Angelique Fraudeau, Júlia Portell-Montserrat, Jonas Tholen, Jiangfeng Zhao, Wojciech P. Galej
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Lipid droplets as substrates for protein phase separation Biophys. J. (IF 3.4) Pub Date : 2024-03-11 Advika Kamatar, Jack P.K. Bravo, Feng Yuan, Liping Wang, Eileen M. Lafer, David W. Taylor, Jeanne C. Stachowiak, Sapun H. Parekh
Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid
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Investigating the ERG a-wave and Retinal Diseases with Rod Equivalent Circuit Model Based on the APD Biophys. J. (IF 3.4) Pub Date : 2024-03-11 Qing-an Ding, Chunyan Liu, Fangfang Ning, Xiaoyuan Li, Binghui Hou, Yuhua Gao, Jianyu Li, Chaoran Gu
Most empirically supported mathematical models of rod cells lack theoretical support from actual physical devices. Therefore, this paper proposes an equivalent circuit model for the rod is proposed based on the photoconductive properties of the avalanche photodetector (APD) and combined with the electrical properties of the rod. The model employs the photodetector to simulate the source of the photocurrent
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The open channel state in anion channelrhodopsin GtACR1 is a red-absorbing intermediate Biophys. J. (IF 3.4) Pub Date : 2024-03-11 Istvan Szundi, David S. Kliger
Anion channelrhodopsin ACR1 is a powerful optogenetic tool to inhibit nerve activity. Its kinetic mechanism was interpreted in terms of the bacteriorhodopsin photocycle, and the L intermediate was assigned to the open channel state. Here, we report the results of the comparison between the time dependence of the channel currents and the time evolutions of the K-like and L-like spectral forms. Based
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Taking mechanomicrobiology from local to global Biophys. J. (IF 3.4) Pub Date : 2024-03-10 W.R. Harcombe
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Structure of the human outer kinetochore KMN network complex Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-08 Stanislau Yatskevich, Jing Yang, Dom Bellini, Ziguo Zhang, David Barford
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Structure of the human KMN complex and implications for regulation of its assembly Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-08 Soumitra Polley, Tobias Raisch, Sabrina Ghetti, Marie Körner, Melina Terbeck, Frauke Gräter, Stefan Raunser, Camilo Aponte-Santamaría, Ingrid R. Vetter, Andrea Musacchio
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Structure and interactions of the endogenous human Commander complex Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-08 Saara Laulumaa, Esa-Pekka Kumpula, Juha T. Huiskonen, Markku Varjosalo
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The ATPase asymmetry: Novel computational insight into coupling diverse FO motors with tripartite F1 Biophys. J. (IF 3.4) Pub Date : 2024-03-08 Shintaroh Kubo, Yasushi Okada
ATP synthase, a crucial enzyme for cellular bioenergetics, operates via the coordinated coupling of an F motor, which presents variable symmetry, and a tripartite F motor. Despite extensive research, the understanding of their coupling dynamics, especially with non-10-fold symmetrical F motors, remains incomplete. This study investigates the coupling patterns between eightfold and ninefold F motors
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Coupling of zinc and GTP binding drives G-domain folding in Acinetobacter baumannii ZigA Biophys. J. (IF 3.4) Pub Date : 2024-03-08 Maximillian K. Osterberg, Ally K. Smith, Courtney Campbell, Daniel J. Deredge, Timothy L. Stemmler, David P. Giedroc
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Mitigating transcription noise via protein sharing in syncytial cells Biophys. J. (IF 3.4) Pub Date : 2024-03-08 Alex Mayer, Jiayu Li, Grace McLaughlin, Amy Gladfelter, Marcus Roper
Bursty transcription allows nuclei to concentrate the work of transcribing mRNA into short, intermittent intervals, potentially reducing transcriptional interference. However, bursts of mRNA production can increase noise in protein abundances. Here, we formulate models for gene expression in syncytia, or multinucleate cells, showing that protein abundance noise may be mitigated locally via spatial
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AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography Acta Cryst. D (IF 2.2) Pub Date : 2024-03-07 Justin E. Miller, Matthew P. Agdanowski, Joshua L. Dolinsky, Michael R. Sawaya, Duilio Cascio, Jose A. Rodriguez, Todd O. Yeates
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Structural determination and modeling of ciliary microtubules Acta Cryst. D (IF 2.2) Pub Date : 2024-03-07 Walton, T., Doran, M.H., Brown, A.
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Guiding the HBO1 complex function through the JADE subunit Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-06 Nitika Gaurav, Akinori Kanai, Catherine Lachance, Khan L. Cox, Jiuyang Liu, Adrian T. Grzybowski, Nehmé Saksouk, Brianna J. Klein, Yosuke Komata, Shuhei Asada, Alexander J. Ruthenburg, Michael G. Poirier, Jacques Côté, Akihiko Yokoyama, Tatiana G. Kutateladze
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How and when to measure mitochondrial inner membrane potentials Biophys. J. (IF 3.4) Pub Date : 2024-03-07 Alicia J. Kowaltowski, Fernando Abdulkader
The scientific literature on mitochondria has increased significantly over the years due to findings that these organelles have widespread roles in the onset and progression of pathological conditions such as metabolic disorders, neurodegenerative and cardiovascular diseases, inflammation, and cancer. Researchers have extensively explored how mitochondrial properties and functions are modified in different
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Interplay between environmental yielding and dynamic forcing modulates bacterial growth Biophys. J. (IF 3.4) Pub Date : 2024-03-07 Anna M. Hancock, Sujit S. Datta
Many bacterial habitats—ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms—are rheologically complex, undergo dynamic external forcing, and have unevenly distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of dispersed in granular hydrogel matrices with
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Hydration water drives the self-assembly of guanosine monophosphate Biophys. J. (IF 3.4) Pub Date : 2024-03-07 Yu Heng Tao, Simon Schulke, Gerhard Schwaab, Gareth L. Nealon, Simone Pezzotti, Stuart I. Hodgetts, Alan R. Harvey, Vincent P. Wallace, Martina Havenith
Guanosine monophosphate (GMP) is a nucleotide that can self-assemble in aqueous solution under certain conditions. An understanding of the process at the molecular level is an essential step to comprehend the involvement of DNA substructures in transcription and replication, as well as their relationship to genetic diseases such as cancer. We present the temperature-dependent terahertz (1.5–12 THz
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Regulatory activity is the default DNA state in eukaryotes Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-06 Ishika Luthra, Cassandra Jensen, Xinyi E. Chen, Asfar Lathif Salaudeen, Abdul Muntakim Rafi, Carl G. de Boer
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Dynamic temperature control in microfluidics for in vivo imaging of cold-sensing in C. elegans Biophys. J. (IF 3.4) Pub Date : 2024-03-06 Sol Ah Lee, Yongmin Cho, William R. Schafer, Hang Lu
The ability to perceive temperature is crucial for most animals. It enables them to maintain their body temperature and swiftly react to noxiously cold or hot objects. is a powerful genetic model for the study of thermosensation as its simple nervous system is well characterized and its transparent body is suited for in vivo functional imaging of neurons. The behavior triggered by experience-dependent
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Mechanical control of cell proliferation patterns in growing epithelial monolayers Biophys. J. (IF 3.4) Pub Date : 2024-03-06 Logan C. Carpenter, Fernanda Pérez-Verdugo, Shiladitya Banerjee
Cell proliferation plays a crucial role in regulating tissue homeostasis and development. However, our understanding of how cell proliferation is controlled in densely packed tissues is limited. Here we develop a computational framework to predict the patterns of cell proliferation in growing epithelial tissues, connecting single-cell behaviors and cell-cell interactions to tissue-level growth. Our
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Heterogeneous sampled subgraph neural networks with knowledge distillation to enhance double-blind compound-protein interaction prediction Structure (IF 5.7) Pub Date : 2024-03-05 Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Identifying binding compounds against a target protein is crucial for large-scale virtual screening in drug development. Recently, network-based methods have been developed for compound-protein interaction (CPI) prediction. However, they are difficult to be applied to unseen (i.e., never-seen-before) proteins and compounds. In this study, we propose SgCPI to incorporate local known interacting networks
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Distinct potassium channel types in brain capillary pericytes Biophys. J. (IF 3.4) Pub Date : 2024-03-05 Maria Sancho, Nicholas R. Klug, Osama F. Harraz, David Hill-Eubanks, Mark T. Nelson
Capillaries, composed of electrically coupled endothelial cells and overlying pericytes, constitute the vast majority of blood vessels in the brain. The most arteriole-proximate three to four branches of the capillary bed are covered by -actin-expressing, contractile pericytes. These mural cells have a distinctive morphology and express different markers compared with their smooth muscle cell (SMC)
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Interaction with stomatin directs human proton channels into cholesterol-dependent membrane domains Biophys. J. (IF 3.4) Pub Date : 2024-03-05 Artem G. Ayuyan, Vladimir V. Cherny, Gustavo Chaves, Boris Musset, Fredric S. Cohen, Thomas E. DeCoursey
Many membrane proteins are modulated by cholesterol. Here we report profound effects of cholesterol depletion and restoration on the human voltage-gated proton channel, hH1, in excised patches but negligible effects in the whole-cell configuration. Despite the presence of a putative cholesterol-binding site, a CARC motif in hH1, mutation of this motif did not affect cholesterol effects. The murine
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Negative lipid membranes enhance the adsorption of TAT-decorated elastin-like polypeptide micelles Biophys. J. (IF 3.4) Pub Date : 2024-03-05 Vivien Walter, Tatiana Schmatko, Pierre Muller, André P. Schroder, Sarah R. MacEwan, Ashutosh Chilkoti, Carlos M. Marques
A cell-penetrating peptide (CPP) is a short amino-acid sequence capable of efficiently translocating across the cellular membrane of mammalian cells. However, the potential of CPPs as a delivery vector is hampered by the strong reduction of its translocation efficiency when it bears an attached molecular cargo. To overcome this problem, we used previously developed diblock copolymers of elastin-like
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Welcoming five new Co-editors Acta Cryst. D (IF 2.2) Pub Date : 2024-03-04 Charles S. Bond, Elspeth F. Garman, Randy J. Read
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Calculation of solvation force in molecular dynamics simulation by deep-learning method Biophys. J. (IF 3.4) Pub Date : 2024-03-04 Jun Liao, Mincong Wu, Junyong Gao, Changjun Chen
Electrostatic calculations are generally used in studying the thermodynamics and kinetics of biomolecules in solvent. Generally, this is performed by solving the Poisson-Boltzmann equation on a large grid system, a process known to be time consuming. In this study, we developed a deep neural network to predict the decomposed solvation free energies and forces of all atoms in a molecule. To train the
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Binding equations for the lipid composition dependence of peripheral membrane-binding proteins Biophys. J. (IF 3.4) Pub Date : 2024-03-02 Daniel Kerr, Tiffany Suwatthee, Sofiya Maltseva, Ka Yee C. Lee
The specific recognition of peripheral membrane-binding proteins for their target membranes is mediated by a complex constellation of various lipid contacts. Despite the inherent complexities of the heterogeneous protein-membrane interface, the binding dependence of such proteins is, surprisingly, often reliably described by simple models such as the Langmuir Adsorption Isotherm or the Hill equation
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TRPV4-dependent Ca2+ influx determines cholesterol dynamics at the plasma membrane Biophys. J. (IF 3.4) Pub Date : 2024-03-02 Yutaro Kuwashima, Masataka Yanagawa, Masashi Maekawa, Mitsuhiro Abe, Yasushi Sako, Makoto Arita
The activities of the transient receptor potential vanilloid 4 (TRPV4), a Ca-permeable nonselective cation channel, are controlled by its surrounding membrane lipids (e.g., cholesterol, phosphoinositides). The transmembrane region of TRPV4 contains a cholesterol recognition amino acid consensus (CRAC) motif and its inverted (CARC) motif located in the plasmalemmal cytosolic leaflet. TRPV4 localizes
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Good reasons for structural biology Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-03-01 Patrick Cramer
The impressive achievements of structural biology leave us in awe, but also raise the question of whether we can still expect major developments in the field in the future. Before I provide my answer to this question, let me briefly reflect on the major advances in structural biology over the past three decades. Thirty years ago, in 1994, the journal Nature Structural Biology (renamed Nature Structural
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Dual mechanisms contribute to enhanced voltage dependence of an electric fish potassium channel Biophys. J. (IF 3.4) Pub Date : 2024-03-01 Jelena Todorovic, Immani Swapna, Antonio Suma, Vincenzo Carnevale, Harold Zakon
The voltage dependence of different voltage-gated potassium channels, described by the voltage at which half of the channels are open (V), varies over a range of 80 mV and is influenced by factors such as the number of positive gating charges and the identity of the hydrophobic amino acids in the channel’s voltage sensor (S4). Here we explore by experimental manipulations and molecular dynamics simulation
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Design of artificial molecular motor inheriting directionality and scalability Biophys. J. (IF 3.4) Pub Date : 2024-02-29 Kenta I. Ito, Yusuke Sato, Shoichi Toyabe
Realizing artificial molecular motors with autonomous functionality and high performance is a major challenge in biophysics. Such motors not only provide new perspectives in biotechnology but also offer a novel approach for the bottom-up elucidation of biological molecular motors. Directionality and scalability are critical factors for practical applications. However, the simultaneous realization of
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Morphodynamics of T-lymphocytes: Scanning to spreading Biophys. J. (IF 3.4) Pub Date : 2024-02-29 Kheya Sengupta, Pierre Dillard, Laurent Limozin
Binding of the T cell receptor complex to its ligand, the subsequent molecular rearrangement, and the concomitant cell-scale shape changes represent the very first steps of adaptive immune recognition. The first minutes of the interaction of T cells and antigen presenting cells have been extensively scrutinized; yet, gaps remain in our understanding of how the biophysical properties of the environment
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Real-time single-molecule imaging of CaMKII-calmodulin interactions Biophys. J. (IF 3.4) Pub Date : 2024-02-28 Shahid Khan, Justin E. Molloy, Henry Puhl, Howard Schulman, Steven S. Vogel
The binding of calcium/calmodulin (CAM) to calcium/calmodulin-dependent protein kinase II (CaMKII) initiates an ATP-driven cascade that triggers CaMKII autophosphorylation. The autophosphorylation in turn increases the CaMKII affinity for CAM. Here, we studied the ATP dependence of CAM association with the actin-binding CaMKIIβ isoform using single-molecule total internal reflection fluorescence microscopy
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Using a probabilistic approach to derive a two-phase model of flow-induced cell migration Biophys. J. (IF 3.4) Pub Date : 2024-02-28 Yaron Ben-Ami, Joe M. Pitt-Francis, Philip K. Maini, Helen M. Byrne
Interstitial fluid flow is a feature of many solid tumors. In vitro experiments have shown that such fluid flow can direct tumor cell movement upstream or downstream depending on the balance between the competing mechanisms of tensotaxis (cell migration up stress gradients) and autologous chemotaxis (downstream cell movement in response to flow-induced gradients of self-secreted chemoattractants).
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Identical sequences, different behaviors: Protein diversity captured at the single-molecule level Biophys. J. (IF 3.4) Pub Date : 2024-02-28 Rafael Tapia-Rojo, Alvaro Alonso-Caballero, Carmen L. Badilla, Julio M. Fernandez
The classical “one sequence, one structure, one function” paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are often assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype.
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Cells on a string: Characterizing cellular structure and dynamics through viscoelastic phenotyping Biophys. J. (IF 3.4) Pub Date : 2024-02-27 Dmitry A. Fedosov, Gerhard Gompper
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Nucleosome spacing controls chromatin spatial structure and accessibility Biophys. J. (IF 3.4) Pub Date : 2024-02-27 Tilo Zülske, Aymen Attou, Laurens Groß, David Hörl, Hartmann Harz, Gero Wedemann
Recent research highlights the significance of the three-dimensional structure of chromatin in regulating various cellular processes, particularly transcription. This is achieved through dynamic chromatin structures that facilitate long-range contacts and control spatial accessibility. Chromatin consists of DNA and a variety of proteins, of which histones play an essential structural role by forming
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Conserved allosteric perturbation of the GTPase domains by region 1 of Ras hypervariable regions Biophys. J. (IF 3.4) Pub Date : 2024-02-27 Xue Gu, Yalong Zhang, Dong Long
Ras proteins are important intracellular signaling hubs that can interact with numerous downstream effectors and upstream regulators through their GTPase domains (G-domains) anchored to plasma membranes by the C-terminal hypervariable regions (HVRs). The biological functions of Ras were proposed to be regulated at multiple levels including the intramolecular G-domain-HVR interactions, of which the