Guangjie Yan, Manhua Pan, Aaron M Keller, Ace George Santiago, Michael Lofgren, Ruma Banerjee, Peng Chen, Tai-Yen Chen
{"title":"Conformation-gated binding underlies kinetic asymmetry and negative cooperativity in ATP:cob(I)alamin adenosyltransferase.","authors":"Guangjie Yan, Manhua Pan, Aaron M Keller, Ace George Santiago, Michael Lofgren, Ruma Banerjee, Peng Chen, Tai-Yen Chen","doi":"10.1016/j.xcrp.2025.102768","DOIUrl":"10.1016/j.xcrp.2025.102768","url":null,"abstract":"<p><p>Vitamin B<sub>12</sub> (cobalamin) is a high-value yet scarce cofactor critical for metabolic homeostasis, necessitating efficient handling mechanisms. ATP:cob(I)alamin adenosyltransferase (MMAB) plays a central role in synthesizing, delivering, and repairing 5'-deoxyadenosylcobalamin (AdoCbl), but the kinetic mechanisms regulating this process, including negative cooperativity, remain unclear. Using single-molecule relative fluorescence spectroscopy, we reveal that conformation-gated binding mechanism, involving a required structural rearrangement prior to the first cofactor association, dictates MMAB's interaction kinetics. This mechanism slows the association of a second AdoCbl, resulting in strong negative cooperativity, favoring the singly bound state, and optimizing AdoCbl handling. This gating mechanism, supported by direct observation of a kinetic intermediate, also contributes to MMAB's preferential handling of AdoCbl over hydroxocobalamin, highlighting MMAB's effective cofactor utilization, supporting bacterial survival in nutrient-limited environments. Furthermore, our approach offers a platform to study cofactor interactions, including cobalamin sensing and gene regulation, shedding light on bacterial adaptation to nutrient fluctuations.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 8","pages":""},"PeriodicalIF":7.3,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12431680/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fathima Hameed Cherilakkudy, Midhun George Thomas, Ann Varghese, Sodiq O Waheed, Anandhu Krishnan, Vincenzo Venditti, Christopher J Schofield, Deyu Li, Christo Z Christov, Tatyana G Karabencheva-Christova
{"title":"Revealing the catalytic mechanism of the Fe(II)/2-oxoglutarate-dependent human epigenetic modifying enzyme ALKBH5.","authors":"Fathima Hameed Cherilakkudy, Midhun George Thomas, Ann Varghese, Sodiq O Waheed, Anandhu Krishnan, Vincenzo Venditti, Christopher J Schofield, Deyu Li, Christo Z Christov, Tatyana G Karabencheva-Christova","doi":"10.1016/j.xcrp.2025.102779","DOIUrl":"10.1016/j.xcrp.2025.102779","url":null,"abstract":"<p><p>ALKBH5 is one of only two known human non-heme Fe(II)/2-oxoglutarate-dependent oxygenases that catalyze the demethylation of N<sup>6</sup>-methyladenine (m<sup>6</sup>A) in single-stranded mRNA, underscoring its role in diverse cancers. Unlike its homolog, the fat mass and obesity-associated protein (FTO), which oxidizes m<sup>6</sup>A to a stable N<sup>6</sup>-hydroxymethyladenine (hm<sup>6</sup>A) intermediate, ALKBH5 demethylates m<sup>6</sup>A, yielding adenine and formaldehyde as products. Here, we integrate molecular dynamics simulations and quantum mechanics/molecular mechanics methods to elucidate ALKBH5's complete catalytic mechanism. Two post-hydroxylation pathways were evaluated: a proton transfer pathway and a Schiff base formation pathway, with the former emerging as the favored mechanism. We identify second-sphere residues Lys132 and Tyr139 as essential contributors to catalysis and demonstrate how Val191 and Tyr133 modulate activity. Dynamic analyses reveal that correlated motions of structural elements such as nucleotide recognition lids NRL1 and NRL2 and increased flexibility of the NRL2 loop in the hm<sup>6</sup>A intermediate may be critical for efficient demethylation.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 8","pages":""},"PeriodicalIF":7.3,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12439684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Subhechchha Paul, Brinthan Kanesalingam, Yan Ma, Julie Villanova, Guillermo Requena, Stanley Chidubem Akpu, Dierk Raabe, Ilenia Battiato, Leora Dresselhaus-Marais
{"title":"A percolating path to green iron.","authors":"Subhechchha Paul, Brinthan Kanesalingam, Yan Ma, Julie Villanova, Guillermo Requena, Stanley Chidubem Akpu, Dierk Raabe, Ilenia Battiato, Leora Dresselhaus-Marais","doi":"10.1016/j.xcrp.2025.102729","DOIUrl":"https://doi.org/10.1016/j.xcrp.2025.102729","url":null,"abstract":"<p><p>About 1.9 gigatons of steel is produced every year, emitting 8% (3.6 gigatons) of global CO<sub>2</sub> in the process. More than 50% of the CO<sub>2</sub> emissions come from a single step of steel production, known as ironmaking. Hydrogen-based direct reduction (HyDR) of iron oxide to iron has emerged as an emission-free ironmaking alternative. However, multiple physical and chemical phenomena ranging from nanometers to meters inside HyDR reactors alter the microstructure and pore networks in iron oxide pellets, in ways that resist gaseous transport of H<sub>2</sub>/H<sub>2</sub>O, slow reaction rates, and disrupt continuous reactor operation. Using synchrotron nano X-ray computed tomography and percolation theory, we quantify the evolution of pores in iron oxide pellets and demonstrate how nanoscale pore connectivity influences micro- and macroscale flow properties such as permeability, diffusivity, and tortuosity. Our modeling framework connects disparate scales and offers opportunities to accelerate HyDR.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 8","pages":"102729"},"PeriodicalIF":7.3,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12374072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144944480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eleftheria Diamanti, Ainhoa Oliden-Sánchez, Daniel Grajales-Hernández, Daniel Andrés-Sanz, Rut Fernández-Marín, Daniel Padro, Jesús Ruíz-Cabello, Ronen Zangi, Fernando López-Gallego
{"title":"The Sabatier principle governs the performance of self-sufficient heterogeneous biocatalysts for redox biotransformations.","authors":"Eleftheria Diamanti, Ainhoa Oliden-Sánchez, Daniel Grajales-Hernández, Daniel Andrés-Sanz, Rut Fernández-Marín, Daniel Padro, Jesús Ruíz-Cabello, Ronen Zangi, Fernando López-Gallego","doi":"10.1016/j.xcrp.2025.102694","DOIUrl":"10.1016/j.xcrp.2025.102694","url":null,"abstract":"<p><p>Self-sufficient heterogeneous biocatalysts (ssHBs), in which enzymes and cofactors are coimmobilized on the same support, provide <i>in situ</i> cofactor regeneration and reduce operating costs. However, the underlying mechanisms remain poorly understood. Here, we present a theoretical model for ssHBs consisting of NAD(P)H-dependent dehydrogenases immobilized on porous agarose-based materials with cofactors coimmobilized through electrostatic interactions via a cationic polymer coating. This model links enzyme activity to cofactor-polymer binding thermodynamics and demonstrates that ssHBs obey the Sabatier principle, where maximum catalytic efficiency is achieved at an intermediate binding strength. Adjustment of pH and ionic strength modulates this interaction, and the resulting activity exhibits the predicted volcano plot. Depending on the reaction conditions, electrostatic complexation is influenced, resulting in the formation of a dense, liquid-like phase inside the particles. Our study directly confirms the Sabatier principle in ssHBs and highlights the crucial role of cofactor binding thermodynamics in optimizing biocatalysis for chemical applications.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 7","pages":"102694"},"PeriodicalIF":7.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12267118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jasmine Cubuk, J Jeremías Incicco, Kathleen B Hall, Alex S Holehouse, Melissa D Stuchell-Brereton, Andrea Soranno
{"title":"The dimerization domain of SARS-CoV-2 nucleocapsid protein is partially disordered and forms a dynamic high-affinity dimer.","authors":"Jasmine Cubuk, J Jeremías Incicco, Kathleen B Hall, Alex S Holehouse, Melissa D Stuchell-Brereton, Andrea Soranno","doi":"10.1016/j.xcrp.2025.102695","DOIUrl":"10.1016/j.xcrp.2025.102695","url":null,"abstract":"<p><p>The SARS-CoV-2 nucleocapsid (N) drives the compaction and packaging of the viral genome. Here, we focused on quantifying the mechanisms that control dimer formation utilizing single-molecule Förster resonance energy transfer to investigate the conformations and energetics of the dimerization domain in the context of the full-length protein. Under monomeric conditions, we observed significantly expanded configurations of the dimerization domain (compared to the folded dimer structure), which is consistent with a dynamic conformational ensemble. The addition of unlabeled protein stabilizes a folded dimer configuration with a high mean transfer efficiency, which is in agreement with predictions based on known structures. Dimerization is characterized by a dissociation constant of ~12 nM at 23°C and is driven by strong enthalpic interactions between the two protein subunits, which originate from the coupled folding and binding. We propose that the retained flexibility of the dimer can affect its interaction with RNA and phase separation propensity.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 7","pages":""},"PeriodicalIF":7.3,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12385586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144944392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Iurii Semenov, Vitalii Kim, Giedre Silkuniene, Andrei G Pakhomov
{"title":"Excitation and polarization of isolated neurons by high-frequency sine waves for temporal interference stimulation.","authors":"Iurii Semenov, Vitalii Kim, Giedre Silkuniene, Andrei G Pakhomov","doi":"10.1016/j.xcrp.2025.102660","DOIUrl":"10.1016/j.xcrp.2025.102660","url":null,"abstract":"<p><p>The capacity of temporal interference (TI) stimulation to target deep brain regions without affecting nearby surface electrodes remains uncertain. Using artifact-free optical recording, we compare excitation patterns and thresholds in hippocampal neurons stimulated by \"pure\" and amplitude-modulated sine waves, representing TI waveforms near electrodes and at the target, respectively. We show that pure 2- and 20-kHz sine waves induce repetitive firing at rates that increase up to 60-90 Hz with stronger electric fields. Beyond this limit, action potentials merge into sustained depolarization, resulting in an excitation block. Modulating the sine waves at 20 Hz aligns firing with amplitude \"beats\" and prevents the excitation block but does not lower excitation thresholds. Thus, off-target TI effects appear unavoidable, though the patterns of neuronal excitation and downstream effects may differ from those at the target. We further analyze membrane charging and relaxation kinetics at nanoscale resolution and confirm an excitation mechanism independent of envelope extraction.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 7","pages":""},"PeriodicalIF":7.3,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12320893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation.","authors":"Anne M Brown, Justin A Lemkul","doi":"10.1016/j.xcrp.2025.102566","DOIUrl":"10.1016/j.xcrp.2025.102566","url":null,"abstract":"<p><p>Computational simulations of biomolecules provide a wealth of information about the thermodynamic landscape of biologically important systems, kinetics of important cellular processes, and the biophysical basis of life. Despite the ubiquity of molecular simulations in biophysical literature, major challenges persist for new practitioners entering the field, and even for experienced computational scientists, in maintaining and distributing their simulation outcomes. Here, we summarize critical obstacles encountered when performing biomolecular simulations and provide best practices for performing simulations that are robust, reproducible, and hypothesis-driven. We also discuss practices that promote improved reproducibility and accessibility using reliable tools and databases.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 5","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"G-quadruplex and i-motif DNA structures form in the promoter of the key innate immune adaptor <i>MYD88</i>.","authors":"Susie Brown, Kennith Swafford, Mason McCrury, Farhana Nasrin, Carlon Q Gragg, Arundhati Chavan, Samrat Roy Choudhury, Jonathan Dickerhoff, Danzhou Yang, Samantha Kendrick","doi":"10.1016/j.xcrp.2025.102560","DOIUrl":"10.1016/j.xcrp.2025.102560","url":null,"abstract":"<p><p>Innate immune responses rely on a critical adaptor protein, MYD88, to bridge extracellular inflammatory signals and transcription factor networks inside the cell. Dysregulation of MYD88 is associated with immunodeficiencies, autoimmunity, and cancer. Here, we identify a stretch of guanine/cytosine-rich DNA in the <i>MYD88</i> promoter capable of adopting stable G-quadruplex and i-Motif structures. Molecular characterization of the i-motif reveals a unique folding pattern with asymmetric lateral loop sizes, a transition pH in line with previously documented i-motifs, and <i>in vitro</i> recognition by the chromatin insulator/transcription factor (CTCF). In exploring the transcriptional role and therapeutic potential of the MYD88 structures, we show the known G-quadruplex ligand, TMPyP4, destabilizes the i-motif, stabilizes the G-quadruplex, and promotes <i>MYD88</i> expression. A ligand, 33353, from the National Cancer Institute (NCI) Diversity Set, also differentially interacts with the two structures yet represses <i>MYD88</i>. This work discovers DNA structures in <i>MYD88</i> that can be pharmacologically leveraged for their ability to control gene expression.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 5","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fanchen Yu, Jinbo Fei, Yi Jia, Tonghui Wang, William F Martin, Junbai Li
{"title":"Chemiosmotic ATP synthesis by minimal protocells.","authors":"Fanchen Yu, Jinbo Fei, Yi Jia, Tonghui Wang, William F Martin, Junbai Li","doi":"10.1016/j.xcrp.2025.102461","DOIUrl":"10.1016/j.xcrp.2025.102461","url":null,"abstract":"<p><p>Energy conservation is crucial to life's origin and evolution. The common ancestor of all cells used ATP synthase to convert proton gradients into ATP. However, pumps generating proton gradients and lipids maintaining proton gradients are not universally conserved across all lineages. A solution to this paradox is that ancestral ATP synthase could harness naturally formed geochemical ion gradients with simpler environmentally provided precursors preceding both proton pumps and biogenic membranes. This runs counter to traditional views that phospholipid bilayers are required to maintain proton gradients. Here, we show that fatty acid membranes can maintain sufficient proton gradients to synthesize ATP by ATP synthase under the steep pH and temperature gradients observed in hydrothermal vent systems. These findings shed substantial light on early membrane bioenergetics, uncovering a functional intermediate in the evolution of chemiosmotic ATP synthesis during protocellular stages postdating the ATP synthase's origin but preceding the advent of enzymatically synthesized cell membranes.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 3","pages":"102461"},"PeriodicalIF":7.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11922820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wenyao Zhang, Christine E Harper, Junsung Lee, Bing Fu, Malissa Ramsukh, Christopher J Hernandez, Peng Chen
{"title":"Transporter excess and clustering facilitate adaptor protein shuttling for bacterial efflux.","authors":"Wenyao Zhang, Christine E Harper, Junsung Lee, Bing Fu, Malissa Ramsukh, Christopher J Hernandez, Peng Chen","doi":"10.1016/j.xcrp.2025.102441","DOIUrl":"10.1016/j.xcrp.2025.102441","url":null,"abstract":"<p><p>Multidrug efflux pumps confer not only antibiotic resistance to bacteria but also cell proliferation. In gram-negative bacteria, the ATP-binding cassette (ABC)-family transporter MacB, the adaptor protein MacA, and the outer membrane protein TolC form the MacA<sub>6</sub>:MacB<sub>2</sub>:TolC<sub>3</sub> assembly to extrude antibiotics and virulence factors. Here, using quantitative single-molecule single-cell imaging, we uncover that, in <i>E. coli</i> cells, there is a large excess of MacB (and TolC) driving the limiting adaptor protein MacA mostly into the MacAB-TolC assembly. Moreover, the excess MacB transporters can dynamically cluster around the assembly, and MacA can dynamically disassemble from the MacAB-TolC assembly, leading to an adaptor protein shuttling mechanism for efficient substrate sequestration from the periplasm toward efflux. We further show that both MacB clustering and MacAB-TolC assembly can be perturbed chemically or physically via microfluidics-based extrusion loading for compromised antibiotic tolerance. These insights may provide opportunities for countering the activities of multidrug efflux systems for antimicrobial treatments.</p>","PeriodicalId":9703,"journal":{"name":"Cell Reports Physical Science","volume":"6 2","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}