Biophysics

Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes

1. Vikram Dalal
2. Brandon T Tan
3. Hanrui Xu
4. Wayland WL Cheng

• Curated by eLife

  eLife Assessment

  The reported cryo-EM imaging of a pentameric ligand-gated ion channel in liposomes as opposed to nanodiscs has both broad implications and contributes valuable methodological advances to the structural investigation of membrane receptors. The comparison of structures assigned to distinct functional states in liposomes versus nanodiscs is convincing, and will aid membrane protein structural biologists in selection of functionally relevant membrane reconstitution environments. This work could be strengthened by a more quantitative presentation of the pore dimension profile leading to the proposed 9' desensitization gate with discussion of the additional apparent constriction at 2' in the desensitized structure, and by a more thorough description of the biochemistry methods for which core parts are not described and/or discussed in sufficient detail.

Reviewed by eLife

Transcriptional coregulation in cis around a contact insulation site revealed by single-molecule microscopy

1. Maciej A Kerlin
2. Ilham Aboulfath-Ladid
3. Julia Roensch
4. Chloé Jaubert
5. Aude Battistella
6. Kyra JE Borgman
7. Antoine Coulon

• Curated by eLife

  eLife Assessment

  This important study combines an innovative experimental approach with mathematical modeling to demonstrate that genes separated by strong topological boundaries can exhibit coordinated transcriptional bursting, providing new insights into how regulatory information is transmitted across the genome. The evidence is solid within the studied locus, but the interpretation and generality of the findings would be strengthened by additional validation using simulated data and broader application beyond a single genomic region. This work will be of interest to cell biologists and biophysicists working on transcription and chromatin.

Reviewed by eLife

Spiral-eyes: A soft active matter model of in vivo corneal epithelial cell migration

1. Kaja Kostanjevec
2. Rastko Sknepnek
3. Jon Martin Collinson
4. Silke Henkes

• Curated by eLife

  eLife Assessment

  This useful study describes a physical mechanism for the emergence of spiral patterns in the outer epithelial layer of the mammalian cornea independent of pre-patterning or guidance cues, using an agent-based model of self-propelled particles with alignment. The model is well constructed, however the central premise of the manuscript, that the spiral patterning of epithelial corneal cells occurs without guidance cues, is incomplete and not fully supported. Several significant questions remain unanswered, such as the role of the corneal curvature or the importance of topological defects. Furthermore, comparison between the model and data are qualitative at best for the moment.

Reviewed by eLife, preLights

Structural mechanisms of PIP2 activation and SEA0400 inhibition in human cardiac sodium-calcium exchanger NCX1

1. Jing Xue
2. Weizhong Zeng
3. Scott John
4. Nicole Attiq
5. Michela Ottolia
6. Youxing Jiang

• Curated by eLife

  eLife Assessment

  Cardiac Ca2+/Na+ exchange is mediated by the NCX1 antiporter, whose activity is tightly regulated. This important manuscript describes the structural basis of activation by the lipid DiC8-PIP2 and inhibition by binding of a small molecule to NCX1. These results provide convincing insights into NCX1 regulation and the structural basis of cellular Ca2+ signaling.

Reviewed by eLife

Multiphase separation in postsynaptic density regulated by membrane geometry via interaction valency and volume

1. Risa Yamada
2. Giovanni B Brandani
3. Shoji Takada

• Curated by eLife

  eLife Assessment

  This valuable study provides a conceptual advance in our understanding of how membrane geometry modulates the balance between specific and non-specific molecular interactions, reversing multiphase morphologies in postsynaptic protein assemblies. Using a mesoscale simulation framework grounded in experimental binding affinities, the authors successfully recapitulate key experimental observations in both solution and membrane-associated systems, providing novel mechanistic insight into how spatial constraints regulate postsynaptic condensate organization. While the evidence supporting the conclusions is largely solid, a few aspects of the analysis and model proposed remain incomplete.

Reviewed by eLife

Domain Coupling in Allosteric Regulation of SthK Measured Using Time-Resolved Transition Metal Ion FRET

1. Pierce Eggan
2. Sharona E. Gordon
3. William N. Zagotta

• Curated by eLife

  eLife Assessment

  This useful work employs transition-metal FRET (tmFRET) to study the cyclic nucleotide binding domain (CNBD) of a bacterial ion channel. The authors employ lifetime measurements of fluorescence to extend their own prior study and observe distance changes within the CNBD domains of a full-length channel; they base these measurements on changes in lifetimes due to tmFRET between a metal at an introduced chelator site and a fluorescent non-canonical amino acid at another site within the channel sequence. This allows the authors to show that coupling of the CNBDs to the rest of the channel stabilizes the CNBDs in their active state relative to an isolated CNBD construct. The data are compelling and of high quality, and support the authors' conclusions.

Reviewed by eLife

Protein Language Model Identifies Disordered, Conserved Motifs Driving Phase Separation

1. Yumeng Zhang
2. Jared Zheng
3. Bin Zhang

• Curated by eLife

  eLife Assessment

  This valuable study presents an analysis of evolutionary conservation in intrinsically disordered regions, identified as key drivers of phase separation, leveraging a protein language model. The strength of evidence is potentially compelling, but a clearer justification of the methods and analyses is needed to fully support the main claims.

Reviewed by eLife

Structural and dynamic impacts of single-atom disruptions to guide RNA interactions within the recognition lobe of Geobacillus stearothermophilus Cas9

1. Helen B Belato
2. Alexa L Knight
3. Alexandra M D'Ordine
4. Chinmai Pindi
5. Zhiqiang Fan
6. Jinping Luo
7. Giulia Palermo
8. Gerwald Jogl
9. George P Lisi

• Curated by eLife

  eLife Assessment

  This study offers valuable insights into the conformational dynamics of the nucleic acid recognition lobe of GeoCas9, a thermophilic Cas9 from Geobacillus stearothermophilus. The authors investigate the influence of local dynamics and allosteric regulation on guide RNA binding affinity and DNA cleavage specificity through molecular dynamics simulations, advanced NMR techniques, RNA binding studies, and mutagenesis. While the mutations studied do not lead to significant changes in GeoCas9 cleavage activity, the study provides convincing evidence for the role of allosteric mechanisms and interdomain communication in Cas9 enzymes, and will be of great interest to biochemists and biophysicists exploring these complex systems.

Reviewed by eLife

Raman flow cytometry using time delay integration

1. Matthew Lindley
2. Toshiki Kubo
3. Stéphanie Devineau
4. Menglu Li
5. Jing Qiao
6. Takuya Yashiro
7. Shiroh Iwanaga
8. Kazuyo Moro
9. Katsumasa Fujita

Reviewed by Arcadia Science

Atomistic Simulation of Voltage Activation of a Truncated BK Channel

1. Zhiguang Jia
2. Jianhan Chen

• Curated by eLife

  eLife Assessment

  This study addresses the structural basis of voltage-activation of BK channels using atomistic simulations of several microseconds, to assess conformational changes that underlie both voltage-sensing and gating of the pore. Simulated effects of voltage on the movement of charged amino acids appear solid as they are generally consistent qualitatively and quantitatively with previous experimental and structural results, providing a potentially valuable way to calculate the contribution of individual charges to voltage-sensitivity. Simulations of conformational changes and interactions associated with channel opening and K+ conduction are likely incomplete owing to the timescale of the simulation and theoretical limitations in simulating K+ and water movement, but nonetheless provide helpful initial predictions and a framework for future improvement. This paper will likely be of interest to ion channel biologists and biophysicists focused on voltage-dependent channel gating mechanisms.

Reviewed by eLife