Biophysics

Pulsed laser lensing for phase modulation in electron microscopy

1. Daniel X. Du
2. Adam C. Bartnik
3. Cameron J. R. Duncan
4. Usama Choudhry
5. Tanya Tabachnik
6. Chaim Sallah
7. Yuki Ogawa
8. Ebrahim Najafi
9. Ding-Shyue Yang
10. Jared M. Maxson
11. Anthony W. P. Fitzpatrick

• Curated by eLife

  eLife Assessment

  This important study introduces a pulsed laser phase plate that generates stable phase contrast in electron microscopy, offering a practical alternative to continuous-wave designs that suffer from optical instabilities and diffraction artifacts. The experimental results demonstrate a controllable and stable electron phase shift, and the evidence supporting the feasibility of this approach for phase-contrast electron microscopy is convincing. Clarifying the agreement between experiment and theory and further elaborating on possible applications would strengthen the manuscript.

Reviewed by eLife

Enhanced bacterial chemotaxis in confined microchannels: Optimal performance in lane widths matching circular swimming radius

1. Caijuan Yue
2. Chi Zhang
3. Rongjing Zhang
4. Junhua Yuan

• Curated by eLife

  eLife Assessment

  This important work examines the effects of side-wall confinement on chemotaxis of swimming bacteria in a shallow microfluidic channel. The authors present convincing experimental evidence, combined with geometric analysis and numerical simulations of simplified models, showing that chemotaxis is enhanced when the distance between the side walls is comparable to the intrinsic radius of chiral circular swimming near open surfaces. This study should be of interest to scientists specializing in bacteria-surface interactions.

Reviewed by eLife

Unraveling the Molecular Mechanisms of ABHD5 Membrane Targeting

1. Amit Kumar
2. Matthew Sanders
3. Huamei Zhang
4. Li Zhou
5. Shahnaz Parveen
6. Miriam C Jensen
7. Thomas JD Jørgensen
8. Christopher V Kelly
9. James G Granneman
10. Yu-ming M Huang

• Curated by eLife

  eLife Assessment

  This study makes a valuable contribution to our understanding of how the lipase regulator ABHD5 may control lipase activity through interactions with lipid droplets and cellular membranes. By combining multiscale molecular dynamics simulations with experimental approaches, the authors provide novel molecular insights into this membrane-protein interaction and present evidence suggesting that the regulatory mechanism depends on protein conformational changes and local membrane remodeling. While much of the evidence supporting the main conclusions is convincing, several aspects of the analysis, interpretation, and discussion remain incomplete. Overall, this work will be of interest to structural and molecular biologists working on lipid metabolism and membrane biophysics.

Reviewed by eLife

Transforming a Fragile Protein Helix into an Ultrastable Scaffold via a Hierarchical AI and Chemistry Framework

1. Jun Qiu
2. Guojin Tang
3. Tianfu Feng
4. Bin Zheng
5. Yuanhao Liu
6. Peng Zheng

• Curated by eLife

  eLife Assessment

  This valuable work describes a computational and experimental workflow that turns a moderately stable α-helical bundle into a very stable fold. The authors advance our understanding of α-helix stabilization and provide a convenient framework with implications for the protein design field. The main claims are supported by convincing evidence through sound and well-validated methods, yet further characterization would strengthen specific conclusions for the design of mechanically, thermally, and chemically stable α-helical bundles.

Reviewed by eLife

Conformational Changes of the ABC Transporter BmrA Depend on Membrane Curvature

1. Alicia Damm
2. Kemil Belhadji
3. Raj Kumar Sadhu
4. Su-Jin Paik
5. Aurélie Di-Cicco
6. John Manzi
7. Michele Castellana
8. Raju Regmi
9. Emmanuel Margeat
10. Maxime Dahan
11. Pierre Sens
12. Daniel Lévy
13. Patricia Bassereau

• Curated by eLife

  eLife Assessment

  This valuable study investigates whether the activity of an ABC transporter, BmrA, can be modulated by mechanical stimuli. The authors develop a single-molecule experimental system to address this question, although aspects of the methodological framework are incomplete. This work also develops a convincing theoretical model to explain the effect of membrane curvature on the conformational transitions observed during the activity cycle of this membrane protein. This study is of interest to the fields of membrane biophysics and membrane transport.

Reviewed by eLife

In silico design and validation of high-affinity RNA aptamers for SARS-CoV-2 comparable to neutralizing antibodies

1. Yanqing Yang
2. Lulu Qiao
3. Yangwei Jiang
4. Zhiye Wang
5. Dong Zhang
6. Damiano Buratto
7. Liquan Huang
8. Ruhong Zhou

• Curated by eLife

  eLife Assessment

  This valuable study introduces CAAMO, a computational framework that combines structure prediction, in silico mutagenesis, molecular simulations, and energy calculations to design RNA aptamers with improved binding affinity. The computational methodology is solid, demonstrating strong theoretical foundations and systematic integration of multiple prediction techniques. However, the experimental validation is incomplete, with methodological weaknesses that limit the strength of support for the computational predictions.

Reviewed by eLife

Invasive cancer cells soften collagen networks and disrupt stress-stiffening via volume exclusion, contractility and adhesion

1. Irène Nagle
2. Margherita Tavasso
3. Ankur D. Bordoloi
4. Iain A.A. Muntz
5. Gijsje H. Koenderink
6. Pouyan E. Boukany

Reviewed by PREreview

Stall force measurement of the kinesin-3 motor KIF1A using a programmable DNA origami nanospring

1. Nobumichi Takamatsu
2. Hiroko Furumoto
3. Takayuki Ariga
4. Mitsuhiro Iwaki
5. Kumiko Hayashi

• Curated by eLife

  eLife Assessment

  Optical tweezers have been instrumental to the determination of mechanical parameters of molecular motors. This study by Takamatsu et al. reports key mechanical parameters of kinesin KIF1A using fluorescence microscopy, wherein the motor is tethered to a DNA nanospring, without the use of an optical trapping apparatus, which represents an exciting development. The approach and the findings reported change current thinking about KIF1A‑mediated transport, with potential implications for understanding human disease. The findings are important and the strength of the evidence is compelling.

Reviewed by eLife

Active regulation of the epidermal growth factor receptor by the membrane bilayer

1. Shwetha Srinivasan
2. Xingcheng Lin
3. Xuyan Chen
4. Raju Regmi
5. Bin Zhang
6. Gabriela S Schlau-Cohen

• Curated by eLife

  eLife Assessment

  The authors describe an interesting approach to studying the dynamics and function of membrane proteins in different lipid environments. The fundamental findings have theoretical and practical implications beyond the study of EGFR to all membrane signalling proteins. The evidence supporting the conclusions is compelling, based on the use of a nanodisk system to study membrane proteins in vitro, combined with state-of-the-art single-molecule FRET. The work will be of broad interest to cell biologists and biochemists.

Reviewed by eLife

Cluster size determines internal structure of transcription factories in human cells

1. Massimiliano Semeraro
2. Giuseppe Negro
3. Giada Forte
4. Antonio Suma
5. Giuseppe Gonnella
6. Peter R Cook
7. Davide Marenduzzo

• Curated by eLife

  eLife Assessment

  This is a valuable polymer model that provides insight into the origin of macromolecular mixed and demixed states within transcription clusters. The simulations are well performed and clearly presented in the context of existing experimental datasets. This compelling study will be of interest to those studying gene expression in the context of chromatin.

Reviewed by eLife