Biophysics

AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network

1. Alisia Fadini
2. Minhuan Li
3. Airlie J. McCoy
4. Thomas C. Terwilliger
5. Randy J. Read
6. Doeke Hekstra
7. Mohammed AlQuraishi

Reviewed by PREreview

A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales

1. Alice Gros
2. Jules Vanaret
3. Valentin Dunsing-Eichenauer
4. Agathe Rostan
5. Philippe Roudot
6. Pierre-François Lenne
7. Léo Guignard
8. Sham Tlili

• Curated by eLife

  eLife Assessment

  This important study introduces a powerful imaging approach that enables deep-tissue visualization in gastruloids using two-photon microscopy, combined with spectral imaging and unmixing to achieve four-color 3D image acquisition. The evidence is compelling that many of the established methods are very helpful (e.g., registration, corrections, signal normalisation, lazy loading bioimage visualisation, spectral decomposition analysis), facilitate the development of quantitative research, and would be of interest to the wider scientific community.

Reviewed by eLife

Atomistic simulation of voltage activation of a truncated BK channel

1. Zhiguang Jia
2. Jianhan Chen

• Curated by eLife

  eLife Assessment

  This valuable 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. The findings, including movement of specific charged residues, combined with the degree to which these movements are coupled to pore movements, provide a solid basis for understanding voltage-gating mechanisms in this class of channels. This paper will likely be of interest to ion channel biologists and biophysicists focused on voltage-dependent channel gating mechanisms.

Reviewed by eLife

Noninvasive ultrasound targeted modulation of calcium influx in splenic immunocytes potentiates antineoplastic immunity attenuating hepatocellular carcinoma proliferation

1. Wei Dong
2. Guihu Wang
3. Senyang Li
4. Yichao Chai
5. Qian Wang
6. Yucheng Li
7. Qiaoman Fei
8. Yujin Zong
9. Jing Geng
10. Pengfei Liu
11. Zongfang Li

• Curated by eLife

  eLife Assessment

  This valuable study presents an innovative noninvasive immunotherapeutic strategy for hepatocellular carcinoma by combining ultrasound stimulation with calcium-loaded nanodroplets to activate splenic immune responses. The authors provide solid preclinical data, including single-cell transcriptomic analyses and evidence of tumor growth suppression, supported by a creative and well-executed methodology. Further validation of the calcium signaling mechanisms and assessment of long-term safety will strengthen the translational potential of this approach. The work will be of broad interest to researchers in oncology, immunotherapy, and biomedical engineering.

Reviewed by eLife

High-resolution cryo-EM structures of small protein–ligand complexes near the theoretical size limit

1. Kunwoong Park
2. Youngki Yoo
3. Hyunbum Jeon
4. Kiju Choi
5. Eunju Kwon
6. Hyun-Ho Lim
7. Dong Young Kim
8. Kyoung Tai No

Reviewed by PREreview

Distinct energetic blueprints diversify function of conserved protein folds

1. Malcolm L. Wells
2. Chenlin Lu
3. Daniel Sultanov
4. Kyle C. Weber
5. Erin Ahern
6. Zhen Gong
7. Ethan Chen
8. Anum Glasgow

Reviewed by PREreview

Toward stable replication of genomic information in pools of RNA molecules

1. Ludwig Burger
2. Ulrich Gerland

• Curated by eLife

  eLife Assessment

  This important theoretical study examines the possibility of encoding genomic information in a collective of short overlapping strands (e.g., the Virtual Circular Genome (VCG) model). The study presents convincing theoretical arguments, simulations and comparisons to experimental data to point at potential features and limitations of such distributed collective encoding of information. The work should be of relevance to colleagues interested in molecular information processing and to those interested in pre-Central Dogma or prebiotic models of self-replication.

Reviewed by eLife

Antigen flexibility supports the avidity of hemagglutinin-specific antibodies at low antigen densities

1. Ananya Benegal
2. Yuanyuan He
3. Katilyn Ho
4. Giselle Groff
5. Zijian Guo
6. Michael D. Vahey

Reviewed by Review Commons

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

1. Vikram Dalal
2. Brandon K 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.

Reviewed by eLife

Coral anthozoan-specific opsins employ a novel chloride counterion for spectral tuning

1. Yusuke Sakai
2. Saumik Sen
3. Tomohiro Sugihara
4. Yukiya Kakeyama
5. Makoto Iwasaki
6. Gebhard FX Schertler
7. Xavier Deupi
8. Mitsumasa Koyanagi
9. Akihisa Terakita

• Curated by eLife

  eLife Assessment

  The authors provide compelling evidence that a chloride ion stabilizes the protonated Schiff base chromophore linkage in the animal rhodopsin Antho2a. This important finding is novel and of major interest to a broad audience, including optogenetics researchers, protein engineers, spectroscopists, and environmental biologists. The study combines state-of-the-art research methods, such as spectroscopic and mutational analyses, which are complemented by QM/MM calculations, and was further improved based on the comments from the reviewers.

Reviewed by eLife