Biophysics

Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA)

1. Thomas GW Graham
2. John Joseph Ferrie
3. Gina M Dailey
4. Robert Tjian
5. Xavier Darzacq

• Curated by eLife

  Evaluation Summary:

  This work develops a new method to probe protein-protein interactions using proximity-assisted photoactivation, in which a receiver fluorophore (longer wavelength) can be photoactivated by the excitation of a nearby sender fluorophore (shorter wavelength). This new method is validated through in-depth characterization, comparison with FRET, and application to known systems of protein-protein interactions. While the new method bears the potential to expand the tool kit for probing protein-protein interactions, further characterizations of its photoactivation properties and comparisons with existing methods would be needed to inform researchers interested to apply this method to their own systems.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Cells use molecular working memory to navigate in changing chemoattractant fields

1. Akhilesh Nandan
2. Abhishek Das
3. Robert Lott
4. Aneta Koseska

• Curated by eLife

  Evaluation Summary:

  This paper addresses how cells can robustly maintain direction during movement by ignoring noise in concentration gradients while also being able to adapt to new signals in those gradients. The authors study this tension in EGFR signaling by postulating a form of cellular memory in a theoretical framework based on dynamical systems and bifurcation theory. The authors also carry out experiments that raise interesting unresolved questions. This paper will be of interest to scientists of all stripes working on cell motility and for theorists who take a dynamical systems view of biological phenomena.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Deciphering a hexameric protein complex with Angstrom optical resolution

1. Hisham Mazal
2. Franz-Ferdinand Wieser
3. Vahid Sandoghdar

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to the structural biology community and people working on cryogenic fluorescence microscopy. This paper is a clear step forward in the use of single-molecule localization microscopy at angstrom resolution, thanks to low-temperature polarized super-resolution imaging and advanced data processing algorithms.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Contributions of the N-terminal intrinsically disordered region of the SARS-CoV-2 nucleocapsid protein to RNA-induced phase separation

1. Milan Zachrdla
2. Adriana Savastano
3. Alain Ibáñez de Opakua
4. Maria-Sol Cima-Omori
5. Markus Zweckstetter

Reviewed by ScreenIT

A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues

1. Chen Chen
2. Veda Sheersh Boorla
3. Ratul Chowdhury
4. Ruth H. Nissly
5. Abhinay Gontu
6. Shubhada K. Chothe
7. Lindsey LaBella
8. Padmaja Jakka
9. Santhamani Ramasamy
10. Kurt J. Vandegrift
11. Meera Surendran Nair
12. Suresh V. Kuchipudi
13. Costas D. Maranas

Reviewed by ScreenIT

Stability and expression of SARS-CoV-2 spike-protein mutations

1. Kristoffer T. Bæk
2. Rukmankesh Mehra
3. Kasper P. Kepp

Reviewed by ScreenIT

Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction

1. Jakub Pospíšil
2. Tomáš Lukeš
3. Justin Bendesky
4. Karel Fliegel
5. Kathrin Spendier
6. Guy M. Hagen

Reviewed by GigaScience

Structural basis of Omicron immune evasion: A comparative computational study of Spike protein-Antibody interaction

1. Darshan Contractor
2. Christoph Globisch
3. Shiv Swaroop
4. Alok Jain

Reviewed by ScreenIT

Hydrodynamic model of fish orientation in a channel flow

1. Maurizio Porfiri
2. Peng Zhang
3. Sean D Peterson

• Curated by eLife

  Evaluation Summary:

  The authors address the problem of fish orienting against the mean flow when deprived of visual cues. They study a simple model of swimming dipole and argue that in the absence of flow-sensing feedback, fluid-structure coupling alone is sufficient to generate upstream orienting behavior, above a given flow speed. A comparison with the experimental literature on fish behavior is attempted.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K+ channel TMEM175

1. SeCheol Oh
2. Fabrizio Marinelli
3. Wenchang Zhou
4. Jooyeon Lee
5. Ho Jeong Choi
6. Min Kim
7. José D Faraldo-Gómez
8. Richard K Hite

• Curated by eLife

  Evaluation Summary:

  This manuscript explores the mechanisms of permeation and selectivity in the unusual potassium-selective ion channel TMEM175, which lacks a canonical selectivity filter. The study is led by molecular dynamics simulations and free energy calculations, complemented by a cryoEM analysis and electrophysiological recordings. The authors propose a novel, single ion-based mechanism of permeation, together with a partial dehydration-driven selectivity mechanism. While in principle exciting and informative, most of the conclusions in the manuscript are based on small differences in calculated values for which an estimation of the uncertainty is lacking, and on the usage of a single physics-based model. This study will appeal to readers interested in the structure and function of ion channels and in molecular mechanisms of ion translocation. It would be strengthened by a thorough exploration of alternative hypotheses.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife