Biophysics

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

Speed variations of bacterial replisomes

1. Deepak Bhat
2. Samuel Hauf
3. Charles Plessy
4. Yohei Yokobayashi
5. Simone Pigolotti

• Curated by eLife

  Evaluation Summary:

  This manuscript uses experiments and theory to characterize the variations in replication speed of E.coli throughout cell cycle. The authors developed a theory to account for fluctuations in the replication velocity as well as a cell-cycle-dependent speed, and by using sequencing data they analyzed the variations in the speed for E. coli. They found that replication speed increases with increasing temperature, and also observed oscillatory patterns in the speed of the replisome, consistent with variations in mutation rate (accuracy) across the genome. These observations suggest a tradeoff between replication speed and accuracy in E.coli.

  (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 agreed to share their name with the authors.)

Reviewed by eLife

High-throughput molecular dynamics-based alchemical free energy calculations for predicting the binding free energy change associated with the common mutations in the spike receptor-binding domain of SARS-CoV-2

1. Rajendra Bhadane
2. Outi M. H. Salo-Ahen

Reviewed by ScreenIT

Cryo-EM structure of the human somatostatin receptor 2 complex with its agonist somatostatin delineates the ligand-binding specificity

1. Yunseok Heo
2. Eojin Yoon
3. Ye-Eun Jeon
4. Ji-Hye Yun
5. Naito Ishimoto
6. Hyeonuk Woo
7. Sam-Yong Park
8. Ji-Joon Song
9. Weontae Lee

• Curated by eLife

  Evaluation Summary:

  This manuscript reports the cryoEM structure of somatostatin receptor 2 (SSTR2) bound to its agonist SST-14 and a heterotrimeric G protein. In addition to presenting the structure itself, the authors include discussion and analysis of ligand recognition and subtype specificity, guided by AlphaFold2 modeling of other somatostatin receptor subtypes. Additional functional data to test the importance of proposed receptor-ligand contacts will be critical to understanding which of the features directly contribute to subtype specificity. Because somatostatin signaling is important in endocrine biology, including in diseases such as acromegaly and some cancers, the work should in principle be of interest to a broad audience.

  (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

In silico screening and testing of FDA approved small molecules to block SARS-CoV-2 entry to the host cell by inhibiting Spike protein cleavage

1. E. Sila Ozdemir
2. Hillary H. Le
3. Adem Yildirim
4. Srivathsan V. Ranganathan

Reviewed by ScreenIT

Characterization of Hydrophobic Interactions of SARS-CoV-2 and MERS-CoV Spike Protein Fusion Peptides Using Single Molecule Force Measurements

1. Cindy Qiu
2. Gary R. Whittaker
3. Samuel H. Gellman
4. Susan Daniel
5. Nicholas L. Abbott

Reviewed by ScreenIT