Biophysics

Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability

1. Gennady Verkhivker

Reviewed by ScreenIT

Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization

1. Matthew C. Chan
2. Kui. K. Chan
3. Erik Procko
4. Diwakar Shukla

Reviewed by ScreenIT

Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant

1. Gennady Verkhivker

Reviewed by ScreenIT

Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family

1. Karthik Ramanadane
2. Monique S Straub
3. Raimund Dutzler
4. Cristina Manatschal

• Curated by eLife

  Evaluation Summary:
  This work elegantly fuses cryo-EM, x-ray crystallography, and in vitro transport experiments to describe the structural basis for functional diversity in the SLC11/NRAMP family of membrane transporters. This work identifies factors responsible for selectivity of classical NRAMPS for transition metal ions (Fe, Mn) and the NRMT clade for alkali metal ion (Mg). Although selectivity is much discussed in transport of divalent metal ions, this is an outstanding example of a study that gets to the bottom of the structural determinants governing this behavior.

  (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 and Reviewer #2 agreed to share their names with the authors.)

Reviewed by eLife

Epithelial-to-mesenchymal transition proceeds through directional destabilization of multidimensional attractor

1. Weikang Wang
2. Dante Poe
3. Yaxuan Yang
4. Thomas Hyatt
5. Jianhua Xing

• Curated by eLife

  Evaluation Summary:

  This is a multifaceted study of the epithelial to mesenchymal transition (EMT) in live cells. EMT is relevant for cancer, development, and wound healing. The authors were able to discern two possible cell transition path categories without multi-color labeling or other advanced experimental approaches, which could be impactful. The study draws on a wide range of experimental, data science, and modelling tools and techniques.

  (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, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Modeling the dynamics of within-host viral infection and evolution predicts quasispecies distributions and phase boundaries separating distinct classes of infections

1. Greyson R. Lewis
2. Wallace F. Marshall
3. Barbara A. Jones

Reviewed by ScreenIT

How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition

1. Kerry Marie Goodman
2. Phinikoula S Katsamba
3. Rotem Rubinstein
4. Göran Ahlsén
5. Fabiana Bahna
6. Seetha Mannepalli
7. Hanbin Dan
8. Rosemary V Sampogna
9. Lawrence Shapiro
10. Barry Honig

• Curated by eLife

  Evaluation Summary:

  This paper is of interest to cell biologists, biochemists and biophysicists interested in how adhesion and signaling proteins at the cell surface help cells (and especially neurons) interact and perform self/non-self-recognition and self-avoidance. The authors provide the first extensive biophysical dataset examining a large subset of potential trans (across two cells) and cis (on the surface of the same cell) interactions between different isoforms of the ~60 clustered protocadherins (cPcdhs). There data show that all tested trans interactions are strictly homophilic and that not all possible cis interactions are equivalent. These results provide additional layers of complexity and constraints on how this protein family can provide neurons with the ability to perform self-recognition and self-avoidance.

  (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

Computational analysis of the effect of SARS-CoV-2 variant Omicron Spike protein mutations on dynamics, ACE2 binding and propensity for immune escape

1. Natalia Teruel
2. Matthew Crown
3. Matthew Bashton
4. Rafael Najmanovich

Reviewed by ScreenIT

Simulation of the omicron variant of SARS-CoV-2 shows broad antibody escape, weakened ACE2 binding, and modest increase in furin binding

1. M. Zaki Jawaid
2. A. Baidya
3. R. Mahboubi-Ardakani
4. Richard L. Davis
5. Daniel L. Cox

Reviewed by ScreenIT

Scanning the RBD-ACE2 molecular interactions in Omicron variant

1. Soumya Lipsa Rath
2. Aditya K. Padhi
3. Nabanita Mandal

Reviewed by ScreenIT