Biophysics

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

Identification of electroporation sites in the complex lipid organization of the plasma membrane

1. Lea Rems
2. Xinru Tang
3. Fangwei Zhao
4. Sergio Pérez-Conesa
5. Ilaria Testa
6. Lucie Delemotte

• Curated by eLife

  Evaluation Summary:

  Using coarse-grained simulations, machine learning analysis and Bayesian inference modeling, the authors explored features that dictate the location and kinetics of electroporation in complex lipid membranes. The resulting understanding and modeling will lead to an effective multi-scale approach for predicting the kinetics of electroporation and guiding the design of experimental protocols for inducing electroporation in broad applications such as tumor treatment, gene therapy and vaccination against cancer.

  (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

Structure of the 5’ untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune system via the human oligoadenylate synthase 1 ^†

1. Emmanuelle Bignon
2. Tom Miclot
3. Alessio Terenzi
4. Giampaolo Barone
5. Antonio Monari

Reviewed by ScreenIT

Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion

1. Joseph H. Lubin
2. Christopher Markosian
3. D. Balamurugan
4. Minh T. Ma
5. Chih-Hsiung Chen
6. Dongfang Liu
7. Renata Pasqualini
8. Wadih Arap
9. Stephen K. Burley
10. Sagar D. Khare

Reviewed by ScreenIT

The Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614 Mutant: Conformational Plasticity and Frustration-Driven Allostery as Energetic Drivers of Highly Transmissible Spike Variant

1. Gennady Verkhivker
2. Steve Agajanian
3. Ryan Kassab
4. Keerthi Krishnan

Reviewed by ScreenIT