Biophysics

Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel

1. Cathrine Bergh
2. Stephanie A Heusser
3. Rebecca Howard
4. Erik Lindahl

• Curated by eLife

  Evaluation Summary:

  This article presents molecular dynamics simulations of the pH-gated pentameric ion channel GLIC, which has been the subject of many structural and functional studies. GLIC can be considered as a model system for pentameric ligand-gated ion channels that are responsible for fast chemical-electrical communication between cells in animals. The findings include the solution of open- and closed-like channel forms, intermediates and a "pre-desensitised" state. The approach reproduces modulation by pH and mutation, surprisingly finding a predominance of closed channels, despite activating conditions, and suggest a role for asymmetry in channel gating. Overall, the sampling of channel dynamics is significant and the description of state interconversions sheds new light on pLGIC mechanisms.

  (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

Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling

1. Gennady M. Verkhivker
2. Steve Agajanian
3. Deniz Yasar Oztas
4. Grace Gupta

Reviewed by ScreenIT

Sequence of the SARS-CoV-2 Spike Transmembrane Domain Encodes Conformational Dynamics

1. Sahil Lall
2. Padmanabhan Balaram
3. M. K. Mathew
4. Shachi Gosavi

Reviewed by ScreenIT

SARS-CoV-2 Variants Are Selecting for Spike Protein Mutations That Increase Protein Stability

1. David Shorthouse
2. Benjamin A. Hall

Reviewed by preLights, ScreenIT

Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes

1. Taniya Bhardwaj
2. Kundlik Gadhave
3. Shivani K. Kapuganti
4. Prateek Kumar
5. Zacharias Faidon Brotzakis
6. Kumar Udit Saumya
7. Namyashree Nayak
8. Ankur Kumar
9. Richa Joshi
10. Bodhidipra Mukherjee
11. Aparna Bhardwaj
12. Krishan Gopal Thakur
13. Neha Garg
14. Michele Vendruscolo
15. Rajanish Giri

Reviewed by ScreenIT

Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium

1. Aujan Mehregan
2. Sergio Pérez-Conesa
3. Yuxuan Zhuang
4. Ahmad Elbahnsi
5. Diletta Pasini
6. Erik Lindahl
7. Rebecca J. Howard
8. Chris Ulens
9. Lucie Delemotte

Reviewed by ScreenIT

Single-Molecule Dynamics of SARS-CoV-2 5’ Cap Recognition by Human eIF4F

1. Hea Jin Hong
2. Matthew G. Guevara
3. Eric Lin
4. Seán E. O’Leary

Reviewed by Rapid Reviews Infectious Diseases, ScreenIT

Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants

1. Vaibhav Upadhyay
2. Alexandra Lucas
3. Sudipta Panja
4. Ryuki Miyauchi
5. Krishna M.G. Mallela

Reviewed by ScreenIT

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

1. Alexander J. Pak
2. Alvin Yu
3. Zunlong Ke
4. John A. G. Briggs
5. Gregory A. Voth

Reviewed by ScreenIT

Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses

1. Tom Miclot
2. Cécilia Hognon
3. Emmanuelle Bignon
4. Alessio Terenzi
5. Marco Marazzi
6. Giampaolo Barone
7. Antonio Monari

Reviewed by ScreenIT