Biophysics

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

Structural Insights of SARS-CoV-2 Spike Protein from Delta and Omicron Variants

1. Ali Sadek
2. David Zaha
3. Mahmoud Salama Ahmed

Reviewed by ScreenIT

Post-Translational Modifications Optimize the Ability of SARS-CoV-2 Spike for Effective Interaction with Host Cell Receptors

1. Karan Kapoor
2. Tianle Chen
3. Emad Tajkhorshid

Reviewed by ScreenIT

Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling

1. Marco Zaccaria
2. Luigi Genovese
3. Brigitte E. Lawhorn
4. William Dawson
5. Andrew S. Joyal
6. Jingqing Hu
7. Patrick Autissier
8. Takahito Nakajima
9. Welkin E. Johnson
10. Ismael Fofana
11. Michael Farzan
12. Babak Momeni

Reviewed by ScreenIT