Biophysics

Sampling alternative conformational states of transporters and receptors with AlphaFold2

1. Diego del Alamo
2. Davide Sala
3. Hassane S Mchaourab
4. Jens Meiler

• Curated by eLife

  Evaluation Summary:

  In this work, del Alamo and colleagues illustrate the ability of recent Deep Learning techniques to predict diverse conformational states in proteins, as opposed to single static models reflecting individual states. Although they are limited to a small number of test cases of membrane proteins, the examples are of interest to members of the community, who are currently unable to reliably model the essential conformational changes required for function, at least until Deep Learning methods can be improved along these lines.

  (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 agreed to share their name with the authors.)”

Reviewed by eLife

Unraveling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent-RNA-Polymerase. An Unusual Active Site Leading to High Replication Rates

1. Emmanuelle Bignon
2. Antonio Monari

Reviewed by ScreenIT

Toward Atomistic Models of Intact SARS-CoV-2 via Martini Coarse-Grained Molecular Dynamics Simulations

1. Dali Wang
2. Jiaxuan Li
3. Lei Wang
4. Yipeng Cao
5. Sai Li
6. Chen Song

Reviewed by ScreenIT

A genetically encoded BRET-based SARS-CoV-2 Mpro protease activity sensor

1. Anupriya M. Geethakumari
2. Wesam S. Ahmed
3. Saad Rasool
4. Asma Fatima
5. S. M. Nasir Uddin
6. Mustapha Aouida
7. Kabir H. Biswas

Reviewed by ScreenIT

Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure

1. Neel Moudgal
2. Grace Arhin
3. Aaron T. Frank

Reviewed by ScreenIT

Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies

1. Carolina Corrêa Giron
2. Aatto Laaksonen
3. Fernando Luís Barroso da Silva

Reviewed by ScreenIT

Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages

1. Nadia M Huisjes
2. Thomas M Retzer
3. Matthias J Scherr
4. Rohit Agarwal
5. Lional Rajappa
6. Barbara Safaric
7. Anita Minnen
8. Karl E Duderstadt

• Curated by eLife

  Evaluation Summary:

  This manuscript reports an open-source platform for the storage and processing of single-molecule, camera-based, imaging data. This platform would facilitate data sharing and reproducibility and would be of great interest to practitioners of single-molecule imaging experiments, both experienced and new to the field. Although the platform requires a bit more testing, troubleshooting, and documenting, it represents significant and important steps towards unifying and standardizing how the field stores and processes data and towards expanding the base of researchers who can easily employ single-molecule imaging methods.

  (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 name with the authors.)

Reviewed by eLife

Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS‐CoV ‐2 variants of concern

1. Seonghan Kim
2. Yi Liu
3. Matthew Ziarnik
4. Sangjae Seo
5. Yiwei Cao
6. X. Frank Zhang
7. Wonpil Im

Reviewed by ScreenIT

Structural Ramifications of Spike Protein D614G Mutation in SARS-CoV-2

1. Hisham M. Dokainish
2. Yuji Sugita

Reviewed by ScreenIT

Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment

1. Md Lokman Hossen
2. Prabin Baral
3. Tej Sharma
4. Bernard Gerstman
5. Prem Chapagain

Reviewed by ScreenIT