Biophysics

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

Investigation of the Effects of N-Linked Glycans on the Stability of the Spike Protein in SARS-CoV-2 by Molecular Dynamics Simulations

1. E.Deniz Tekin

Reviewed by ScreenIT

Single-molecule analysis of the entire perfringolysin O pore formation pathway

1. Conall McGuinness
2. James C Walsh
3. Charles Bayly-Jones
4. Michelle A Dunstone
5. Michelle P Christie
6. Craig J Morton
7. Michael W Parker
8. Till Böcking

• Curated by eLife

  Evaluation Summary:

  This paper presents a single-molecule, multi-color microscopy study of the real-time assembly of perfringolysin O, a member of the membrane attack complex perforin cholesterol-dependent cytolysin superfamily. With the ability to resolve different states of the species in the reaction, simultaneously with membrane leakage, this work informs on key aspects of the mechanism including identifying potential assemblies involved in membrane lysis, and how membrane binding, oligomerization, and pore transitioning depends on concentration and pH. While some additional controls are needed to clarify the interpretation of the results, this study will be of interest to many, including those studying cytolysin mechanisms, but also the broader field of single-molecule studies of membrane binding proteins.

  (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 #3 agreed to share their name with the authors.)

Reviewed by eLife

Self-organization of kinetochore-fibers in human mitotic spindles

1. William Conway
2. Robert Kiewisz
3. Gunar Fabig
4. Colm P Kelleher
5. Hai-Yin Wu
6. Maya Anjur-Dietrich
7. Thomas Müller-Reichert
8. Daniel J Needleman

• Curated by eLife

  Evaluation Summary:

  Conway and colleagues use a combination of experiments and theory to test models for how kinetochore-fibers are born in mammalian spindles. Their work is consistent with a model where kinetochore-fibers primarily nucleate de novo at kinetochores, rather than arise from search-and-capture of microtubules. This work should be of interest to experimentalists and theorists broadly interested in self-organization, and in cell division.

  (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 #3 agreed to share their name with the authors.)

Reviewed by eLife

Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies

1. Luke K Davis
2. Ian J Ford
3. Bart W Hoogenboom

• Curated by eLife

  Evaluation Summary:

  This theoretical study describes the interaction of a planar brush or film of the resident unstructured components of the nuclear pore complex (NPC) called nucleoporins (FG-nups) and different nuclear transport receptors (NTRs). The authors describe impacts of competitive binding that give rise to enrichment of the NTRs, NTF2 and importin-beta, at different depths of the FG-nup film, which could relate to experimental observations in other studies, as well as evidence that crowding could promote the rate of nuclear transport by modulating FG-NTR binding/unbinding. The conclusions were found to be generally supported by the data, relevant to the field of nuclear transport, and able to make specific predictions that can be experimentally tested in the future, although previous studies in the field and the novelty could be better described.

  (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. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Computational study of the furin cleavage domain of SARS-CoV-2: delta binds strongest of extant variants

1. M. Zaki Jawaid
2. A. Baidya
3. S. Jakovcevic
4. J. Lusk
5. R. Mahboubi-Ardakani
6. N. Solomon
7. G. Gonzalez
8. J. Arsuaga
9. M. Vazquez
10. R.L. Davis
11. D.L. Cox

Reviewed by ScreenIT