Biophysics

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

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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

Autophagy and evasion of immune system by SARS-CoV-2. Structural features of the Non-structural protein 6 from Wild Type and Omicron viral strains interacting with a model lipid bilayer. ^†

1. Emmanuelle Bignon
2. Marco Marazzi
3. Stéphanie Grandemange
4. Antonio Monari

Reviewed by ScreenIT

Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants

1. Andrei Neamtu
2. Francesca Mocci
3. Aatto Laaksonen
4. Fernando L. Barroso da Silva

Reviewed by ScreenIT

Structural and computational insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction

1. Jun Lan
2. Xinheng He
3. Yifei Ren
4. Ziyi Wang
5. Huan Zhou
6. Shilong Fan
7. Chenyou Zhu
8. Dongsheng Liu
9. Bin Shao
10. Tie-Yan Liu
11. Qisheng Wang
12. Linqi Zhang
13. Jiwan Ge
14. Tong Wang
15. Xinquan Wang

Reviewed by ScreenIT

Hydrodynamics of spike proteins dictate a transport-affinity competition for SARS-CoV-2 and other enveloped viruses

1. Nicolas Moreno
2. Daniela Moreno-Chaparro
3. Florencio Balboa Usabiaga
4. Marco Ellero

Reviewed by ScreenIT

Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant

1. Zhen Cui
2. Pan Liu
3. Nan Wang
4. Lei Wang
5. Kaiyue Fan
6. Qianhui Zhu
7. Kang Wang
8. Ruihong Chen
9. Rui Feng
10. Zijing Jia
11. Minnan Yang
12. Ge Xu
13. Boling Zhu
14. Wangjun Fu
15. Tianming Chu
16. Leilei Feng
17. Yide Wang
18. Xinran Pei
19. Peng Yang
20. Xiaoliang Sunney Xie
21. Lei Cao
22. Yunlong Cao
23. Xiangxi Wang

Reviewed by ScreenIT