Biophysics

Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9

1. Lukasz Nierzwicki
2. Kyle W East
3. Uriel N Morzan
4. Pablo R Arantes
5. Victor S Batista
6. George P Lisi
7. Giulia Palermo

• Curated by eLife

  Evaluation Summary:

  This is a comprehensive study combining solution NMR with molecular dynamics simulations to uncover the effects of three key mutations in the Cas9 HNH domain that increase CRISP-Cas9 complex specificity and reduce off-target activity. Through the analysis of these three different mutations, the authors concluded that by tuning the conformational dynamics of the HNH module in the CRISP-Cas9 complex, it is possible to control the function and specificity of the system. Combined these findings could have important implications for the design of new variants for this important gene editing complex.

  (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

Physical observables to determine the nature of membrane-less cellular sub-compartments

1. Mathias L Heltberg
2. Judith Miné-Hattab
3. Angela Taddei
4. Aleksandra M Walczak
5. Thierry Mora

• Curated by eLife

  Evaluation Summary:

  There has been a lively debate recently concerning the multiplicity of reported observations of phase-separated compartments inside of cells. Specifically, some claims of phase separation have been challenged, and an alternative model put forward in which clustering of observed particles is due to a clustering of binding sites with no phase separation. The current study does an admirable job of proposing and analyzing ways of distinguishing these two scenarios.

  (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

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

1. Anda Trifan
2. Defne Gorgun
3. Zongyi Li
4. Alexander Brace
5. Maxim Zvyagin
6. Heng Ma
7. Austin Clyde
8. David Clark
9. Michael Salim
10. David J. Hardy
11. Tom Burnley
12. Lei Huang
13. John McCalpin
14. Murali Emani
15. Hyenseung Yoo
16. Junqi Yin
17. Aristeidis Tsaris
18. Vishal Subbiah
19. Tanveer Raza
20. Jessica Liu
21. Noah Trebesch
22. Geoffrey Wells
23. Venkatesh Mysore
24. Thomas Gibbs
25. James Phillips
26. S. Chakra Chennubhotla
27. Ian Foster
28. Rick Stevens
29. Anima Anandkumar
30. Venkatram Vishwanath
31. John E. Stone
32. Emad Tajkhorshid
33. Sarah A. Harris
34. Arvind Ramanathan

Reviewed by ScreenIT

Low-affinity integrin states have faster ligand-binding kinetics than the high-affinity state

1. Jing Li
2. Jiabin Yan
3. Timothy A Springer

• Curated by eLife

  Evaluation Summary:

  Li, Yan and Springer report ligand binding on- and off-rates for three different conformations of α4β1 as well as α5β1 integrin. This is the first report that provides these numbers, which are important to understand the 'mode of integrin activation'. The study is - from a technical stand point - flawlessly performed and the calculated data is in perfect agreement with the previously published data.

  (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

A mechano-osmotic feedback couples cell volume to the rate of cell deformation

1. Larisa Venkova
2. Amit Singh Vishen
3. Sergio Lembo
4. Nishit Srivastava
5. Baptiste Duchamp
6. Artur Ruppel
7. Alice Williart
8. Stéphane Vassilopoulos
9. Alexandre Deslys
10. Juan Manuel Garcia Arcos
11. Alba Diz-Muñoz
12. Martial Balland
13. Jean-François Joanny
14. Damien Cuvelier
15. Pierre Sens
16. Matthieu Piel

• Curated by eLife

  Evaluation Summary:

  The paper by Venkova et al. is a comprehensive study of mammalian cell volume dynamics during the common cellular process of adhesion and spreading on a flat substrate, osmotic changes, and mechanical confinement. The paper reveals a complex interplay between cell water/ion regulation, cytoskeletal processes, and mechanical deformation of the cell. The topic is important in cell physiology and should be of considerable interest to cell biologists, mechanobiologists and biophysicists.

  (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

The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection

1. Marta F. M. Vieira
2. Guillem Hernandez
3. Qiyun Zhong
4. Miguel Arbesú
5. Tiago Veloso
6. Tiago Gomes
7. Maria L. Martins
8. Hugo Monteiro
9. Carlos Frazão
10. Gad Frankel
11. Andreas Zanzoni
12. Tiago N. Cordeiro

Reviewed by Review Commons

How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations

1. Soumya Lipsa Rath
2. Madhusmita Tripathy
3. Nabanita Mandal

Reviewed by ScreenIT

Dynamic allostery highlights the evolutionary differences between the CoV-1 and CoV-2 main proteases

1. Paul Campitelli
2. Jin Lu
3. S. Banu Ozkan

Reviewed by ScreenIT

Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes

1. Stefan T Huber
2. Edin Sarajlic
3. Roeland Huijink
4. Felix Weis
5. Wiel H Evers
6. Arjen J Jakobi

• Curated by eLife

  Evaluation Summary:

  Sample preparation for single-particle electron cryo-microscopy (cryo-EM) remains a bottleneck of this technique. The sample ice thickness cannot be accurately controlled, molecules may display strongly preferred orientations that make more elaborate data collection schemes necessary, and the sample may degrade at the air-water interface before it is finally frozen. In their pioneering work, the authors describe a prototype of a new microfluidic device that addresses some of these problems, including a refreshingly objective and critical discussion about the pros and cons of this novel approach. While some development will be required for this method to become mainstream, it has the potential to become a powerful alternative to the conventional workflow of single-particle cryo-EM, enabling full automation and making sample preparation highly reproducible.

  (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, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Mechanistic Insights into the Effects of Key Mutations on SARS-CoV-2 RBD-ACE2 Binding

1. Abhishek Aggarwal
2. Supriyo Naskar
3. Nikhil Maroli
4. Biswajit Gorai
5. Narendra M. Dixit
6. Prabal K. Maiti

Reviewed by ScreenIT