Biophysics

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

An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation

1. Rui Fang
2. Jason Hon
3. Mengying Zhou
4. Ying Lu

• Curated by eLife

  Evaluation Summary:

  AAA+ ATPases consume chemical energy in form of ATP to catalyze essential cellular reactions. Here, computational and biochemical approaches are used to model how the six subunits of the AAA+ ATPase Rpt1-6 coordinate their enzymatic activity with each other to exert unidirectional pulling forces on target polypeptide chains that promote protein unfolding. Although the technical aspects of the work are sometimes difficult to follow, the findings indicate that the order in which ATPase active sites fire is generally sequential, much like a rotary engine. The system can tolerate "misfires" - instances in which a subunit fails to hydrolyze ATP - by skipping the problematic subunit. The work should appeal to the broad AAA+ community and researchers trying to understand the biophysical principles by which complex biological machines operate.

  (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

Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes

1. Beibei Wang
2. Changqing Zhong
3. D. Peter Tieleman

Reviewed by ScreenIT

Fast ATP-dependent Subunit Rotation in Reconstituted F _o F ₁ -ATP Synthase Trapped in Solution

1. Thomas Heitkamp
2. Michael Börsch

• Curated by Biophysics Colab

  Endorsement statement (21 September 2021)

  The preprint by Heitkamp and Börsch describes visualization of the fast ATP-dependent subunit rotation in reconstituted FoF1-ATP synthase using single-molecule FRET techniques. Using a highly innovative method for trapping single molecules, the authors were able to see the static and dynamic disorder of enzymes in solution, not possible in previous studies. The work makes important contributions to both understanding the structural dynamics of FoF1-ATP synthase and the development of methodologies to study single-molecule dynamics of other proteins in solution.

  (This endorsement refers to version 5 of this preprint, which was peer reviewed by Biophysics Colab.)

Reviewed by Biophysics Colab

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin

1. Pawel M. Wydorski
2. Jerzy Osipiuk
3. Benjamin T. Lanham
4. Christine Tesar
5. Michael Endres
6. Elizabeth Engle
7. Robert Jedrzejczak
8. Vishruth Mullapudi
9. Karolina Michalska
10. Krzysztof Fidelis
11. David Fushman
12. Andrzej Joachimiak
13. Lukasz A. Joachimiak

Reviewed by ScreenIT

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

1. Weria Pezeshkian
2. Fabian Grünewald
3. Oleksandr Narykov
4. Senbao Lu
5. Valeria Arkhipova
6. Alexey Solodovnikov
7. Tsjerk A. Wassenaar
8. Siewert J. Marrink
9. Dmitry Korkin

Reviewed by ScreenIT

Mitoxantrone dihydrochloride, an FDA approved drug, binds with SARS-CoV-2 NSP1 C-terminal

1. Prateek Kumar
2. Taniya Bhardwaj
3. Rajanish Giri

Reviewed by ScreenIT

Structure-activity relationships of B.1.617 and other SARS-CoV-2 spike variants

1. Tzu-Jing Yang
2. Pei-Yu Yu
3. Yuan-Chih Chang
4. Ning-En Chang
5. Yu-Xi Tsai
6. Kang-Hao Liang
7. Piotr Draczkowski
8. Bertina Lin
9. Yong-Sheng Wang
10. Yu-Chun Chien
11. Kay-Hooi Khoo
12. Han-Chung Wu
13. Shang-Te Danny Hsu

Reviewed by ScreenIT