Biochemistry

Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA

1. Jan Philip Wurm

• Curated by eLife

  Evaluation Summary:

  This manuscript is interesting to a broad audience in the general fields of RNA and structural biology. It provides detailed and important molecular insight into one of the mechanisms by which ATP-fueled RNA helicases can cause the local destabilisation of terminal base-pairs and eventually contribute to RNA structure remodelling and it is a prime example of how crystallographic high-resolution snapshots of conformational intermediates can be combined with sophisticated NMR techniques and assays into a comprehensive model. The manuscript would benefit from a broader and more explicit comparative discussion including the limitations of the proposed model, because DbpA is a rather specialised RNA helicase and because the double-stranded RNA substrates were specifically designed to exclusively investigate unwinding from the side of a short 5'-overhang.

  (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 #2 agreed to share their name with the authors.

Reviewed by eLife

Antibacterial potency of type VI amidase effector toxins is dependent on substrate topology and cellular context

1. Atanas Radkov
2. Anne L Sapiro
3. Sebastian Flores
4. Corey Henderson
5. Hayden Saunders
6. Rachel Kim
7. Steven Massa
8. Samuel Thompson
9. Chase Mateusiak
10. Jacob Biboy
11. Ziyi Zhao
12. Lea M Starita
13. William L Hatleberg
14. Waldemar Vollmer
15. Alistair B Russell
16. Jean-Pierre Simorre
17. Spencer Anthony-Cahill
18. Peter Brzovic
19. Beth Hayes
20. Seemay Chou

Reviewed by Review Commons

SARS-CoV-2 spike variants differ in their allosteric response to linoleic acid

1. A. Sofia F. Oliveira
2. Deborah K. Shoemark
3. Andrew D. Davidson
4. Imre Berger
5. Christiane Schaffitzel
6. Adrian J. Mulholland

Reviewed by ScreenIT

The free fatty acid–binding pocket is a conserved hallmark in pathogenic β-coronavirus spike proteins from SARS-CoV to Omicron

1. Christine Toelzer
2. Kapil Gupta
3. Sathish K. N. Yadav
4. Lorna Hodgson
5. Maia Kavanagh Williamson
6. Dora Buzas
7. Ufuk Borucu
8. Kyle Powers
9. Richard Stenner
10. Kate Vasileiou
11. Frederic Garzoni
12. Daniel Fitzgerald
13. Christine Payré
14. Gunjan Gautam
15. Gérard Lambeau
16. Andrew D. Davidson
17. Paul Verkade
18. Martin Frank
19. Imre Berger
20. Christiane Schaffitzel

Reviewed by ScreenIT

Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release

1. Brianna Bibel
2. Elad Elkayam
3. Steve Silletti
4. Elizabeth A Komives
5. Leemor Joshua-Tor

• Curated by eLife

  Evaluation Summary:

  This paper provides well documented and solid biochemical data to show how phosphorylation of AGO2 modulate its binding to target mRNAs, releasing the complex to allow its recycling in the cell via electrostatic repulsion. This result could explain how a small amount of Ago proteins could target a very large number of mRNA molecules . The data support the key claims of the manuscript, and the approaches used are rigorous. This very well-written and elegant study will be of great interest to those working in the miRNA field as it addresses important open questions concerning the dynamic regulation of mIRNA-mediated gene repression.

  (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

Redox regulation of the SARS-CoV-2 main protease provides new opportunities for drug design

1. Lisa-Marie Funk
2. Gereon Poschmann
3. Ashwin Chari
4. Fabian Rabe von Pappenheim
5. Kim-Maren Stegmann
6. Antje Dickmanns
7. Nora Eulig
8. Marie Wensien
9. Elham Paknia
10. Gabi Heyne
11. Elke Penka
12. Arwen R. Pearson
13. Carsten Berndt
14. Tobias Fritz
15. Sophia Bazzi
16. Jon Uranga
17. Ricardo A. Mata
18. Matthias Dobbelstein
19. Rolf Hilgenfeld
20. Ute Curth
21. Kai Tittmann

Reviewed by ScreenIT

Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants

1. Hiam R. S. Arruda
2. Tulio M. Lima
3. Renata G. F. Alvim
4. Fernanda B. A. Victorio
5. Daniel P. B. Abreu
6. Federico F. Marsili
7. Karen D. Cruz
8. Patricia Sosa-Acosta
9. Mauricio Quinones-Vega
10. Jéssica de S. Guedes
11. Fábio C. S. Nogueira
12. Jerson L. Silva
13. Leda R. Castilho
14. Guilherme A. P. de Oliveira

Reviewed by ScreenIT

A potent synthetic nanobody with broad-spectrum activity neutralizes SARS-Cov-2 virus and Omicron variant through a unique binding mode

1. Dongping Zhao
2. Liqin Liu
3. Xinlin Liu
4. Jinlei Zhang
5. Yuqing Yin
6. Linli Luan
7. Dingwen Jiang
8. Xiong Yang
9. Lei Li
10. Hualong Xiong
11. Dongming Xing
12. Qingbing Zheng
13. Ningshao Xia
14. Yuyong Tao
15. Shaowei Li
16. Haiming Huang

Reviewed by ScreenIT

Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex

1. Kanwal Kayastha
2. Alexander Katsyv
3. Christina Himmrich
4. Sonja Welsch
5. Jan M Schuller
6. Ulrich Ermler
7. Volker Müller

• Curated by eLife

  Evaluation Summary:

  This paper describes a new structure for a complex between a bifurcating electron transfer flavoprotein (ETF) and its client dehydrogenase. Because electrons are being supplied by the dehydrogenase, the ETF executes confurcation in contrast to all of those elucidated so far, which function in the opposite direction to effect bifurcation. As electron-confurcation and electron-bifurcation have emerged as important paradigms of cellular bioenergetics, the data reported herein pave the way for future exploration of similar electron transfer systems and lay the ground for understanding their structural basis. The work will be of relevance to all who are interested in the mechanisms of enzymes.

  (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

Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike

1. Victoria Stalls
2. Jared Lindenberger
3. Sophie M.-C. Gobeil
4. Rory Henderson
5. Rob Parks
6. Maggie Barr
7. Margaret Deyton
8. Mitchell Martin
9. Katarzyna Janowska
10. Xiao Huang
11. Aaron May
12. Micah Speakman
13. Esther Beaudoin
14. Bryan Kraft
15. Xiaozhi Lu
16. Robert J. Edwards
17. Amanda Eaton
18. David C. Montefiori
19. Wilton B. Williams
20. Kevin O. Saunders
21. Kevin Wiehe
22. Barton F. Haynes
23. Priyamvada Acharya

Reviewed by ScreenIT