Biochemistry

Cooperation among c-subunits of FoF1-ATP synthase in rotation-coupled proton translocation

1. Noriyo Mitome
2. Shintaroh Kubo
3. Sumie Ohta
4. Hikaru Takashima
5. Yuto Shigefuji
6. Toru Niina
7. Shoji Takada

• Curated by eLife

  Evaluation Summary:

  This is an interesting manuscript describing for the first time experimentally the cooperative effects of mutations to individual key Glu residues in the c-ring of ATP synthase. The main result is that mutations in nearby c subunits are less inhibitory than those in subunits further apart in the ring. This is explained on the basis of MD/MC simulations as a shared waiting time for delayed proton uptake in case of neighboring subunits, which appears logical. Overall the manuscript is well presented, but with some caveats. The works will be of interest to specialists in bioenergetics, and to a wider biochemical, biophysical and structural biology audience.

  (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 names with the authors.)

Reviewed by eLife

Modeling SARS-CoV-2 spike/ACE2 protein–protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context

1. Vincenzo Tragni
2. Francesca Preziusi
3. Luna Laera
4. Angelo Onofrio
5. Ivan Mercurio
6. Simona Todisco
7. Mariateresa Volpicella
8. Anna De Grassi
9. Ciro Leonardo Pierri

Reviewed by ScreenIT

Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif

1. Ramiro Lorenzo
2. Lucas A. Defelipe
3. Lucio Aliperti
4. Stephan Niebling
5. Tânia F. Custódio
6. Christian Löw
7. Jennifer J. Schwarz
8. Kim Remans
9. Patricio O. Craig
10. Lisandro H. Otero
11. Sebastián Klinke
12. María García-Alai
13. Ignacio E. Sánchez
14. Leonardo G. Alonso

Reviewed by ScreenIT

Intra-Helical Salt Bridge Contribution to Membrane Protein Insertion

1. Gerard Duart
2. John Lamb
3. Juan Ortiz-Mateu
4. Arne Elofsson
5. Ismael Mingarro

Reviewed by Review Commons

Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer

1. Kushol Gupta
2. Ying Wen
3. Nisha S Ninan
4. Amanda C Raimer
5. Robert Sharp
6. Ashlyn M Spring
7. Kathryn L Sarachan
8. Meghan C Johnson
9. Gregory D Van Duyne
10. A Gregory Matera

• Curated by eLife

  Summary:

  The manuscript describes a very detailed mutagenesis analysis of the dimerization / oligomerization behavior of the protein Survival Motor Neuron. Mutations in this protein cause Spinal Muscular Atrophy. Analysis of disease causing mutations show a correlation with their impact on oligomerization. A structural model that includes different domains of the protein involved in oligomerization is built from these analyses.

  This analysis is an excellent source for researchers working in the field of SMN proteins. A mechanistic interpretation of how changes in the oligomerization lead to the disease or impact the formation of membraneless organelles, is however missing. Thus, the manuscript provides an enormous amount of important mutational analysis data but does not lead to a significant advancement in our understanding of the disease mechanism.

  (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

SARS-CoV-2 beta variant substitutions alter spike glycoprotein receptor binding domain structure and stability

1. Daniel L. Moss
2. Jay Rappaport

Reviewed by ScreenIT

Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations

1. Tzu-Jing Yang
2. Pei-Yu Yu
3. Yuan-Chih Chang
4. Kang-Hao Liang
5. Hsian-Cheng Tso
6. Meng-Ru Ho
7. Wan-Yu Chen
8. Hsiu-Ting Lin
9. Han-Chung Wu
10. Shang-Te Danny Hsu

Reviewed by ScreenIT

AKAP79 enables calcineurin to directly suppress protein kinase A activity

1. Timothy W Church
2. Parul Tewatia
3. Saad Hannan
4. João Antunes
5. Olivia Eriksson
6. Trevor G Smart
7. Jeanette Hellgren Kotaleski
8. Matthew G Gold

• Curated by eLife

  Evaluation Summary:

  This manuscript will be of interest to neuroscientists as well as a broad audience of cell biologists, as it provides new insight into the myriad of cellular functions regulated by the well-studied cAMP-dependent protein kinase, PKA. Rigorous biochemical data supports a model for PKA inactivation wherein dephosphorylation of the PKA regulatory subunit within a multiprotein complex leads to rapid capture of the PKA catalytic subunit limiting signaling duration. Overall, the biochemical data and modeling support the conclusions although a few details can be addressed further and the in vivo data remains preliminary. The work nevertheless presents exciting findings that provide a tantalizing mechanism to selectively modulate PKA activity at precise subcellular locations.

  (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 names with the authors.)

Reviewed by eLife

Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis

1. Florian Kabinger
2. Carina Stiller
3. Jana Schmitzová
4. Christian Dienemann
5. Goran Kokic
6. Hauke S. Hillen
7. Claudia Höbartner
8. Patrick Cramer

Reviewed by ScreenIT

Nanopore Dwell Time Analysis Permits Sequencing and Conformational Assignment of Pseudouridine in SARS-CoV-2

1. Aaron M. Fleming
2. Nicole J. Mathewson
3. Shereen A. Howpay Manage
4. Cynthia J. Burrows

Reviewed by ScreenIT