Biochemistry

Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP

1. Sarah R Hansen
2. David S White
3. Mark Scalf
4. Ivan R Corrêa
5. Lloyd M Smith
6. Aaron A Hoskins

• Curated by eLife

  Evaluation Summary:

  This study extends previous work from the same group on the mechanism of 5' splice site recognition using co-localization single-molecule spectroscopy. There are three important conclusions: 1) the association of the U1 snRNP with the 5' splice site is largely determined by the snRNP itself and does not require other splicing factors; 2) sequence features of the 5' splice site determine whether a short-lived complex with U1 dissociates or transitions into a longer-lived, "productive" complex, potentially mediated by stabilized contacts with U1 associated proteins; and 3) the ability to form the longer-lived complex cannot be accurately predicted by base-pairing potential alone, as presumed by many predictive algorithms. Currently, a test for the role of specific protein-RNA contacts is lacking; additionally, a comparison with other nucleic acid recognition events is missing, particularly those also showing a two-step binding mechanism. This work will be of interest to colleagues in the splicing field as well as to others in fields where nucleic acid recognition by snRNPs plays a major role.

  (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

A Single-Component Luminescent Biosensor for the SARS-CoV-2 Spike Protein

1. Matthew Ravalin
2. Heegwang Roh
3. Rahul Suryawanshi
4. G. Renuka Kumar
5. John E. Pak
6. Melanie Ott
7. Alice Y. Ting

Reviewed by ASAPbio crowd review

Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

1. Yitong Li
2. Vijaya Kumar Balakrishnan
3. Michael Rowse
4. Cheng-Guo Wu
5. Anastasia Phoebe Bravos
6. Vikash K Yadav
7. Ylva Ivarsson
8. Stefan Strack
9. Irina V Novikova
10. Yongna Xing

• Curated by eLife

  Evaluation Summary:

  Xing and colleagues present a cryoEM structure of the protein phosphatase 2A (PP2A)-B56 holoenzyme in complex with protein phosphatase methyltransferase-1 (PME-1). The structure reveals that PME-1 blocks the substrate binding site of PP2A by inserting an unstructured loop. This unexpected inhibitory mechanism is also coupled to a large conformation change in the PP2A-B56 holoenzyme and PME-1. Combined with biochemical and cellular assays, the authors suggest how PME-1 can regulate p53-mediated DNA damage responses via inhibiting PP2A. This manuscript will be of importance for structural biologists as well as colleagues in the p53 field.

  (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

Membrane-mediated dimerization potentiates PIP5K lipid kinase activity

1. Scott D Hansen
2. Albert A Lee
3. Benjamin R Duewell
4. Jay T Groves

• Curated by eLife

  Evaluation Summary:

  This paper is of interest for a wide range of readers who study the biology of lipid modifying enzymes, especially as it relates to interfacial reaction kinetics in biological membranes. This study aimed to obtain detailed biochemical insights into the mutual relationship between PI(4,5)P2 lipids and their kinase PIP5K, which engage in an exciting pattern-forming reaction on membranes. The authors find cooperative recruitment of PIP5K to the membrane, oligomerization-enhanced catalytic efficiency and indications of allosteric regulation. Although of very high interest and featuring mostly convincing data, there are concerns about the interpretation of whether the observed phenomenon is dimer specific or related to higher-order oligomerization. In addition, there are inconsistencies in the data presentation.

  (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

An auto-inhibited state of protein kinase G and implications for selective activation

1. Rajesh Sharma
2. Jeong Joo Kim
3. Liying Qin
4. Philipp Henning
5. Madoka Akimoto
6. Bryan VanSchouwen
7. Gundeep Kaur
8. Banumathi Sankaran
9. Kevin R MacKenzie
10. Giuseppe Melacini
11. Darren E Casteel
12. Friedrich W Herberg
13. Choel Kim

• Curated by eLife

  Evaluation Summary:

  This reported crystal structure of nearly-full-length cGMP-dependent protein kinase β (PGK1β) provides new insights into how the activity of the PKG catalytic domain is held in check by intramolecular interactions between both the upstream regulatory cGMP-binding domains and the autoinhibitory segment and the catalytic domain, and how cGMP binding to the cGMP-binding domains can relieve these inhibitory constraints leading to an increase in catalytic activity. The structure of the activating PKGIα R177Q CNB-A domain mutant, which resembles a cGMP-bound wild type CNB-A domain, provides a nice explanation for how this point mutation activates PKG Iα and leads to the development of the TAAD (Thoracic Aortic Aneurysms and Dissections) syndrome. The work will be of specific interest to the cyclic nucleotide community, and to the broader signaling community in general.

  (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

PH domain-mediated autoinhibition and oncogenic activation of Akt

1. Hwan Bae
2. Thibault Viennet
3. Eunyoung Park
4. Nam Chu
5. Antonieta Salguero
6. Michael J Eck
7. Haribabu Arthanari
8. Philip A Cole

• Curated by eLife

  Evaluation Summary:

  Bae et al. examine the regulatory role of the PH domain of the AKT Ser/ Thr kinase, finding a key set of interactions that mediate autoinhibitory interactions between PH and kinase domains. The work provides additional mechanistic understanding of the E17K mutation, a common variant in human cancers. This manuscript will be of great interest to scientists focused on protein kinase regulation and molecular mechanisms that control signal transduction.

  (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

Glutamine metabolism modulates chondrocyte inflammatory response

1. Manoj Arra
2. Gaurav Swarnkar
3. Naga Suresh Adapala
4. Syeda Kanwal Naqvi
5. Lei Cai
6. Muhammad Farooq Rai
7. Srikanth Singamaneni
8. Gabriel Mbalaviele
9. Robert Brophy
10. Yousef Abu-Amer

• Curated by eLife

  Evaluation Summary:

  This manuscript focuses on identifying how metabolism can influence the response of cartilage cells to inflammation. This has relevance to the painful disease known as osteoarthritis. Modulation of cell metabolism in the right direction can serve to protect joint cartilage from the negative effects of inflammation which causes onset and disease progression.

  (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

Fusion with heat-resistant obscure (Hero) proteins have the potential to improve the molecular property of recombinant proteins

1. Eri Morimoto
2. Kotaro Tsuboyama
3. Yukihide Tomari

Reviewed by ASAPbio crowd review

Translational Activity Controls Ribophagic Flux and Turnover of Distinct Ribosome Pools

1. Jakob Trendel
2. Milan Aleksić
3. Matilde Bertolini
4. Marco Jochem
5. Günter Kramer
6. Stefan Pfeffer
7. Bernd Bukau
8. Jeroen Krijgsveld

Reviewed by ASAPbio crowd review

Increasing protein stability by inferring substitution effects from high-throughput experiments

1. Rasmus Krogh Norrild
2. Kristoffer Enøe Johansson
3. Charlotte O’Shea
4. Jens Preben Morth
5. Kresten Lindorff-Larsen
6. Jakob Rahr Winther

Reviewed by ASAPbio crowd review