Biophysics

Extracellular vimentin as a target against SARS-CoV-2 host cell invasion

1. Łukasz Suprewicz
2. Maxx Swoger
3. Sarthak Gupta
4. Ewelina Piktel
5. Fitzroy J. Byfield
6. Daniel V. Iwamoto
7. Danielle Germann
8. Joanna Reszeć
9. Natalia Marcińczyk
10. Robert J. Carroll
11. Marzena Lenart
12. Krzysztof Pyrc
13. Paul Janmey
14. J.M. Schwarz
15. Robert Bucki
16. Alison Patteson

Reviewed by Rapid Reviews Infectious Diseases, PREreview, ScreenIT

Allosteric communication in Class A β-lactamases occurs via Cooperative Coupling of Loop Dynamics

1. Ioannis Galdadas
2. Shen Qu
3. Ana Sofia F Oliveria
4. Edgar Olehnovics
5. Andrew R Mack
6. Maria F Mojica
7. Pratul K Agarwal
8. Catherine L Tooke
9. Francesco L Gervasio
10. James Spencer
11. Robert A Bonomo
12. Adrian J Mulholland
13. Shozeb Haider

• Curated by eLife

  Evaluation Summary:

  This manuscript presents a computational study aiming to understand the allosteric signaling propagation pathway in two class-A beta-lactamases. The results of this study will be of interest to the readers in the fields of beta-lactamase, antibiotic resistance, and enzyme allostery.

  (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. Reviewers #1, #2, and #3 agreed to share their names with the authors.)

Reviewed by eLife

StormGraph: A graph-based algorithm for quantitative clustering analysis of diverse single-molecule localization microscopy data

1. Joshua M. Scurll
2. Libin Abraham
3. Da Wei Zheng
4. Reza Tafteh
5. Keng C. Chou
6. Michael R. Gold
7. Daniel Coombs

Reviewed by eLife

Spatiotemporal dynamics of PIEZO1 localization controls keratinocyte migration during wound healing

1. Jesse R. Holt
2. Wei-Zheng Zeng
3. Elizabeth L. Evans
4. Seung-Hyun Woo
5. Shang Ma
6. Hamid Abuwarda
7. Meaghan Loud
8. Ardem Patapoutian
9. Medha M. Pathak

• Curated by eLife

  Evaluation Summary:

  The manuscript links a critical physiological function of the skin, wound healing to the ability of skin cells to migrate and the modification of migration by the mechanosensitive ion channel Piezo1. The topic of the manuscript is timely, relevant and would be of interest to a broad audience. The experimental design followed by the authors is straightforward and elegant, and the majority of the conclusions are well supported by the results.

  (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

Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2

1. Yihu Xie
2. Bradley P. Clarke
3. Yong Joon Kim
4. Austin L. Ivey
5. Pate S. Hill
6. Yi Shi
7. Yi Ren

• Curated by eLife

  Evaluation Summary:

  This is an interesting paper describing the structure of the yeast THO:Sub2 complex and how it interacts with the SR like protein Gbp2. The paper extends what we have learned from two recently published Tho:Sub2 complex structures by the Conti and Plaschka groups in two ways. Firstly, it shows how Gbp2 interacts with the THO complex. Secondly, it reveals a substantially different orientation between THO:Sub2 protomers compared with the earlier structure, so provides more information on the flexibility and range of movements that the two protomers might make with respect to each other. The structural inferences are supported by some biochemical experiments but mechanistically the work has limitations, similar to other recent cryo-EM structures of this complex. However, this is an important structure of wide interest to people working on gene expression in eukaryotes and it undoubtedly advances the 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. The reviewers opted to remain anonymous to the authors.)

Reviewed by eLife

Spurious regulatory connections dictate the expression‐fitness landscape of translation factors

1. Jean‐Benoît Lalanne
2. Darren J Parker
3. Gene‐Wei Li

Reviewed by Review Commons

Conformational dynamics of auto-inhibition in the ER calcium sensor STIM1

1. Stijn van Dorp
2. Ruoyi Qiu
3. Ucheor B Choi
4. Minnie M Wu
5. Michelle Yen
6. Michael Kirmiz
7. Axel T Brunger
8. Richard S Lewis

• Curated by eLife

  Evaluation Summary:

  This study uses complementary approaches to advance our mechanistic understanding of STIM1 activation, with elegant single molecule methods providing new details on STIM1 structure and dynamics. Full length STIM1 in a cellular environment was probed by crosslinking, but the same has not yet been possible with single-molecule Förster resonance energy transfer (smFRET).

  (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

Voltage-clamp fluorometry analysis of structural rearrangements of ATP-gated channel P2X2 upon hyperpolarization

1. Rizki Tsari Andriani
2. Yoshihiro Kubo

• Curated by eLife

  Evaluation Summary:

  This study will be of broad interest to ion channel researchers interested in understanding the fundamental mechanisms of voltage-sensing. The researchers use a novel approach to determine the mechanism of voltage-sensing in a channel that lacks a canonical voltage-sensing domain.

  (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 names with the authors.)

Reviewed by eLife

The propofol binding sites of prokaryotic voltage-gated sodium channels

1. Elaine Yang
2. Weiming Bu
3. Antonio Suma
4. Vincenzo Carnevale
5. Kimberly C. Grasty
6. Patrick Loll
7. Kellie Woll
8. Natarajan Bhanu
9. Benjamin A. Garcia
10. Roderic G. Eckenhoff
11. Manuel Covarrubias

Reviewed by eLife

Confinement Discerns Swarmers from Planktonic Bacteria

1. Weijie Chen
2. Neha Mani
3. Hamid Karani
4. Hao Li
5. Sridhar Mani
6. Jay X. Tang

• Curated by eLife

  Summary: In this paper, the authors proposed a new approach by mounting a PDMS microwells of specific sizes on agar surface to confine swarming and planktonic SM3 cells. They found swarming bacteria exhibit a "single-swirl" motion pattern and concentrated planktonic bacteria exhibit "multi-swirls" motion pattern in the diameter range of 31-90 μm. The phase diagram shows that in smaller wells concentrated planktonic SM3 forms a single vortex and in larger wells swarming SM3 also breaks into mesoscale vortices.

  In addition, they conducted systematic experiments to explore parameters defining the divergence of motion patterns in confinement including cell density, cell length, cell speed and surfactant. They concluded that the single swirl pattern depends on cohesive cell-cell interaction mediated by biochemical factors removable through matrix dilution.

  This paper gives a new method to discern swarmers from planktonic bacteria and carefully studies the factors that influence the formation of bacterial vortices under restriction.

Reviewed by eLife