Biophysics

Structural basis of ion – substrate coupling in the Na+-dependent dicarboxylate transporter VcINDY

1. David B. Sauer
2. Jennifer J. Marden
3. Joseph C. Sudar
4. Jinmei Song
5. Christopher Mulligan
6. Da-Neng Wang

• Curated by Biophysics Colab

  Endorsement statement (28 June 2022)

  Sauer et al. describe two cryo-EM structures of the Na⁺-dependent dicarboxylate transporter VcINDY in two inward-facing states. The high-quality structural data, complemented by NMR-inspired analysis, functional assays and cysteine accessibility measurements, reveal crucial conformational changes induced by Na⁺ binding to apo VcINDY that result in formation of the substrate-binding site. This is a strong manuscript that provides an important contribution to our understanding of the transport mechanism in the SLC13/DASS family of transporters, several members of which have critical physiological functions. The work will be of interest to researchers working on this and other ion-coupled transporter families.

  (This endorsement by Biophysics Colab refers to the version of record for this work, which is linked to and has been revised from the original preprint following peer review.)

Reviewed by Biophysics Colab

The role of surface adhesion on the macroscopic wrinkling of biofilms

1. Steffen Geisel
2. Eleonora Secchi
3. Jan Vermant

• Curated by eLife

  Evaluation Summary:

  The wrinkling of growing biofilms is considered in this paper experimentally in a clever set of experiments in a microfluidic setup that reveals aspects of the onset of the wrinkling instability and the formation of hollow channels within which bacteria move. Variations in the adhesive properties of the underlying surface are shown to affect the instability. While the results will surely be of interest to researchers in a range of areas, the connection with theoretical results needs further development.

  (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

On the origin of universal cell shape variability in confluent epithelial monolayers

1. Souvik Sadhukhan
2. Saroj Kumar Nandi

• Curated by eLife

  Evaluation Summary:

  By theoretically analysing the energy of a confluent epithelial tissue, the authors unveil the reason for nearly universal shape fluctuations that have been reported earlier. With a better justification of some of the underlying approximations used by the authors, the manuscript would be relevant for all people with an interest in tissue structure and dynamics.

  (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

Viscoelastic properties of suspended cells measured with shear flow deformation cytometry

1. Richard Gerum
2. Elham Mirzahossein
3. Mar Eroles
4. Jennifer Elsterer
5. Astrid Mainka
6. Andreas Bauer
7. Selina Sonntag
8. Alexander Winterl
9. Johannes Bartl
10. Lena Fischer
11. Shada Abuhattum
12. Ruchi Goswami
13. Salvatore Girardo
14. Jochen Guck
15. Stefan Schrüfer
16. Nadine Ströhlein
17. Mojtaba Nosratlo
18. Harald Herrmann
19. Dorothea Schultheis
20. Felix Rico
21. Sebastian Johannes Müller
22. Stephan Gekle
23. Ben Fabry

• Curated by eLife

  Evaluation Summary:

  This paper describes a microfluidic approach to determine the viscoelastic properties of living cells from their deformation in a fluid flow. Its implementation seems accessible and the method offers the possibility to perform measurements on a large number of cells. This technique could eventually be used in many laboratories, including those not specialized in cell mechanics.

  (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 name with the authors.)

Reviewed by eLife

Unfolding and identification of membrane proteins in situ

1. Nicola Galvanetto
2. Zhongjie Ye
3. Arin Marchesi
4. Simone Mortal
5. Sourav Maity
6. Alessandro Laio
7. Vincent Torre

• Curated by eLife

  Evaluation Summary:

  This paper presents a method to identify membrane proteins in native cell membranes based on a combination of single molecule AFM and an unsupervised clustering procedure to identify clusters of single-protein curves. This original approach represents a definitive step forward for AFM technology and methodology, which can generally only be used to characterize purified biomolecules of known identity. The work will be of interest to all students of membrane biology and especially membrane proteins.

  (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 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Mitochondrial mRNA localization is governed by translation kinetics and spatial transport

1. Ximena G. Arceo
2. Elena F. Koslover
3. Brian M. Zid
4. Aidan I. Brown

Reviewed by Review Commons

Adsorption of pulmonary and exogeneous surfactants on SARS-CoV-2 spike protein

1. Kolattukudy P. Santo
2. Alexander V. Neimark

Reviewed by ScreenIT

Excitatory and inhibitory D-serine binding to the NMDA receptor

1. Remy A Yovanno
2. Tsung Han Chou
3. Sarah J Brantley
4. Hiro Furukawa
5. Albert Y Lau

• Curated by eLife

  Evaluation Summary:

  Activation of NMDA receptors requires two co-agonists: Glutamate which binds to the GluN2 subunit and glycine/D-serine which binds to the GluN1 subunit. In the present manuscript, the authors address the interaction of D-serine, which is a less studied co-agonist than glycine, with the GluN1 and GluN2A subunits using molecular simulations as well as electrophysiology experiments. Surprisingly they find that D-serine interacts with the GluN2 subunit, further expanding our molecular understanding of NMDA receptor structure-function.

  (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

SARS-CoV-2 Main Protease: a Kinetic Approach

1. Thierry Rebetez

Reviewed by ScreenIT

Transient exposure of a buried phosphorylation site in an autoinhibited protein

1. Simone Orioli
2. Carl G. Henning Hansen
3. Kresten Lindorff-Larsen

• Curated by eLife

  Evaluation Summary:

  The manuscript describes a metadynamics simulation-based characterization of the binding and unbinding dynamics of a buried phosphorylated residue in the inhibitory module to the functional domain of Vav1, in an effort to shed lights on the autoinhibition mechanism. The work led to a conformation-selection scenario of the event. The authors discussed the inconsistency between the computational findings and the NMR data, in terms of the free energy differences between the bound and unbound states. Further justification is required for the somewhat ad hoc choice of three collective variables for the metadynamics simulations, including two that are highly correlated.

  (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