Biophysics

Analyzing SARS CoV-2 Patient Data Using Quantum Supervised Machine Learning

1. Zara Yu

Reviewed by ScreenIT

Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate PF-07321332

1. Jian Li
2. Cheng Lin
3. Xuelan Zhou
4. Fanglin Zhong
5. Pei Zeng
6. Yang Yang
7. Yuting Zhang
8. Bo Yu
9. Xiaona Fan
10. Peter J. McCormick
11. Rui Fu
12. Yang Fu
13. Haihai Jiang
14. Jin Zhang

Reviewed by ScreenIT

Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

1. Nicolai Tidemand Johansen
2. Marta Bonaccorsi
3. Tone Bengtsen
4. Andreas Haahr Larsen
5. Frederik Grønbæk Tidemand
6. Martin Cramer Pedersen
7. Pie Huda
8. Jens Berndtsson
9. Tamim Darwish
10. Nageshewar Rao Yepuri
11. Anne Martel
12. Thomas Günther Pomorski
13. Andrea Bertarello
14. Mark Sansom
15. Mikaela Rapp
16. Ramon Crehuet
17. Tobias Schubeis
18. Kresten Lindorff-Larsen
19. Guido Pintacuda
20. Lise Arleth

• Curated by eLife

  Evaluation Summary:

  Magnesium is an essential metal that is involved in vital biological processes. Using a model system, the authors discovered the presence of a conformational equilibrium between different unligated states that may explain the mechanism of magnesium transport. The combination of several different approach support the hypothesis that molecular motion is involved in the transport mechanism of Mg2+ ions.

  (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

The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates

1. Keith J Mickolajczyk
2. Paul Dominic B Olinares
3. Brian T Chait
4. Shixin Liu
5. Tarun M Kapoor

• Curated by eLife

  Evaluation Summary:

  Mickolajczyk et al. report the development of a new optical tweezers-based unbinding-force assay to characterize the interaction between the MIDAS domain of the mechanoenzyme Mdn1 and the ubiquitin-like (UBL) domain-containing ribosomal proteins Rsa1 and Ytm1. The authors show that the bond between MIDAS and Rsa1/Ytm1 can be best explained by a catch-slip bond behavior. The observations suggest that catch bonding between MIDAS and UBL domains plays a key role in the Mdn1-mediated ribosomal biogenesis. The reported results will be of interesting for the ribosomal and single-molecule biophysics communities and the developed DNA-tether-based optical tweezers assay will be useful for characterizing other molecular bonds.

  (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

The molecular mechanism of load adaptation by branched actin networks

1. Tai-De Li
2. Peter Bieling
3. Julian Weichsel
4. R Dyche Mullins
5. Daniel A Fletcher

• Curated by eLife

  Evaluation Summary:

  This in vitro study proposes to explain why branched actin filament networks, similar to the ones encountered in migrating cells, become denser when they grow against a mechanical load. This question is of broad interest, and has long been waiting for a molecular-scale explanation. Building on their previously published tools and results, the authors perform a series of elegant and clever experiments, and convincingly identify key molecular mechanisms. Importantly, the results also confirm the Brownian ratchet model for actin assembly. This study captures several important features of branched filament networks, and should become a reference on the topic.

  (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

Ligand binding remodels protein side-chain conformational heterogeneity

1. Stephanie A Wankowicz
2. Saulo H de Oliveira
3. Daniel W Hogan
4. Henry van den Bedem
5. James S Fraser

• Curated by eLife

  Evaluation Summary:

  This work attempts to extract information about protein thermodynamics from X-ray crystallography data, which is a challenging problem. This work presents a comprehensive examination of the structural transitions associated with small molecule binding to proteins. The heterogenous pattern of order parameter changes in response to ligand binding implies that the approach is identifying new information. This work offers insights into ligand binding affinity and specificity mechanisms, suggesting that distal (allosteric) perturbations represent a possible avenue to modulate protein 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. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Lactoferricins impair the cytosolic membrane of Escherichia coli within a few seconds and accumulate inside the cell

1. Enrico F Semeraro
2. Lisa Marx
3. Johannes Mandl
4. Ilse Letofsky-Papst
5. Claudia Mayrhofer
6. Moritz PK Frewein
7. Haden L Scott
8. Sylvain Prévost
9. Helmut Bergler
10. Karl Lohner
11. Georg Pabst

• Curated by eLife

  Evaluation Summary:

  This paper presents groundbreaking data on the effects of antimicrobial peptides on bacterial cells, obtained by time resolved small angle X-ray and neutron scattering experiments coupled to stopped-flow mixing. Application of this approach to cells is highly innovative and provides ms time resolution, and information on multiple length scales (from conformational changes in the cell, to structural changes in the membranes). This is an important extension of the effort of the scientific community to study model membranes. The main result is that the peptides reach the cytosol in a few seconds, accumulating to high concentrations. The data analysis should be improved, and many conclusions are speculative, in particular on the mechanism of entry of the peptides.

  (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

Unsupervised Bayesian Ising Approximation for decoding neural activity and other biological dictionaries

1. Damián G Hernández
2. Samuel J Sober
3. Ilya Nemenman

• Curated by eLife

  Evaluation Summary:

  Hernandez et al use an elegant mathematical framework to build a novel tool for extracting unusually frequent (or infrequent) patterns in multidimensional biological data when only a small number of measurements are available. This is a common problem in many biological settings, so the tool could potentially be used to answer a wide range of statistically hard questions. As a first demonstration of its use, the authors show that the new tool can be used to reveal novel properties about neural responses in zebra finches during song generation.

  (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

Conformational decoupling in acid-sensing ion channels uncovers mechanism and stoichiometry of PcTx1-mediated inhibition

1. Stephanie A Heusser
2. Christian B Borg
3. Janne M Colding
4. Stephan A Pless

• Curated by eLife

  Evaluation Summary:

  This work provides direct evidence that PcTx1, a modulator commonly used to study acid-sensing ion channels, induces a conformational change that persists long after an effect on the channel activity has dissipated. The data support this central claim of the paper and invite future investigation of the precise mechanism. The work is of general interest to those studying ion channel biophysics and pharmacology and is a fine example of the power of combined functional and fluorescence measurements.

  (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

Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern

1. Nabanita Mandal
2. Aditya K. Padhi
3. Soumya Lipsa Rath

Reviewed by ScreenIT