Biophysics

Computational model of the full-length TSH receptor

1. Mihaly Mezei
2. Rauf Latif
3. Terry F Davies

• Curated by eLife

  Evaluation Summary:

  This manuscript presents the first molecular dynamics (MD) simulations of full-length membrane-bound Thyroid Stimulating Hormone Receptor (TSHR). The authors find that its linker region (LR) is disordered, contrasting previous models. While this is largely a solid study that would interest researchers working in computational modeling, thyroid hormone metabolism, and signaling, the rationale for the arbitrarily chosen starting model and unclear mechanistic relevance need to be clarified further.

  (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

Rabphilin 3A binds the N-peptide of SNAP-25 to promote SNARE complex assembly in exocytosis

1. Tianzhi Li
2. Qiqi Cheng
3. Shen Wang
4. Cong Ma

• Curated by eLife

  Evaluation Summary:

  Li et al. use biochemical binding analysis to explore the role of Rabphilin 3A in dense-core vesicle exocytosis in neuroendocrine PC12 cells and in an in vitro SNARE assembly assay. They propose that the Rph3A binding to SNAP25 pre-structures the protein to efficiently assemble with Syntaxin and VAMP2, and thus, promoting the vesicle docking and priming process. This work will be of interest to scientists studying the molecular basis of synaptic vesicle release.

  (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

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times

1. Fengbin Wang
2. Chi Ho Chan
3. Victor Suciu
4. Khawla Mustafa
5. Madeline Ammend
6. Dong Si
7. Allon I Hochbaum
8. Edward H Egelman
9. Daniel R Bond

• Curated by eLife

  Evaluation Summary:

  This manuscript reports the CryoEM structure of OmcZ cytochrome nanowires of Geobacter sulfurreducens, the third cytochrome nanowire of Geobacter to be structurally resolved. OmcZ differs structurally from these previously determined nanowire structures, showing a different heme chain configuration. Based on these and other differences the authors speculate about the evolutionary origin of these nanowires and the mechanism of long-range electron transport. This manuscript is an important contribution to the field of electron transfer and will be of interest to everyone working in electron transfer and filament formation and interested in their evolution.

  (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

Membrane curvature governs the distribution of Piezo1 in live cells

1. Shilong Yang
2. Xinwen Miao
3. Steven Arnold
4. Boxuan Li
5. Alan T. Ly
6. Huan Wang
7. Matthew Wang
8. Xiangfu Guo
9. Medha M. Pathak
10. Wenting Zhao
11. Charles D. Cox
12. Zheng Shi

• Curated by Biophysics Colab

  Endorsement statement (6 December 2022)

  The preprint by Yang et al. asks how the shape of the membrane influences the localization of mechanosensitive Piezo channels. The authors use a creative approach involving methods that distort the plasma membrane by generating blebs and artificial filopodia. They convincingly show that curvature of the lipid environment influences Piezo1 localization, such that increased curvature causes channel depletion, and that application of the chemical modulator Yoda1 is sufficient to allow channels to enter filopodia. The study provides support for a provocative “flattening model” of Yoda1 action, and should inspire future studies by researchers interested in mechanosensitive channels and membrane curvature.

  (This endorsement by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

Reviewed by Biophysics Colab

Architecture of the chikungunya virus replication organelle

1. Timothée Laurent
2. Pravin Kumar
3. Susanne Liese
4. Farnaz Zare
5. Mattias Jonasson
6. Andreas Carlson
7. Lars-Anders Carlson

Reviewed by Review Commons

Ranking Peptide Binders by Affinity with AlphaFold**

1. Liwei Chang
2. Alberto Perez

Reviewed by Arcadia Science

Versatile patterns in the actin cortex of motile cells: Self-organized pulses can coexist with macropinocytic ring-shaped waves

1. Arik Yochelis
2. Sven Flemming
3. Carsten Beta

• Curated by eLife

  Evaluation Summary:

  Individual cells may act in response to stimuli or in a self-organized fashion. The relative weight of these two modes determines in the end to which degree cells or rather organs/organisms carry function. This study reports an example of very complex self-organization of actin waves as the coexistence of slowly moving broad waves of high F-actin concentration and rapidly propagating planar F-actin pulses. The paper is interesting for everybody interested in conceptual questions like signalling versus self-organization, in cellular morpho-dynamics and theory of dynamic patterns.

  (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

Dilated cardiomyopathy mutation E525K in human beta-cardiac myosin stabilizes the interacting-heads motif and super-relaxed state of myosin

1. David V Rasicci
2. Prince Tiwari
3. Skylar ML Bodt
4. Rohini Desetty
5. Fredrik R Sadler
6. Sivaraj Sivaramakrishnan
7. Roger Craig
8. Christopher M Yengo

• Curated by eLife

  Evaluation Summary:

  This study seeks to develop the use of a FRET-based sensor for the formation of the folded 'interacting heads motif' structure for cardiac myosin, which is thought by some to represent a super-relaxed state with lower basal ATPase activity. This study offers some evidence that there is a relationship between the super-relaxed state and the 'interacting heads motif' structure, and that a specific dilated cardiomyopathy mutant in this myosin stabilizes the 'interacting heads motif' conformation. This paper will be of interest to muscle and cardiovascular biologists as it provides important insights into the correlation of structural and functional states of motor proteins in the context of cardiac muscle. The data qualitatively support this correlation and suggest a new mode of action of disease-causing mutations that lead to impaired contractile 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 #2 agreed to share their name with the authors.)

Reviewed by eLife

In situ single particle classification reveals distinct 60S maturation intermediates in cells

1. Bronwyn A Lucas
2. Kexin Zhang
3. Sarah Loerch
4. Nikolaus Grigorieff

• Curated by eLife

  Evaluation Summary:

  This paper explores the use of 2D high-resolution template-matching (2DTM) to locate and discriminate highly similar macromolecules within cryo-EM images of focused ion beam-milled cells. It demonstrates that differences in the 2DTM signal-to-noise ratios for located targets against multiple search templates can effectively segregate a mixed population of similar structures, as well as present a formal analysis strategy for probabilistic assignment of species within the mixed population. Because the identification of distinct structural states of macromolecular complexes inside the cell is a fundamental problem in 3D visual proteomics, this paper will be of broad interest to both structural and cell biologists.

  (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 name with the authors.)

Reviewed by eLife

Trapped Pore Waters in the Open Proton Channel H _V 1

1. Danila Boytsov
2. Stefania Brescia
3. Gustavo Chaves
4. Sabina Koefler
5. Christof Hannesschlaeger
6. Christine Siligan
7. Nikolaus Goessweiner‐Mohr
8. Boris Musset
9. Peter Pohl

Reviewed by Review Commons