Biophysics

Tension-Induced Stiffening of Cytoskeletal Components Regulates Cardiomyocyte Contractility

1. Mohammad Jafari
2. Sisir Datla
3. Elliot L. Elson
4. Brian E. Carlson
5. Tetsuro Wakatsuki
6. Farid Alisafaei

Reviewed by PREreview

Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications

1. Rasa Giniūnaitė
2. Rahul Sharma
3. John H. Maddocks
4. Skirmantas Kriaučionis
5. Daiva Petkevičiūtė-Gerlach

• Curated by eLife

  eLife Assessment

  This valuable simulation study proposes a new coarse-grained model to explain the effects of CpG methylation on nucleosome wrapping energy and nucleosome positioning. The evidence to support the claims in the paper looks solid and this work will be of interest to the researchers working on gene regulation and mechanisms of DNA methylation.

Reviewed by eLife

Quantifying the shape of cells - from Minkowski tensors to p-atic orders

1. Lea Happel
2. Griseldis Oberschelp
3. Valeriia Grudtsyna
4. Harish P Jain
5. Rastko Sknepnek
6. Amin Doostmohammadi
7. Axel Voigt

• Curated by eLife

  eLife Assessment

  This important work describes a set of parameters that give a robust description of shape features of cells in tissues. The evidence for the usefulness of these parameters is solid. The work should be of interest for anybody analyzing epithelial dynamics, but more details about the analysis of experimental images are necessary and some streamlining of the text would increase the accessibility of the material for non-specialists.

Reviewed by eLife

Phase-Space Dynamics Reveal Structured and Chaotic Motility in Human Sperm via DTW Clustering

1. Athanasia Sergounioti
2. Efstathios Alonaris
3. Dimitrios Rigas

Reviewed by PREreview

DIRseq: a method for predicting drug-interacting residues of intrinsically disordered proteins from sequences

1. Matthew MacAinsh
2. Sanbo Qin
3. Huan-Xiang Zhou

• Curated by eLife

  eLife Assessment

  This study presents a sequence-based method for predicting drug-interacting residues in intrinsically disordered proteins (IDPs), addressing an important challenge in understanding small-molecule:IDP interactions. The findings have solid support in illustrative examples that underscore the role of aromatic interactions. While predicted binding sites remain coarse, validation was done on a total of 10 IDPs, four of which thoroughly and six others less so. The method builds on previous work from the authors, with necessarily ad hoc modifications, and offers a starting point for further exploration in this emerging field.

Reviewed by eLife

AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2

1. Matteo Cagiada
2. F. Emil Thomasen
3. Sergey Ovchinnikov
4. Charlotte M. Deane
5. Kresten Lindorff-Larsen

Reviewed by PREreview

Molecular Drivers of RNA Phase Separation

1. V Ramachandran
2. DA Potoyan

Reviewed by PREreview

Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes

1. Dario D’Asaro
2. Jean-Michel Arbona
3. Vinciane Piveteau
4. Aurèle Piazza
5. Cédric Vaillant
6. Daniel Jost

Reviewed by Review Commons

Atypical collective oscillatory activity in cardiac tissue uncovered by optogenetics

1. Alexander S Teplenin
2. Nina N Kudryashova
3. Rupamanjari Majumder
4. Antoine AF de Vries
5. Alexander V Panfilov
6. Daniël Pijnappels
7. Tim De Coster

• Curated by eLife

  eLife Assessment

  This important work provides mechanistic insights into the development of cardiac arrhythmia and establishes a new experimental use case for optogenetics in studying cardiac electrophysiology. The agreement between computational models and experimental observations provides a convincing level of evidence that wave train-induced pacemaker activity can originate in continuously depolarized tissue, with the limitation that there may be differences between depolarization arising from constant optogenetic stimulation, as opposed to pathophysiological tissue depolarization. Future experiments in vivo and in other tissue preparations would extend the generality of these findings.

Reviewed by eLife

Conduction pathway for potassium through the E. coli pump KdpFABC

1. Adel Hussein
2. Xihui Zhang
3. Bjørn Panyella Pedersen
4. David L Stokes

• Curated by eLife

  eLife Assessment

  This valuable study provides new insights into the movement of ions through the bacterial pump KdpFABC, which regulates intracellular potassium concentration, by solving a 2.1 Å cryo-EM structure of the nanodisc-embedded active wild-type protein, and carrying out mutagenesis and activity assays. Although the structural data and analysis are solid, additional information about other structural classes identified in the EM data, as well as a discussion of relevant work done by others, would further strengthen these findings. The description of the activity assays is currently incomplete because more information is required to rigorously assess these experiments. This work will be of interest to the membrane transporter and channel communities and to microbiologists interested in osmoregulation and potassium homeostasis.

Reviewed by eLife