Biophysics

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 Petkevičiūteė-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

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

Dimerization and dynamics of human angiotensin-I converting enzyme revealed by cryo-EM and MD simulations

1. Jordan M Mancl
2. Xiaoyang Wu
3. Minglei Zhao
4. Wei-Jen Tang

• Curated by eLife

  eLife Assessment

  This study shows, for the first time, the structure and snapshots of the dynamics of the full-length soluble Angiotensin-I converting enzyme dimer. The combination of structural and computational analyses provides compelling evidence that reveals the conformational dynamics of the complex and key regions mediating the conformational change. This fundamental work illustrates how conformational heterogeneity can be used to gain insights into protein function.

Reviewed by eLife

Emergence of specific binding and catalysis from a designed generalist binding protein

1. Yuda Chen
2. Sagar Bhattacharya
3. Lena Bergmann
4. Galen J. Correy
5. Sophia K. Tan
6. Kaipeng Hou
7. Justin Biel
8. Lei Lu
9. Ian Bakanas
10. Alexander N. Volkov
11. Ivan V. Korendovych
12. Nicholas F. Polizzi
13. James S. Fraser
14. William F. DeGrado

Reviewed by Arcadia Science

Expanding automated multiconformer ligand modeling to macrocycles and fragments

1. Jessica Flowers
2. Nathaniel Echols
3. Galen J Correy
4. Priyadarshini Jaishankar
5. Takaya Togo
6. Adam R Renslo
7. Henry van den Bedem
8. James S Fraser
9. Stephanie A Wankowicz

• Curated by eLife

  eLife Assessment

  The work presents a valuable extension of qFit-ligand, a computational method for modeling conformational heterogeneity of ligands in X-ray crystallography and cryo-EM density maps. The authors provide solid evidence of improved capabilities through careful validation against the previous version, particularly in expanding ligand sampling within conformational space. Such improvements suggest practical utility for challenging applications, including macrocyclic compound modeling and crystallographic drug fragment screening.

Reviewed by Arcadia Science, eLife

Impacts of structural properties of myosin II filaments on force generation

1. Shihang Ding
2. Pei-En Chou
3. Shinji Deguchi
4. Taeyoon Kim

• Curated by eLife

  eLife Assessment

  The authors present a useful agent-based model to study the tensile force generated by myosin mini-filaments in actin systems (bundles and networks); by numerically solving a mechanical model of myosin-II filaments, the authors provide insights into how the geometry of the molecular components and their elastic responses determine the force production. This work is of interest to biophysicists (in particular theoreticians) investigating force generation of motor molecules from a biomechanical engineering and physics perspective. The authors convincingly show that cooperative effects between multiple myosin filaments can enhance the total force generated, but not the efficiency of force generation (force per myosin) if passive cross-linkers are present. This work would benefit from a more extensive discussion of the physiological relevance of the results in view of the existing experimental literature, and how the principles that govern the behavior could be different for different motor proteins.

Reviewed by eLife

Quantifying Intracellular Mechanosensitive Response upon Spatially Defined Mechano-Chemical Triggering

1. Elaheh Zare-Eelanjegh
2. Renard TM Lewis
3. Ines Lüchtefeld
4. Ulrike Kutay
5. Tomaso Zambelli

• Curated by eLife

  eLife Assessment

  This valuable study provides evidence that the integration of the nuclear envelope into the endoplasmic reticulum provides a mechanism for mechanical integration across this continuous membrane system. If robustly demonstrated, this work would open up new avenues for studying organelle membrane tension homeostasis. While the evidence is largely convincing and carefully quantified, a key limitation is the absence of data demonstrating that microinjection of cytoskeleton-depolymerizing drugs locally disrupts the target network.

Reviewed by eLife