Biophysics

Decoding phase separation of prion-like domains through data-driven scaling laws

1. M Julia Maristany
2. Anne Aguirre Gonzalez
3. Jorge R Espinosa
4. Jan Huertas
5. Rosana Collepardo-Guevara
6. Jerelle A Joseph

• Curated by eLife

  eLife Assessment

  The authors performed extensive coarse-grained molecular dynamics simulations of 140 different prion-like domain variants to interrogate how specific amino acid substitutions determine the driving forces for phase separation. The analyses are solid, and the derived predictive scaling laws can aid in identifying potential phase-separating regions in uncharacterized proteins. Overall, this is a valuable contribution to the field of biomolecular condensates. It exemplifies how data-driven methodologies can uncover new insights into complex biological phenomena.

Reviewed by eLife

Toward Stable Replication of Genomic Information in Pools of RNA Molecules

1. Ludwig Burger
2. Ulrich Gerland

• Curated by eLife

  eLife Assessment

  This important theoretical study examines the possibility of encoding genomic information in a collective of short overlapping strands (e.g., the Virtual Circular Genome (VCG) model). The study presents solid theoretical arguments, simulations and comparisons to experimental data to point at potential features and limitations of such distributed collective encoding of information. The work should be of relevance to colleagues interested in molecular information processing and to those interested in pre-Central Dogma or prebiotic models of self-replication.

Reviewed by eLife

Mechanical imbalance between normal and transformed cells drives epithelial homeostasis through cell competition

1. Praver Gupta
2. Sayantani Kayal
3. Nobuyuki Tanimura
4. Shilpa P Pothapragada
5. Harish K Senapati
6. Padmashree Devendran
7. Yasuyuki Fujita
8. Dapeng Bi
9. Tamal Das

• Curated by eLife

  eLife Assessment

  In this important study, the authors combine innovative experimental approaches, including direct compressibility measurements and traction force analyses, with theoretical modeling to propose that wild-type cells exert compressive forces on softer HRasV12-transformed cells, influencing competition outcomes. The data generally provide solid evidence that transformed epithelial cells exhibit higher compressibility than wild-type cells, a property linked to their compaction during mechanical cell competition. However, the study would benefit from further characterization of how compression affects the behavior of HRasV12 cells and clearer causal links between compressibility and competition outcomes.

Reviewed by eLife

Cluster size determines morphology of transcription factories in human cells

1. Massimiliano Semeraro
2. Giuseppe Negro
3. Giada Forte
4. Antonio Suma
5. Giuseppe Gonnella
6. Peter R Cook
7. Davide Marenduzzo

• Curated by eLife

  eLife Assessment

  This is a valuable polymer model that provides insight into the origin of macromolecular mixed and demixed states within transcription clusters. The well-performed and clearly presented simulations will be of interest to those studying gene expression in the context of chromatin. While the study is generally solid, it could benefit from a more direct comparison with existing experimental data sets as well as further discussion of the limits of the underlying model assumptions.

Reviewed by eLife

De novo identification of universal cell mechanics gene signatures

1. Marta Urbanska
2. Yan Ge
3. Maria Winzi
4. Shada Abuhattum
5. Syed Shafat Ali
6. Maik Herbig
7. Martin Kräter
8. Nicole Toepfner
9. Joanne Durgan
10. Oliver Florey
11. Martina Dori
12. Federico Calegari
13. Fidel-Nicolás Lolo
14. Miguel Ángel del Pozo
15. Anna Taubenberger
16. Carlo Vittorio Cannistraci
17. Jochen Guck

• Curated by eLife

  eLife Assessment

  This important study uses machine learning-based network analysis on transcriptomic data from different tissue cell types to identify a small set of conserved (pan-tissue) genes associated with changes in cell mechanics. The new method, which provides a new type of approach for mechanobiology, is accessible, compelling, and well-validated using in silico and experimental approaches. The study provides motivation for researchers to test hypotheses concerning the identified five-gene network, and the method will be strengthened over time with expanded sets of validations, such as testing genes with hitherto unknown roles and different perturbation techniques.

Reviewed by eLife

Effects of residue substitutions on the cellular abundance of proteins

1. Thea K Schulze
2. Kresten Lindorff-Larsen

• Curated by eLife

  eLife Assessment

  This valuable study presents a thorough analysis of protein abundance changes caused by amino acid substitutions, using structural context to improve predictive accuracy. By deriving substitution response matrices based on solvent accessibility, the authors demonstrate that simple structural features can predict abundance effects with accuracy comparable to complex methods such as free energy calculations. The strength of the evidence is solid, supported by robust experimental design and comprehensive analyses. This work is expected to be of interest to broad audiences as it offers practical tools for analyzing mutational effects and insights into the structural basis of proteostasis.

Reviewed by eLife, PREreview

Structure and function of the human mitochondrial MRS2 channel

1. Zhihui He
2. Yung-Chi Tu
3. Chen-Wei Tsai
4. Jonathan Mount
5. Jingying Zhang
6. Ming-Feng Tsai
7. Peng Yuan

• Curated by Biophysics Colab

  Evaluation Statement (14 June 2024)

  The study by He et al. explores the structure and mechanisms of the human mitochondrial RNA splicing 2 (MRS2) protein, predicted to form Mg2+-selective channels in the mitochondrial inner membrane based on homology to the CorA family of prokaryotic Mg2+ channels. The authors use an innovative biochemical strategy to express MRS2 and perform single particle reconstructions in the absence and presence of key divalent cations. High resolution reconstructions of the pentameric channel reveal binding sites for Mg2+ and Ca2+, and electrophysiological investigations suggest that MRS2 is a Ca2+-regulated, cation-selective, Mg2+-permeable channel, in contrast to the Mg2+-regulated, Mg2+-selective CorA channel. This is an important study with interesting structural and functional observations, which will motivate further investigations of a potential role for MRS2 in mitochondrial Ca2+ signaling.

  Biophysics Colab recommends this study to scientists interested in the structure, function and regulation of cation channels as well as those working on mitochondrial transport.

  Biophysics Colab has evaluated this study as one that meets the following criteria:

  - Rigorous methodology

  - Transparent reporting

  - Appropriate interpretation

  (This evaluation 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

Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding

1. Sukrit Singh
2. Vytautas Gapsys
3. Matteo Aldeghi
4. David Schaller
5. Aziz M. Rangwala
6. Jessica B. White
7. Joseph P. Bluck
8. Jenke Scheen
9. William G. Glass
10. Jiaye Guo
11. Sikander Hayat
12. Bert L. de Groot
13. Andrea Volkamer
14. Clara D. Christ
15. Markus A. Seeliger
16. John D. Chodera

Reviewed by PREreview

Torsion is a Dynamic Regulator of DNA Replication Stalling and Reactivation

1. Xiaomeng Jia
2. Xiang Gao
3. Shuming Zhang
4. James T. Inman
5. Yifeng Hong
6. Anupam Singh
7. Smita Patel
8. Michelle D. Wang

Reviewed by PREreview

Physiological magnetic field strengths help magnetotactic bacteria navigate in simulated sediments

1. Agnese Codutti
2. Mohammad A Charsooghi
3. Konrad Marx
4. Elisa Cerdá-Doñate
5. Omar Muñoz
6. Paul Zaslansky
7. Vitali Telezki
8. Tom Robinson
9. Damien Faivre
10. Stefan Klumpp

• Curated by eLife

  eLife Assessment

  This study presents valuable experimental and numerical results on the motility of a magnetotactic bacterium living in sedimentary environments, particularly in environments of varying magnetic field strengths. The evidence supporting the claims of the authors is compelling and the study will be of specific relevance to biophysicists interested in bacterial motility.

Reviewed by eLife