Biophysics

AlphaFold-SFA: accelerated sampling of cryptic pocket opening by fusing AlphaFold, slow feature analysis and metadynamics

1. Shray Vats
2. Pär Söderhjelm
3. Soumendranath Bhakat

Reviewed by Biophysics Colab

Mechanism of Dimer Selectivity and Binding Cooperativity of BRAF Inhibitors

1. Joseph Clayton
2. Aarion Romany
3. Evangelia Matenoglou
4. Evripidis Gavathiotis
5. Poulikos I. Poulikakos
6. Jana Shen

• Curated by eLife

  eLife assessment

  This important work illuminates the dynamics of BRAF in both its monomeric and dimeric forms, with or without inhibitors, combining traditional techniques and sophisticated computational analyses. The evidence presented is convincing and suggests a potential allosteric effect, though substantiating the exact mechanism will require further studies. The work has implications for understanding kinase signaling and the development of potential drug candidates. This study will be of interest to structural biologists, medicinal chemists, and pharmacologists.

Reviewed by eLife

An Integrated Machine Learning Approach Delineates an Entropic Expansion Mechanism for the Binding of a Small Molecule to α -Synuclein

1. Sneha Menon
2. Subinoy Adhikari
3. Jagannath Mondal

• Curated by eLife

  eLife assessment

  This study describes the application of machine learning and Markov state models to characterize the binding mechanism of alpha-Synuclein to the small molecule Fasudil. The results suggest that entropic expansion can explain such binding. However, the simulations and analyses in their present form are inadequate.

Reviewed by eLife

Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription

1. Yi-Che Chang
2. Sofia A. Quinodoz
3. Clifford P. Brangwynne

• Curated by eLife

  eLife assessment

  This valuable study establishes a method for live-cell imaging, tracking, and quantification of Alu elements marking euchromatic regions of the nucleus. The method will help characterize the relationship between chromatin dynamics and transcriptional activity. While the findings are largely consistent with previous reports, characterization of the technique is incomplete and could benefit from additional controls.

Reviewed by eLife

Intracellular mechanical fingerprint reveals cell type specific mechanical tuning

1. Till M. Muenker
2. Bart E. Vos
3. Timo Betz

• Curated by eLife

  eLife assessment

  Münker and colleagues use an optical tweezer setup to apply oscillatory forces to endocytosed/phagocytosed glass beads over a wide frequency range (from ~1 to 1000 Hz) and probe cytoplasmic material properties at multiple time scales in six different cell types. Using statistical methods and principal component analysis, they find that the active and passive mechanical properties of cells can be described by 6 parameters (from power law fits) that allow characterizing the viscous and elastic nature of the cytoplasmic material as well as an effective active energy driven by cellular metabolism. Overall, this is very well done and important work, using convincing and state-of-the-art methods, albeit with some limitations related to the way the beads are internalized.

Reviewed by eLife

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, although the novelty of the findings should be discussed in connection with the previous works. This work will be of interest to the researchers working on gene regulation and mechanisms of DNA methylation.

Reviewed by eLife

Biophysics of microRNA-34a targeting and its influence on down-regulation

1. Lara Sweetapple
2. David M Kosek
3. Elnaz Banijamali
4. Walter Becker
5. Juliane Müller
6. Christina Karadiakos
7. Lorenzo Baronti
8. Ileana Guzzetti
9. Dimitri Schritt
10. Alan Chen
11. Emma R Andersson
12. Katja Petzold

Reviewed by Review Commons

Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern

1. Callum M Ives
2. Linh Nguyen
3. Carl A Fogarty
4. Aoife M Harbison
5. Yves Durocher
6. John Klassen
7. Elisa Fadda

• Curated by eLife

  eLife assessment

  This study presents an important finding on the structural role of glycosylation at position N343 of the SARS-CoV-2 spike protein's receptor-binding domain in maintaining its stability, with implications across different variants of concern. The evidence supporting the claims of the authors is convincing, since appropriate and validated methodology in line with current state-of-the-art has been approached. The work will be of interest to evolutionary virologists.

Reviewed by eLife

Potassium-mediated bacterial chemotactic response

1. Chi Zhang
2. Rongjing Zhang
3. Junhua Yuan

• Curated by eLife

  eLife assessment

  In this important study, the authors report a novel measurement of the Escherichia coli chemotactic response and demonstrate that these bacteria display an attractant response to potassium, which is connected to intracellular pH level. The experimental evidence provided is convincing and the work will be of interest to microbiologists studying chemotaxis.

Reviewed by eLife

Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion

1. Tianyu Yuan
2. Hao Yan
3. Kevin C. Li
4. Ivan Surovtsev
5. Megan C. King
6. Simon G. J. Mochrie

Reviewed by Review Commons