Biophysics

A complete map of specificity encoding for a partially fuzzy protein interaction

1. Taraneh Zarin
2. Ben Lehner

Reviewed by PREreview

Cryo-EM structure and biochemical analysis of human chemokine receptor CCR8

1. Qi Peng
2. Haihai Jiang
3. Xinyu Cheng
4. Na Wang
5. Sili Zhou
6. Yuting Zhang
7. Tingting Yang
8. Yixiang Chen
9. Wei Zhang
10. Sijia Lv
11. Weiwei Nan
12. JianFei Wang
13. Guo-Huang Fan
14. Jian Li
15. Jin Zhang

Reviewed by PREreview

The mechanism of mammalian proton-coupled peptide transporters

1. Simon M Lichtinger
2. Joanne L Parker
3. Simon Newstead
4. Philip C Biggin

• Curated by eLife

  eLife assessment

  This study provides important insight into the mechanisms of proton-coupled oligopeptide transporters. It uses enhanced-sampling molecular dynamics (MD), backed by cell-based assays, revealing the importance of protonation of selected residues for PepT2 function. The simulation approaches are convincing, using long MD simulations, constant-pH MD and free energy calculations. Overall, the work has led to findings that will appeal to structural biologists, biochemists, and biophysicists studying membrane transporters.

Reviewed by eLife

Insulator-based dielectrophoresis-assisted separation of insulin secretory vesicles

1. Mahta Barekatain
2. Yameng Liu
3. Ashley Archambeau
4. Vadim Cherezov
5. Scott Fraser
6. Kate L White
7. Mark A Hayes

• Curated by eLife

  eLife assessment

  This paper presents a new method for separating organelles in an unbiased way. The method is applied to the separation of distinct subpopulations of insulin vesicles. There are concerns around whether the vesicles measured are in fact insulin vesicles and whether the observed changes in vesicle populations upon glucose stimulation are biologically meaningful, and thus it is difficult to assess at this stage how well the technique performs. This paper is likely to be of wide interest to cell biologists studying a variety of compartments, as well as to researchers in the beta cell field.

Reviewed by eLife

AlphaFold-SFA: accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics

1. Shray Vats
2. Raitis Bobrovs
3. Pär Söderhjelm
4. Soumendranath Bhakat

Reviewed by Biophysics Colab

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 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, 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