Biophysics

Differential conformational dynamics in two type-A RNA-binding domains drive the double-stranded RNA recognition and binding

1. Firdousi Parvez
2. Devika Sangpal
3. Harshad Paithankar
4. Zainab Amin
5. Jeetender Chugh

• Curated by eLife

  eLife assessment

  This study presents a useful comparison of the dynamic properties of two RNA-binding domains. The data collection and analysis are solid, making excellent use of a suite of NMR experiments and ITC data. Nonetheless, reported evidence was found to only partially support the proposed connection between the backbone dynamics of the tandem domains and their RNA binding activity. This work will be of interest to biophysicists working on RNA-binding proteins.

Reviewed by eLife

OpenNucleome for high-resolution nuclear structural and dynamical modeling

1. Zhuohan Lao
2. Kartik D Kamat
3. Zhongling Jiang
4. Bin Zhang

• Curated by eLife

  eLife assessment

  This important work significantly advances the field of computational modelling of genome organisation through the development of OpenNucleome. The evidence supporting the tool's effectiveness is compelling, as the authors compare their predictions with experimental data. It is anticipated that OpenNucleome will attract significant interest from the biophysics and genomics communities.

Reviewed by eLife

Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts

1. Po-Lin Chiu
2. Juan D Orjuela
3. Bert L de Groot
4. Camilo Aponte Santamaría
5. Thomas Walz

• Curated by eLife

  eLife assessment

  This manuscript aims to unravel the contribution of cholesterol to aquaporin-0 (AQP0) tetramer array formation within lens membranes. Compelling electron crystallography data are combined with solid molecular dynamics experiments to identify a specific cholesterol binding site of significance to protein clustering within lipid rafts. The important work advances our understanding of membrane biology and will be of broad interest to membrane transport biologists, biochemists, and structural biologists.

Reviewed by eLife

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