Biophysics

eLife assessment

Single-particle tomography (SPT) is a useful method to determine the structure of proteins imaged in situ. This important work presents an easy-to-use tool for SPT that approximates the use of 2D tomographic projections using a "pseudo-subtomogram" data structure, chosen to facilitate implementation within the existing Relion codebase. The examples shown provide solid support for the claims about the efficacy of the approach.

eLife assessment

The goal of this study is to identify allosteric modulators of a SLC-1 amino acid transporter, ASCT2, which has been implicated in cancer progression. By combining computational and docking methods with functional measurements, this study provides solid evidence for specific aspects of allosteric SLC-1 inhibition mechanisms. The findings are important to transporter mechanism and pharmacology.

eLife assessment

The authors measure the work output of shrinking mammalian microtubules, reporting results of fundamental importance that advance our mechanistic understanding of how shrinking microtubules exert forces on chromosomes during cell division. Carefully performed, technically advanced experiments and model-based quantitative data analysis provide compelling evidence for the authors' conclusions. This work will be of interest for cell biologists interested in cell division, biophysicists interested in force production by biopolymers, and structural biologists interested in microtubule dynamics.

eLife assessment

This paper, which provides useful information on the assembly of volume-regulated anions channels formed by LRRC8 proteins, will be of interest scientists in the field of ion channels. The authors report the structure of a LRRC8C-LRRC8A chimera with native functional properties as a heptameric complex with a lipid-filled pore. This is very interesting and well-presented work, but the evidence supporting the physiological relevance of the heptameric assembly and the hypothesized role of lipids is still incomplete.

eLife Assessment:

Predicting the effect of mutations on protein stability is important both for protein engineering and for helping to decipher the effects of genetic and clinical mutations. The machine learning methodology introduce here is timely in view of the millions of AlphaFold model structures that are now becoming available, which could hypothetically be examined through approaches such as this one. The methodology presented is valuable, but the manuscript would benefit from a substantial amount of comparative data to provide more compelling evidence for the validity of the methods.

eLife assessment

This work is of high relevance to developmental and quantitative biologists with an interest in morphogen-mediated position decoding. A general mathematical model formulation is presented that is nevertheless accessible to a broad audience. Model tests via perturbation experiments in the Drosophila wing disc look promising and inspire a new round of data generation.

eLife assessment

The replication protein A (RPA) plays a critical role in DNA replication, DNA repair, and recombination by interacting with various proteins. This paper describes the structure of an N-terminus OB-fold of the 70kD subunit of human replication protein A (RPA70N or DNA-binding domain-F) bound to peptides from five different proteins, HELB, ATRIP, BLM, RMI1, and WRN. This paper provides useful knowledge regarding the structural flexibility of RPA70N in the binding to the different interacting peptides. The structural and biochemical analyses of the interaction of RPA70N with the different peptides provide solid evidence for the presented conclusion. The work will be of interest to those studying DNA replication, recombination and repair.

eLife assessment

This study provides new experimental data and detailed modeling of the partitioning of low copy plasmids under the control of the ParABS system in bacteria. The dynamics of the partition complex is tracked over many generations, providing useful data to constrain the models. The authors propose a model which can manifest either regular positioning or oscillations depending on the model parameters. The research will be of interest to biologists and biophysicists interested in cellular dynamics and internal organization in bacteria.

eLife assessment

This work addresses the mechanisms of action of the transmembrane proteins TMEM87A and TMEM87B, which are thought to play a role in protein transport, but have been implicated in other processes as well, such as signaling and acting as mechanosensitive ion channels. The study represents an important advance of the understanding of this poorly characterized family of proteins. While the structure is of low resolution, it is well interpreted, and authors take good advantage of AlphaFold2 to gain insights into potential function. The work is of interest to colleagues studying transporters and ion channels.

eLife assessment

The work by Kim et al., used synthetic constructs in Drosophila to examine the relationship between regulators (activator/repressor) and transcription initiation. By measuring regulator concentrations and the corresponding RNA polymerase initiation rates in different synthetic constructs and using a thermodynamic model, the authors concluded that that higher-order cooperativities between the repressor on adjacent binding sites, and that between the repressor and RNA polymerase are needed to explain the observed response curves in RNA polymerase loading rate. This work targets a challenging question in eukaryotic transcription regulation, where higher-order cooperativity between different molecular components, in addition to simple transcription factor binding and unbinding, is often necessary to account for observed promoter behaviors when multiple elements (repressors, mediators, activators) exist.