Structural Biology and Molecular Biophysics

eLife assessment

This fundamental study examines the human voltage-gated chloride channel CLC-2. A compelling approach that combines cryo-EM, electrophysiology, and computational analysis provides convincing support for a "ball and chain" mechanism of inactivation. This and other findings regarding the gating and inhibition mechanisms of the channel are fundamentally interesting to ion channel physiologists.

eLife assessment

One of the most promising strategies in development of drugs targeting kinases is provided by using allosteric control that allows specific regulation and study of kinase function without directly targeting the active site. This important work reviews convincingly the current repertoire of tools for regulating the activity of protein kinases with the ultimate goal of developing novel approaches in treating diseases associated with signal dysregulation.

eLife assessment

This manuscript will provide a valuable method to evaluate the safety of MR in patients with orthopaedic implants, which is required in clinics. A strength of the work is that the in-silicon testbed is solid, based on the widely available human project, and validated. In addition, the toolbox will be open for clinical practice.

eLife assessment

This study provides an important demonstration of how the false-positive rate of high-resolution 2D template matching to find particles of a given target structure in 2D cryo-EM images (2DTM) relates to overfitting the data towards the template. The authors present new methods to measure the amount of model bias that gets introduced in high-resolution features of such maps, with compelling evidence that high-resolution features that are not present in the template can still be reconstructed in 3D from images obtained by 2DTM. The paper could be strengthened by the inclusion of a more elaborate discussion (and possibly additional experiments) to describe the limitations of 2DTM for smaller target structures.

eLife assessment

This important study describes the discovery and further engineering of a red light-activated, chloride-conducting Channelrhodopsin (ACR) that could be used to inhibit neuronal activity. The authors were able to demonstrate some inhibition of neuronal activities in vitro and in vivo with 635 nm light, however the study was incomplete. Adequate controls and direct comparisons to the performance of already-established variants were missing, making it difficult to confirm the future utility of MsACR1 and raACR1.

eLife assessment

This study provides a valuable starting point for unraveling the molecular basis of the pathological phenotypes of the repeat expansion in the gene associated with open reading frame 72 in human chromosome 9. The coarse-grained simulation method used by the authors goes beyond the state of the art, investigating a compelling number of binding partners. The evidence supporting the claims of the authors is solid, although validation of the results is needed to further strengthen the major conclusions of the work. The work will be of broad interest to biophysicists and biochemists.

eLife assessment

Using a novel micropipette-based, minimally invasive approach in combination with theoretical and computational analysis, this important work probes tissue mechanics in the Drosophila embryo. The authors provide compelling evidence for the applicability of their method, which reveals important differences between the mechanical properties on the apical and basal tissue sides. This work should be of broad interest to scientists studying tissue mechanics, membranes, and developmental processes.

eLife assessment

The manuscript describes a set of detailed modeling and experimental studies to disentangle the respective roles of gap junctional electrical vs. metabolic coupling mechanisms in the synchronization of islet activity. This is of interest due to the importance of islet synchronization and generally islet network properties in the regulation of insulin secretion from the pancreas. The significance of the findings was judged to be mostly important and the strength of evidence provided was judged to be mostly solid overall.

eLife assessment

This study, of interest to cell biologists, presents valuable findings on the positioning mechanics of microtubule asters in Drosophila embryo explants. While the experimental setting is artificial (centrosomes are detached from nuclei and the cell cycle is arrested in interphase in these explants), it extends the framework of aster positioning from recently published work. The authors reach the conclusion that asters interact via pushing forces, an interesting conclusion supported by solid evidence. The identification of motors and MAPs functioning in the aster positioning mechanism would further strengthen the study.

eLife assessment

The current manuscript offers important updates to qFit , the state-of-the art tool for modeling alternative conformations of protein molecules based on high resolution X-ray diffraction or Cryo-EM data. While the authors provide convincing examples of qFit's performance, these are restricted to selected test cases. This manuscript will be of interest to structural biologists and protein biochemists more generally.

eLife assessment:

This valuable study, of interest for students of the biology of genomes, uses simulations in combination with published data to examine how many TADs remain after cohesin depletion. The authors suggest that a significant subset of chromosome conformations do not require cohesin, and that knowledge of specific epigenetic states can be used to identify regions of the genome that still interact in the absence of cohesin. The theoretical approaches and quantitative analysis are state-of-the-art, and the data quality and strength of the conclusions are solid. However, because "physical boundaries (of domains?)" in the model appear to be a consequence of preserved TADs, rather than the other way around, the functional insights are limited.

eLife assessment

This valuable study illuminates molecular movements of acid-sensing ion channels by combining compelling advanced chemical biology and biophysical techniques. The evidence for the main claim, lack of interaction of molecular termini, is solid and challenges prior models. Some other claims warrant further evidence. This work will pique interest in the ion channel signaling field, providing a fresh perspective.

eLife assessment

This valuable study reports multi-scale molecular dynamics simulations to investigate a class of highly potent antibodies that simultaneously engage with the HIV-1 Envelope trimer and the viral membrane. The work provides insights into how broadly neutralizing antibodies associate with lipids proximal to membrane-associated epitopes to drive neutralization. However, the evidence for rules for lipid recognition in antibodies is still incomplete. In addition, the text would benefit from clearer subsections that delineate discrete mechanistic discoveries.

eLife assessment

The authors use a previously described technology of designing soluble transmembrane-targeting peptides, to interfere with the receptor function of the T cell receptor (TCR), which provides useful insights into the molecular mechanism of T cell activation. The designed PITCR peptide has functional effects, but the evidence for the proposed mechanism is still incomplete. With further data to support the conclusion, results from this study will be of interest to those studying the TCR as well as those seeking to use the TCR or its derivatives in synthetic biology studies and immunotherapy.

eLife assessment

The authors have developed a compelling coarse-grained simulation approach for nucleosome-nucleosome interactions within a chromatin array. The data presented are solid and provide new insights that allow for predictions of how chromatin interactions might occur in vivo, but some of the claims should be tempered. The tools will be valuable for the chromosome biology field.

eLife assessment

This important study presents findings with broad implications for the use of AlphaFold2 models in ligand binding pose modeling, a common task in protein structure modeling. The computational experiments and analyses provide compelling results for the GPCR protein family data, but the conclusions are likely to apply also to other proteins and they will therefore be of interest to biophysicists, physical chemists, structural biologists, and anyone interested or involved in structure-based ligand discovery.

eLife assessment

This exceptional work substantially advances our understanding of the mechanics of the Reissner's fibre (RF) by performing in-vivo experiments that track and analyze the behavior of the RF when it is cut and the behavior of ciliated cells touching the RF when contact is interrupted. The data is valuable and the conclusions are compelling. The work will be of broad interest to many research communities including developmental neuroscience and cilia biology.

eLife assessment

This manuscript reports the fundamental finding that an oligomeric protein kinase, CaMKII, can be phosphorylated by another molecule of the holoenzyme in a manner that does not involve subunit exchange. The evidence for the main conclusion is compelling, supported by several independent experiments. If independently confirmed in future, the study will stand as having provided a novel regulatory mechanism for the autophosphorylation of this kinase. The work will be of broad interest to molecular and cellular neuroscientists as well as biochemists.

eLife assessment

The authors describe the dynamics underlying allostery of the adenosine A1 receptor, providing valuable insights into the receptor's activation pathway. The enhanced sampling molecular dynamics simulations of available structural data, followed by network analysis, reveal transient conformational states and communication between functional regions. The authors carefully state the limitations of their work, including the restricted convergence of the free energy landscape and missing water-mediated hydrogen bond coordination. Collectively, they provide a convincing framework for advancing rational design strategies of specific modulators with desired modes of action.

[Editors' note: this was originally reviewed and assessed by Biophysics Colab]

Evaluation statement (16 June 2023)

Maria-Solano and Choi present the dynamics underlying allostery of the adenosine A1 receptor, providing valuable insights into the receptor's activation pathway. The enhanced sampling molecular dynamics simulations of available structural data, followed by network analysis, reveal transient conformational states and communication between functional regions. The authors carefully state the limitations of their work, including the restricted convergence of the free energy landscape and missing water-mediated hydrogen bond coordination. Collectively, the findings provide a convincing framework to advance rational design strategies of specific modulators with desired modes of action.

Biophysics Colab considers this to be a convincing study and recommends it to scientists interested in the structural dynamics, allosteric pathway activations, and free energy landscapes of GPCRs.

(This evaluation by Biophysics Colab refers to version 5 of this preprint, which has been revised in response to peer review of versions 3 and 4.)

eLife assessment

Cryo-EM has become the dominant method in structural biochemistry, and making more efficient use of expensive microscope time is therefore of broad interest to academic and industrial users. The authors identify a bottleneck in cryoEM data collection, namely path optimization, and provide a valuable machine-learning model to overcome this bottleneck. The solid data presented suggests their model can replace a human operator to automate efficient data collection.