Biophysics

The Glycan-Specificity of the Pineapple Lectin AcmJRL and its Carbohydrate-Dependent Binding of the SARS-CoV-2 Spike Protein

1. Joscha Meiers
2. Jan Dastbaz
3. Sebastian Adam
4. Sari Rasheed
5. Susanne H. Kirsch
6. Peter Meiser
7. Peter Gross
8. Rolf Müller
9. Alexander Titz

Reviewed by ScreenIT

A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging

1. Xingbo Yang
2. Gloria Ha
3. Daniel J Needleman

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to scientists who use imaging approaches to study cellular metabolism. It presents a new coarse-grained model for inferring mitochondrial NADH oxidation from NAD(P)H fluorescence lifetime imaging in mouse oocytes. The modeling is thoughtfully and clearly presented, but the validity of some key assumptions of the model and the overall generalizability of the method to other cell types could be strengthened.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

A Theory of Synaptic Transmission

1. Bin Wang
2. Olga K. Dudko

• Curated by eLife

  Evaluation Summary:

  The present MS describes an effort to create a general mathematical model of synaptic neurotransmission. The authors invested great efforts to create a complex model of the presynaptic mechanisms. This is an exceptionally challenging task and it falls short of a true general theory. Nonetheless, the model will be an important addition to an emerging field attempting to generate predictive models of complex neuronal biophysical processes, including synaptic transmission.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript.The reviewers remained anonymous to the authors.)

Reviewed by eLife

Structural basis for substrate selection by the SARS-CoV-2 replicase

1. Brandon F. Malone
2. Jason K. Perry
3. Paul Dominic B. Olinares
4. Hery W. Lee
5. James Chen
6. Todd C. Appleby
7. Joy Y. Feng
8. John P. Bilello
9. Honkit Ng
10. Johanna Sotiris
11. Mark Ebrahim
12. Eugene Y. D. Chua
13. Joshua H. Mendez
14. Ed T. Eng
15. Robert Landick
16. Matthias Götte
17. Brian T. Chait
18. Elizabeth A. Campbell
19. Seth A. Darst

Reviewed by ScreenIT

Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography

1. Alberto Borsatto
2. Obaeda Akkad
3. Ioannis Galdadas
4. Shumeng Ma
5. Shymaa Damfo
6. Shozeb Haider
7. Frank Kozielski
8. Carolina Estarellas
9. Francesco Luigi Gervasio

• Curated by eLife

  eLife assessment

  SARS-CoV-2 nonstructural protein (Nsp1) has emerged as an attractive target as it plays an important role in modulating the host and viral gene expression. This study describes multiple druggable sites in Nsp1. A 1.1Å co-crystal structure of Nsp1 with a fragment, together with computational studies, provides a framework for the rational design of potential antiviral candidates. This important study is methodologically convincing and will be of interest to researchers in the fields of structural virology and rational drug design.

Reviewed by eLife, ScreenIT

Novel analytical tools reveal that local synchronization of cilia coincides with tissue-scale metachronal waves in zebrafish multiciliated epithelia

1. Christa Ringers
2. Stephan Bialonski
3. Mert Ege
4. Anton Solovev
5. Jan Niklas Hansen
6. Inyoung Jeong
7. Benjamin M Friedrich
8. Nathalie Jurisch-Yaksi

• Curated by eLife

  Evaluation Summary:

  This is a comprehensive, in vivo study of motile cilia dynamics, organisation and coordination in the larval zebrafish nose. The authors used a combination of highly quantitative imaging methods and transgenics to visualise the properties of multiciliated cells in this model organism - with particular emphasis on measuring the spatiotemporal coherence and organisation of cilia across the organ, and on the discovery of large-scale metachronal waves. With the aid of a computational model, the authors also explored the implications of metachronal ciliary action for fluid pumping.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies

1. Rachel A Banks
2. Vahe Galstyan
3. Heun Jin Lee
4. Soichi Hirokawa
5. Athena Ierokomos
6. Tyler D Ross
7. Zev Bryant
8. Matt Thomson
9. Rob Phillips

• Curated by eLife

  Evaluation Summary:

  This study investigates on how weight loss by bariatric surgery or weight-matched dietary intervention impairs breast cancer growth as well as immunotherapy. This study can potentially provide some therapeutic intervention strategies on combining vertical sleeve gastrectomy and immunotherapy in treating breast cancer.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

In situ architecture and membrane fusion of SARS-CoV-2 Delta variant

1. Yutong Song
2. Hangping Yao
3. Nanping Wu
4. Jialu Xu
5. Zheyuan Zhang
6. Cheng Peng
7. Shibo Li
8. Weizheng Kong
9. Yong Chen
10. Miaojin Zhu
11. Jiaqi Wang
12. Danrong Shi
13. Chongchong Zhao
14. Xiangyun Lu
15. Martín Echavarría Galindo
16. Sai Li

Reviewed by ScreenIT

Effect on the conformations of the spike protein of SARS‐CoV‐2 due to mutation

1. Aayatti Mallick Gupta
2. Jaydeb Chakrabarti

Reviewed by ScreenIT

Structural basis of ion – substrate coupling in the Na+-dependent dicarboxylate transporter VcINDY

1. David B. Sauer
2. Jennifer J. Marden
3. Joseph C. Sudar
4. Jinmei Song
5. Christopher Mulligan
6. Da-Neng Wang

• Curated by Biophysics Colab

  Endorsement statement (28 June 2022)

  Sauer et al. describe two cryo-EM structures of the Na⁺-dependent dicarboxylate transporter VcINDY in two inward-facing states. The high-quality structural data, complemented by NMR-inspired analysis, functional assays and cysteine accessibility measurements, reveal crucial conformational changes induced by Na⁺ binding to apo VcINDY that result in formation of the substrate-binding site. This is a strong manuscript that provides an important contribution to our understanding of the transport mechanism in the SLC13/DASS family of transporters, several members of which have critical physiological functions. The work will be of interest to researchers working on this and other ion-coupled transporter families.

  (This endorsement by Biophysics Colab refers to the version of record for this work, which is linked to and has been revised from the original preprint following peer review.)

Reviewed by Biophysics Colab