Biophysics

CaMKII autophosphorylation can occur between holoenzymes without subunit exchange

1. Iva Lučić
2. Léonie Héluin
3. Pin-Lian Jiang
4. Alejandro G Castro Scalise
5. Cong Wang
6. Andreas Franz
7. Florian Heyd
8. Markus C Wahl
9. Fan Liu
10. Andrew JR Plested

• Curated by eLife

  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.

Reviewed by eLife

How accurately can one predict drug binding modes using AlphaFold models?

1. Masha Karelina
2. Joseph J Noh
3. Ron O Dror

• Curated by eLife

  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.

Reviewed by eLife

Emergence of flagella-like oscillations in single microtubules driven by collective dynein transport

1. Shivani A. Yadav
2. Neha Khetan
3. Dhruv Khatri
4. Chaitanya A. Athale

Reviewed by Review Commons

Biomimetic actin cortices shape cell-sized lipid vesicles

1. Lucia Baldauf
2. Felix Frey
3. Marcos Arribas Perez
4. Miroslav Mladenov
5. Michael Way
6. Timon Idema
7. Gijsje H. Koenderink

Reviewed by Arcadia Science

Dynamic allosteric networks drive adenosine A1 receptor activation and G-protein coupling

1. Miguel A Maria-Solano
2. Sun Choi

• Curated by eLife

  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]

• Curated 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.)

Reviewed by eLife, Biophysics Colab

Optimized path planning surpasses human efficiency in cryo-EM imaging

1. Yilai Li
2. Quanfu Fan
3. Ziping Xu
4. Emma Rose Lee
5. John Cohn
6. Veronique Demers
7. Ja Young Lee
8. Lucy Yip
9. Michael A. Cianfrocco
10. Seychelle M. Vos

• Curated by eLife

  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.

Reviewed by eLife

Conformational dynamics of lipid transfer domains provide a general framework to decode their functional mechanism

1. Sriraksha Srinivasan
2. Andrea Di Luca
3. Arun T. John Peter
4. Charlotte Gehin
5. Museer A. Lone
6. Thorsten Hornemann
7. Giovanni D’Angelo
8. Stefano Vanni

Reviewed by Review Commons

Free energy landscapes of KcsA inactivation

1. Sergio Pérez-Conesa
2. Lucie Delemotte

• Curated by eLife

  eLife assessment

  In this valuable study, advanced simulation methodologies are used to extract the mechanisms of inactivation for the potassium ion channel KcsA. The string method approach provides solid evidence that reveal features associated with the interplay between gate size and collapse of the selectivity filter, as well as remarkable differences between different force fields. While this manuscript does not address recent discoveries in K channel inactivation involving dilated selectivity filter structures obtained by Xray and cryo-EM, it does help us understand the KcsA constriction process. With added descriptions and analysis of collective variables, improved reproducibility of results, consistency between string method free energies and unbiased simulations, and improved transition rate calculation, this manuscript will be of interest to the ion channel field.

Reviewed by eLife

Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike

1. Ahmad Reza Mehdipour
2. Gerhard Hummer

Reviewed by ScreenIT

Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex

1. James Chen
2. Brandon Malone
3. Eliza Llewellyn
4. Michael Grasso
5. Patrick M.M. Shelton
6. Paul Dominic B. Olinares
7. Kashyap Maruthi
8. Edward T. Eng
9. Hasan Vatandaslar
10. Brian T. Chait
11. Tarun M. Kapoor
12. Seth A. Darst
13. Elizabeth A. Campbell

Reviewed by ScreenIT