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A list by Biophysics Colab

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  1. 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

    5 evaluationsAppears in 7 listsLatest version Latest activity

  2. Modulation of cannabinoid receptor signaling by endocannabinoids

    1. Kaavya Krishna Kumar
    2. Michael J. Robertson
    3. Elina Thadhani
    4. Haoqing Wang
    5. Carl-Mikael Suomivuori
    6. Alexander S. Powers
    7. Lipin Ji
    8. Spyros P. Nikas
    9. Maria Gerasi
    10. Kiran Vemuri
    11. Ron O. Dror
    12. Asuka Inoue
    13. Alexandros Makriyannis
    14. Georgios Skiniotis
    15. Brian Kobilka
    Appears in 1 listLatest version

  9. Cryo-EM structures of an LRRC8 chimera with native functional properties reveal heptameric assembly

    1. Hirohide Takahashi
    2. Toshiki Yamada
    3. Jerod S Denton
    4. Kevin Strange
    5. Erkan Karakas

    • Curated by eLife

      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.

    Reviewed by eLife

    4 evaluationsAppears in 2 listsLatest version Latest activity

  11. Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules

    1. Yufeng Zhou
    2. John H Lewis
    3. Zhe Lu

    • Curated by eLife

      eLife assessment

      This paper presents a single-molecule polarization microscopy study aimed at monitoring the arginine/agmatine antiporter AdiC as it transiently exchanges between conformational states. This approach measures how a bis-TMR fluorophore anchored onto helix 6a changes its orientation in the microscope, and the authors identify four states that they propose correspond to the key steps in the transport cycle (inward-open, inward occluded, outward occluded and outward open). This is a cutting-edge and challenging approach that sets the stage for direct measurements of conformational equilibria and will thus be of interest to anyone studying transport mechanisms. However, additional investigation is required to validate the robustness of the post-processing of the single-molecule data to yield the four-state model compared to alternate models, to test the robustness of the data with transport mutants/conditions that would slow or eliminate states, and to consolidate transitions that are observed that conflict with previous observations of obligatory coupling in AdiC.

    Reviewed by eLife

    5 evaluationsAppears in 2 listsLatest version Latest activity

  14. Allosteric Regulation of a Synaptic Vesicle Glutamate Transporter

    1. Fei Li
    2. Jacob Eriksen
    3. Juan A. Oses-Prieto
    4. Yessica K. Gomez
    5. Hongfei Xu
    6. Janet Finer-Moore
    7. Phuong Nguyen
    8. Alisa Bowen
    9. Andrew Nelson
    10. Alma Burlingame
    11. Michael Grabe
    12. Robert M. Stroud
    13. Robert H. Edwards
    Appears in 1 listLatest version

  16. Computational design of peptides to target NaV1.7 channel with high potency and selectivity for the treatment of pain

    1. Phuong T Nguyen
    2. Hai M Nguyen
    3. Karen M Wagner
    4. Robert G Stewart
    5. Vikrant Singh
    6. Parashar Thapa
    7. Yi-Je Chen
    8. Mark W Lillya
    9. Anh Tuan Ton
    10. Richard Kondo
    11. Andre Ghetti
    12. Michael W Pennington
    13. Bruce Hammock
    14. Theanne N Griffith
    15. Jon T Sack
    16. Heike Wulff
    17. Vladimir Yarov-Yarovoy

    • Curated by eLife

      eLife assessment

      The authors of this manuscript set out to improve on a peptide, ProTxII, which had been previously put forward as a promising blocker of Nav1.7 channels and thus offers a possible non-opiate way to block pain. They develop a useful computational workflow that is based on in silico manipulations of the interaction of ProTxII with a Na channel structure determined previously and evaluation of the predicted mutations with electrophysiology. The authors succeed in producing two peptides with improved selectivity for Nav1.7 over other subtypes and capable of producing ion channel block at low concentrations and the experimental evidence presented is solid, and the general applicability of the method is compelling.

    Reviewed by eLife

    4 evaluationsAppears in 2 listsLatest version Latest activity

  18. Computational model of the full-length TSH receptor

    1. Mihaly Mezei
    2. Rauf Latif
    3. Terry F Davies

    • Curated by eLife

      Evaluation Summary:

      This manuscript presents the first molecular dynamics (MD) simulations of full-length membrane-bound Thyroid Stimulating Hormone Receptor (TSHR). The authors find that its linker region (LR) is disordered, contrasting previous models. While this is largely a solid study that would interest researchers working in computational modeling, thyroid hormone metabolism, and signaling, the rationale for the arbitrarily chosen starting model and unclear mechanistic relevance need to be clarified further.

      (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

    4 evaluationsAppears in 2 listsLatest version Latest activity

  20. Ion channel thermodynamics studied with temperature jumps measured at the cell membrane

    1. Carlos A.Z. Bassetto
    2. Bernardo I. Pinto
    3. Ramon Latorre
    4. Francisco Bezanilla

    • Curated by Biophysics Colab

      Evaluation statement (17 January 2024)

      The study by Bassetto Jr. et al. presents an elegant and pioneering technique to rapidly manipulate membrane temperature by up to 10 ºC in less than 1.5 ms, thereby enabling high temporal resolution of the temperature dependence of ion channel currents. The approach combines the cut-open oocyte voltage clamp technique with laser illumination to heat the sub-membrane melanosome layer. Temperature is quantified from observed changes in membrane capacitance. Recordings of Kir1.1, TRPM8, and TRPV1 channels are used to validate the effectiveness of the technique. A limitation is that, in its current form, the technique can be used only on melanosome-containing Xenopus oocyte membranes.

      Biophysics Colab recommends this study to scientists working on the temperature dependence of ion channels and other membrane proteins.

      Biophysics Colab has evaluated this study as one that meets the following criteria:

      • Rigorous methodology
      • Transparent reporting
      • Appropriate interpretation

      (This evaluation 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

    3 evaluationsAppears in 4 listsLatest version Latest activity
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