Latest preprint reviews

1. Intracellular Helix-Loop-Helix Domain Modulates Inactivation Kinetics of Mammalian TRPV5 and TRPV6 Channels

   This article has 5 authors:

   1. Lisandra Flores-Aldama
   2. Daniel Bustos
   3. Deny Cabezas-Bratesco
   4. Wendy Gonzalez
   5. Sebastian E. Brauchi

   This article has been curated by 1 group:

   • Curated by Biophysics Colab

     Evaluation statement (1 September 2023)

     Flores-Aldama and colleagues set out to identify molecular determinants of fast inactivation in the TRPV6 ion channel, a mechanism not observed in the closely related TRPV5 channel. The work focuses on a helix-loop-helix (HLH) motif, located at the interface between several important regions for channel gating. Using molecular dynamics simulations and analysis of mutations, the authors identify pairs of amino acid residues in a structural triad formed by the HLH, S2-S3 linker, and transmembrane domains, which show different conformations in the available TRPV5 and TRPV6 cryo-EM structures. An important aspect of the study is that some of the structural hypotheses were derived from an evolutionary analysis of sequences from orthologues of both channels, demonstrating the value of this type of analysis.

     Biophysics Colab considers this to be a convincing study and recommends it to scientists interested in the molecular determinants of ion channel gating.

     (This evaluation 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

2. Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

   This article has 4 authors:

   1. Dongxue Yang
   2. Zhiyu Zhao
   3. Emad Tajkhorshid
   4. Eric Gouaux

   This article has been curated by 1 group:

   • Curated by Biophysics Colab

     Evaluation statement (24 May 2023)

     Yang et al. present valuable information about ligand interactions with the serotonin transporter SERT, innovatively purified from pig brain using Fab fragments. The approach of using natively expressed SERT is notable for its potential insight into binding of endogenous membrane components such as lipids. Data distinguishing binding of the psychostimulants methamphetamine and cocaine add to our knowledge of substrate and inhibitor interactions with SERT and allow direct comparison with the closely related dopamine transporter DAT. The authors carefully state the limitations of their findings, including the possibility that the monomeric transporter stable in detergent micelles might exist in a multimeric state in native membranes.

     Biophysics Colab considers this to be a convincing study and recommends it to scientists interested in the structure, mechanism and ligand interactions of neurotransmitter transporters.

     (This evaluation by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

   Reviewed by Biophysics Colab

3. Tuning aromatic contributions by site-specific encoding of fluorinated phenylalanine residues in bacterial and mammalian cells

   This article has 12 authors:

   1. Grace D. Galles
   2. Daniel T. Infield
   3. Colin J. Clark
   4. Marcus L. Hemshorn
   5. Shivani Manikandan
   6. Frederico Fazan
   7. Ali Rasouli
   8. Emad Tajkhorshid
   9. Jason D. Galpin
   10. Richard B. Cooley
   11. Ryan A. Mehl
   12. Christopher A. Ahern

   This article has been curated by 1 group:

   • Curated by Biophysics Colab

     Endorsement statement (3 October 2022)

     The preprint by Galles et al. reports the generation of pyrrolysine-based aminoacyl-tRNA synthetases capable of incorporating fluorinated phenylalanine non-canonical amino acids into proteins expressed in either bacteria or mammalian cells. For the most extensively characterized synthetases, fluorinated phenylalanine derivatives were successfully incorporated into GFP and two membrane proteins (CFTR and Nav1.5) at expression levels adequate for biochemical studies, suggesting that the approach could be combined with multiple different structural and biophysical techniques. The work provides a valuable tool that will enable the functional role of cation-pi interactions to be interrogated in both soluble and integral membrane proteins.

     (This endorsement by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

   Reviewed by Biophysics Colab

4. Interpreting the molecular mechanisms of disease variants in human transmembrane proteins

   This article has 4 authors:

   1. Johanna Katarina Sofie Tiemann
   2. Henrike Zschach
   3. Kresten Lindorff-Larsen
   4. Amelie Stein

   Reviewed by Biophysics Colab

5. Activation-pathway transitions in human voltage-gated proton channels revealed by a non-canonical fluorescent amino acid

   This article has 4 authors:

   1. Esteban Suárez-Delgado
   2. Maru Orozco-Contreras
   3. Gisela E Rangel-Yescas
   4. Leon D Islas

   This article has been curated by 1 group:

   • Curated by Biophysics Colab

     Endorsement statement (22 December 2022)

     The preprint by Suarez-Delgado et al. explores the mechanisms by which the Hv1 voltage-activated proton channel is dependent upon transmembrane voltage and pH by incorporating the small fluorescent non-canonical amino acid Anap into the S4 helix and monitoring its fluorescence. Anap spectra suggest the fluorophore resides in an aqueous environment and moves relative to a quenching aromatic residue (F150) in the S2 helix upon depolarization. Two kinetically distinct components of fluorescence change support the presence of at least three conformational states in the activation pathway of Hv1. Measurements using different pH gradients suggest that S4 movement and channel opening are similarly affected by pH gradients. This is the first study to incorporate Anap into Hv1, and provide a rigorous and thorough characterization of how the fluorophore can be used to explore mechanisms of gating and regulation, paving the way for future studies. The work will be of interest to physiologists and biophysicists investigating membrane protein mechanisms using non-canonical fluorescent amino acids.

     (This endorsement by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

   Reviewed by Biophysics Colab

6. Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter

   This article has 6 authors:

   1. Diego del Alamo
   2. Lillian DeSousa
   3. Rahul M. Nair
   4. Suhaila Rahman
   5. Jens Meiler
   6. Hassane S. Mchaourab

   Reviewed by Biophysics Colab

7. Activation mechanism of the human Smoothened receptor

   This article has 3 authors:

   1. Prateek D. Bansal
   2. Soumajit Dutta
   3. Diwakar Shukla

   This article has been curated by 1 group:

   • Curated by Biophysics Colab

     Evaluation statement (22 August 2023)

     Bansal et al. present an atomistic view of the transition cascade of the class F GPCR Smoothened (Smo). The extensive long-range molecular dynamics simulations together with stochastic modelling provide theoretical insight into Smo activation and how this is modulated by different ligands. The work identifies testable hypotheses for functional studies of Smo and other class F GPCRs. Future simulations of regions beyond the seven-transmembrane bundle, particularly the cysteine-rich domain, will afford a more complete understanding of receptor activation.

     Biophysics Colab considers this to be a convincing computational study and recommends it to scientists interested in the conformational dynamics of class F GPCRs.

     (This evaluation by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

   Reviewed by Biophysics Colab

8. Membrane curvature governs the distribution of Piezo1 in live cells

   This article has 12 authors:

   1. Shilong Yang
   2. Xinwen Miao
   3. Steven Arnold
   4. Boxuan Li
   5. Alan T. Ly
   6. Huan Wang
   7. Matthew Wang
   8. Xiangfu Guo
   9. Medha M. Pathak
   10. Wenting Zhao
   11. Charles D. Cox
   12. Zheng Shi

   This article has been curated by 1 group:

   • Curated by Biophysics Colab

     Endorsement statement (6 December 2022)

     The preprint by Yang et al. asks how the shape of the membrane influences the localization of mechanosensitive Piezo channels. The authors use a creative approach involving methods that distort the plasma membrane by generating blebs and artificial filopodia. They convincingly show that curvature of the lipid environment influences Piezo1 localization, such that increased curvature causes channel depletion, and that application of the chemical modulator Yoda1 is sufficient to allow channels to enter filopodia. The study provides support for a provocative “flattening model” of Yoda1 action, and should inspire future studies by researchers interested in mechanosensitive channels and membrane curvature.

     (This endorsement by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

   Reviewed by Biophysics Colab

9. Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter

   This article has 17 authors:

   1. Martin F. Peter
   2. Jan A. Ruland
   3. Peer Depping
   4. Niels Schneberger
   5. Emmanuele Severi
   6. Jonas Moecking
   7. Karl Gatterdam
   8. Sarah Tindall
   9. Alexandre Durand
   10. Veronika Heinz
   11. Jan Peter Siebrasse
   12. Paul-Albert Koenig
   13. Matthias Geyer
   14. Christine Ziegler
   15. Ulrich Kubitscheck
   16. Gavin H. Thomas
   17. Gregor Hagelueken

   This article has been curated by 1 group:

   • Curated by Biophysics Colab

     Endorsement statement (5 August 2022)

     Peter et al. describe the first experimentally validated structural model of a canonical member of the TRAP family of transporters, Haemophilus influenzae (Hi)SiaPQM, which transports sialic acid into bacteria. By elegantly combining a cryo-EM structure of the HiSiaQM dimer, AlphaFoldmodels, and sequence, biochemical, and mutational analyses, the authors shed light on the fold and domain organization of the tripartite HiSiaPQM holocomplex. The authors also propose a structure-based model for its transport mechanism: substrate recognition is "outsourced" to the substrate binding protein (P protein) by the QM proteins, which in turn use an elevator mechanism to transport sialic acid across the membrane. The work is rigorous and convincing, and it presents valuable findings that will be of interest to scientists investigating transporters with an elevator-type mechanism as well as membrane transport more generally.

     (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

10. Calcineurin-fusion facilitates Cryo-EM Structure Determination of a Family A GPCR

    This article has 8 authors:

    1. Jun Xu
    2. Geng Chen
    3. Haoqing Wang
    4. Sheng Cao
    5. Jie Heng
    6. Xavier Deupi
    7. Yang Du
    8. Brian K. Kobilka

    Reviewed by Biophysics Colab