Reviewed articles

ATP-release pannexin channels are gated by lysophospholipids

1. Erik Henze
2. Russell N Burkhardt
3. Bennett William Fox
4. Tyler J Schwertfeger
5. Eric Gelsleichter
6. Kevin Michalski
7. Lydia Kramer
8. Margret Lenfest
9. Jordyn M Boesch
10. Hening Lin
11. Frank C Schroeder
12. Toshimitsu Kawate

• Curated by eLife

  eLife Assessment

  Pannexin (Panx) channels are a family of poorly understood large-pore channels that mediate the release of substrates like ATP from cells, yet the physiological stimuli that activate these channels remain poorly understood. The study by Henze et al. describes an elegant approach wherein activity-guided fractionation of mouse liver led to the discovery that lysophospholipids (LPCs) activate Panx1 and Panx2 channels expressed in cells or reconstituted into liposomes. The authors provide compelling evidence that LPC-mediated activation of Panx1 is involved in joint pain and that Panx1 channels are required for the established effects of LPC on inflammasome activation in monocytes, suggesting that Panx channels play a role in inflammatory pathways. Overall, this important study reports a previously unanticipated mechanism wherein LPCs directly activate Panx channels. The work will be of interest to scientists investigating phospholipids, Panx channels, purinergic signalling and inflammation.

  [Editors' note: this paper was reviewed and curated by Biophysics Colab]

• Curated by Biophysics Colab

  Evaluation Statement (5 February 2025)

  Pannexin (Panx) channels are a family of poorly understood large-pore channels that mediate the release of substrates like ATP from cells, yet the physiological stimuli that activate these channels remain poorly understood. The preprint by Henze et al. describes an elegant approach wherein activity-guided fractionation of mouse liver led to the discovery that lysophospholipids (LPCs) activate Panx1 and Panx2 channels expressed in cells or reconstituted into liposomes. The authors provide evidence that LPC-mediated activation of Panx1 is involved in joint pain and that Panx1 channels are required for the established effects of LPC on inflammasome activation in monocytes, suggesting that Panx channels play a role in inflammatory pathways. Overall, this important study reports a previously unanticipated mechanism wherein LPCs directly activate Panx channels.

  Biophysics Colab recommends this study to scientists investigating phospholipids, Panx channels, purinergic signalling and inflammation.

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

  • Rigorous methodology
  • Transparent reporting
  • Appropriate interpretation

  (This evaluation refers to version 3 of this preprint, which has been revised in response to peer review of versions 1 and 2.)

Reviewed by eLife, Biophysics Colab

Structure and function of the human mitochondrial MRS2 channel

1. Zhihui He
2. Yung-Chi Tu
3. Chen-Wei Tsai
4. Jonathan Mount
5. Jingying Zhang
6. Ming-Feng Tsai
7. Peng Yuan

• Curated by Biophysics Colab

  Evaluation Statement (14 June 2024)

  The study by He et al. explores the structure and mechanisms of the human mitochondrial RNA splicing 2 (MRS2) protein, predicted to form Mg2+-selective channels in the mitochondrial inner membrane based on homology to the CorA family of prokaryotic Mg2+ channels. The authors use an innovative biochemical strategy to express MRS2 and perform single particle reconstructions in the absence and presence of key divalent cations. High resolution reconstructions of the pentameric channel reveal binding sites for Mg2+ and Ca2+, and electrophysiological investigations suggest that MRS2 is a Ca2+-regulated, cation-selective, Mg2+-permeable channel, in contrast to the Mg2+-regulated, Mg2+-selective CorA channel. This is an important study with interesting structural and functional observations, which will motivate further investigations of a potential role for MRS2 in mitochondrial Ca2+ signaling.

  Biophysics Colab recommends this study to scientists interested in the structure, function and regulation of cation channels as well as those working on mitochondrial transport.

  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

Macromolecular condensation is unlikely to buffer intracellular osmolality

1. Alan R. Kay
2. Zahra Aminzare

• Curated by Biophysics Colab

  Evaluation Statement (30 January 2025)

  Kay and Aminzare discuss a claim made in a prior publication that macromolecular condensation acts as a water buffering mechanism in cells to compensate for the effects of osmotic shock. The authors argue that, although such a buffer could temporarily maintain a transmembrane osmolality differential, this differential would drive water across the membrane to reach a steady-state in which osmolality within the cell equals osmolality outside the cell. Using the well-established pump-leak model for osmotic water transport, they further show that the timescale at which a water buffer could maintain a modest 10% osmolality differential across the membrane is at most one minute for a typical animal cell.

  Biophysics Colab recommends this study to researchers working on membrane transport, intracellular water buffering, and condensate biology.

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

  • Rigorous methodology
  • Transparent reporting
  • Appropriate interpretation

Reviewed by Biophysics Colab

AlphaFold-SFA: accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics

1. Shray Vats
2. Raitis Bobrovs
3. Pär Söderhjelm
4. Soumendranath Bhakat

Reviewed by Biophysics Colab

The folding-limited nucleation of curli hints at an evolved safety mechanism for functional amyloid production

1. Jolyon K. Claridge
2. Chloe Martens
3. Brajabandhu Pradhan
4. Frank Sobott
5. Mike Sleutel
6. Han Remaut

Reviewed by Biophysics Colab

Structural basis of closed groove scrambling by a TMEM16 protein

1. Zhang Feng
2. Omar E. Alvarenga
3. Alessio Accardi

• Curated by Biophysics Colab

  Evaluation statement (17 January 2024; revised 31 January 2024)

  Feng and colleagues investigate the molecular basis of lipid scrambling in a fungal member of the TMEM16 family of Ca²⁺-dependent lipid scramblases. These proteins possess a groove in their 3D structure that has been implicated in lipid scrambling, which the authors investigate in the absence and presence of Ca²⁺ using a combination of cryo-EM structure determination, mutagenesis and functional assays. Their closed-groove structure reveals a continuous file of lipid molecules around the catalytic groove region, providing a structural basis for lipid interaction with the protein. Additionally, the authors capture three novel states of TMEM16, completing the picture of conformational transitions that this protein undergoes. Strikingly, the authors show that both structure and distribution of the protein’s conformations depend on lipid composition and nanodisc scaffold protein.

  Biophysics Colab considers this to be exceptional work and recommends it to scientists interested in plasma membrane lipid homeostasis and cryoEM.

  (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

Semi‐synthetic nanobody‐ligand conjugates exhibit tunable signaling properties and enhanced transcriptional outputs at neurokinin receptor‐1

1. Nayara Braga Emidio
2. Ross W. Cheloha

Reviewed by Biophysics Colab

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

Structure of an open KATP channel reveals tandem PIP2 binding sites mediating the Kir6.2 and SUR1 regulatory interface

1. Camden M. Driggers
2. Yi-Ying Kuo
3. Phillip Zhu
4. Assmaa ElSheikh
5. Show-Ling Shyng

• Curated by Biophysics Colab

  Evaluation statement (10 January 2024)

  Driggers et al. is an elegant study that reports the structure of an open KATP channel complex formed from the Q52R diabetes mutation of the pore-forming subunit Kir 6.2, the sulfonylurea receptor (SUR1), and long-chain phosphatidylinositol 4,5-bisphosphate (PIP2) – a key lipid that stabilizes the open state of the channel and regulates inhibition by intracellular ATP. The structure reveals one PIP2 site related to that seen in other Kir channels as well as a second unanticipated one where the lipid snuggles into the interface between Kir6.2 and a region of SUR1 previously implicated in promoting the open state of KATP. This important finding helps to explain how PIP2 exerts such a profound regulatory influence on KATP.

  Biophysics Colab considers this to be a convincing study and recommends it to scientists working on KATP and other membrane proteins regulated by PIP2.

  (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

Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain

1. Sandra Seljeset
2. Oksana Sintsova
3. Yuhong Wang
4. Hassan Y. Harb
5. Timothy Lynagh

• Curated by Biophysics Colab

  Evaluation statement (8 March 2024)

  Seljeset et al. investigate the mechanism by which NMDA receptors are activated by co-agonists glutamate and glycine. By mutating residue Asp732 in the glycine-binding site, they generate receptors activated by glutamate, and not glycine, but inhibited by glycine antagonists. Conventional and unnatural amino acid mutagenesis reveals that Asp732 interacts with nearby residues to influence channel gating as well as ligand binding. Furthermore, a homomeric receptor from Trichoplax adhaerens, which has a tyrosine in the homologous position, displays constitutive activity that becomes glycine-dependent when the tyrosine is mutated to aspartate. The study is valuable because it reveals the importance of position 732 for controlling ligand potency and channel activity in glutamate receptors, which should lead to a better understanding of how these receptors are primed for channel opening.

  Biophysics Colab recommends this study to scientists interested in the structure and function of glutamate receptors

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

  • Rigorous methodology
  • Transparent reporting
  • Appropriate interpretation

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

Reviewed by Biophysics Colab

Structural insights into the organization and channel properties of human Pannexin isoforms 1 and 3

1. Nazia Hussain
2. Ashish Apotikar
3. Shabareesh Pidathala
4. Sourajit Mukherjee
5. Ananth Prasad Burada
6. Sujit Kumar Sikdar
7. Vinothkumar R. Kutti
8. Aravind Penmatsa

Reviewed by Biophysics Colab

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

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

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

• 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

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

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

• 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

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

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

• 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

Interpreting the molecular mechanisms of disease variants in human transmembrane proteins

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

Reviewed by Biophysics Colab

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

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

• 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

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

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

Activation mechanism of the human Smoothened receptor

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

• 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

Membrane curvature governs the distribution of Piezo1 in live cells

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

• 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