Transporter Physics Meets Genomics

Published 16 May 2024 in Molecular Cell (doi 10.1016/j.molcel.2024.04.008):

The full spectrum of SLC22 OCT1 mutations illuminates the bridge between drug transporter biophysics and pharmacogenomics

Sook Wah Yee, Christian B Macdonald, Darko Mitrovic, Xujia Zhou, Megan L Koleske, Jia Yang, Dina Buitrago Silva, Patrick Rockefeller Grimes, Donovan D Trinidad, Swati S More, Linda Kachuri, John S Witte, Lucie Delemotte, Kathleen M Giacomini, Willow Coyote-Maestas

Mutations in transporters can impact an individual’s response to drugs and cause many diseases. Few variants in transporters have been evaluated for their functional impact. Here, we combine saturation mutagenesis and multi-phenotypic screening to dissect the impact of 11,213 missense single-amino-acid deletions, and synonymous variants across the 554 residues of OCT1, a key liver xenobiotic transporter. By quantifying in parallel expression and substrate uptake, we find that most variants exert their primary effect on protein abundance, a phenotype not commonly measured alongside function. Using our mutagenesis results combined with structure prediction and molecular dynamic simulations, we develop accurate structure-function models of the entire transport cycle, providing biophysical characterization of all known and possible human OCT1 polymorphisms. This work provides a complete functional map of OCT1 variants along with a framework for integrating functional genomics, biophysical modeling, and human genetics to predict variant effects on disease and drug efficacy.

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Allosteric Contacts of Cholesterol

Published 15 May 2024 in the Journal of Physical Chemistry B (doi 10.1021/acs.jpcb.4c01703):

Allosteric cholesterol site in glycine receptors characterized through molecular simulations

Farzaneh Jalalypour, Rebecca J Howard, Erik Lindahl

Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to gating by the glycine agonist, interactions with lipids and other compounds in the surrounding membrane environment modulate their function, but molecular details of these interactions remain unclear, in particular, for cholesterol. Here, we report coarse-grained simulations in a model neuronal membrane for three zebrafish glycine receptor structures representing apparent resting, open, and desensitized states. We then converted the systems to all-atom models to examine detailed lipid interactions. Cholesterol bound to the receptor at an outer-leaflet intersubunit site, with a preference for the open and desensitized versus resting states, indicating that it can bias receptor function. Finally, we used short atomistic simulations and iterative amino acid perturbations to identify residues that may mediate allosteric gating transitions. Frequent cholesterol contacts in atomistic simulations clustered with residues identified by perturbation analysis and overlapped with mutations influencing channel function and pathology. Cholesterol binding at this site was also observed in a recently reported pig heteromeric glycine receptor. These results indicate state-dependent lipid interactions relevant to allosteric transitions of glycine receptors, including specific amino acid contacts applicable to biophysical modeling and pharmaceutical design.

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Grattis Dr Mitrovic

Members of Molecular Biophysics Stockholm joined family and friends in celebrating Darko Mitrovic‘s successful spikning and defense of his PhD in Applied Physics, Combining Evolution and Physics through Machine Learning to Decipher Molecular Mechanisms. Darko nailed his thesis at SciLifeLab on 2 May, and defended it at KTH Royal Institute of Technology on 15 May, with Professor Gerhard Hummer (Max Planck Institute, Frankfurt, Germany) as opponent. Associate Professor Lucie Delemotte led a toast to her advisee of nearly four years, as he transitions to a postdoctoral fellowship.


TRP on Acid

Published 26 April 2024 in EMBO Journal (doi 10.1038/s44318-024-00106-4):

Functional and structural insights into activation of TRPV2 by weak acids

Ferdinand M Haug, Ruth A Pumroy, Akshay Sridhar, Sebastian Pantke, Florian Dimek, Tabea C Fricke, Axel Hage, Christine Herzog, Frank G Echtermeyer, Jeanne de la Roche, Adrian Koh, Abhay Kotecha, Rebecca J Howard, Erik Lindahl, Vera Moiseenkova-Bell°, Andreas Leffler°

Transient receptor potential (TRP) ion channels are involved in the surveillance or regulation of the acid-base balance. Here, we demonstrate that weak carbonic acids, including acetic acid, lactic acid, and CO2 activate and sensitize TRPV2 through a mechanism requiring permeation through the cell membrane. TRPV2 channels in cell-free inside-out patches maintain weak acid-sensitivity, but protons applied on either side of the membrane do not induce channel activation or sensitization. The involvement of proton modulation sites for weak acid-sensitivity was supported by the identification of titratable extracellular (Glu495, Glu561) and intracellular (His521) residues on a cryo-EM structure of rat TRPV2 (rTRPV2) treated with acetic acid. Molecular dynamics simulations as well as patch clamp experiments on mutant rTRPV2 constructs confirmed that these residues are critical for weak acid-sensitivity. We also demonstrate that the pore residue Glu609 dictates an inhibition of weak acid-induced currents by extracellular calcium. Finally, TRPV2-expression in HEK293 cells is associated with an increased weak acid-induced cytotoxicity. Together, our data provide new insights into weak acids as endogenous modulators of TRPV2.

°Corresponding authors

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A Correction to Droplet Friction

Published 19 March 2024 in Physical Review Fluids (doi 10.1103/PhysRevFluids.9.034002):

Near-wall depletion and layering affect contact line friction of multicomponent liquids

Michele Pellegrino, Berk Hess

The main causes of energy dissipation in micro- and nanoscale wetting are viscosity and liquid-solid friction localized in the three-phase contact line region. Theoretical models predict the contact line friction coefficient to correlate with the shear viscosity of the wetting fluid. Experiments conducted to investigate such correlation have not singled out a unique scaling law between the two coefficients. We perform molecular dynamics simulations of liquid water-glycerol droplets wetting silicalike surfaces, aimed to demystify the effect of viscosity on contact line friction. The viscosity of the fluid is tuned by changing the relative mass fraction of glycerol in the mixture and it is estimated both via equilibrium and nonequilibrium molecular dynamics simulations. Contact line friction is measured directly by inspecting the velocity of the moving contact line and the microscopic contact angle. It is found that the scaling between contact line friction and viscosity is sublinear, contrary to the prediction of molecular kinetic theory. The disagreement is explained by accounting for the depletion of glycerol in the near-wall region. A correction is proposed, based on multicomponent molecular kinetic theory and the definition of a rescaled interfacial friction coefficient.

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Simulating Biosensors

Published 1 February 2024 in Protein Engineering, Design and Selection (doi 10.1093/protein/gzae003):

Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids

Nandan Haloi*, Shan Huang*, Aaron L Nichols, Eve J Fine, Nicholas J Friesenhahn, Christopher B Marotta, Dennis A Dougherty, Erik Lindahl, Rebecca J Howard, Stephen L Mayo, Henry A Lester

We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for ∆F/F0vs [nicotine] (δ-slope, 2.7 μM−1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the ‘candle snuffer’ mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.

Read the full publication here.

*These authors contributed equally.


Grattis Dr Rovšnik

Members of Molecular Biophysics Stockholm joined family and friends in celebrating Urška Rovšnik‘s successful spikning and defense of her PhD in Biochemistry, Structural transitions of proton-gated ion channels: Involving pH sensing, heterogeneity and lipid interactions. Urška nailed her thesis at SciLifeLab on 15 January, and defended it there on 31 January, with Dr Hugues Nury (Institut de Biologie Structurale, Grenoble, France) as opponent. Professor Erik Lindahl and Ligand-Gated Ion Channels team-lead Reba Howard led a toast to their advisee of over five years, as she prepares for a postdoctoral position at Gothenburg University.


Multidisciplinary Lipid Discovery

Published 30 January 2024 in eLife (doi 10.7554/eLife.86016.3):

Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM

Cathrine Bergh, Urška Rovšnik, Rebecca J Howard, Erik Lindahl

Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane domain of several ion channels. However, structural details of such lipid contacts remain elusive, partly due to limited resolution of these regions in experimental structures. Here, we discovered multiple lipid interactions in the channel GLIC by integrating cryo-electron microscopy and large-scale molecular simulations. We identified 25 bound lipids in the GLIC closed state, a conformation where none, to our knowledge, were previously known. Three lipids were associated with each subunit in the inner leaflet, including a buried interaction disrupted in mutant simulations. In the outer leaflet, two intrasubunit sites were evident in both closed and open states, while a putative intersubunit site was preferred in open-state simulations. This work offers molecular details of GLIC-lipid contacts particularly in the ill-characterized closed state, testable hypotheses for state-dependent binding, and a multidisciplinary strategy for modeling protein-lipid interactions.

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Automating CpHMD

Published 12 January 2024 in The Journal of Chemical Information and Modeling (doi 10.1021/acs.jcim.3c01313):

phbuilder: A tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS

Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev*, Berk Hess*

Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constant pH implementation was incorporated into the GROMACS MD package. Although this implementation provides good accuracy and performance, manual modification and the preparation of simulation input files are required, which can be complicated, tedious, and prone to errors. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH MD simulations for GROMACS by modifying the input structure and topology as well as generating the necessary parameter files. phbuilder can prepare constant pH simulations from both initial structures and existing simulation systems, and it also provides functionality for performing titrations and single-site parametrizations of new titratable group types. The tool is freely available at We anticipate that phbuilder will make constant pH simulations easier to set up, thereby making them more accessible to the GROMACS user community.

Read the full publication here.

*Co-corresponding authors


Grattis Dr McComas

Members of Molecular Biophysics Stockholm joined family and friends in celebrating Sarah McComas‘ successful spikning and defense of her PhD in Biochemistry, The molecular basis for substrate recognition and gating in sugar transporters. Sarah nailed her thesis at SciLifeLab on 27 November, and defended it 8 December at Stockholm University, with Professor Philip Biggin (University of Oxford) as opponent. Along with her supervisor Professor David Drew, the Membrane Protein Modeling team led a toast to their colleague of over five years.


Adrenergic AI

Published 10 November 2023 in The Journal of Physical Chemistry B (doi 10.1021/acs.jpcb.3c04897):

Coevolution-driven method for efficiently simulating conformational changes in proteins reveals molecular details of ligand effects in the β2AR receptor

Darko Mitrovic, Yue Chen, Antoni Marciniak, Lucie Delemotte

With the advent of AI-powered structure prediction, the scientific community is inching closer to solving protein folding. An unresolved enigma, however, is to accurately, reliably, and deterministically predict alternative conformational states that are crucial for the function of, e.g., transporters, receptors, or ion channels where conformational cycling is innately coupled to protein function. Accurately discovering and exploring all conformational states of membrane proteins has been challenging due to the need to retain atomistic detail while enhancing the sampling along interesting degrees of freedom. The challenges include but are not limited to finding which degrees of freedom are relevant, how to accelerate the sampling along them, and then quantifying the populations of each micro- and macrostate. In this work, we present a methodology that finds relevant degrees of freedom by combining evolution and physics through machine learning and apply it to the conformational sampling of the β2 adrenergic receptor. In addition to predicting new conformations that are beyond the training set, we have computed free energy surfaces associated with the protein’s conformational landscape. We then show that the methodology is able to quantitatively predict the effect of an array of ligands on the β2 adrenergic receptor activation through the discovery of new metastable states not present in the training set. Lastly, we also stake out the structural determinants of activation and inactivation pathway signaling through different ligands and compare them to functional experiments to validate our methodology and potentially gain further insights into the activation mechanism of the β2 adrenergic receptor.

Read the full publication here.


Grattis Dr Zhuang

Members and friends of Molecular Biophysics Stockholm celebrated Yuxuan Zhuang‘s successful spikning and defense of his PhD from Stockholm University in Biophysics, Simulating Functional Cycles and Drug Modulation in Ligand-Gated Ion Channels. Yuxuan nailed his thesis on 6 October, and defended it 19 October at SciLifeLab, with Professor Grace Brannigan (Rutgers University – Camden, NJ) as opponent. Professor Erik Lindahl and Integrative Structural Biology team-lead Reba Howard led a toast to their advisee of over five years, as he heads to a Wallenberg Foundation Postdoctoral Scholarship at Stanford University.


Resolving Rho1

Published 1 September 2023 in Neuron (doi 10.1016/j.neuron.2023.08.006):

Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor

John Cowgill*, Chen Fan*, Nandan Haloi, Yuxuan Zhuang, Rebecca J Howard°, Erik Lindahl°

The neurotransmitter γ-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABAARs). Pharmacological properties of ρ-type GABAARs are particularly distinctive, yet the structural basis for their specialization remains unclear. Here, we present cryo-EM structures of a lipid-embedded human ρ1 GABAAR, including a partial intracellular domain, under apo, inhibited, and desensitized conditions. An apparent resting state, determined first in the absence of modulators, was recapitulated with the specific inhibitor (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid and blocker picrotoxin and provided a rationale for bicuculline insensitivity. Comparative structures, mutant recordings, and molecular simulations with and without GABA further explained the sensitized but slower activation of ρ1 relative to canonical subtypes. Combining GABA with picrotoxin also captured an apparent uncoupled intermediate state. This work reveals structural mechanisms of gating and modulation with applications to ρ-specific pharmaceutical design and to our biophysical understanding of ligand-gated ion channels.

*Contributed equally
°Corresponding authors

Read the full publication here.


Alchemical Atlas

Published 31 August 2023 in The Protein Journal (doi 10.1007/s10930-023-10137-1):

On the path to optimal alchemistry

Magnus Lundborg, Jack Lidmar, Berk Hess

Alchemical free energy calculations have become a standard and widely used tool, in particular for calculating and comparing binding affinities of drugs. Although methods to compute such free energies have improved significantly over the last decades, the choice of path between the end states of interest is usually still the same as two decades ago. We will show that there is a fundamentally arbitrary, implicit choice of parametrization of this path. To address this, the notion of the length of a path or a metric is required. A metric recently introduced in the context of the accelerated weight histogram method also proves to be very useful here. We demonstrate that this metric can not only improve the efficiency of sampling along a given path, but that it can also be used to improve the actual choice of path. For a set of relevant use cases, the combination of these improvements can increase the efficiency of alchemical free energy calculations by up to a factor 16.

Read the full publication here.


New Sites for Steroids

Published 22 August 2023 in Nature Communications (doi 10.1038/s41467-023-40800-1):

Structural insights into opposing actions of neurosteroids on GABAA receptors

Dagimhiwat H Legesse, Chen Fan, Jinfeng Teng, Yuxuan Zhuang, Rebecca J Howard, Colleen M Noviello, Erik Lindahl, Ryan E Hibbs

γ-Aminobutyric acid type A (GABAA) receptors mediate fast inhibitory signaling in the brain and are targets of numerous drugs and endogenous neurosteroids. A subset of neurosteroids are GABAA receptor positive allosteric modulators; one of these, allopregnanolone, is the only drug approved specifically for treating postpartum depression. There is a consensus emerging from structural, physiological and photolabeling studies as to where positive modulators bind, but how they potentiate GABA activation remains unclear. Other neurosteroids are negative modulators of GABAA receptors, but their binding sites remain debated. Here we present structures of a synaptic GABAA receptor bound to allopregnanolone and two inhibitory sulfated neurosteroids. Allopregnanolone binds at the receptor-bilayer interface, in the consensus potentiator site. In contrast, inhibitory neurosteroids bind in the pore. MD simulations and electrophysiology support a mechanism by which allopregnanolone potentiates channel activity and suggest the dominant mechanism for sulfated neurosteroid inhibition is through pore block.

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EBSA-Stockholm 2023

More than twenty current and former members of Molecular Biophysics Stockholm had the rare opportunity to be visited by over 1000 scientists at the biannual Congress of the European Biophysical Societies’ Association (EBSA), held 31 July–4 August for its first time in Stockholm. The event culminated months of preparation by Congress Co-Chair Erik Lindahl, and included selected oral presentations by Nandan Haloi and Marie Lycksell, as well as poster awards to Anton Jansen and Antoni Marciniak (pictured at bottom).


Density Fitting, Fast & Gentle

Published online 31 July 2023 in PLOS Computational Biology (doi 10.1371/journal.pcbi.1011255):

Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach

Christian Blau, Linnea YvonnesdotterErik Lindahl

Better detectors and automated data collection have generated a flood of high-resolution cryo-EM maps, which in turn has renewed interest in improving methods for determining structure models corresponding to these maps. However, automatically fitting atoms to densities becomes difficult as their resolution increases and the refinement potential has a vast number of local minima. In practice, the problem becomes even more complex when one also wants to achieve a balance between a good fit of atom positions to the map, while also establishing good stereochemistry or allowing protein secondary structure to change during fitting. Here, we present a solution to this challenge using a maximum likelihood approach by formulating the problem as identifying the structure most likely to have produced the observed density map. This allows us to derive new types of smooth refinement potential—based on relative entropy—in combination with a novel adaptive force scaling algorithm to allow balancing of force-field and density-based potentials. In a low-noise scenario, as expected from modern cryo-EM data, the relative-entropy based refinement potential outperforms alternatives, and the adaptive force scaling appears to aid all existing refinement potentials. The method is available as a component in the GROMACS molecular simulation toolkit.

Read the full publication here.


Profiling Permeation Enhancers

Published online 18 July 2023 in Journal of Chemical Information and Modeling (doi 10.1021/acs.jcim.3c00625):

Understanding drug skin permeation enhancers using molecular dynamics simulations

Christian WennbergMagnus LundborgErik Lindahl, Lars Norlén

Our skin constitutes an effective permeability barrier that protects the body from exogenous substances but concomitantly severely limits the number of pharmaceutical drugs that can be delivered transdermally. In topical formulation design, chemical permeation enhancers (PEs) are used to increase drug skin permeability. In vitro skin permeability experiments can measure net effects of PEs on transdermal drug transport, but they cannot explain the molecular mechanisms of interactions between drugs, permeation enhancers, and skin structure, which limits the possibility to rationally design better new drug formulations. Here we investigate the effect of the PEs water, lauric acid, geraniol, stearic acid, thymol, ethanol, oleic acid, and eucalyptol on the transdermal transport of metronidazole, caffeine, and naproxen. We use atomistic molecular dynamics (MD) simulations in combination with developed molecular models to calculate the free energy difference between 11 PE-containing formulations and the skin’s barrier structure. We then utilize the results to calculate the final concentration of PEs in skin. We obtain an RMSE of 0.58 log units for calculated partition coefficients from water into the barrier structure. We then use the modified PE-containing barrier structure to calculate the PEs’ permeability enhancement ratios (ERs) on transdermal metronidazole, caffeine, and naproxen transport and compare with the results obtained from in vitro experiments. We show that MD simulations are able to reproduce rankings based on ERs. However, strict quantitative correlation with experimental data needs further refinement, which is complicated by significant deviations between different measurements. Finally, we propose a model for how to use calculations of the potential of mean force of drugs across the skin’s barrier structure in a topical formulation design.

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MD-Fitting a Membrane Protein

Published 11 July 2023 in Biophysical Journal (doi 10.1016/j.bpj.2023.05.033):

Automated simulation-based membrane protein refinement into cryo-EM data

Linnea Yvonnesdotter, Urška Rovšnik, Christian Blau, Marie Lycksell, Rebecca J Howard, Erik Lindahl

The resolution revolution has increasingly enabled single-particle cryogenic electron microscopy (cryo-EM) reconstructions of previously inaccessible systems, including membrane proteins—a category that constitutes a disproportionate share of drug targets. We present a protocol for using density-guided molecular dynamics simulations to automatically refine atomistic models into membrane protein cryo-EM maps. Using adaptive force density-guided simulations as implemented in the GROMACS molecular dynamics package, we show how automated model refinement of a membrane protein is achieved without the need to manually tune the fitting force ad hoc. We also present selection criteria to choose the best-fit model that balances stereochemistry and goodness of fit. The proposed protocol was used to refine models into a new cryo-EM density of the membrane protein maltoporin, either in a lipid bilayer or detergent micelle, and we found that results do not substantially differ from fitting in solution. Fitted structures satisfied classical model-quality metrics and improved the quality and the model-to-map correlation of the x-ray starting structure. Additionally, the density-guided fitting in combination with generalized orientation-dependent all-atom potential was used to correct the pixel-size estimation of the experimental cryo-EM density map. This work demonstrates the applicability of a straightforward automated approach to fitting membrane protein cryo-EM densities. Such computational approaches promise to facilitate rapid refinement of proteins under different conditions or with various ligands present, including targets in the highly relevant superfamily of membrane proteins.

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Formulating Fructose Flux

Published 5 July 2023 in eLife (doi 10.7554/eLife.84808):

Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5

Sarah E McComas, Tom Reichenbach, Darko Mitrovic, Claudia Alleva, Marta Bonaccorsi, Lucie Delemotte, David Drew

In mammals, glucose transporters (GLUT) control organism-wide blood-glucose homeostasis. In human, this is accomplished by 14 different GLUT isoforms, that transport glucose and other monosaccharides with varying substrate preferences and kinetics. Nevertheless, there is little difference between the sugar-coordinating residues in the GLUT proteins and even the malarial Plasmodium falciparum transporter PfHT1, which is uniquely able to transport a wide range of different sugars. PfHT1 was captured in an intermediate ‘occluded’ state, revealing how the extracellular gating helix TM7b has moved to break and occlude the sugar-binding site. Sequence difference and kinetics indicated that the TM7b gating helix dynamics and interactions likely evolved to enable substrate promiscuity in PfHT1, rather than the sugar-binding site itself. It was unclear, however, if the TM7b structural transitions observed in PfHT1 would be similar in the other GLUT proteins. Here, using enhanced sampling molecular dynamics simulations, we show that the fructose transporter GLUT5 spontaneously transitions through an occluded state that closely resembles PfHT1. The coordination of D-fructose lowers the energetic barriers between the outward- and inward-facing states, and the observed binding mode for D-fructose is consistent with biochemical analysis. Rather than a substrate-binding site that achieves strict specificity by having a high affinity for the substrate, we conclude GLUT proteins have allosterically coupled sugar binding with an extracellular gate that forms the high-affinity transition-state instead. This substrate-coupling pathway presumably enables the catalysis of fast sugar flux at physiological relevant blood-glucose concentrations.

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Coevolving Sugar Transport

Published 5 July 2023 in eLife (doi 10.7554/eLife.84805):

Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning

Darko Mitrovic, Sarah E McComas, Claudia Alleva, Marta Bonaccorsi, David Drew, Lucie Delemotte

Sugar porters (SPs) represent the largest group of secondary-active transporters. Some members, such as the glucose transporters (GLUTs), are well known for their role in maintaining blood glucose homeostasis in mammals, with their expression upregulated in many types of cancers. Because only a few sugar porter structures have been determined, mechanistic models have been constructed by piecing together structural states of distantly related proteins. Current GLUT transport models are predominantly descriptive and oversimplified. Here, we have combined coevolution analysis and comparative modeling, to predict structures of the entire sugar porter superfamily in each state of the transport cycle. We have analyzed the state-specific contacts inferred from coevolving residue pairs and shown how this information can be used to rapidly generate free-energy landscapes consistent with experimental estimates, as illustrated here for the mammalian fructose transporter GLUT5. By comparing many different sugar porter models and scrutinizing their sequence, we have been able to define the molecular determinants of the transport cycle, which are conserved throughout the sugar porter superfamily. We have also been able to highlight differences leading to the emergence of proton-coupling, validating, and extending the previously proposed latch mechanism. Our computational approach is transferable to any transporter, and to other protein families in general.

Read the full publication here.



Published 28 June 2023 in the British Journal of Pharmacology (doi 10.1111/bph.16183):

Subtype-specific modulation of human Kv7 channels by the anticonvulsant cannabidiol through a lipid-exposed pore-domain site

Michael Pökl, Akshay Sridhar, Damon JA Frampton, Veronika A Linhart, Lucie Delemotte, Sara I Liin

Background and Purpose
Cannabidiol (CBD) is used clinically as an anticonvulsant. However, its precise mechanism of action has remained elusive. CBD was recently demonstrated to enhance the activity of the neuronal KV7.2/7.3 channel, which may be one important contributor to CBD’s anticonvulsant effect. Curiously, CBD inhibits the closely related cardiac KV7.1/KCNE1 channel. However, whether and how CBD affects other KV7 subtypes remains unstudied, and the CBD interaction sites mediating these diverse effects remain unknown.

Experimental approach
Here, we used electrophysiology, molecular dynamics simulations, molecular docking, and site-directed mutagenesis to address these open questions.

Key results
We found that CBD modulates the activity of all human KV7 subtypes and that the effects are subtype-dependent. CBD enhanced the activity of KV7.2-7.5 subtypes, seen as a V50 shift towards more negative voltages or increased maximum conductance. In contrast, CBD inhibited the KV7.1 and KV7.1/KCNE1 channels, seen as a V50 shift towards more positive voltages and reduced conductance. In KV7.2 and KV7.4, we propose a CBD interaction site at the subunit interface in the pore domain which overlaps with the interaction site of other compounds, notably the anticonvulsant retigabine. However, CBD relies on other residues for its effects than the conserved tryptophan that is critical for retigabine effects. We propose a similar, though not identical CBD site in KV7.1, with a non-conserved phenylalanine being important.

Conclusions and implications
We identify novel targets of CBD, contributing to a better understanding of CBD’s clinical effects, and provide mechanistic insights into how CBD modulates different KV7 subtypes.

Read the full publication here.


Bulges in Eukaryotic Navs

Published 21 June 2023 in Journal of Physical Chemistry Letters (doi 10.1021/acs.jpclett.3c00803):

Modulation of pore opening of eukaryotic sodium channels by π-helices in S6

Koushik Choudhury, Lucie Delemotte

Voltage-gated sodium channels are heterotetrameric sodium selective ion channels that play a central role in electrical signaling in excitable cells. With recent advances in structural biology, structures of eukaryotic sodium channels have been captured in several distinct conformations corresponding to different functional states. The secondary structure of the pore lining S6 helices of subunits DI, DII, and DIV has been captured with both short π-helix stretches and in fully α-helical conformations. The relevance of these secondary structure elements for pore gating is not yet understood. Here, we propose that a π-helix in at least DI-S6, DIII-S6, and DIV-S6 results in a fully conductive state. On the other hand, the absence of π-helix in either DI-S6 or DIV-S6 yields a subconductance state, and its absence from both DI-S6 and DIV-S6 yields a nonconducting state. This work highlights the impact of the presence of a π-helix in the different S6 helices of an expanded pore on pore conductance, thus opening new doors toward reconstructing the entire conformational landscape along the functional cycle of Nav Channels and paving the way to the design of state-dependent modulators.

Read the full publication here.


Calculating HCN Coupling

Published 21 June 2023 in eLife (doi 10.7554/eLife.80303):

Interplay between VSD, pore, and membrane lipids in electromechanical coupling in HCN channels

Ahmad Elbahnsi, John Cowgill, Verena Burtscher, Linda Wedemann, Luise Zeckey, Baron Chanda, Lucie Delemotte

Hyperpolarized-activated and cyclic nucleotide-gated (HCN) channels are the only members of the voltage-gated ion channel superfamily in mammals that open upon hyperpolarization, conferring them pacemaker properties that are instrumental for rhythmic firing of cardiac and neuronal cells. Activation of their voltage-sensor domains (VSD) upon hyperpolarization occurs through a downward movement of the S4 helix bearing the gating charges, which triggers a break in the alpha-helical hydrogen bonding pattern at the level of a conserved Serine residue. Previous structural and molecular simulation studies had however failed to capture pore opening that should be triggered by VSD activation, presumably because of a low VSD/pore electromechanical coupling efficiency and the limited timescales accessible to such techniques. Here, we have used advanced modeling strategies, including enhanced sampling molecular dynamics simulations exploiting comparisons between non-domain swapped voltage-gated ion channel structures trapped in closed and open states to trigger pore gating and characterize electromechanical coupling in HCN1. We propose that the coupling mechanism involves the reorganization of the interfaces between the VSD helices, in particular S4, and the pore-forming helices S5 and S6, subtly shifting the balance between hydrophobic and hydrophilic interactions in a ‘domino effect’ during activation and gating in this region. Remarkably, our simulations reveal state-dependent occupancy of lipid molecules at this emergent coupling interface, suggesting a key role of lipids in hyperpolarization-dependent gating. Our model provides a rationale for previous observations and a possible mechanism for regulation of HCN channels by the lipidic components of the membrane.

Read the full publication here.


Grattis till Dr Bergh

Members of Molecular Biophysics Stockholm joined family and friends in celebrating Cathrine Bergh’s successful spikning and defense of her PhD from KTH in Applied Physics, From static structures to free energy landscapes: characterizing conformational transitions in biological macromolecules. Cathrine nailed her thesis on 29 May, and defended it 13 June at SciLifeLab, with Professor Gerhard Hummer (Max Planck Institute of Biophysics) as opponent. Professor Erik Lindahl and Ligand-Gated Ion Channels team-lead Reba Howard led a toast to their advisee of over five years, as she prepares to join the GROMACS software development team.