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Yee SW, Macdonald CB, Mitrovic D, Zhou X, Koleske ML, Yang J, Buitrago Silva D, Rockefeller Grimes P, Trinidad DD, More SS, Kachuri L, Witte JS, Delemotte L, Giacomini KM, Coyote-Maestas W. The full spectrum of SLC22 OCT1 mutations illuminates the bridge between drug transporter biophysics and pharmacogenomics. Mol Cell 2024:S1097-2765(24)00323-X. [PMID: 38703769 DOI: 10.1016/j.molcel.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/04/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024]
Abstract
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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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christian B Macdonald
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Darko Mitrovic
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick Rockefeller Grimes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donovan D Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Swati S More
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden.
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA.
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2
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Clatot J, Currin CB, Liang Q, Pipatpolkai T, Massey SL, Helbig I, Delemotte L, Vogels TP, Covarrubias M, Goldberg EM. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proc Natl Acad Sci U S A 2024; 121:e2307776121. [PMID: 38194456 PMCID: PMC10801864 DOI: 10.1073/pnas.2307776121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/17/2023] [Indexed: 01/11/2024] Open
Abstract
De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium (K+) channel subunit Kv3.2 are a recently described cause of developmental and epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr) was identified via exome sequencing in a patient with DEE. Relative to wild-type Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing shift in the voltage dependence of activation, accelerated activation, and delayed deactivation consistent with a relative stabilization of the open conformation, along with increased current density. Leveraging the cryogenic electron microscopy (cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix of the T1 domain promotes a relative stabilization of the open conformation of the channel, which underlies the observed gain of function. A multicompartment computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition in cerebral cortex circuits to explain the resulting epilepsy.
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Affiliation(s)
- Jerome Clatot
- Division of Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- The Epilepsy Neurogenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia,PA19104
| | | | - Qiansheng Liang
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA19107
| | - Tanadet Pipatpolkai
- Department of Applied Physics, Science for Life Laboratory, Royal Institute of Technology, SolnaSE-171 21, Sweden
| | - Shavonne L. Massey
- Division of Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- The Epilepsy Neurogenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia,PA19104
- The Department of Neurology, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104
| | - Ingo Helbig
- Division of Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- The Epilepsy Neurogenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia,PA19104
- The Department of Neurology, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, Royal Institute of Technology, SolnaSE-171 21, Sweden
| | - Tim P. Vogels
- The Institute of Science and Technology Austria, Klosterneuburg3400, Austria
| | - Manuel Covarrubias
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA19107
| | - Ethan M. Goldberg
- Division of Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- The Epilepsy Neurogenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia,PA19104
- The Department of Neurology, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104
- The Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104
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3
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Stevens-Sostre WA, Flores-Aldama L, Bustos D, Li J, Morais-Cabral JH, Delemotte L, Robertson GA. An intracellular hydrophobic nexus critical for hERG1 channel slow deactivation. Biophys J 2024:S0006-3495(24)00026-2. [PMID: 38219015 DOI: 10.1016/j.bpj.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/17/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Slow deactivation is a critical property of voltage-gated K+ channels encoded by the human Ether-à-go-go-Related Gene 1 (hERG). hERG1 channel deactivation is modulated by interactions between intracellular N-terminal Per-Arnt-Sim (PAS) and C-terminal cyclic nucleotide-binding homology (CNBh) domains. The PAS domain is multipartite, comprising a globular domain (gPAS; residues 26-135) and an N-terminal PAS-cap that is further subdivided into an initial unstructured "tip" (residues 1-12) and an amphipathic α-helical region (residues 13-25). Although the PAS-cap tip has long been considered the effector of slow deactivation, how its position near the gating machinery is controlled has not been elucidated. Here, we show that a triad of hydrophobic interactions among the gPAS, PAS-cap α helix, and the CNBh domains is required to support slow deactivation in hERG1. The primary sequence of this "hydrophobic nexus" is highly conserved among mammalian ERG channels but shows key differences to fast-deactivating Ether-à-go-go 1 (EAG1) channels. Combining sequence analysis, structure-directed mutagenesis, electrophysiology, and molecular dynamics simulations, we demonstrate that polar serine substitutions uncover an intermediate deactivation mode that is also mimicked by deletion of the PAS-cap α helix. Molecular dynamics simulation analyses of the serine-substituted channels show an increase in distance among the residues of the hydrophobic nexus, a rotation of the intracellular gating ring, and a retraction of the PAS-cap tip from its receptor site near the voltage sensor domain and channel gate. These findings provide compelling evidence that the hydrophobic nexus coordinates the respective components of the intracellular gating ring and positions the PAS-cap tip to control hERG1 deactivation gating.
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Affiliation(s)
- Whitney A Stevens-Sostre
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Lisandra Flores-Aldama
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Daniel Bustos
- Centro de Investigación de Estudios Avanzados Del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica Del Maule, Talca, Chile; Laboratorio de Bioinformática y Química Computacional (LBQC), Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica Del Maule, Talca, Chile
| | - Jin Li
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - João H Morais-Cabral
- Instituto de Investigação e Inovação Em Saude da Universidade Do Porto (i3S); Instituto de Biologia Molecular e Celular, Universidade Do Porto, Porto, Portugal
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Gail A Robertson
- Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
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4
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Pökl M, Sridhar A, Frampton DJA, Linhart VA, Delemotte L, Liin SI. Subtype-specific modulation of human K V 7 channels by the anticonvulsant cannabidiol through a lipid-exposed pore-domain site. Br J Pharmacol 2023; 180:2956-2972. [PMID: 37377025 DOI: 10.1111/bph.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/16/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND AND PURPOSE Cannabidiol (CBD) is used clinically as an anticonvulsant. Its precise mechanism of action has remained unclear. CBD was recently demonstrated to enhance the activity of the neuronal KV 7.2/7.3 channel, which may be one important contributor to CBD anticonvulsant effect. Curiously, CBD inhibits the closely related cardiac KV 7.1/KCNE1 channel. Whether and how CBD affects other KV 7 subtypes remains uninvestigated 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 questions. KEY RESULTS We found that CBD modulates the activity of all human KV 7 subtypes and that the effects are subtype dependent. CBD enhanced the activity of KV 7.2-7.5 subtypes, seen as a V50 shift towards more negative voltages or increased maximum conductance. In contrast, CBD inhibited the KV 7.1 and KV 7.1/KCNE1 channels, seen as a V50 shift towards more positive voltages and reduced conductance. In KV 7.2 and KV 7.4, we propose a CBD interaction site at the subunit interface in the pore domain that 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 KV 7.1, with a non-conserved phenylalanine being important. CONCLUSIONS AND IMPLICATIONS We identify novel targets of CBD, contributing to a better understanding of CBD clinical effects and provide mechanistic insights into how CBD modulates different KV 7 subtypes.
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Affiliation(s)
- Michael Pökl
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Damon J A Frampton
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Veronika A Linhart
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Sara I Liin
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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5
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Mitrovic D, Chen Y, Marciniak A, Delemotte L. Coevolution-Driven Method for Efficiently Simulating Conformational Changes in Proteins Reveals Molecular Details of Ligand Effects in the β2AR Receptor. J Phys Chem B 2023; 127:9891-9904. [PMID: 37947090 PMCID: PMC10683026 DOI: 10.1021/acs.jpcb.3c04897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
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.
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Affiliation(s)
- Darko Mitrovic
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Yue Chen
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Antoni Marciniak
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Lucie Delemotte
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
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6
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Mitrovic D, McComas SE, Alleva C, Bonaccorsi M, Drew D, Delemotte L. Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning. eLife 2023; 12:e84805. [PMID: 37405846 DOI: 10.7554/elife.84805] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/25/2023] [Indexed: 07/06/2023] Open
Abstract
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.
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Affiliation(s)
- Darko Mitrovic
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Sarah E McComas
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Claudia Alleva
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marta Bonaccorsi
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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7
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McComas SE, Reichenbach T, Mitrovic D, Alleva C, Bonaccorsi M, Delemotte L, Drew D. Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5. eLife 2023; 12:e84808. [PMID: 37405832 DOI: 10.7554/elife.84808] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/21/2023] [Indexed: 07/06/2023] Open
Abstract
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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Affiliation(s)
- Sarah E McComas
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Tom Reichenbach
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Darko Mitrovic
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Claudia Alleva
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marta Bonaccorsi
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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Choudhury K, Delemotte L. Modulation of Pore Opening of Eukaryotic Sodium Channels by π-Helices in S6. J Phys Chem Lett 2023:5876-5881. [PMID: 37341700 DOI: 10.1021/acs.jpclett.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
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.
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Affiliation(s)
- Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-171 65 Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-171 65 Solna, Sweden
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9
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Elbahnsi A, Cowgill J, Burtscher V, Wedemann L, Zeckey L, Chanda B, Delemotte L. Interplay between VSD, pore and membrane lipids in electromechanical coupling in HCN channels. eLife 2023; 12:e80303. [PMID: 37341381 DOI: 10.7554/elife.80303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/20/2023] [Indexed: 06/22/2023] Open
Abstract
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.
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Affiliation(s)
- Ahmad Elbahnsi
- Department of Applied Physics of Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - John Cowgill
- Department of Applied Physics of Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Verena Burtscher
- Department of Anesthesiology, Washington University in St. Louis, Saint Louis, United States
| | - Linda Wedemann
- Department of Applied Physics of Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Luise Zeckey
- Department of Applied Physics of Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Baron Chanda
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, United States
| | - Lucie Delemotte
- Department of Applied Physics of Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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10
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Yee SW, Macdonald C, Mitrovic D, Zhou X, Koleske ML, Yang J, Silva DB, Grimes PR, Trinidad D, More SS, Kachuri L, Witte JS, Delemotte L, Giacomini KM, Coyote-Maestas W. The full spectrum of OCT1 (SLC22A1) mutations bridges transporter biophysics to drug pharmacogenomics. bioRxiv 2023:2023.06.06.543963. [PMID: 37333090 PMCID: PMC10274788 DOI: 10.1101/2023.06.06.543963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Membrane transporters play a fundamental role in the tissue distribution of endogenous compounds and xenobiotics and are major determinants of efficacy and side effects profiles. Polymorphisms within these drug transporters result in inter-individual variation in drug response, with some patients not responding to the recommended dosage of drug whereas others experience catastrophic side effects. For example, variants within the major hepatic Human organic cation transporter OCT1 (SLC22A1) can change endogenous organic cations and many prescription drug levels. To understand how variants mechanistically impact drug uptake, we systematically study how all known and possible single missense and single amino acid deletion variants impact expression and substrate uptake of OCT1. We find that human variants primarily disrupt function via folding rather than substrate uptake. Our study revealed that the major determinants of folding reside in the first 300 amino acids, including the first 6 transmembrane domains and the extracellular domain (ECD) with a stabilizing and highly conserved stabilizing helical motif making key interactions between the ECD and transmembrane domains. Using the functional data combined with computational approaches, we determine and validate a structure-function model of OCT1s conformational ensemble without experimental structures. Using this model and molecular dynamic simulations of key mutants, we determine biophysical mechanisms for how specific human variants alter transport phenotypes. We identify differences in frequencies of reduced function alleles across populations with East Asians vs European populations having the lowest and highest frequency of reduced function variants, respectively. Mining human population databases reveals that reduced function alleles of OCT1 identified in this study associate significantly with high LDL cholesterol levels. Our general approach broadly applied could transform the landscape of precision medicine by producing a mechanistic basis for understanding the effects of human mutations on disease and drug response.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Christian Macdonald
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Darko Mitrovic
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Sweden
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Patrick Rockefeller Grimes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Donovan Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, United States
| | - Swati S More
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
- Current address: Center for Drug Design (CDD), College of Pharmacy, University of Minnesota, Minnesota, United States
| | - Linda Kachuri
- Epidemiology and Population Health, Stanford University, California, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | - John S Witte
- Epidemiology and Population Health, Stanford University, California, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Sweden
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
- Quantitative Biosciences Institute, University of California, San Francisco, United States
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11
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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. bioRxiv 2023:2023.05.02.538537. [PMID: 37205542 PMCID: PMC10187166 DOI: 10.1101/2023.05.02.538537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation, such as temperature and simulation length, and identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore collected MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and increase populating and standardizing metadata to reuse this valuable matter.
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Affiliation(s)
- Johanna K. S. Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Magdalena Szczuka
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de Toulouse, 205 route de Narbonne, 31400, Toulouse, France
| | - Lisa Bouarroudj
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Mohamed Oussaren
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | | | - Rebecca J. Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de Toulouse, 205 route de Narbonne, 31400, Toulouse, France
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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12
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Panel N, Vo DD, Kahlous NA, Hübner H, Tiedt S, Matricon P, Pacalon J, Fleetwood O, Kampen S, Luttens A, Delemotte L, Kihlberg J, Gmeiner P, Carlsson J. Design of Drug Efficacy Guided by Free Energy Simulations of the β2‐Adrenoceptor. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202218959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Nicolas Panel
- Uppsala University: Uppsala Universitet Cell and Molecular Biology SWEDEN
| | - Duc Duy Vo
- Uppsala University: Uppsala Universitet SWEDEN
| | - Nour Aldin Kahlous
- Uppsala University: Uppsala Universitet Cell and Molecular Biology SWEDEN
| | - Harald Hübner
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg Chemistry and Pharmacy GERMANY
| | - Stephanie Tiedt
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg Chemistry and Pharmacy GERMANY
| | - Pierre Matricon
- Uppsala University: Uppsala Universitet Cell and Molecular Biology SWEDEN
| | - Jody Pacalon
- Uppsala University: Uppsala Universitet Cell and Molecular Biology SWEDEN
| | | | - Stefanie Kampen
- Uppsala University: Uppsala Universitet Cell and Molecular Biology SWEDEN
| | - Andreas Luttens
- Uppsala University: Uppsala Universitet Cell and Molecular Biology SWEDEN
| | - Lucie Delemotte
- KTH Royal Institute of Technology: Kungliga Tekniska Hogskolan Applied Physics SWEDEN
| | - Jan Kihlberg
- Uppsala University: Uppsala Universitet Chemistry-BMC SWEDEN
| | - Peter Gmeiner
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg Chemistry and Pharmacy GERMANY
| | - Jens Carlsson
- Uppsala University Dept. of Cell and Molecular Biology Husargatan 3 Box 596 751 24 Uppsala SWEDEN
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13
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Panel N, Vo DD, Kahlous NA, Hübner H, Tiedt S, Matricon P, Pacalon J, Fleetwood O, Kampen S, Luttens A, Delemotte L, Kihlberg J, Gmeiner P, Carlsson J. Design of Drug Efficacy Guided by Free Energy Simulations of the β2-Adrenoceptor. Angew Chem Int Ed Engl 2023; 62:e202218959. [PMID: 36914577 DOI: 10.1002/anie.202218959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/16/2023]
Abstract
G protein-coupled receptors (GPCR) play important roles in physiological processes and are modulated by drugs that either activate or block signaling. Rational design of the pharmacological efficacy profiles of GPCR ligands could enable the development of more efficient drugs, but is challenging even if high-resolution receptor structures are available. We performed molecular dynamics simulations of the β2 adrenergic receptor (β2R) in active and inactive conformations to assess if binding free energy calculations can predict differences in ligand efficacy for closely related compounds. Previously identified ligands were successfully classified into groups with comparable efficacy profiles based on the calculated shift in ligand affinity upon activation. A series of ligands were then predicted and synthesized, leading to the discovery of partial agonists with nanomolar potencies and novel scaffolds. Our results demonstrate that free energy simulations enable design of ligand efficacy and the same approach can be applied to other GPCR drug targets.
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Affiliation(s)
- Nicolas Panel
- Uppsala University: Uppsala Universitet, Cell and Molecular Biology, SWEDEN
| | - Duc Duy Vo
- Uppsala University: Uppsala Universitet, , SWEDEN
| | - Nour Aldin Kahlous
- Uppsala University: Uppsala Universitet, Cell and Molecular Biology, SWEDEN
| | - Harald Hübner
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Chemistry and Pharmacy, GERMANY
| | - Stephanie Tiedt
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Chemistry and Pharmacy, GERMANY
| | - Pierre Matricon
- Uppsala University: Uppsala Universitet, Cell and Molecular Biology, SWEDEN
| | - Jody Pacalon
- Uppsala University: Uppsala Universitet, Cell and Molecular Biology, SWEDEN
| | | | - Stefanie Kampen
- Uppsala University: Uppsala Universitet, Cell and Molecular Biology, SWEDEN
| | - Andreas Luttens
- Uppsala University: Uppsala Universitet, Cell and Molecular Biology, SWEDEN
| | - Lucie Delemotte
- KTH Royal Institute of Technology: Kungliga Tekniska Hogskolan, Applied Physics, SWEDEN
| | - Jan Kihlberg
- Uppsala University: Uppsala Universitet, Chemistry-BMC, SWEDEN
| | - Peter Gmeiner
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Chemistry and Pharmacy, GERMANY
| | - Jens Carlsson
- Uppsala University, Dept. of Cell and Molecular Biology, Husargatan 3 Box 596, 751 24, Uppsala, SWEDEN
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14
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Marciniak A, Mitrovic D, Delemotte L. Molecular determinants of distinctive opioid receptor subtype affinities. Biophys J 2023; 122:511a. [PMID: 36784643 DOI: 10.1016/j.bpj.2022.11.2719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Antoni Marciniak
- Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Darko Mitrovic
- Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lucie Delemotte
- Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
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15
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Choudhury K, Howard RJ, Delemotte L. An α-π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb. J Gen Physiol 2022; 155:213748. [PMID: 36515966 PMCID: PMC9754703 DOI: 10.1085/jgp.202213214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Voltage-gated sodium channels play an important role in electrical signaling in excitable cells. In response to changes in membrane potential, they cycle between nonconducting and conducting conformations. With recent advances in structural biology, structures of sodium channels have been captured in several distinct conformations, which are thought to represent different functional states. However, it has been difficult to capture the intrinsically transient open state. We recently showed that a proposed open state of the bacterial sodium channel NavMs was not conductive and that a conformational change involving a transition to a π-helix in the pore-lining S6 helix converted this structure into a conducting state. However, the relevance of this structural feature in other sodium channels, and its implications for the broader gating cycle, remained unclear. Here, we propose a comparable open state of another class of bacterial channel from Aliarcobacter butzleri (NavAb) with characteristic pore hydration, ion permeation, and drug binding properties. Furthermore, we show that a π-helix transition can lead to pore opening and that such a conformational change blocks fenestrations in the inner helix bundle. We also discover that a region in the C-terminal domain can undergo a disordering transition proposed to be important for pore opening. These results support a role for a π-helix transition in the opening of NavAb, enabling new proposals for the structural annotation and drug modulation mechanisms in this important sodium channel model.
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Affiliation(s)
- Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Rebecca J. Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden,Correspondence to Lucie Delemotte:
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16
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Westerlund AM, Sridhar A, Dahl L, Andersson A, Bodnar AY, Delemotte L. Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin. PLoS Comput Biol 2022; 18:e1010583. [PMID: 36206305 PMCID: PMC9581412 DOI: 10.1371/journal.pcbi.1010583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/19/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Calmodulin (CaM) is a calcium sensor which binds and regulates a wide range of target-proteins. This implicitly enables the concentration of calcium to influence many downstream physiological responses, including muscle contraction, learning and depression. The antipsychotic drug trifluoperazine (TFP) is a known CaM inhibitor. By binding to various sites, TFP prevents CaM from associating to target-proteins. However, the molecular and state-dependent mechanisms behind CaM inhibition by drugs such as TFP are largely unknown. Here, we build a Markov state model (MSM) from adaptively sampled molecular dynamics simulations and reveal the structural and dynamical features behind the inhibitory mechanism of TFP-binding to the C-terminal domain of CaM. We specifically identify three major TFP binding-modes from the MSM macrostates, and distinguish their effect on CaM conformation by using a systematic analysis protocol based on biophysical descriptors and tools from machine learning. The results show that depending on the binding orientation, TFP effectively stabilizes features of the calcium-unbound CaM, either affecting the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the bound domain. The conclusions drawn from this work may in the future serve to formulate a complete model of pharmacological modulation of CaM, which furthers our understanding of how these drugs affect signaling pathways as well as associated diseases. Calmodulin (CaM) is a calcium-sensing protein which makes other proteins dependent on the surrounding calcium concentration by binding to these proteins. Such protein-protein interactions with CaM are vital for calcium to control many physiological pathways within the cell. The antipsychotic drug trifluoperazine (TFP) inhibits CaM’s ability to bind and regulate other proteins. Here, we use molecular dynamics simulations together with Markov state modeling and machine learning to understand the structural and dynamical features by which TFP bound to the one domain of CaM prevents association to other proteins. We find that TFP encourages CaM to adopt a conformation that is like the one stabilized in absence of calcium: depending on the binding orientation of TFP, the drug indeed either affects the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the domain. Understanding TFP binding is a first step towards designing better drugs targeting CaM.
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Affiliation(s)
- Annie M. Westerlund
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Leo Dahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Alma Andersson
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- Division of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna-Yaroslava Bodnar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- * E-mail:
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17
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Chi G, Liang Q, Sridhar A, Cowgill JB, Sader K, Radjainia M, Qian P, Castro-Hartmann P, Venkaya S, Singh NK, McKinley G, Fernandez-Cid A, Mukhopadhyay SMM, Burgess-Brown NA, Delemotte L, Covarrubias M, Dürr KL. Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain. Nat Commun 2022; 13:4087. [PMID: 35840580 PMCID: PMC9287412 DOI: 10.1038/s41467-022-29594-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/24/2022] [Indexed: 11/26/2022] Open
Abstract
Kv3 channels have distinctive gating kinetics tailored for rapid repolarization in fast-spiking neurons. Malfunction of this process due to genetic variants in the KCNC1 gene causes severe epileptic disorders, yet the structural determinants for the unusual gating properties remain elusive. Here, we present cryo-electron microscopy structures of the human Kv3.1a channel, revealing a unique arrangement of the cytoplasmic tetramerization domain T1 which facilitates interactions with C-terminal axonal targeting motif and key components of the gating machinery. Additional interactions between S1/S2 linker and turret domain strengthen the interface between voltage sensor and pore domain. Supported by molecular dynamics simulations, electrophysiological and mutational analyses, we identify several residues in the S4/S5 linker which influence the gating kinetics and an electrostatic interaction between acidic residues in α6 of T1 and R449 in the pore-flanking S6T helices. These findings provide insights into gating control and disease mechanisms and may guide strategies for the design of pharmaceutical drugs targeting Kv3 channels.
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Affiliation(s)
- Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Qiansheng Liang
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, UK
| | - Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH, Solna, Sweden
| | - John B Cowgill
- Department of Applied Physics, Science for Life Laboratory, KTH, Solna, Sweden
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Mazdak Radjainia
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Shayla Venkaya
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exscientia Ltd., The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | - Nanki Kaur Singh
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Gavin McKinley
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Alejandra Fernandez-Cid
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exact Sciences Ltd., The Sherard Building, Edmund Halley Road, The Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Shubhashish M M Mukhopadhyay
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exscientia Ltd., The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exact Sciences Ltd., The Sherard Building, Edmund Halley Road, The Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH, Solna, Sweden
| | - Manuel Covarrubias
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, UK
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
- OMass Therapeutics, Ltd., The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK.
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18
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Frampton DJA, Choudhury K, Nikesjö J, Delemotte L, Liin SI. Subtype-specific responses of hKv7.4 and hKv7.5 channels to polyunsaturated fatty acids reveal an unconventional modulatory site and mechanism. eLife 2022; 11:77672. [PMID: 35642964 PMCID: PMC9159753 DOI: 10.7554/elife.77672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
The KV7.4 and KV7.5 subtypes of voltage-gated potassium channels play a role in important physiological processes such as sound amplification in the cochlea and adjusting vascular smooth muscle tone. Therefore, the mechanisms that regulate KV7.4 and KV7.5 channel function are of interest. Here, we study the effect of polyunsaturated fatty acids (PUFAs) on human KV7.4 and KV7.5 channels expressed in Xenopus oocytes. We report that PUFAs facilitate activation of hKV7.5 by shifting the V50 of the conductance versus voltage (G(V)) curve toward more negative voltages. This response depends on the head group charge, as an uncharged PUFA analogue has no effect and a positively charged PUFA analogue induces positive V50 shifts. In contrast, PUFAs inhibit activation of hKV7.4 by shifting V50 toward more positive voltages. No effect on V50 of hKV7.4 is observed by an uncharged or a positively charged PUFA analogue. Thus, the hKV7.5 channel's response to PUFAs is analogous to the one previously observed in hKV7.1-7.3 channels, whereas the hKV7.4 channel response is opposite, revealing subtype-specific responses to PUFAs. We identify a unique inner PUFA interaction site in the voltage-sensing domain of hKV7.4 underlying the PUFA response, revealing an unconventional mechanism of modulation of hKV7.4 by PUFAs.
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Affiliation(s)
- Damon J A Frampton
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Johan Nikesjö
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sara I Liin
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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19
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Delemotte L, Garcia SL, Rodríguez-Gijón A, Sezgin E, Vihervaara A. Uniting diversity to create a more inclusive academic environment. J Cell Sci 2022; 135:275020. [PMID: 35411385 DOI: 10.1242/jcs.259977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Rems L, Tang X, Zhao F, Pérez-Conesa S, Testa I, Delemotte L. Identification of electroporation sites in the complex lipid organization of the plasma membrane. eLife 2022; 11:e74773. [PMID: 35195069 PMCID: PMC8912918 DOI: 10.7554/elife.74773] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon termed electroporation is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrhythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study, we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. Additionally, by analysing poration kinetics with Bayesian survival analysis we show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.
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Affiliation(s)
- Lea Rems
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Ljubljana, Faculty of Electrical EngineeringLjubljanaSlovenia
| | - Xinru Tang
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Fangwei Zhao
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Ilaria Testa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
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21
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Delemotte L, Fleetwood O, Chen Y, Pérez Conesa S. Details of G-protein coupled receptor activation via data-driven molecular modeling. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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22
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Mitrovic D, Drew D, Delemotte L. Integration of family-wide information to probe the conformational landscape of sugar transporters. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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23
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McComas S, Drew D, Delemotte L. Free energy surface of a sugar transporter in the presence and absence of substrate. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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24
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Cowgill J, Yvonnesdotter L, Blau C, Howard RJ, Lindahl ER, Delemotte L. Atomic models from low resolution maps with density-guided MD simulations. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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25
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Chen Y, Fleetwood O, Pérez Conesa S, Delemotte L. Allosteric effect of nanobody binding on ligand-specific active states of the β2-adrenergic receptor. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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26
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Abstract
TRP channels have been heavily pursued as cryo-electron microscopy targets since they rang in the "resolution revolution." Although widespread in eukaryotes, a fungal TRP channel structure was missing. In this issue of Structure, Ahmed et al. (2022) present structural insights into the regulation of yeast TRPY1 by Ca2+ and lipids.
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Affiliation(s)
- Ute A Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence "Balance of the Microverse", 07743 Jena, Germany; Center for Biomolecular Magnetic Resonance, Goethe-University, 60438 Frankfurt, Germany.
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
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27
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Choudhury K, Kasimova MA, McComas S, Howard RJ, Delemotte L. An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine. Biophys J 2022; 121:11-22. [PMID: 34890580 PMCID: PMC8758419 DOI: 10.1016/j.bpj.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Voltage-gated sodium (Nav) channels play critical roles in propagating action potentials and otherwise manipulating ionic gradients in excitable cells. These channels open in response to membrane depolarization, selectively permeating sodium ions until rapidly inactivating. Structural characterization of the gating cycle in this channel family has proved challenging, particularly due to the transient nature of the open state. A structure from the bacterium Magnetococcus marinus Nav (NavMs) was initially proposed to be open, based on its pore diameter and voltage-sensor conformation. However, the functional annotation of this model, and the structural details of the open state, remain disputed. In this work, we used molecular modeling and simulations to test possible open-state models of NavMs. The full-length experimental structure, termed here the α-model, was consistently dehydrated at the activation gate, indicating an inability to conduct ions. Based on a spontaneous transition observed in extended simulations, and sequence/structure comparison to other Nav channels, we built an alternative π-model featuring a helix transition and the rotation of a conserved asparagine residue into the activation gate. Pore hydration, ion permeation, and state-dependent drug binding in this model were consistent with an open functional state. This work thus offers both a functional annotation of the full-length NavMs structure and a detailed model for a stable Nav open state, with potential conservation in diverse ion-channel families.
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Affiliation(s)
- Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Marina A. Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah McComas
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rebecca J. Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden,Corresponding author
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28
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Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L. Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. J Chem Inf Model 2021; 61:6024-6037. [PMID: 34780174 PMCID: PMC8715506 DOI: 10.1021/acs.jcim.1c00826] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nanobody binding
stabilizes G-protein-coupled receptors (GPCR)
in a fully active state and modulates their affinity for bound ligands.
However, the atomic-level basis for this allosteric regulation remains
elusive. Here, we investigate the conformational changes induced by
the binding of a nanobody (Nb80) on the active-like β2 adrenergic
receptor (β2AR) via enhanced sampling molecular dynamics simulations.
Dimensionality reduction analysis shows that Nb80 stabilizes structural
features of the β2AR with an ∼14 Å outward movement
of transmembrane helix 6 and a close proximity of transmembrane (TM)
helices 5 and 7, and favors the fully active-like conformation of
the receptor, independent of ligand binding, in contrast to the conditions
under which no intracellular binding partner is bound, in which case
the receptor is only stabilized in an intermediate-active state. This
activation is supported by the residues located at hotspots located
on TMs 5, 6, and 7, as shown by supervised machine learning methods.
Besides, ligand-specific subtle differences in the conformations assumed
by intracellular loop 2 and extracellular loop 2 are captured from
the trajectories of various ligand-bound receptors in the presence
of Nb80. Dynamic network analysis further reveals that Nb80 binding
triggers tighter and stronger local communication networks between
the Nb80 and the ligand-binding sites, primarily involving residues
around ICL2 and the intracellular end of TM3, TM5, TM6, as well as
ECL2, ECL3, and the extracellular ends of TM6 and TM7. In particular,
we identify unique allosteric signal transmission mechanisms between
the Nb80-binding site and the extracellular domains in conformations
modulated by a full agonist, BI167107, and a G-protein-biased partial
agonist, salmeterol, involving mainly TM1 and TM2, and TM5, respectively.
Altogether, our results provide insights into the effect of intracellular
binding partners on the GPCR activation mechanism, which should be
taken into account in structure-based drug discovery.
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Affiliation(s)
- Yue Chen
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Sergio Pérez-Conesa
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
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29
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Moiseenkova-Bell V, Delemotte L, Minor DL. Ion Channels: Intersection of Structure, Function, and Pharmacology. J Mol Biol 2021; 433:167102. [PMID: 34119491 DOI: 10.1016/j.jmb.2021.167102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vera Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Daniel L Minor
- Cardiovascular Research Institute, Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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30
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Elbahnsi A, Delemotte L. Structure and Sequence-based Computational Approaches to Allosteric Signal Transduction: Application to Electromechanical Coupling in Voltage-gated Ion Channels. J Mol Biol 2021; 433:167095. [PMID: 34107281 DOI: 10.1016/j.jmb.2021.167095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/17/2022]
Abstract
Allosteric signaling underlies the function of many biomolecules, including membrane proteins such as ion channels. Experimental methods have enabled specific quantitative insights into the coupling between the voltage sensing domain (VSD) and the pore gate of voltage-gated ion channels, located tens of Ångström apart from one another, as well as pinpointed specific residues and domains that participate in electromechanical signal transmission. Nevertheless, an overall atomic-level resolution picture is difficult to obtain from these methods alone. Today, thanks to the cryo-EM resolution revolution, we have access to high resolution structures of many different voltage-gated ion channels in various conformational states, putting a quantitative description of the processes at the basis of these changes within our close reach. Here, we review computational methods that build on structures to detect and characterize allosteric signaling and pathways. We then examine what has been learned so far about electromechanical coupling between VSD and pore using such methods. While no general theory of electromechanical coupling in voltage-gated ion channels integrating results from all these methods is available yet, we outline the types of insights that could be achieved in the near future using the methods that have not yet been put to use in this field of application.
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Affiliation(s)
- Ahmad Elbahnsi
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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31
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Carnevale V, Delemotte L, Howard RJ. Molecular Dynamics Simulations of Ion Channels. Trends Biochem Sci 2021; 46:621-622. [PMID: 33941431 DOI: 10.1016/j.tibs.2021.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA
| | - Lucie Delemotte
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
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32
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Pérez-Conesa S, Keeler EG, Zhang D, Delemotte L, McDermott AE. Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel. J Chem Phys 2021; 154:165102. [PMID: 33940802 PMCID: PMC9250420 DOI: 10.1063/5.0040649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As the first potassium channel with an x-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related, in particular, to the allosteric coupling between its gates remain open. The many currently available x-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms. Since these studies have required mutations, complexation with antibodies, and substitution of detergents in place of lipids, examining the channel under more native conditions is desirable. Solid-state nuclear magnetic resonance (SSNMR) can be used to study the wild-type protein under activating conditions (low pH), at room temperature, and in bacteriomimetic liposomes. In this work, we sought to structurally assign the activated state present in SSNMR experiments. We used a combination of molecular dynamics (MD) simulations, chemical shift prediction algorithms, and Bayesian inference techniques to determine which of the most plausible x-ray structures resolved to date best represents the activated state captured in SSNMR. We first identified specific nuclei with simulated NMR chemical shifts that differed significantly when comparing partially open vs fully open ensembles from MD simulations. The simulated NMR chemical shifts for those specific nuclei were then compared to experimental ones, revealing that the simulation of the partially open state was in good agreement with the SSNMR data. Nuclei that discriminate effectively between partially and fully open states belong to residues spread over the sequence and provide a molecular level description of the conformational change.
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Affiliation(s)
- Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Eric G Keeler
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Dongyu Zhang
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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33
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Ghovanloo MR, Choudhury K, Bandaru TS, Fouda MA, Rayani K, Rusinova R, Phaterpekar T, Nelkenbrecher K, Watkins AR, Poburko D, Thewalt J, Andersen OS, Delemotte L, Goodchild SJ, Ruben PC. Cannabidiol inhibits the skeletal muscle Nav1.4 by blocking its pore and by altering membrane elasticity. J Gen Physiol 2021; 153:211970. [PMID: 33836525 PMCID: PMC8042605 DOI: 10.1085/jgp.202012701] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/13/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cannabidiol (CBD) is the primary nonpsychotropic phytocannabinoid found in Cannabis sativa, which has been proposed to be therapeutic against many conditions, including muscle spasms. Among its putative targets are voltage-gated sodium channels (Navs), which have been implicated in many conditions. We investigated the effects of CBD on Nav1.4, the skeletal muscle Nav subtype. We explored direct effects, involving physical block of the Nav pore, as well as indirect effects, involving modulation of membrane elasticity that contributes to Nav inhibition. MD simulations revealed CBD's localization inside the membrane and effects on bilayer properties. Nuclear magnetic resonance (NMR) confirmed these results, showing CBD localizing below membrane headgroups. To determine the functional implications of these findings, we used a gramicidin-based fluorescence assay to show that CBD alters membrane elasticity or thickness, which could alter Nav function through bilayer-mediated regulation. Site-directed mutagenesis in the vicinity of the Nav1.4 pore revealed that removing the local anesthetic binding site with F1586A reduces the block of INa by CBD. Altering the fenestrations in the bilayer-spanning domain with Nav1.4-WWWW blocked CBD access from the membrane into the Nav1.4 pore (as judged by MD). The stabilization of inactivation, however, persisted in WWWW, which we ascribe to CBD-induced changes in membrane elasticity. To investigate the potential therapeutic value of CBD against Nav1.4 channelopathies, we used a pathogenic Nav1.4 variant, P1158S, which causes myotonia and periodic paralysis. CBD reduces excitability in both wild-type and the P1158S variant. Our in vitro and in silico results suggest that CBD may have therapeutic value against Nav1.4 hyperexcitability.
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Affiliation(s)
- Mohammad-Reza Ghovanloo
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada.,Department of Cellular and Molecular Biology, Xenon Pharmaceuticals, Burnaby, BC, Canada.,Science for Life Laboratory, Department of Physics, Royal Institute of Technology, Solna, Sweden
| | - Koushik Choudhury
- Science for Life Laboratory, Department of Physics, Royal Institute of Technology, Solna, Sweden
| | - Tagore S Bandaru
- Science for Life Laboratory, Department of Physics, Royal Institute of Technology, Solna, Sweden
| | - Mohamed A Fouda
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada.,Department of Pharmacology and Toxicology, Alexandria University, Alexandria, Egypt
| | - Kaveh Rayani
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
| | - Tejas Phaterpekar
- Department of Molecular Biology and Biochemistry/Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Karen Nelkenbrecher
- Department of Cellular and Molecular Biology, Xenon Pharmaceuticals, Burnaby, BC, Canada
| | - Abeline R Watkins
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Damon Poburko
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Jenifer Thewalt
- Department of Molecular Biology and Biochemistry/Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Physics, Royal Institute of Technology, Solna, Sweden
| | - Samuel J Goodchild
- Department of Cellular and Molecular Biology, Xenon Pharmaceuticals, Burnaby, BC, Canada
| | - Peter C Ruben
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
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34
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Silverå Ejneby M, Gromova A, Ottosson NE, Borg S, Estrada-Mondragón A, Yazdi S, Apostolakis P, Elinder F, Delemotte L. Resin-acid derivatives bind to multiple sites on the voltage-sensor domain of the Shaker potassium channel. J Gen Physiol 2021; 153:211862. [PMID: 33683319 PMCID: PMC7944402 DOI: 10.1085/jgp.202012676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/30/2020] [Accepted: 01/27/2021] [Indexed: 01/10/2023] Open
Abstract
Voltage-gated potassium (KV) channels can be opened by negatively charged resin acids and their derivatives. These resin acids have been proposed to attract the positively charged voltage-sensor helix (S4) toward the extracellular side of the membrane by binding to a pocket located between the lipid-facing extracellular ends of the transmembrane segments S3 and S4. By contrast to this proposed mechanism, neutralization of the top gating charge of the Shaker KV channel increased resin-acid-induced opening, suggesting other mechanisms and sites of action. Here, we explore the binding of two resin-acid derivatives, Wu50 and Wu161, to the activated/open state of the Shaker KV channel by a combination of in silico docking, molecular dynamics simulations, and electrophysiology of mutated channels. We identified three potential resin-acid-binding sites around S4: (1) the S3/S4 site previously suggested, in which positively charged residues introduced at the top of S4 are critical to keep the compound bound, (2) a site in the cleft between S4 and the pore domain (S4/pore site), in which a tryptophan at the top of S6 and the top gating charge of S4 keeps the compound bound, and (3) a site located on the extracellular side of the voltage-sensor domain, in a cleft formed by S1-S4 (the top-VSD site). The multiple binding sites around S4 and the anticipated helical-screw motion of the helix during activation make the effect of resin-acid derivatives on channel function intricate. The propensity of a specific resin acid to activate and open a voltage-gated channel likely depends on its exact binding dynamics and the types of interactions it can form with the protein in a state-specific manner.
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Affiliation(s)
- Malin Silverå Ejneby
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Arina Gromova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nina E Ottosson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Stina Borg
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Samira Yazdi
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Panagiotis Apostolakis
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Elinder
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
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35
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Fleetwood O, Delemotte L. Identification of Ligand-Specific G-Protein Coupled Receptor States and Prediction of Downstream Efficacy Via Data-Driven Modeling. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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36
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Pérez Conesa S, Keeler EG, McDermott AE, Delemotte L. Informing NMR Experiments with Molecular Dynamics Simulations to Characterize the Dominant Open State of KcsA. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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37
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Fleetwood O, Carlsson J, Delemotte L. Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling. eLife 2021; 10:60715. [PMID: 33506760 PMCID: PMC7886328 DOI: 10.7554/elife.60715] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/27/2021] [Indexed: 12/22/2022] Open
Abstract
Ligand binding stabilizes different G protein-coupled receptor states via a complex allosteric process that is not completely understood. Here, we have derived free energy landscapes describing activation of the β2 adrenergic receptor bound to ligands with different efficacy profiles using enhanced sampling molecular dynamics simulations. These reveal shifts toward active-like states at the Gprotein-binding site for receptors bound to partial and full agonists, and that the ligands modulate the conformational ensemble of the receptor by tuning protein microswitches. We indeed find an excellent correlation between the conformation of the microswitches close to the ligand binding site and in the transmembrane region and experimentally reported cyclic adenosine monophosphate signaling responses. Dimensionality reduction further reveals the similarity between the unique conformational states induced by different ligands, and examining the output of classifiers highlights two distant hotspots governing agonism on transmembrane helices 5 and 7.
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Affiliation(s)
- Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
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38
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Kang PW, Westerlund AM, Shi J, White KM, Dou AK, Cui AH, Silva JR, Delemotte L, Cui J. Calmodulin acts as a state-dependent switch to control a cardiac potassium channel opening. Sci Adv 2020; 6:6/50/eabd6798. [PMID: 33310856 PMCID: PMC7732179 DOI: 10.1126/sciadv.abd6798] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/27/2020] [Indexed: 05/09/2023]
Abstract
Calmodulin (CaM) and phosphatidylinositol 4,5-bisphosphate (PIP2) are potent regulators of the voltage-gated potassium channel KCNQ1 (KV7.1), which conducts the cardiac I Ks current. Although cryo-electron microscopy structures revealed intricate interactions between the KCNQ1 voltage-sensing domain (VSD), CaM, and PIP2, the functional consequences of these interactions remain unknown. Here, we show that CaM-VSD interactions act as a state-dependent switch to control KCNQ1 pore opening. Combined electrophysiology and molecular dynamics network analysis suggest that VSD transition into the fully activated state allows PIP2 to compete with CaM for binding to VSD. This leads to conformational changes that alter VSD-pore coupling to stabilize open states. We identify a motif in the KCNQ1 cytosolic domain, which works downstream of CaM-VSD interactions to facilitate the conformational change. Our findings suggest a gating mechanism that integrates PIP2 and CaM in KCNQ1 voltage-dependent activation, yielding insights into how KCNQ1 gains the phenotypes critical for its physiological function.
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Affiliation(s)
- Po Wei Kang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Annie M Westerlund
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Kelli McFarland White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Alex K Dou
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Amy H Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Jonathan R Silva
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Lucie Delemotte
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA.
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39
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Pantazis A, Kaneko M, Angelini M, Steccanella F, Westerlund AM, Lindström SH, Nilsson M, Delemotte L, Saitta SC, Olcese R. Tracking the motion of the K V1.2 voltage sensor reveals the molecular perturbations caused by a de novo mutation in a case of epilepsy. J Physiol 2020; 598:5245-5269. [PMID: 32833227 PMCID: PMC8923147 DOI: 10.1113/jp280438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
KEY POINTS KV1.2 channels, encoded by the KCNA2 gene, regulate neuronal excitability by conducting K+ upon depolarization. A new KCNA2 missense variant was discovered in a patient with epilepsy, causing amino acid substitution F302L at helix S4, in the KV1.2 voltage-sensing domain. Immunocytochemistry and flow cytometry showed that F302L does not impair KCNA2 subunit surface trafficking. Molecular dynamics simulations indicated that F302L alters the exposure of S4 residues to membrane lipids. Voltage clamp fluorometry revealed that the voltage-sensing domain of KV1.2-F302L channels is more sensitive to depolarization. Accordingly, KV1.2-F302L channels opened faster and at more negative potentials; however, they also exhibited enhanced inactivation: that is, F302L causes both gain- and loss-of-function effects. Coexpression of KCNA2-WT and -F302L did not fully rescue these effects. The proband's symptoms are more characteristic of patients with loss of KCNA2 function. Enhanced KV1.2 inactivation could lead to increased synaptic release in excitatory neurons, steering neuronal circuits towards epilepsy. ABSTRACT An exome-based diagnostic panel in an infant with epilepsy revealed a previously unreported de novo missense variant in KCNA2, which encodes voltage-gated K+ channel KV1.2. This variant causes substitution F302L, in helix S4 of the KV1.2 voltage-sensing domain (VSD). F302L does not affect KCNA2 subunit membrane trafficking. However, it does alter channel functional properties, accelerating channel opening at more hyperpolarized membrane potentials, indicating gain of function. F302L also caused loss of KV1.2 function via accelerated inactivation onset, decelerated recovery and shifted inactivation voltage dependence to more negative potentials. These effects, which are not fully rescued by coexpression of wild-type and mutant KCNA2 subunits, probably result from the enhancement of VSD function, as demonstrated by optically tracking VSD depolarization-evoked conformational rearrangements. In turn, molecular dynamics simulations suggest altered VSD exposure to membrane lipids. Compared to other encephalopathy patients with KCNA2 mutations, the proband exhibits mild neurological impairment, more characteristic of patients with KCNA2 loss of function. Based on this information, we propose a mechanism of epileptogenesis based on enhanced KV1.2 inactivation leading to increased synaptic release preferentially in excitatory neurons, and hence the perturbation of the excitatory/inhibitory balance of neuronal circuits.
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Affiliation(s)
- Antonios Pantazis
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
- Wallenberg Center for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Maki Kaneko
- Center for Personalized Medicine, Children's Hospital, Los Angeles, Los Angeles, CA, USA
- Division of Genomic Medicine, Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Marina Angelini
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Federica Steccanella
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Annie M Westerlund
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah H Lindström
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Michelle Nilsson
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sulagna C Saitta
- Department of Obstetrics and Gynecology and Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Riccardo Olcese
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Brain Research Institute, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
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40
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Westerlund AM, Fleetwood O, Pérez-Conesa S, Delemotte L. Network analysis reveals how lipids and other cofactors influence membrane protein allostery. J Chem Phys 2020; 153:141103. [DOI: 10.1063/5.0020974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Annie M. Westerlund
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Oliver Fleetwood
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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41
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Rems L, Kasimova MA, Testa I, Delemotte L. Pulsed Electric Fields Can Create Pores in the Voltage Sensors of Voltage-Gated Ion Channels. Biophys J 2020; 119:190-205. [PMID: 32559411 PMCID: PMC7335976 DOI: 10.1016/j.bpj.2020.05.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/21/2022] Open
Abstract
Pulsed electric fields are increasingly used in medicine to transiently increase the cell membrane permeability via electroporation to deliver therapeutic molecules into the cell. One type of event that contributes to this increase in membrane permeability is the formation of pores in the membrane lipid bilayer. However, electrophysiological measurements suggest that membrane proteins are affected as well, particularly voltage-gated ion channels (VGICs). The molecular mechanisms by which the electric field could affects these molecules remain unidentified. In this study, we used molecular dynamics simulations to unravel the molecular events that take place in different VGICs when exposing them to electric fields mimicking electroporation conditions. We show that electric fields can induce pores in the voltage-sensor domains (VSDs) of different VGICs and that these pores form more easily in some channels than in others. We demonstrate that poration is more likely in VSDs that are more hydrated and are electrostatically more favorable for the entry of ions. We further show that pores in VSDs can expand into so-called complex pores, which become stabilized by lipid headgroups. Our results suggest that such complex pores are considerably more stable than conventional lipid pores, and their formation can lead to severe unfolding of VSDs from the channel. We anticipate that such VSDs become dysfunctional and unable to respond to changes in transmembrane voltage, which is in agreement with previous electrophysiological measurements showing a decrease in the voltage-dependent transmembrane ionic currents after pulse treatment. Finally, we discuss the possibility of activation of VGICs by submicrosecond-duration pulses. Overall, our study reveals a new, to our knowledge, mechanism of electroporation through membranes containing VGICs.
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Affiliation(s)
- Lea Rems
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Marina A Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Ilaria Testa
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden.
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42
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Abstract
![]()
Agonist
binding to G protein-coupled receptors (GPCRs) leads to
conformational changes in the transmembrane region that activate cytosolic
signaling pathways. Although high-resolution structures of different
receptor states are available, atomistic details of allosteric signaling
across the membrane remain elusive. We calculated free energy landscapes
of β2 adrenergic receptor activation using atomistic
molecular dynamics simulations in an optimized string of swarms framework,
which shed new light on how microswitches govern the equilibrium between
conformational states. Contraction of the extracellular binding site
in the presence of the agonist BI-167107 is obligatorily coupled to
conformational changes in a connector motif located in the core of
the transmembrane region. The connector is probabilistically coupled
to the conformation of the intracellular region. An active connector
promotes desolvation of a buried cavity, a twist of the conserved
NPxxY motif, and an interaction between two conserved tyrosines in
transmembrane helices 5 and 7 (Y–Y motif), which lead to a
larger population of active-like states at the G protein binding site.
This coupling is augmented by protonation of the strongly conserved
Asp792.50. The agonist binding site hence communicates
with the intracellular region via a cascade of locally connected microswitches.
Characterization of these can be used to understand how ligands stabilize
distinct receptor states and contribute to development drugs with
specific signaling properties. The developed simulation protocol can
likely be transferred to other class A GPCRs.
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Affiliation(s)
- Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , SE-751 05 Uppsala , Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , SE-751 05 Uppsala , Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
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43
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Fleetwood O, Kasimova MA, Westerlund AM, Delemotte L. Molecular Insights from Conformational Ensembles via Machine Learning. Biophys J 2020; 118:765-780. [PMID: 31952811 PMCID: PMC7002924 DOI: 10.1016/j.bpj.2019.12.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/21/2019] [Accepted: 12/16/2019] [Indexed: 01/04/2023] Open
Abstract
Biomolecular simulations are intrinsically high dimensional and generate noisy data sets of ever-increasing size. Extracting important features from the data is crucial for understanding the biophysical properties of molecular processes, but remains a big challenge. Machine learning (ML) provides powerful dimensionality reduction tools. However, such methods are often criticized as resembling black boxes with limited human-interpretable insight. We use methods from supervised and unsupervised ML to efficiently create interpretable maps of important features from molecular simulations. We benchmark the performance of several methods, including neural networks, random forests, and principal component analysis, using a toy model with properties reminiscent of macromolecular behavior. We then analyze three diverse biological processes: conformational changes within the soluble protein calmodulin, ligand binding to a G protein-coupled receptor, and activation of an ion channel voltage-sensor domain, unraveling features critical for signal transduction, ligand binding, and voltage sensing. This work demonstrates the usefulness of ML in understanding biomolecular states and demystifying complex simulations.
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Affiliation(s)
- Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Marina A Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Annie M Westerlund
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden.
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44
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Kang PW, Westerlund AM, Shi J, McFarland White K, Dou AK, Silva JR, Delemotte L, Cui J. Calmodulin Functionally Couples the KCNQ1 Channel Voltage-Sensing and Pore Domains. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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45
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Qureshi AA, Suades A, Matsuoka R, Brock J, McComas SE, Nji E, Orellana L, Claesson M, Delemotte L, Drew D. The molecular basis for sugar import in malaria parasites. Nature 2020; 578:321-325. [PMID: 31996846 DOI: 10.1038/s41586-020-1963-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 01/03/2020] [Indexed: 12/11/2022]
Abstract
Elucidating the mechanism of sugar import requires a molecular understanding of how transporters couple sugar binding and gating events. Whereas mammalian glucose transporters (GLUTs) are specialists1, the hexose transporter from the malaria parasite Plasmodium falciparum PfHT12,3 has acquired the ability to transport both glucose and fructose sugars as efficiently as the dedicated glucose (GLUT3) and fructose (GLUT5) transporters. Here, to establish the molecular basis of sugar promiscuity in malaria parasites, we determined the crystal structure of PfHT1 in complex with D-glucose at a resolution of 3.6 Å. We found that the sugar-binding site in PfHT1 is very similar to those of the distantly related GLUT3 and GLUT5 structures4,5. Nevertheless, engineered PfHT1 mutations made to match GLUT sugar-binding sites did not shift sugar preferences. The extracellular substrate-gating helix TM7b in PfHT1 was positioned in a fully occluded conformation, providing a unique glimpse into how sugar binding and gating are coupled. We determined that polar contacts between TM7b and TM1 (located about 15 Å from D-glucose) are just as critical for transport as the residues that directly coordinate D-glucose, which demonstrates a strong allosteric coupling between sugar binding and gating. We conclude that PfHT1 has achieved substrate promiscuity not by modifying its sugar-binding site, but instead by evolving substrate-gating dynamics.
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Affiliation(s)
- Abdul Aziz Qureshi
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Albert Suades
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rei Matsuoka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Joseph Brock
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sarah E McComas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Emmanuel Nji
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Laura Orellana
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Magnus Claesson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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46
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Kasimova MA, Tewari D, Cowgill JB, Ursuleaz WC, Lin JL, Delemotte L, Chanda B. Helix breaking transition in the S4 of HCN channel is critical for hyperpolarization-dependent gating. eLife 2019; 8:e53400. [PMID: 31774399 PMCID: PMC6904216 DOI: 10.7554/elife.53400] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/19/2022] Open
Abstract
In contrast to most voltage-gated ion channels, hyperpolarization- and cAMP gated (HCN) ion channels open on hyperpolarization. Structure-function studies show that the voltage-sensor of HCN channels are unique but the mechanisms that determine gating polarity remain poorly understood. All-atom molecular dynamics simulations (~20 μs) of HCN1 channel under hyperpolarization reveals an initial downward movement of the S4 voltage-sensor but following the transfer of last gating charge, the S4 breaks into two sub-helices with the lower sub-helix becoming parallel to the membrane. Functional studies on bipolar channels show that the gating polarity strongly correlates with helical turn propensity of the substituents at the breakpoint. Remarkably, in a proto-HCN background, the replacement of breakpoint serine with a bulky hydrophobic amino acid is sufficient to completely flip the gating polarity from inward to outward-rectifying. Our studies reveal an unexpected mechanism of inward rectification involving a linker sub-helix emerging from HCN S4 during hyperpolarization.
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Affiliation(s)
- Marina A Kasimova
- Science for Life Laboratory, Department of Applied PhysicsKTH Royal Institute of TechnologyStockholmSweden
| | - Debanjan Tewari
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
| | - John B Cowgill
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Graduate program in BiophysicsUniversity of WisconsinMadisonUnited States
| | | | - Jenna L Lin
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Graduate program in BiophysicsUniversity of WisconsinMadisonUnited States
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied PhysicsKTH Royal Institute of TechnologyStockholmSweden
| | - Baron Chanda
- Department of NeuroscienceUniversity of Wisconsin-MadisonMadisonUnited States
- Department of Biomolecular ChemistryUniversity of Wisconsin-MadisonMadisonUnited States
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47
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Abstract
Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with limited noise. This has remained a formidable task, despite a plethora of existing clustering methods. We present InfleCS, a novel method for extracting well-defined core states from free energy landscapes. The method is based on a Gaussian mixture free energy estimator and exploits the shape of the estimated density landscape. The core states that naturally arise from the clustering allow for detailed characterization of the conformational ensemble. The clustering quality is evaluated on three toy models with different properties, where the method is shown to consistently outperform other conventional and state-of-the-art clustering methods. Finally, the method is applied to a temperature enhanced molecular dynamics simulation of Ca2+-bound Calmodulin. Through the free energy landscape, we discover a pathway between a canonical and a compact state, revealing conformational changes driven by electrostatic interactions.
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Affiliation(s)
- Annie M Westerlund
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
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48
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Abraham M, Apostolov R, Barnoud J, Bauer P, Blau C, Bonvin AMJJ, Chavent M, Chodera J, Čondić-Jurkić K, Delemotte L, Grubmüller H, Howard RJ, Jordan EJ, Lindahl E, Ollila OHS, Selent J, Smith DGA, Stansfeld PJ, Tiemann JKS, Trellet M, Woods C, Zhmurov A. Sharing Data from Molecular Simulations. J Chem Inf Model 2019; 59:4093-4099. [PMID: 31525920 DOI: 10.1021/acs.jcim.9b00665] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/ ). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.
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Affiliation(s)
- Mark Abraham
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Rossen Apostolov
- PDC Center for High Performance Computing, School of Electrical Engineering and Computer Science , KTH Royal Institute of Technology , 114 28 Stockholm , Sweden
| | | | - Paul Bauer
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Christian Blau
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | | | | | - John Chodera
- Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Karmen Čondić-Jurkić
- Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Open Force Field Consortium , https://openforcefield.org/consortium/
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry , 37077 Goettingen , Germany
| | - Rebecca J Howard
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics , Stockholm University , Box 1031, SE-171 21 Solna , Sweden
| | - E Joseph Jordan
- Science for Life Laboratory, Department of Biochemistry and Biophysics , Stockholm University , Box 1031, SE-171 21 Solna , Sweden
| | - Erik Lindahl
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics , Stockholm University , Box 1031, SE-171 21 Solna , Sweden
| | - O H Samuli Ollila
- Institute of Biotechnology , University of Helsinki , 00100 Helsinki , Finland
| | - Jana Selent
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) & Department of Experimental and Health Sciences , Pompeu Fabra University , 08002 Barcelona , Spain
| | - Daniel G A Smith
- The Molecular Sciences Software Institute , Blacksburg , Virginia 24060 , United States
| | | | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, Faculty of Medicine , University Leipzig , Leipzig 04107 , Germany
| | - Mikael Trellet
- Faculty of Science , Utrecht University , Bijvoet Center, Utrecht , The Netherlands
| | | | - Artem Zhmurov
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
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49
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Delemotte L, Westerlund AM, Blau C. Robust Estimation of Free Energy Landscapes from Gaussian Mixture Models with Cross-Validation. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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50
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Pantazis A, Kaneko M, Westerlund AM, Delemotte L, Saitta S, Olcese R. A De Novo Mutation Associated with Epilepsy Enhances KV1.2 Voltage Dependence, Suppressing Neuronal Excitability. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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