| 1. |
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A Beginner's Guide to Swedish Academia
- 2022
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Samlingsverk (redaktörskap) (övrigt vetenskapligt/konstnärligt)abstract
- As new to the Swedish research system, one is faced with a series of questions, about what applies to qualifications, what the networks look like, but also practical issues. To make things easier, YAS has developed a guide for international researchers, to help navigate Swedish academia and remove time-consuming obstacles.
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| 2. |
- Abraham, Mark James, et al.
(författare)
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Sharing Data from Molecular Simulations
- 2019
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Ingår i: Journal of Chemical Information and Modeling. - : AMER CHEMICAL SOC. - 1549-9596 .- 1549-960X. ; 59:10, s. 4093-4099
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Tidskriftsartikel (refereegranskat)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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| 3. |
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| 4. |
- Amarouch, Mohamed-Yassine, et al.
(författare)
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Biophysical Characterization of Epigallocatechin-3-Gallate Effect on the Cardiac Sodium Channel Na(v)1.5
- 2020
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Ingår i: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 25:4
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Tidskriftsartikel (refereegranskat)abstract
- Epigallocatechin-3-Gallate (EGCG) has been extensively studied for its protective effect against cardiovascular disorders. This effect has been attributed to its action on multiple molecular pathways and transmembrane proteins, including the cardiac Na(v)1.5 channels, which are inhibited in a dose-dependent manner. However, the molecular mechanism underlying this effect remains to be unveiled. To this aim, we have characterized the EGCG effect on Na(v)1.5 using electrophysiology and molecular dynamics (MD) simulations. EGCG superfusion induced a dose-dependent inhibition of Na(v)1.5 expressed in tsA201 cells, negatively shifted the steady-state inactivation curve, slowed the inactivation kinetics, and delayed the recovery from fast inactivation. However, EGCG had no effect on the voltage-dependence of activation and showed little use-dependent block on Na(v)1.5. Finally, MD simulations suggested that EGCG does not preferentially stay in the center of the bilayer, but that it spontaneously relocates to the membrane headgroup region. Moreover, no sign of spontaneous crossing from one leaflet to the other was observed, indicating a relatively large free energy barrier associated with EGCG transport across the membrane. These results indicate that EGCG may exert its biophysical effect via access to its binding site through the cell membrane or via a bilayer-mediated mechanism.
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| 5. |
- Andersson, Alma E. V., et al.
(författare)
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Exploring the Viral Channel Kcv(PBCV-1) Function via Computation
- 2018
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Ingår i: Journal of Membrane Biology. - : SPRINGER. - 0022-2631 .- 1432-1424. ; 251:3, s. 419-430
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Tidskriftsartikel (refereegranskat)abstract
- Viral potassium channels (Kcv) are homologous to the pore module of complex -selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of conduction and channel gating. In this work, we construct a homology model of the open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.
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| 6. |
- Carnevale, Vincenzo, et al.
(författare)
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Molecular Dynamics Simulations of Ion Channels
- 2021
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Ingår i: TIBS -Trends in Biochemical Sciences. Regular ed.. - : Elsevier BV. - 0968-0004 .- 1362-4326. ; 46:7, s. 621-622
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 7. |
- Chen, Yue, et al.
(författare)
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Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the beta 2 Adrenergic Receptor
- 2021
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Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 61:12, s. 6024-6037
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Tidskriftsartikel (refereegranskat)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 beta 2 adrenergic receptor (beta 2AR) via enhanced sampling molecular dynamics simulations. Dimensionality reduction analysis shows that Nb80 stabilizes structural features of the beta 2AR with an similar to 14 angstrom 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 intermediateactive 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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| 8. |
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| 9. |
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| 10. |
- Chi, Gamma, et al.
(författare)
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Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain
- 2022
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)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 alpha 6 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. Here, Chi et al. report cryo-EM structures of the human Kv3.1a channel, revealing a unique arrangement of the cytoplasmic T1 domain, which allows the interactions with the C-terminal axonal targeting motif and key components of the gating machinery. These findings provide insights into the functional relevance of previously unknown interdomain interactions in Kv3 channels and may guide the design of new pharmaceutical drugs.
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| 11. |
- Choudhury, Koushik, et al.
(författare)
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An alpha-pi transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb
- 2022
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Ingår i: The Journal of General Physiology. - : Rockefeller University Press. - 0022-1295 .- 1540-7748. ; 155:2
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Tidskriftsartikel (refereegranskat)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 pi-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 pi-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 pi-helix transition in the opening of NavAb, enabling new proposals for the structural annotation and drug modulation mechanisms in this important sodium channel model. We propose a new conformational cycle for NavAb wherein an alpha- to pi-helix transition in S6 and disordering of the neck region of the C-terminal domain is important for pore opening.
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| 12. |
- Choudhury, Koushik, et al.
(författare)
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An open state of a voltage-gated sodium channel involving a p-helix and conserved pore-facing asparagine
- 2022
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 121:1, s. 11-22
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Tidskriftsartikel (refereegranskat)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 cc-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 p-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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| 13. |
- Choudhury, Koushik
(författare)
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Gating and modulation mechanism of voltage gated sodium channels
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Voltage-gated sodium channels (Nav channels) play an essential role in nerve impulse conduction in excitable cells. Thus, these channels are involved in several neurological and muscular disorders. Understanding their mechanism of functioning is essential for designing drugs targeting them. These are tetrameric membrane proteins that selectively transport sodium ions across the membrane. They regulate ion flow by cycling through three main functional states - resting state, open state, and inactivated state. Structural biology techniques have captured Nav channels in several functional states. However, most of the structures are captured in the inactivated state. Although it is quite challenging to capture the open state experimentally because of its transient nature, several structures of bacterial and eukaryotic Nav channels have been captured in the putative open state. However, a rigorous functional annotation of these open-state structures awaits. I performed molecular dynamics simulations to show that the experimental bacterial Nav channels captured in the putative open state, the pore was dehydrated and had a high free energy barrier for ion/drug permeation suggesting that these structures do not correspond to a functional open state. The pore-lining helices of these channels are ? helical. Sequence/structure conservation analysis showed the possibility of ?-helices in the pore-lining helices. Introducing ?-helices in the middle of these pore-lining helices hydrated the pore and removed the free energy barrier for ion/drug permeation. The ?-helices might also be relevant for pore opening as they dehydrate the peripheral cavities/reduce the interactions between the hydrophobic pore-lining residues and hence allow the opening of the hydrophobic pore. Additionally, I also determined a disordered region in the C-terminal domain which is known to be relevant to pore opening.I also studied the effect of ?-helices on drug access and binding to sodium channels. I found that ?-helices in the bacterial Nav channel blocked the fenestrations irrespective of the pore diameter thus inhibiting drug access through the fenestrations. Exploring further on drug binding, I investigated lidocaine binding to different functional states which revealed that the drug binds in different orientations and positions across the functional states. This implies that there might be a change in the lidocaine-binding affinity as the channel cycles through different functional states. I also investigated the drug binding site and access pathway of cannabidiol in sodium channels and the effect of cannabidiol on membrane properties. Our computational results were complemented by experimental results. Molecular dynamics simulations suggest that cannabidiol does not affect the membrane rigidity and causes an ordering of the membrane methylenes, which is in excellent agreement with the NMR results. Mutagenesis experiments show that cannabidiol blocks the pore by interacting with a phenylalanine residue which is in good agreement with our docking results. Adiabatic biased molecular dynamics simulations were performed to confirm the pathway for CBD to reach the pore is through the fenestrations in the ion channel. The idea of investigating the relevance of ?-helices in pore-lining helices was extended to eukaryotic Nav channels as well. Eukaryotic channels are heterotetrameric, so the pore lining helices of different subunits might contribute differently to the channel function. I concluded that increasing the number of ?-helices not only increased the pore hydration and ion conductance but also reduced the barrier for ion permeation. ?-helices in pore-lining helices of subunit-I and subunit-IV in an expanded pore are essential for a functional open state.Putting the above results together, I show that the bacterial experimental structures initially proposed to represent open states might correspond instead to inactivated states. In eukaryotes, the experimental structure initially proposed to represent the open state corresponds to a sub-conductance open state. Thus, I propose that a ? to ? helix transition and vice-versa might be relevant to the gating of Nav channels. By showing these results I would like to highlight the importance of rigorously annotating experimental structures and assigning their functional states. Finally, I would also like to highlight the power of molecular dynamics simulations to not only rigorously annotate experimental structures but also to provide atomistic details to explain experimental results.
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| 14. |
- Choudhury, Koushik, et al.
(författare)
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Modulation of pore opening of Eukaryotic sodium channels by π-helices in S6
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Annan publikation (övrigt vetenskapligt/konstnärligt)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 subunit 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 sub-conductance state, and its absence from both DI-S6 and DIV-S6 yields a non-conducting 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 towards 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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| 15. |
- Choudhury, Koushik, et al.
(författare)
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Modulation of Pore Opening of Eukaryotic Sodium Channels by π-Helices in S6
- 2023
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 14:25, s. 5876-5881
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Tidskriftsartikel (refereegranskat)abstract
- Voltage-gated sodium channels are heterotetrameric sodiumselectiveion channels that play a central role in electrical signaling in excitablecells. With recent advances in structural biology, structures of eukaryoticsodium channels have been captured in several distinct conformationscorresponding to different functional states. The secondary structureof the pore lining S6 helices of subunits DI, DII, and DIV has beencaptured with both short & pi;-helix stretches and in fully & alpha;-helicalconformations. The relevance of these secondary structure elementsfor pore gating is not yet understood. Here, we propose that a & pi;-helixin at least DI-S6, DIII-S6, and DIV-S6 results in a fully conductivestate. On the other hand, the absence of & pi;-helix in either DI-S6or DIV-S6 yields a subconductance state, and its absence from bothDI-S6 and DIV-S6 yields a nonconducting state. This work highlightsthe impact of the presence of a & pi;-helix in the different S6helices of an expanded pore on pore conductance, thus opening newdoors toward reconstructing the entire conformational landscape alongthe functional cycle of Nav Channels and paving the way to the design of state-dependent modulators.
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| 16. |
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| 17. |
- Clatot, Jerome, et al.
(författare)
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A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction
- 2024
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 121:3
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Tidskriftsartikel (refereegranskat)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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| 18. |
- Cournia, Zoe, et al.
(författare)
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Membrane Protein Structure, Function, and Dynamics : a Perspective from Experiments and Theory
- 2015
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Ingår i: Journal of Membrane Biology. - : Springer. - 0022-2631 .- 1432-1424. ; 248:4, s. 611-640
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Tidskriftsartikel (refereegranskat)abstract
- Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
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| 19. |
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| 20. |
- Damenti, Martina, et al.
(författare)
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Quantitative and functional assessment of Arc n-meric states in membrane interaction and AMPA receptor endocytosis
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Arc (or Arg3.1), Activity Regulated-Cytoskeleton associated-protein is pivotal to mediate plastic responses in neuronal cells. In vitro and in vivo studies suggest its ability to form high- and low-order oligomers which are potentially involved in neuronal trafficking. Despite its important function, no direct observation of Arc oligomers in cells has been presented due to its highly regulated spatiotemporal expression, the small size of the structures, the lack of appropriate labelling strategies and the background associated to free diffusing cytosolic proteins. Here, we take advantage of several complementary advanced fluorescence microscopy and spectroscopy techniques to observe and quantify Arc oligomeric states in cellular environment especially in the synapses. In cells, we uncovered Arc-Arc intermolecular interactions, Arc tendency to form liquid condensates and to interact with lipid bilayers. High-order oligomers are found to localize at the excitatory synaptic compartment and to directly affects AMPA receptor surface levels. Together, our observations support the model by which Arc oligomerization mediates plasma- membrane negative inward curvature favoring AMPA receptors endocytosis.
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| 21. |
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| 22. |
- Delemotte, Lucie
(författare)
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Chapter 7 : Bridging the Gap between Atomistic Molecular Dynamics Simulations and Wet-lab Experimental Techniques: Applications to Membrane Proteins
- 2021
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Ingår i: RSC Theoretical and Computational Chemistry Series. - : Royal Society of Chemistry. ; , s. 247-286
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Bokkapitel (refereegranskat)abstract
- Molecular dynamics (MD) simulations provide atomistic insights into not only the structure, but also the dynamics and ensemble properties of (bio-)molecular systems, hence providing a direct link to functional characterization using wet-lab experiments. The models, algorithms and hardware needed to conduct MD simulations have matured, meaning that reliable estimates of ensemble properties can now be obtained. However, the choice of model and protocol is non-trivial and cannot be fully automated yet, therefore an understanding of the models, the algorithms and the insights that can be obtained, and of how they can be combined with the output of other techniques, is necessary. This chapter provides a description of the MD algorithm, including extensions of the methodology to generate conformational ensembles representing functional states. The insights that MD simulations can provide into membrane protein functions are then illustrated using case studies. They are classified according to whether they provide testable hypotheses, provide molecular-level interpretation of experimental observables, or they exploit experimental data to drive the sampling of simulations towards biological timescales.
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| 23. |
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| 24. |
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| 25. |
- Delemotte, Lucie, et al.
(författare)
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Molecular Dynamics
- 2023
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Ingår i: Textbook of Ion Channels Volume I. - : Informa UK Limited. ; , s. 253-273
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Molecular dynamics (MD) simulations have emerged as a powerful tool to complement structural and functional studies of ion channels. By solving the classical equations of motion of a system of particles encompassing the ion channel embedded in a near-native environment (lipidic bilayer and ionic solution), this technique indeed allows the practitioner to monitor the response of the system to an applied stimulus and to characterize conformational ensembles with an atomistic resolution. This chapter reviews the basic principles of the MD simulation algorithm and of the analysis of its output, before introducing applications of the technique in the field of ion channel biophysics. It covers in particular how to apply the stimuli of interest to the ion channel field, such as change in transmembrane voltage, pH or mechanical properties of the membrane, how to detect sensing of these stimuli, how to measure gating, ion conduction and selectivity, lipid modulation, allostery, and the effect of mutations.
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| 26. |
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| 27. |
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| 28. |
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| 29. |
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| 30. |
- Elbahnsi, Ahmad, et al.
(författare)
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Interplay between VSD, pore, and membrane lipids in electromechanical coupling in HCN channels
- 2023
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Ingår i: eLIFE. - : eLife Sciences Publications, Ltd. - 2050-084X. ; 12
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Tidskriftsartikel (refereegranskat)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 hyperpolar-ization, 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 electrome-chanical 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 observa-tions and a possible mechanism for regulation of HCN channels by the lipidic components of the membrane.
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| 31. |
- Elbahnsi, Ahmad, et al.
(författare)
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Structure and Sequence-based Computational Approaches to Allosteric Signal Transduction : Application to Electromechanical Coupling in Voltage-gated Ion Channels
- 2021
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 433:17
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Forskningsöversikt (refereegranskat)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 Angstrom 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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| 32. |
- Fernandez-Marino, Ana I., et al.
(författare)
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Gating interaction maps reveal a noncanonical electromechanical coupling mode in the Shaker K+ channel
- 2018
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Ingår i: Nature Structural & Molecular Biology. - : Nature Publishing Group. - 1545-9993 .- 1545-9985. ; 25:4, s. 320-326
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Tidskriftsartikel (refereegranskat)abstract
- Membrane potential regulates the activity of voltage-dependent ion channels via specialized voltage-sensing modules, but the mechanisms involved in coupling voltage-sensor movement to pore opening remain unclear owing to a lack of resting state structures and robust methods to identify allosteric pathways. Here, using a newly developed interaction-energy analysis, we probe the interfaces of the voltage-sensing and pore modules in the Drosophila Shaker K+ channel. Our measurements reveal unexpectedly strong equilibrium gating interactions between contacts at the S4 and S5 helices in addition to those between S6 and the S4-S5 linker. Network analysis of MD trajectories shows that the voltage-sensor and pore motions are linked by two distinct pathways: a canonical pathway through the S4-S5 linker and a hitherto unknown pathway akin to rack-and-pinion coupling involving the S4 and S5 helices. Our findings highlight the central role of the S5 helix in electromechanical transduction in the voltage-gated ion channel (VGIC) superfamily.
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| 33. |
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| 34. |
- Fleetwood, Oliver, et al.
(författare)
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Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches
- 2020
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Ingår i: Biochemistry. - : AMER CHEMICAL SOC. - 0006-2960 .- 1520-4995. ; 59:7, s. 880-891
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Tidskriftsartikel (refereegranskat)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 beta(2) 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 Asp79(2.50). 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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| 35. |
- Fleetwood, Oliver, 1990-, et al.
(författare)
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Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling
- 2021
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Ingår i: eLIFE. - : eLife Sciences Publications, Ltd. - 2050-084X. ; 10
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Tidskriftsartikel (refereegranskat)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 beta(2) 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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| 36. |
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| 37. |
- Fleetwood, Oliver, et al.
(författare)
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Molecular Insights from Conformational Ensembles via Machine Learning
- 2020
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Ingår i: Biophysical Journal. - : Biophysical Society. - 0006-3495 .- 1542-0086. ; 118:3, s. 765-780
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Tidskriftsartikel (refereegranskat)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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| 38. |
- Fleetwood, Oliver, 1990-
(författare)
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New approaches to data-driven analysis and enhanced sampling simulations of G protein-coupled receptors
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Proteins are large biomolecules that carry out specific functions within living organisms. Understanding how proteins function is a massive scientific challenge with a wide area of applications. In particular, by controlling protein function we may develop therapies for many diseases. To understand a protein’s function, we need to consider its full conformational ensemble, and not only a single snapshot of a structure. Allosteric signaling is a factor often driving protein conformation change, where the binding of a molecule to one site triggers a response in another part of the protein. G protein-coupled receptors (GPCRs) are transmembrane proteins that bind molecules outside the membrane, which enables coupling to a G protein in their intracellular domain. Understanding the complex allosteric process governing this mechanism could have a significant impact on the development of novel drugs.Molecular dynamics (MD) is a computational method that can capture protein conformational change at an atomistic level. However, MD is a computationally expensive approach to simulating proteins, and is thus infeasible for many applications. Enhanced sampling techniques have emerged to reduce the computational cost of standard MD. Another challenge with MD is to extract useful information and distinguish signal from noise in an MD trajectory. Data-driven methods can streamline analysis of protein simulations and improve our understanding of biomolecular systems.Paper 1 and 2 contain methodological developments to analyze the results of MD in a data-driven manner. We provide methods that create interpretable maps of important molecular features from protein simulations (Paper 1) and identify allosteric communication pathways in biological systems (Paper 2). As a result, more insights can be extracted from MD trajectories. Our approach is generalizable and can become useful to analyze complex simulations of various biomolecular systems. In Paper 3 and 4, we combine the aforementioned methodological advancements with enhanced sampling techniques to study a prototypical GPCR, the β2 adrenergic receptor. First, we make improvements to the string method with swarms of trajectories and derive the conformational change and free energy along the receptor’s activation pathway. Next, we identify key molecular microswitches directly or allosterically controlled by orthosteric ligands and show how these couple to a shift in probability of the receptor’s active state. In Paper 4, we also find that ligands induce ligand-specific states, and the molecular basis governing these states. These new approaches generate insights compatible with previous simulation and experimental studies at a relatively low computational cost. Our work also provides new insights into the molecular basis of allosteric communication in membrane proteins, and might become a useful tool in the design of novel GPCR drugs.
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| 39. |
- Frampton, Damon, et al.
(författare)
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Subtype-specific responses of hKv7.4 and hKv7.5 channels to polyunsaturated fatty acids reveal an unconventional modulatory site and mechanism
- 2022
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Ingår i: eLIFE. - : eLife Sciences Publications, Ltd. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- The K(V)7.4 and K(V)7.5 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 K(V)7.4 and K(V)7.5 channel function are of interest. Here, we study the effect of polyunsaturated fatty acids (PUFAs) on human K(V)7.4 and KV7.5 channels expressed in Xenopus oocytes. We report that PUFAs facilitate activation of hK(V)7.5 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 V-50 shifts. In contrast, PUFAs inhibit activation of hK(V)7.4 by shifting V-50 toward more positive voltages. No effect on V-50 of hK(V)7.4 is observed by an uncharged or a positively charged PUFA analogue. Thus, the hK(V)7.5 channel's response to PUFAs is analogous to the one previously observed in hK(V)7.1-7.3 channels, whereas the hK(V)7.4 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 hK(V)7.4 by PUFAs.
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| 40. |
- Galleano, Iacopo, et al.
(författare)
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Functional cross-talk between phosphorylation and disease-causing mutations in the cardiac sodium channel Na(v)1.5
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:33
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Tidskriftsartikel (refereegranskat)abstract
- The voltage-gated sodium channel Nav1.5 initiates the cardiac action potential. Alterations of its activation and inactivation properties due to mutations can cause severe, life-threatening arrhythmias. Yet despite intensive research efforts, many functional aspects of this cardiac channel remain poorly understood. For instance, Nav1.5 undergoes extensive posttranslational modification in vivo, but the functional significance of these modifications is largely unexplored, especially under pathological conditions. This is because most conventional approaches are unable to insert metabolically stable posttranslational modification mimics, thus preventing a precise elucidation of the contribution by these modifications to channel function. Here, we overcome this limitation by using protein semisynthesis of Nav1.5 in live cells and carry out complementary molecular dynamics simulations. We introduce metabolically stable phosphorylation mimics on both wild-type (WT) and two pathogenic long-QT mutant channel backgrounds and decipher functional and pharmacological effects with unique precision. We elucidate the mechanism by which phosphorylation of Y1495 impairs steady-state inactivation in WT Nav1.5. Surprisingly, we find that while the Q1476R patient mutation does not affect inactivation on its own, it enhances the impairment of steady-state inactivation caused by phosphorylation of Y1495 through enhanced unbinding of the inactivation particle. We also show that both phosphorylation and patient mutations can impact Nav1.5 sensitivity toward the clinically used antiarrhythmic drugs quinidine and ranolazine, but not flecainide. The data highlight that functional effects of Nav1.5 phosphorylation can be dramatically amplified by patient mutations. Our work is thus likely to have implications for the interpretation of mutational phenotypes and the design of future drug regimens.
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| 41. |
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| 42. |
- Ghovanloo, Mohammad-Reza, et al.
(författare)
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Cannabidiol inhibits the skeletal muscle Nav1.4 by blocking its pore and by altering membrane elasticity
- 2021
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Ingår i: The Journal of General Physiology. - : Rockefeller University Press. - 0022-1295 .- 1540-7748. ; 153:5
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Tidskriftsartikel (refereegranskat)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 gramicidinbased 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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| 43. |
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| 44. |
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| 45. |
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| 46. |
- Gianti, Eleonora, et al.
(författare)
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On the role of water density fluctuations in the inhibition of a proton channel
- 2016
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Ingår i: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. - : NATL ACAD SCIENCES. - 0027-8424. ; 113:52, s. E8359-E8368
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Tidskriftsartikel (refereegranskat)abstract
- Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.
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| 47. |
- Groome, J. R., et al.
(författare)
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Gating pore currents in sodium channels
- 2018
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Ingår i: Handbook of Experimental Pharmacology. - Cham : Springer. - 0171-2004 .- 1865-0325. ; , s. 371-399
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Tidskriftsartikel (refereegranskat)abstract
- Voltage-gated sodium channels belong to the superfamily of voltage-gated cation channels. Their structure is based on domains comprising a voltage sensor domain (S1–S4 segments) and a pore domain (S5–S6 segments). Mutations in positively charged residues of the S4 segments may allow protons or cations to pass directly through the gating pore constriction of the voltage sensor domain; these anomalous currents are referred to as gating pore or omega (ω) currents. In the skeletal muscle disorder hypokalemic periodic paralysis, and in arrhythmic dilated cardiomyopathy, inherited mutations of S4 arginine residues promote omega currents that have been shown to be a contributing factor in the pathogenesis of these sodium channel disorders. Characterization of gating pore currents in these channelopathies and with artificial mutations has been possible by measuring the voltage-dependence and selectivity of these leak currents. The basis of gating pore currents and the structural basis of S4 movement through the gating pore has also been studied extensively with molecular dynamics. These simulations have provided valuable insight into the nature of S4 translocation and the physical basis for the effects of mutations that promote permeation of protons or cations through the gating pore.
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| 48. |
- Harpole, Tyler J., et al.
(författare)
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Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations
- 2018
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Ingår i: Biochimica et Biophysica Acta - Biomembranes. - : Elsevier. - 0005-2736 .- 1879-2642. ; 1860:4, s. 909-926
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Forskningsöversikt (refereegranskat)abstract
- The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables.
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| 49. |
- Hellmich, Ute A., et al.
(författare)
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TRP channels : branching out into the fungal kingdom
- 2022
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 30:1, s. 2-4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)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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| 50. |
- Howard, Rebecca J., et al.
(författare)
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Permeating disciplines : Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport
- 2018
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Ingår i: Biochimica et Biophysica Acta - Biomembranes. - : ELSEVIER SCIENCE BV. - 0005-2736 .- 1879-2642. ; 1860:4, s. 927-942
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Forskningsöversikt (refereegranskat)abstract
- Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process for example with neuroactive drugs demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin Mcllwain.
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