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  • 1.
    Andersson, Magnus
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Mattle, Daniel
    Sitsel, Oleg
    Nielsen, Anna Marie
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    White, Stephen H.
    Nissen, Poul
    Gourdon, Pontus
    Transport Pathway in Cu+ P-Type ATPases2014Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 427A-427AArtikkel i tidsskrift (Annet vitenskapelig)
  • 2. Gronberg, Christina
    et al.
    Sitsel, Oleg
    Lindahl, Erik
    Gourdon, Pontus
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport2016Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, nr 11, s. 2417-2429Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cu+-specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu+-binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu+ entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu+ delivery. Mutational analyses and simulations in the presence and absence of Cu+ predict that the ion-entry path involves two ion-binding sites: one transient Met148-Cys382 site and one intramembranous site formed by trigonal coordination to Cys384, Asn689, and Met717. The results reconcile earlier biochemical and x-ray absorption data and provide a molecular understanding of ion entry in Cu+-transporting P-type ATPases.

  • 3. Hariharan, Parameswaran
    et al.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Jiang, Xiaoxu
    Pardon, Els
    Steyaert, Jan
    Kaback, H. Ronald
    Guan, Lan
    Thermodynamics of Nanobody Binding to Lactose Permease2016Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 55, nr 42, s. 5917-5926Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Camelid nanobodies (Nbs) raised against the outward-facing conformer of a double-Trp mutant of the lactose permease of Escherichia coli (LacY) stabilize the permease in outward-facing conformations. Isothermal titration calorimetry is applied herein to dissect the binding thermodynamics of two Nbs, one that markedly improves access to the sugar-binding site and another that dramatically increases the affinity for galactoside. The findings presented here show that both enthalpy and entropy contribute favorably to binding of the Nbs to wild-type (WT) LacY and that binding of Nb to double-Trp mutant G46W/G262W is driven by a greater enthalpy at an entropic penalty. Thermodynamic analyses support the interpretation that WT LacY is stabilized in outward-facing conformations like the double-Trp mutant with closure of the cytoplasmic cavity through conformational selection. The LacY conformational transition required for ligand binding is reflected by a favorable entropy increase. Molecular dynamics simulations further suggest that the entropy increase likely stems from release of immobilized water molecules primarily from the cytoplasmic cavity upon closure.

  • 4. Jiang, X.
    et al.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Chau, B. T.
    Wong, L. Y.
    Villafuerte, M. K. R.
    Kaback, H. R.
    Role of Conserved Gly-Gly Pairs on the Periplasmic Side of LacY2016Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 55, nr 31, s. 4326-4332Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    On the periplasmic side of LacY, two conserved Gly-Gly pairs in helices II and XI (Gly46 and Gly370, respectively) and helices V and VIII (Gly159 and Gly262, respectively) allow close packing of each helix pair in the outward (periplasmic)-closed conformation. Previous studies demonstrate that replacing one Gly residue in each Gly-Gly pair with Trp leads to opening of the periplasmic cavity with abrogation of transport activity, but an increased rate of galactoside binding. To further investigate the role of the Gly-Gly pairs, 11 double-replacement mutants were constructed for each pair at positions 46 (helix II) and 262 (helix VIII). Replacement with Ala or Ser results in decreased but significant transport activity, while replacements with Thr, Val, Leu, Asn, Gln, Tyr, Trp, Glu, or Lys exhibit very little or no transport. Remarkably, however, the double mutants bind galactoside with affinities 10-20-fold higher than that of the pseudo-WT or WT LacY. Moreover, site-directed alkylation of a periplasmic Cys replacement indicates that the periplasmic cavity becomes readily accessible in the double-replacement mutants. Molecular dynamics simulations with the WT and double-Leu mutant in the inward-open/outward-closed conformation provide support for this interpretation. 

  • 5. Jiang, X.
    et al.
    Villafuerte, M. K. R.
    Andersson, Magnus
    University of California at Irvine, United States.
    White, S. H.
    Kaback, H. R.
    Galactoside-binding site in LacY2014Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 53, nr 9, s. 1536-1543Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although an X-ray crystal structure of lactose permease (LacY) has been presented with bound galactopyranoside, neither the sugar nor the residues ligating the sugar can be identified with precision at ∼3.5 Å. Therefore, additional evidence is important for identifying side chains likely to be involved in binding. On the basis of a clue from site-directed alkylation suggesting that Asn272, Gly268, and Val264 on one face of helix VIII might participate in galactoside binding, molecular dynamics simulations were conducted initially. The simulations indicate that Asn272 (helix VIII) is sufficiently close to the galactopyranosyl ring of a docked lactose analogue to play an important role in binding, the backbone at Gly268 may be involved, and Val264 does not interact with the bound sugar. When the three side chains are subjected to site-directed mutagenesis, with the sole exception of mutant Asn272 → Gln, various other replacements for Asn272 either markedly decrease affinity for the substrate (i.e., high KD) or abolish binding altogether. However, mutant Gly268 → Ala exhibits a moderate 8-fold decrease in affinity, and binding by mutant Val264 → Ala is affected only minimally. Thus, Asn272 and possibly Gly268 may comprise additional components of the galactoside-binding site in LacY.

  • 6. Kimanius, Dari
    et al.
    Pettersson, Ingrid
    Schluckebier, Gerd
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholm University, Sweden.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    SAXS-Guided Metadynamics2015Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 7, s. 3491-3498Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The small-angle X-ray scattering (SAXS) methodology enables structural characterization of biological macromolecules in solution. However, because SAXS provides low-dimensional information, several potential structural configurations can reproduce the experimental scattering profile, which severely complicates the structural refinement process. Here, we present a bias-exchange metadynamics refinement protocol that incorporates SAXS data as collective variables and therefore tags all possible configurations with their corresponding free energies, which allows identification of a unique structural solution. The method has been implemented in PLUMED and combined with the GROMACS simulation package, and as a proof of principle, we explore the Trp-cage protein folding landscape.

  • 7. Kimanius, Dari
    et al.
    White, Stephen
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. Stockholm University, Sweden.
    Kaback, Ronald
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik.
    Uptake Dynamics in the LacY Membrane Protein Transporter2017Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, nr 3, s. 128A-128AArtikkel i tidsskrift (Annet vitenskapelig)
  • 8.
    Lindahl, Viveca
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Gourdon, Pontus
    Department of Biomedical Sciences, University of Copenhagen, Denmark.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to functionInngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aquaporin TIP2;1 is a protein channel that is permeable to both water and ammonia. Thestructural origin of ammonia selectivity remains obscure, but experiments have revealed that adouble mutation renders it impermeable to ammonia without affecting water permeability. Here,we aim to reproduce and explain these observations by performing an extensive mutationalstudy using microsecond long molecular dynamics simulations, applying two popular force fields.We calculate permeabilities and free energy profiles along the channel axis, for ammonia andwater. For one force field, the permeability of the double mutant decreases by a factor of 2.5 forwater and a factor of 4 for ammonia, thus increasing the selectivity for water. We attribute thiseffect to decreased entropy of water in the pore, due to the observed increase in pore–waterinteractions and narrower pore. Additionally, we observe spontaneous opening and closing ofthe pore on the cytosolic side, which suggests a gating mechanism for the pore. Our resultsshow that sampling methods and simulation times are sufficient to delineate even subtle effectsof mutations on structure and function and to capture important long-timescale events, butalso underline the importance of improving models further.

  • 9.
    Lindahl, Viveca
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gourdon, Pontus
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 2995Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.

  • 10. Nyblom, Maria
    et al.
    Poulsen, Hanne
    Gourdon, Pontus
    Reinhard, Linda
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Fedosova, Natalya
    Nissen, Poul
    Crystal Structure of Na+, K+-ATPase in the Na+-Bound State2013Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 342, nr 6154, s. 123-127Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Na+, K+-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na+ and K+ across the plasma membrane-a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K+-bound or ouabain-blocked forms. We present the crystal structure of a Na+-bound Na+, K+-ATPase as determined at 4.3 angstrom resolution. Compared with the K+-bound form, large conformational changes are observed in the a subunit whereas the beta and gamma subunit structures are maintained. The locations of the three Na+ sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na+ from IIIb through IIIa, followed by exchange of Na+ for K+ at sites I and II, is suggested.

  • 11. Nys, Mieke
    et al.
    Farinha, Ana
    Wijckmans, Eveline
    Brams, Marijke
    Yoluk, Özge
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Ulens, Chris
    The Crystal Structure of ELIC in Complex with Chlorpromazine Unexpectedly Unveils an Allosteric Binding Site in the Ligand-Binding Domain2016Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, nr 3, s. 457A-457AArtikkel i tidsskrift (Annet vitenskapelig)
  • 12. Nys, Mieke
    et al.
    Wijckmans, Eveline
    Farinha, Ana
    Yoluk, Özge
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Brams, Marijke
    Spurny, Radovan
    Peigneur, Steve
    Tytgat, Jan
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholm University, Sweden.
    Ulens, Chris
    Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine2016Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, nr 43, s. E6696-E6703Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pentameric ligand-gated ion channels or Cys-loop receptors are responsible for fast inhibitory or excitatory synaptic transmission. The antipsychotic compound chlorpromazine is a widely used tool to probe the ion channel pore of the nicotinic acetylcholine receptor, which is a prototypical Cys-loop receptor. In this study, we determine the molecular determinants of chlorpromazine binding in the Erwinia ligand-gated ion channel (ELIC). We report the X-ray crystal structures of ELIC in complex with chlorpromazine or its brominated derivative bromopromazine. Unexpectedly, we do not find a chlorpromazine molecule in the channel pore of ELIC, but behind the beta 8-beta 9 loop in the extracellular ligand-binding domain. The beta 8-beta 9 loop is localized downstream from the neurotransmitter binding site and plays an important role in coupling of ligand binding to channel opening. In combination with electrophysiological recordings from ELIC cysteine mutants and a thiol-reactive derivative of chlorpromazine, we demonstrate that chlorpromazine binding at the beta 8-beta 9 loop is responsible for receptor inhibition. We further use molecular-dynamics simulations to support the X-ray data and mutagenesis experiments. Together, these data unveil an allosteric binding site in the extracellular ligand-binding domain of ELIC. Our results extend on previous observations and further substantiate our understanding of a multisite model for allosteric modulation of Cys-loop receptors.

  • 13.
    Ravishankar, Harsha
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Barth, Andreas
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Probing the activity of a recombinant Zn2+-transporting P-type ATPase2017Inngår i: Biopolymers, ISSN 0006-3525, E-ISSN 1097-0282Artikkel i tidsskrift (Fagfellevurdert)
  • 14. Wang, Kaituo
    et al.
    Sitsel, Oleg
    Meloni, Gabriele
    Autzen, Henriette Elisabeth
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Klymchuk, Tetyana
    Nielsen, Anna Marie
    Rees, Douglas C.
    Nissen, Poul
    Gourdon, Pontus
    Structure and mechanism of Zn2+-transporting P-type ATPases2014Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 514, nr 7523, s. 518-+Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Zinc is an essential micronutrient for all living organisms. It is required for signalling and proper functioning of a range of proteins involved in, for example, DNA binding and enzymatic catalysis(1). In prokaryotes and photosynthetic eukaryotes, Zn2+-transporting P-type ATPases of class IB (ZntA) are crucial for cellular redistribution and detoxification of Zn2+ and related elements(2,3). Here we present crystal structures representing the phosphoenzyme ground state (E2P) and a dephosphorylation intermediate (E2.P-i) of ZntA from Shigella sonnei, determined at 3.2 angstrom and 2.7 angstrom resolution, respectively. The structures reveal a similar fold to Cu+-ATPases, with an amphipathic helix at the membrane interface. A conserved electronegative funnel connects this region to the intramembranous high-affinity ion-binding site and may promote specific uptake of cellular Zn2+ ions by the transporter. The E2P structure displays a wide extracellular release pathway reaching the invariant residues at the high-affinity site, including C392, C394 and D714. The pathway closes in the E2.P-i state, in which D714 interacts with the conserved residue K693, which possibly stimulates Zn2+ release as a built-in counter ion, as has been proposed for H+-ATPases. Indeed, transport studies in liposomes provide experimental support for ZntA activity without counter transport. These findings suggest a mechanistic link between P-IB-type Zn2+-ATPases and P-III-type H+-ATPases and at the same time show structural features of the extracellular release pathway that resemble P-II-type ATPases such as the sarcoplasmic/endoplasmic reticulum Ca2+-ATPase(4,5) (SERCA) and Na+, K+-ATPase(6). These findings considerably increase our understanding of zinc transport in cells and represent new possibilities for biotechnology and biomedicine.

  • 15. Yazdi, Samira
    et al.
    Stein, Matthias
    Elinder, Fredrik
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Lindahl, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. Stockholms universitet, Sweden.
    The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel2016Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 12, nr 1, artikkel-id e1004704Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Voltage-gated potassium (K-V) channels are membrane proteins that respond to changes in membrane potential by enabling K+ ion flux across the membrane. Polyunsaturated fatty acids (PUFAs) induce channel opening by modulating the voltage-sensitivity, which can provide effective treatment against refractory epilepsy by means of a ketogenic diet. While PUFAs have been reported to influence the gating mechanism by electrostatic interactions to the voltage-sensor domain (VSD), the exact PUFA-protein interactions are still elusive. In this study, we report on the interactions between the Shaker K-V channel in open and closed states and a PUFA-enriched lipid bilayer using microsecond molecular dynamics simulations. We determined a putative PUFA binding site in the open state of the channel located at the protein-lipid interface in the vicinity of the extracellular halves of the S3 and S4 helices of the VSD. In particular, the lipophilic PUFA tail covered a wide range of non-specific hydrophobic interactions in the hydrophobic central core of the protein-lipid interface, while the carboxylic head group displayed more specific interactions to polar/charged residues at the extracellular regions of the S3 and S4 helices, encompassing the S3-S4 linker. Moreover, by studying the interactions between saturated fatty acids (SFA) and the Shaker K-V channel, our study confirmed an increased conformational flexibility in the polyunsaturated carbon tails compared to saturated carbon chains, which may explain the specificity of PUFA action on channel proteins.

  • 16. Yazdi, Sammy
    et al.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Elinder, Fredrik
    Stein, Matthias
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Molecular Characterization of the Binding of Polyunsaturated Fatty Acids to a Voltage-Gated Potassium Channel2014Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 739A-739AArtikkel i tidsskrift (Annet vitenskapelig)
  • 17.
    Yoluk, Ozge
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Heusser, Stephanie
    SciLifeLab, Solna, Sweden.;Stockholm Univ, S-10691 Stockholm, Sweden..
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Orellana, Laura
    KTH.
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Stockholm, Sweden..
    Gating Ritual: Simulations of Gating in Glutamate-Gated Chloride Channel2015Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 431A-431AArtikkel i tidsskrift (Annet vitenskapelig)
  • 18.
    Yoluk, Ozge
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Lindahl, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. Stockholm Univ, Dept Biochem & Biophys, Ctr Biomembrane Res.
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Conformational Gating Dynamics in the GluCl Anion-Selective Chloride Channel2015Inngår i: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 6, nr 8, s. 1459-1467Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cys-loop receptors are central to propagation of signals in the nervous system. The gating of the membrane-spanning pore is triggered by structural rearrangements in the agonist-binding site, located some so A away from the pore. A sequential conformational change, propagating from the ligand-binding site to the pore, has been proposed to govern gating in all Cys-loop receptors. Here, we identify structural and dynamic components of the conformational gating in the eukaryotic glutamate-gated chloride channel (GluCl) by means of molecular dynamics (MD) simulations with and without the L-glutamate agonist bound. A significant increase in pore opening and accompanying hydration is observed in the presence of glutamate. Potential of mean force calculations reveal that the barrier for ion passage drops from 15 kcal/mol to 5-10 kcal/mol with the agonist bound. This appears to be explained by agonist binding that leads to significant changes in the intersubunit hydrogen-bonding pattern, which induce a slight tilt of the extracellular domain relative to the transmembrane domain in the simulations. This rearrangement is subtle, but correspond to the direction of the quaternary twist observed as a key difference between open and closed X-ray structures. While the full reversible gating is still a much slower process, the observed structural dynamics sheds new light on the early stages of how the agonist influences the extracellular domain, how the extracellular domain interacts with the transmembrane domain, and how changes in the transmembrane domain alter the free energy of ion passage.

  • 19.
    Yoluk, Özge
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Riederer, Erika A.
    Andersson, Magnus
    Klement, Goran
    Trudell, James R.
    Bertaccini, Edward J.
    Howard, Rebecca J.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Contribution of Structural Elements to Activation and Allosteric Modulation in an Anionic Ligand-Gated Ion Channel2014Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 547A-547AArtikkel i tidsskrift (Annet vitenskapelig)
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