Direct Binding of Phosphatidylglycerol at Specific Sites Modulates
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bioRxiv preprint doi: https://doi.org/10.1101/722512; this version posted August 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 6 7 8 9 Direct Binding of Phosphatidylglycerol at Specific Sites Modulates 10 Desensitization of a Pentameric Ligand-Gated Ion Channel 11 12 13 Ailing Tong1, John T. Petroff II1, Fong-Fu Hsu2, Philipp A. M. Schmidpeter3, Crina M. Nimigean3, 14 Liam Sharp4, Grace Brannigan4,5, Wayland W. L. Cheng1,* 15 16 From the Departments of 1Anesthesiology, and 2Internal Medicine, Mass Spectrometry 17 Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington 18 University in St. Louis, MO, USA, 3Departments of Anesthesiology, and Physiology and 19 Biophysics, Weill Cornell Medicine, NY, USA, and the 4Center for Computational and Integrative 20 Biology and 5Department of Physics, Rutgers University, Camden, NJ, USA. 21 22 23 *To whom correspondence should be addressed: Professor Wayland W. L. Cheng, Department 24 of Anesthesiology, Washington University School of Medicine, Campus Box 8054, St. Louis, MO 25 63110. Telephone: (314)273-7958; E-mail: [email protected] 26 bioRxiv preprint doi: https://doi.org/10.1101/722512; this version posted August 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 27 Abstract 28 Pentameric ligand-gated ion channels (pLGICs) are essential determinants of synaptic 29 transmission, and are modulated by specific lipids including anionic phospholipids. The exact 30 modulatory effect of anionic phospholipids in pLGICs and the mechanism of this effect are not 31 well understood. Using native mass spectrometry, coarse-grained molecular dynamics 32 simulations and functional assays, we show that the anionic phospholipid, 1-palmitoyl-2-oleoyl- 33 phosphatidylglycerol (POPG), preferentially binds to and stabilizes the pLGIC, Erwinia ligand- 34 gated ion channel (ELIC), and decreases ELIC desensitization. Mutations of five arginines located 35 in the interfacial regions of the transmembrane domain (TMD) reduce POPG binding, and a 36 subset of these mutations increase ELIC desensitization. In contrast, the L240A mutant known to 37 decrease ELIC desensitization, increases POPG binding. The results support a mechanism by 38 which POPG stabilizes the open state of ELIC relative to the desensitized state by direct binding 39 at specific sites. 40 41 Introduction 42 Pentameric ligand-gated ion channels (pLGICs) are essential determinants of synaptic 43 transmission, and the targets of many allosteric modulators including general anesthetics and 44 anti-epileptics (1). These ion channels are embedded in a heterogeneous and dynamic lipid 45 environment (2), and the presence of specific lipids fine-tunes the function of pLGICs and may 46 play a role in regulating neuronal excitability and drug sensitivity (3-5). One nearly ubiquitous 47 example is that of anionic phospholipids, which are known to modulate pentameric ligand-gated 48 ion channels (pLGICs) such as the nicotinic acetylcholine receptor (nAchR) (6), as well as inward 49 rectifying potassium channels (7), K(2P) channels (8), voltage-gated potassium channels (9, 10), 50 and cyclic nucleotide-gated channels (11). In pLGICs, anionic phospholipids have been shown to 51 shift the conformational equilibrium of the channel from an uncoupled or desensitized state to a 52 resting state, in which agonist binding is effectively coupled to channel activation (12-14). 2 bioRxiv preprint doi: https://doi.org/10.1101/722512; this version posted August 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 53 Studies of lipid modulation of ion channel function including modulation of pLGICs have 54 focused on two central questions: 1) what is the exact effect of the lipid on channel function and 55 structure, and 2) is the effect attributable to direct binding of the lipid at specific sites? Torpedo 56 nAchR channel activity measured from flux assays (6, 15, 16) and agonist-induced conformational 57 changes (13, 17) depend on anionic phospholipids. However, only a few studies have employed 58 fast solution changes to measure current responses of pLGICs in model membranes (18), which 59 is necessary to distinguish the effect of lipids on channel gating, specifically transitions between 60 resting, open and desensitized states. With regard to lipid binding, early studies using electron 61 paramagnetic resonance (EPR) of spin-labeled lipids or lipid-induced modification of fluorescent 62 probes revealed an immobilized layer of lipids surrounding nAchRs that is enriched for certain 63 phospholipids (19, 20) with lipids occupying specific sites (21, 22). These approaches are, 64 however, an indirect means to examine lipid binding to ion channels. More recently, crystal 65 structures of the pLGIC, Gloeobacter ligand-gated ion channel (GLIC), revealed bound, co- 66 purified phospholipids in a putative open structure, and the absence of one of these phospholipids 67 in a locally-closed structure (23, 24). Similarly, a putative desensitized structure of GLIC with a 68 bound polyunsaturated fatty acid showed loss of the aforementioned phospholipid density that is 69 bound to the open state (25). Both of these studies suggest that bound phospholipids at specific 70 sites stabilize the open state of the channel, although the identity of these lipids remains unknown. 71 Furthermore, the absence of a lipid density in a crystal structure is not necessarily an indication 72 of lack of binding. 73 Native mass spectrometry (MS) has proven to be a powerful tool to directly measure 74 binding of endogenous and exogenous lipids to membrane proteins (26, 27). In addition, coarse- 75 grained molecular dynamics (MD) simulations provide a complementary approach to examine 76 lipid interactions with membrane-embedded pLGICs at time scales that allow equilibration of lipid 77 binding sites (28, 29). We sought to determine whether phospholipids bind directly and selectively 78 to a pLGIC by native MS and coarse-grained MD simulations, and whether specific binding 3 bioRxiv preprint doi: https://doi.org/10.1101/722512; this version posted August 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 79 interactions modulate channel function by measuring ELIC activity in liposomes of defined lipid 80 composition. Erwinia ligand-gated ion channel (ELIC), a prototypical pLGIC and biochemically 81 tractable target, is also sensitive to its lipid environment. ELIC was found to be inactive when 82 reconstituted in 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) membranes fused to Xenopus 83 oocyte membranes, similar to the nAchR (30). After optimizing native MS for ELIC, we 84 demonstrate that phospholipids directly bind to ELIC, with more binding observed for the anionic 85 phospholipid, 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) compared to zwitterionic 86 phospholipids, 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) and POPC. Consistent 87 with this finding, coarse-grained simulations of ELIC in a lipid bilayer show enrichment of annular 88 POPG compared to POPC or POPE. In addition, POPG selectively stabilizes ELIC against 89 thermal denaturation indicative of a specific binding interaction, and reduces channel 90 desensitization. Mutations of five arginines at the transmembrane domain (TMD) intracellular and 91 extracellular interfaces decrease POPG binding while a subset of these mutations increase 92 desensitization. Likewise, the L240A mutant, which reduces desensitization, increases POPG 93 binding. The results support the hypothesis that anionic phospholipids stabilize the open state of 94 pLGICs by direct binding to sites in the TMD adjacent to the lipid-facing transmembrane helix 4 95 (TM4) (3). 96 97 Results 98 99 Selective binding of phospholipids to ELIC 100 Native MS of ELIC purified in dodecyl maltoside (DDM) was optimized on a Q-Exactive 101 EMR mass spectrometer as previously described (27). Optimal desolvation of the pentamer 102 required activation energies that resulted in some dissociation into tetramer and monomer (Fig. 103 1A). Nevertheless, both the pentamer and tetramer species showed multiple bound small 104 molecules of ~750 Da, likely corresponding to co-purified phospholipids (up to 8 and 6 lipids per 105 multimer were observed for the pentamer and tetramer, respectively) (Fig. 1A). To determine the 4 bioRxiv preprint doi: https://doi.org/10.1101/722512; this version posted August 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Figure 1. POPG binds selectively to ELIC. (A) Native MS spectra of ELIC in DDM, C10E5, and C10E5 with 12 µM POPG. Left shows full spectra and right shows deconvoluted spectra. (B) Deconvoluted spectra of ELIC in 12 µM of the indicated phospholipid. (C) Plot of the average number of bound phospholipids per pentamer at varying concentrations of POPG, POPE and POPC (n=3-6, ±SD). 106 identity of these lipids, we performed a lipid extraction from the purified ELIC preparation, and 107 analyzed the