Membrane-associated Conformation Research Articles

Chloride intracellular channel (CLIC) proteins function as fusogens

Chloride Intracellular Channel (CLIC) family members uniquely transition between soluble and membrane-associated conformations. Despite decades of extensive functional and structural studies, CLICs’ function as ion channels remains debated, rendering our understanding of their physiological role incomplete. Here, we expose the function of CLIC5 as a fusogen. We demonstrate that purified CLIC5 directly interacts with the membrane and induces fusion, as reflected by increased liposomal diameter and lipid and content mixing between liposomes. Moreover, we show that this activity is facilitated by acidic pH, a known trigger for CLICs’ transition to a membrane-associated conformation, and that increased exposure of the hydrophobic inter-domain interface is crucial for this process. Finally, mutation of a conserved hydrophobic interfacial residue diminishes the fusogenic activity of CLIC5 in vitro and impairs excretory canal extension in C. elegans in vivo. Together, our results unravel the long-sought physiological role of these enigmatic proteins.

Targeted Delivery of Adamantylated Peptidoglycan Immunomodulators in Lipid Nanocarriers: NMR Shows That Cargo Fragments Are Available on the Surface.

We present an in-depth investigation of the membrane interactions of peptidoglycan (PGN)-based immune adjuvants designed for lipid-based delivery systems using NMR spectroscopy. The derivatives contain a cargo peptidoglycan (PGN) dipeptide fragment and an adamantyl group, which serves as an anchor to the lipid bilayer. Furthermore, derivatives with a mannose group that can actively target cell surface receptors on immune cells are also studied. We showed that the targeting mannose group and the cargo PGN fragment are both available on the lipid bilayer surface, thereby enabling interactions with cognate receptors. We found that the nonmannosylated compounds are incorporated stronger into the lipid assemblies than the mannosylated ones, but the latter compounds penetrate deeper in the bilayer. This might be explained by stronger electrostatic interactions available for zwitterionic nonmannosylated derivatives as opposed to the compounds in which the charged N-terminus is capped by mannose groups. The higher incorporation efficiency of the nonmannosylated compounds correlated with a larger relative enhancement in immune stimulation activities upon lipid incorporation compared to that of the derivatives with the mannose group. The chirality of the adamantyl group also influenced the incorporation efficiency, which in turn correlated with membrane-associated conformations that affect possible intermolecular interactions with lipid molecules. These findings will help in improving the development of PGN-based immune adjuvants suitable for delivery in lipid nanoparticles.

Architecture of the pore forming toxin sticholysin I in membranes

Sticholysin I (StI) is a toxin produced by the sea anemone Stichodactyla helianthus and belonging to the actinoporins family. Upon binding to sphingomyelin-containing membranes StI forms oligomeric pores, thereby leading to cell death. According to recent controversial experimental evidences, the pore architecture of actinoporins is a debated topic. Here, we investigated the StI topology in membranes by site-directed spin labeling and electron paramagnetic resonance spectroscopy. The results reveal that StI in membrane exhibits an oligomeric architecture with heterogeneous stoichiometry of predominantly eight or nine protomers, according to the available structural models. The StI topology resembles the conic pore structure reported for the actinoporin fragaceatoxin C. Our data show that StI coexists in two membrane-associated conformations, with the N-terminal segment either attached to the protein core or inserted in the membrane forming the pore. This finding suggests a ‘pre-pore’ to ‘pore’ transition determined by a conformational change that detaches the N-terminal segment.

Membrane-Associated Conformation of HIV-1 Nef Investigated with Hydrogen Exchange Mass Spectrometry at a Langmuir Monolayer.

In the companion paper to this work, we described development of a new type of hydrogen exchange (HX) mass spectrometry (MS) measurement that integrates Langmuir monolayers. With Langmuir monolayers, the lipid packing density can be reproducibly controlled and changed as desired. Analysis of HX in proteins that may undergo conformational changes as a function of lipid packing (for example, conformational rearrangements after insertion into a lipid layer) are then possible. We previously used neutron reflection to characterize just such a conformational change in the myristoylated HIV-1 Nef protein (myrNef): at high lipid packing density, myrNef could not insert into the lipids and maintained a compact conformation adjacent to the monolayer, whereas at lower lipid packing density, myrNef was able to insert N-terminal arm residues, causing displacement of the core domain away from the monolayer. In order to locate where conformation may have been altered by lipid association, we applied the HX MS Langmuir monolayer method to myrNef associated with monolayers of packing densities identical to those used for the prior neutron reflection measurements. The results show that the N-terminal region and the C-terminal unstructured loop undergo conformational changes when associated with a low density lipid monolayer. The results are not consistent with the hypothesis of myrNef dimerization upon membrane association in the absence of other myrNef binding partners. The HX MS Langmuir monolayer method provides new and meaningful information for myrNef that helps explain necessary conformational changes required for function at the membrane.

Conformational heterogeneity of α-synuclein in membrane

α-Synuclein (αS) is a natively disordered protein in solution, thought to be involved in the fusion of neurotransmitter vesicles to cellular membranes during neurotransmission. Monomeric αS has been previously characterized in two distinct membrane-associated conformations: a broken-helix structure, and an extended helix. By employing atomistic molecular dynamics and a novel membrane representation with significantly enhanced lipid mobility (HMMM), we investigate the process of spontaneous membrane binding of αS and the conformational dynamics of monomeric αS in its membrane-bound form.By repeatedly placing helical αS monomers in solution above a planar lipid bilayer and observing their spontaneous association and its spontaneous insertion into the membrane during twenty independent unbiased simulations, we are able to characterize αS in its membrane-bound state, suggesting that αS has a highly variable membrane insertion depth at equilibrium. Our simulations also capture two distinct states of αS, the starting broken-helix conformation seen in the micelle bound NMR structures, and a semi-extended helix. Analysis of lipid distributions near αS monomers indicates that the transition to a semi-extended helix is facilitated by concentration of phosphatidyl-serine headgroups along the inner edge of the protein. Such a lipid-mediated transition between helix–turn–helix and extended conformations of αS may also occur in vivo, and may be important for the physiological function of αS.

The Discreet Charm of the Curve

The Discreet Charm of the Curve

The Conformation of Membrane-Associated HIV Nef and its Interactions with Hck

Nef is one of several HIV-1 accessory proteins and directly contributes to AIDS progression. Nef has no catalytic activity but instead realizes its functions by interacting with cellular proteins. Nef is myristoylated on the N-terminus, associates with membranes, and undergoes a transition from a solution conformation to a membrane-associated conformation. It has been hypothesized that conformational rearrangement enables membrane-associated Nef to interact with cellular proteins. Despite its obvious disease importance, there is little or no direct information about the conformation of membrane-bound Nef. In this work we used neutron reflection to reveal details of the conformation of membrane-bound Nef. The conformation of myristoylated Nef was studied upon binding to Langmuir monolayers of negatively-charged lipids. By adjusting the surface pressure, the extent of insertion of the myristate group could be controlled. At sufficiently high surface pressure such that the myristate group did not insert, adsorbed Nef was in a condensed state with the core domain directly against the lipid headgroups. At lower surface pressure such that the myristate group inserted into the membrane, adsorbed Nef was found to be in an extended state with the core domain displaced ∼ 70 A from the lipid headgroups. Thus, insertion of the myristate group triggers a conformational transition to an open configuration. This may have important ramifications for the ability of Nef to interact with host proteins. Prior work has shown that Nef interaction with the SH3 domains of Src-family kinases is a common early event in HIV-infected cells that generates important downstream signals essential for viral pathogenesis. We will report on the ability of membrane-bound Nef in each conformation to interact with the SH3 domain of Hck.

Molecular dynamics simulation of HIV-1 fusion domain-membrane complexes: Insight into the N-terminal gp41 fusion mechanism

To understand how viral proteins fuse with the cell membrane, a process that is important for the initial stages of infection, the conformation of the membrane-bound viral fusion peptides (FPs) must be identified. Here, molecular dynamics (MD) simulations were performed to investigate the conformation of the FP-16 and FP-23 of human immunodeficiency virus (HIV) bound to a dimyristoyl phosphatidylcholine (DMPC) bilayer. All FPs were found to penetrate into the bilayer despite the different initial orientations. In addition, the inclusion of residues 17 to 23 was found to play significant role in the fusion ability. Each of the FPs adopts at least two distinct conformations (predominantly α-helical and β-structures) while association with membrane. The peptide seriously affects structural and dynamical parameter of the contacted lipids. The previously experimental data together with our simulation data reveal that fusion ability depends on the membrane-associated conformation and alignment of the peptide.

Conformational Change of HIV Nef upon Insertion into Lipid Membranes Resolved by Neutron Reflectivity

Nef is one of several HIV-1 accessory proteins and directly contributes to AIDS progression. Nef has no catalytic activity but instead realizes its functions by interacting with cellular proteins. Nef is myristoylated on the N-terminus, associates with membranes, and undergoes a transition from a solution conformation to a membrane-associated conformation. It has been hypothesized that conformational rearrangement enables membrane-associated Nef to interact with cellular proteins. Despite its obvious disease importance, there is little or no direct information about the conformation of membrane-bound Nef. In this work we used neutron reflection to reveal details of the conformation of membrane-bound Nef. The conformation of myristoylated Nef was studied upon binding to Langmuir monolayers of negatively-charged lipids. By adjusting the surface pressure, the extent of insertion of the myristate group could be controlled. At sufficiently high surface pressure such that the myristate group did not insert, adsorbed Nef was in a condensed state with the core domain directly against the lipid headgroups. At lower surface pressure such that the myristate group inserted into the membrane, adsorbed Nef was found to be in an extended state with the core domain displaced ∼ 70 A from the lipid headgroups. Thus, insertion of the myristate group triggers a conformational transition to an open configuration. This has important ramifications for the ability of Nef to interact with host proteins.

The Conformation and Activity of Membane-Bound HIV Nef Studied by Neutron Reflectivity

Nef is one of six HIV-1 accessory proteins and directly contributes to AIDS progression. Nef has no catalytic activity but instead realizes its functions by interacting with cellular proteins. Nef is myristoylated on the N-terminus, associates with membranes, and may undergo a transition from a solution conformation to a membrane-associated conformation. It has been hypothesized that conformational rearrangement enables membrane-associated Nef to interact with cellular proteins. Despite its obvious disease importance, there is little or no direct information about the conformation of membrane-bound Nef. In this work we used neutron reflection to reveal details of the conformation of membrane-bound Nef. The conformation of membrane-bound Nef, and its ability to bind to the SH3 domain of Hck, was found to depend upon the mode of membrane binding. In solution Nef in known to bind the SH3 domain of Hck with high affinity (kd = 250 nM). In one mode, Nef was bound through an N-terminal His tag to Langmuir monolayers of DPPC mixed with a synthetic metal-chelating lipid (Biophys. J. 99, 1940, 2010). In that case, for a range of pH and salt concentration the core domain of membrane-bound Nef lies within a few angstroms of the lipid headgroups and a portion of the protein, presumably from the N-terminal arm, is inserted. In this conformation, Nef does not bind the SH3 domain of Hck. However, upon binding to negatively-charged membranes in absence of an interaction through the N-terminus, the core domain of Nef is displaced from the membrane, and binding of SH3 occurs. The ramifications of the these results for the actions of Nef in-vivo will be discussed.

Neutron Reflectometry Study of the Conformation of HIV Nef Bound to Lipid Membranes

Nef is an HIV-1 accessory protein that directly contributes to AIDS progression. Nef is myristoylated on the N-terminus, associates with membranes, and may undergo a transition from a solution conformation to a membrane-associated conformation. It has been hypothesized that conformational rearrangement enables membrane-associated Nef to interact with cellular proteins. Despite its medical relevance, to our knowledge there is no direct information about the conformation of membrane-bound Nef. In this work, we used neutron reflection to reveal what we believe are the first details of the conformation of membrane-bound Nef. The conformation of Nef was probed upon binding to Langmuir monolayers through the interaction of an N-terminal His tag with a synthetic metal-chelating lipid, which models one of the possible limiting cases for myr-Nef. The data indicate that residues are inserted into the lipid headgroups during interaction, and that the core domain lies directly against the lipid headgroups, with a thickness of ∼40 Å. Binding of Nef through the N-terminal His tag apparently facilitates insertion of residues, as no insertion occurred upon binding of Nef through weak electrostatic interactions in the absence of the specific interaction through the His tag.

A Study of the Conformation of HIV Nef Bound to Lipid Membranes by Neutron Reflectivity

Nef is one of six HIV-1 accessory proteins and directly contributes to AIDS progression. Nef associates with membranes and may require a transition from a solution conformation to a membrane-associated conformation. It has been hypothesized that a transition from a “closed” conformational form to an “open” form enables interaction of Nef with cellular proteins. Despite its obvious disease importance, there is little or no direct information about the conformation of membrane-bound Nef. In this work we used neutron reflection to reveal details of the conformation of membrane-bound Nef. Nef was bound through an N-terminal His tag to Langmuir monolayers of DPPC mixed with a synthetic metal-chelating lipid. Several methods were found to achieve a dense monomolecular layer of membrane-bound Nef, despite its tendency to form oligomers at high concentration. At the conditions of this initial study (65% DSIDA 35 mol% DPPC, 20 mM Tris, 20 C, pH 8.2), for the large majority of the bound population the core domain of membrane-bound Nef lies within a few A of the lipid headgroups. The N-terminal arm is directly against the lipid headgroups with a small portion inserted. The results also indicate that the disordered loop extends from the core domain into the solution. The data also suggest that for a very small fraction of the bound population the N-terminal arm extends normal to the membrane and the core domain is displaced ∼50 A from the membrane. Some ramifications of these results for the activity of Nef are discussed.

The N-Terminal Domain of Bcl-xL Reversibly Binds Membranes in a pH-Dependent Manner

Bcl-xL regulates apoptosis by maintaining the integrity of the mitochondrial outer membrane by adopting both soluble and membrane-associated forms. The membrane-associated conformation does not require a conserved, C-terminal transmembrane domain and appears to be inserted into the bilayer of synthetic membranes as assessed by membrane permeabilization and critical surface pressure measurements. Membrane association is reversible and is regulated by the cooperative binding of approximately two protons to the protein. Two acidic residues, Glu153 and Asp156, that lie in a conserved hairpin of Bcl-xLDeltaTM appear to be important in this process on the basis of a 16% increase in the level of membrane association of the double mutant E153Q/D156N. Contrary to that for the wild type, membrane permeabilization for the mutant is not correlated with membrane association. Monolayer surface pressure measurements suggest that this effect is primarily due to less membrane penetration. These results suggest that E153 and D156 are important for the Bcl-xLDeltaTM conformational change and that membrane binding can be distinct from membrane permeabilization. Taken together, these studies support a model in which Bcl-xL activity is controlled by reversible insertion of its N-terminal domain into the mitochondrial outer membrane. Future studies with Bcl-xL mutants such as E153Q/D156N should allow determination of the relative contributions of membrane binding, insertion, and permeabilization to the regulation of apoptosis.

Helix periodicity, topology, and dynamics of membrane‐associated α‐Synuclein

The protein alpha-Synuclein (aS) is a synaptic vesicle-associated regulator of synaptic strength and dopamine homeostasis with a pathological role in Parkinson's disease. The normal function of aS depends on a membrane-associated conformation that is adopted upon binding to negatively charged lipid surfaces. Previously we found that the membrane-binding domain of aS is helical and suggested that it may exhibit an unusual structural periodicity. Here we present a study of the periodicity, topology, and dynamics of detergent micelle-bound aS using paramagnetic spin labels embedded in the micelle or attached to the protein. We show that the helical region of aS completes three full turns every 11 residues, demonstrating the proposed 11/3 periodicity. We also find that the membrane-binding domain is partially buried in the micelle surface and bends toward the hydrophobic interior, but does not traverse the micelle. Deeper submersion of certain regions within the micelle, including the unique lysine-free sixth 11-residue repeat, is observed and may be functionally important. There are no long-range tertiary contacts within this domain, indicating a highly extended configuration. The backbone dynamics of the micelle-bound region are relatively uniform with a slight decrease in flexibility observed toward the C-terminal end. These results clarify the topological features of aS bound to membrane-mimicking detergent micelles, with implications for aS function and pathology.

Modifications of cysteine residues in the solution and membrane-associated conformations of phosphatidylinositol transfer protein have differential effects on lipid transfer activity.

The alpha isoforms of mammalian phosphatidylinositol transfer protein (PITP) contain four conserved Cys residues. In this investigation, a series of thiol-modifying reagents, both alkylating and mixed disulfide-forming, was employed to define the accessibility of these residues and to evaluate their role in protein-mediated intermembrane phospholipid transport. Isolation and analysis of chemically modified peptides and site-directed mutagenesis of each Cys residue to Ala were also performed. Soluble, membrane-associated, and denatured preparations of wild-type and mutant rat PITPs were studied. Under denaturing conditions, all four Cys residues could be detected spectrophotometrically by chemical reaction with 4,4'-dipyridyl disulfide or 5,5'-dithiobis(2-nitrobenzoate). In the native protein, two of the four Cys residues were sensitive to some but not all thiol-modifying reagents, with discrimination based on the charge and hydrophobicity of the reagent and the conformation of the protein. With the soluble conformation of PITP, achieved in the absence of phospholipid vesicles, the surface-exposed Cys(188) was chemically modified without consequence to lipid transfer activity. Cys(188) exhibited an apparent pK(a) of 7.6. The buried Cys(95), which constitutes part of the phospholipid substrate binding site, was covalently modified upon transient association of PITP with a membrane surface. The Cys-to-Ala mutations showed that neither Cys(95) nor Cys(188) was essential for lipid transfer activity. However, chemical modification of Cys(95) resulted in the loss of lipid transfer activity. These results demonstrate that the Cys residues of PITP can be assigned to several different classes of chemical reactivity. Of particular interest is Cys(95), whose sulfhydryl group becomes exposed to modification in the membrane-associated conformation of PITP. Furthermore, the inhibition of PITP activity by thiol-modifying reagents is a result of steric hindrance of phospholipid substrate binding.

The structure of the membrane-binding 38 C-terminal residues from bovine PP3 determined by liquid- and solid-state NMR spectroscopy.

The secondary structure and membrane-associated conformation of a synthetic peptide corresponding to the putative membrane-binding C-terminal 38 residues of the bovine milk component PP3 was determined using 1H NMR in methanol, CD in methanol and SDS micelles, and 15N solid-state NMR in planar phospholipid bilayers. The solution NMR and CD spectra reveal that the PP3 peptide in methanol and SDS predominantly adopts an alpha-helical conformation extending over its entire length with a potential bend around residue 19. 15N solid-state NMR of two PP3 peptides 15N-labelled at the Gly7 and Ala32 positions, respectively, and dissolved in dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol phospholipid bilayers shows that the peptide is associated to the membrane surface with the amphipathic helix axis oriented parallel to the bilayer surface.

The orientation and dynamics of substance P in lipid environments.

The membrane-associated conformation of substance P (RPKPQQFFGLM-NH2) has been previously proposed to be the NK1-receptor-active conformation. In this work, NMR methods are applied to explore the orientation and dynamics of substance P at lipid surfaces for which the peptide's three-dimensional structure had been previously determined. Here the presence of dodecylphosphocholine (DPC) or sodium dodecylsulfate (SDS) micelles has been found to cause sequence specific changes in the acid- and base-catalyzed amide proton exchange rates relative to the solution state values. On binding of substance P to SDS micelles, the FFG portion showed the largest decreases in the base-catalyzed amide exchange rates. Similar sequence-specific changes in substance P are observed in the presence of DPC micelles, albeit at much weaker levels due to fast exchange between free and bound forms of the peptide. These differences are attributed to the location of the amide protons either in the surface double layer (via electrostatic effect) or inserted into the polar head group region of the micelles (via low dielectric). The sequence-specific effects of micelle association were also observed in the homonuclear nonselective spin-lattice relaxation time; these, in combination with spin-spin relaxation times, were used to calculate correlation times for the backbone amide protons. These data combined with paramagnetic broadening observations on peptide protons in the presence of spin-labeled lipids yield a detailed model of the interaction of substance P with lipid surfaces.

Binding of Molten Globule-like Conformations to Lipid Bilayers: STRUCTURE OF NATIVE AND PARTIALLY FOLDED α-LACTALBUMIN BOUND TO MODEL MEMBRANES

The effect of membrane binding on the structure and stability of several conformers of alpha-lactalbumin was studied by infrared spectroscopy, circular dichroism, and fluorescence spectroscopy. In solution, under experimental conditions where all conformers interact with negatively charged membranes, they show significant conformational differences. However, binding to negatively charged membranes, which causes considerable changes in the structure of these conformers, leads to a remarkably similar protein conformation. The membrane-associated conformations are characterized by 1) a high helical content, greater than any of those found in solution, 2) a lack of stable tertiary structure, and 3) the disappearance of their thermotropic transition. These observations indicate that association with negatively charged membranes induces a conformational change within alpha-lactalbumin to a flexible, molten globule-like state.

Mapping a membrane-associated conformation of colicin Ia.

Channel-forming colicins exist in at least two different membrane-associated conformations: a voltage-independent closed-channel state and a voltage-dependent open-channel state. In a voltage-independent membrane-associated conformation, we find that two major regions of colicin Ia are protected from pepsin proteolysis after association with negatively charged membranes. In contrast, colicin Ia is rapidly and completely proteolyzed in the absence of membranes. The major protected region includes an electrophysiologically defined C-terminal channel-forming domain as well as 96 residues upstream of this region. Approximately 100 residues spanning Ala79- approximately Arg189 within the N-terminal domain are protected as well. The first N-terminal 76 residues of colicin Ia and a large region which includes much of the putative central receptor-binding domain are not protected from proteolysis. Both N- and C-termini of protected peptides have been identified using a combination of gel electrophoresis, N-terminal sequencing, and mass spectrometry, thereby defining specific residues that are located on the outside of the lipid bilayer. These data suggest a role for regions other than the electrophysiologically defined C-terminal channel-forming domain in membrane insertion and channel formation.