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Logo of jbcThe Journal of Biological Chemistry
J Biol Chem. 2013 December 6; 288(49): 35266–35276.
Published online 2013 October 23. doi:  10.1074/jbc.M113.508408
PMCID: PMC3853275

Mechanism of Transport Modulation by an Extracellular Loop in an Archaeal Excitatory Amino Acid Transporter (EAAT) Homolog*


Secondary transporters in the excitatory amino acid transporter family terminate glutamatergic synaptic transmission by catalyzing Na+-dependent removal of glutamate from the synaptic cleft. Recent structural studies of the aspartate-specific archaeal homolog, GltPh, suggest that transport is achieved by a rigid body, piston-like movement of the transport domain, which houses the substrate-binding site, between the extracellular and cytoplasmic sides of the membrane. This transport domain is connected to an immobile scaffold by three loops, one of which, the 3–4 loop (3L4), undergoes substrate-sensitive conformational change. Proteolytic cleavage of the 3L4 was found to abolish transport activity indicating an essential function for this loop in the transport mechanism. Here, we demonstrate that despite the presence of fully cleaved 3L4, GltPh is still able to sample conformations relevant for transport. Optimized reconstitution conditions reveal that fully cleaved GltPh retains some transport activity. Analysis of the kinetics and temperature dependence of transport accompanied by direct measurements of substrate binding reveal that this decreased transport activity is not due to alteration of the substrate binding characteristics but is caused by the significantly reduced turnover rate. By measuring solute counterflow activity and cross-link formation rates, we demonstrate that cleaving 3L4 severely and specifically compromises one or more steps contributing to the movement of the substrate-loaded transport domain between the outward- and inward-facing conformational states, sparing the equivalent step(s) during the movement of the empty transport domain. These results reveal a hitherto unknown role for the 3L4 in modulating an essential step in the transport process.

Keywords: Amino Acid Transport, Chemical Modification, Glutamate, Membrane Transport, Reconstitution of Membrane Transporters, Transporters, Protein Cross-linking


Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system, mediating synaptic transmission by activating receptors in post-synaptic neurons (1). Glutamate is removed by reuptake into glia and neurons by members of the EAAT2 family, which transport one glutamate molecule into the cell coupled to three Na+ ions and one H+ accompanied by the countertransport of one K+ ion (2). EAATs are members of the dicarboxylate/amino acid:cation symporter family (TCDB code 2.A.23) that also includes members that transport dicarboxylates and other amino acids (35). GltPh, from the archaeon Pyrococcus horikoshii, is 30% identical to the EAATs (6) and transports aspartate (l-Asp); it is the only dicarboxylate/amino acid:cation symporter member for which there is high resolution structural information (710). GltPh is an excellent model for the EAATs with similar functional properties, including the co-transport of substrate with three Na+ ions (11, 12) and the presence of a thermodynamically uncoupled anion conductance (13). However, GltPh does not require K+ to recycle the glutamate-free transporter from inward-facing to outward-facing states, instead recycling in a substrate- and ion-free state (11).

GltPh, like other members of the EAAT family, is a trimer; each protomer consists of eight transmembrane helices and two re-entrant hairpin loops, the tips of which, along with transmembrane helices 7 and 8, form the substrate-binding site (Fig. 1A) (7, 14). Each protomer is organized into two distinct domains as follows: a stationary trimerization domain that mediates all intersubunit contacts, and a mobile transport domain that fully encompasses the substrate-binding site (9, 15). Cross-linking, structural and computational studies, and more recently, electron paramagnetic resonance (EPR) spectroscopy suggest a model in which the transport domain moves ~18 Å and rotates ~30° through the trimerization domain (9, 1618). In a simple kinetic scheme for GltPh; l-Asp and three Na+ ions bind to the outward-facing state (OFS) (Fig. 1B, step 1), facilitating this dramatic conformational change and resulting in a piston-like movement of the substrate-binding site across the membrane (Fig. 1B, step 2). In our scheme, this step includes the formation of an occluded outward-facing state (“closing,” perhaps by HP2 closure), the large scale translocation of the domain, and the transition from “inward-occluded” to “inward-open” substrate-bound states (“opening”). The substrates are released into the cytoplasm from this inward-facing state (IFS) (Fig. 1B, step 3), and the empty transport domain transitions from the IFS back to OFS to restart the cycle (Fig. 1B, step 4; note that in the mammalian isoforms K+ is bound for this step). This return step also presumably includes closing and opening steps to permit the translocation step of the occluded apo-transporter (whose structure was recently published (19)).

Detergent-solubilized GltPh can be trapped in the IFS when 3L4 is cleaved. A, structure of l-Asp-bound GltPh (Protein Data Bank accession 1XFH(7)) showing the K55C and A364C mutations (blue balls) in relation to HP1 (yellow), HP2 (red), and 3L4 (green ...

The trimerization domain is attached to the transport domain by three loops connecting transmembrane helices 2–3, 3–4 (3L4), and 5–6 (7). Comparison of the outward-facing and inward-facing crystal structures reveals distinct conformational changes in 2–3 and 5–6 loops; however, 3L4 was either unresolved or involved in lattice-packing interactions, meaning that the true structure of 3L4 is unknown (7, 9). The 21-amino acid, proline-rich 3L4 undergoes substrate-dependent conformational changes, as demonstrated by limited trypsin proteolysis analysis and fluorescein 5-maleimide accessibility experiments (20). Furthermore, cleaving the protein backbone within 3L4, by means of an engineered Factor X protease recognition site, resulted in almost complete loss of transport activity despite the protein maintaining its structural integrity (20). This novel observation revealed that 3L4 plays a critical role in the transport cycle.

In this work, we probe the role of 3L4 in the mechanism of l-Asp transport by GltPh using cross-linking, binding, and transport assays. We demonstrate that cleaving 3L4 specifically inhibits one of the components of the translocation step of the substrate-loaded transport domain of GltPh while sparing the equivalent component of the translocation of the substrate-free apo-translocation domain, a conclusion with important implications for the overall mechanism of transport.


Protein Expression and Purification

All mutations were made using the QuikChange II site-directed mutagenesis kit (Agilent Technologies), and all cysteine substitutions were introduced into a Cys-less GltPh mutant wherein the single native cysteine had been mutated to serine (C321S), which is fully active (20). Purification of wild-type GltPh and its variants was performed essentially as described previously (11). A culture of Escherichia coli TOP10 cells harboring the appropriate expression vector was grown to mid-log phase, and expression was induced by addition of 0.1% (w/v) l-arabinose. Cells were lysed by sonication, and membranes were isolated by multiple centrifugation steps.

Membranes containing overexpressed His-tagged protein were solubilized by addition of n-dodecyl β-d-maltopyranoside (DDM, Anatrace) and incubated for 1 h at 4 °C with nickel-nitrilotriacetic acid Superflow resin (Qiagen) pre-equilibrated with buffer containing 20 mm Tris-HCl, pH 7.4, 200 mm NaCl, 5 mm l-glutamate, 0.5 mm tris(2-carboxyethyl)phosphine, and 2 mm DDM. Contaminants were removed by washing with 20 column volumes of the same buffer plus 40 mm imidazole. Bound protein was eluted by addition of the same buffer plus 250 mm imidazole. The His tag was removed by incubation overnight at room temperature with thrombin in a ratio of 10 units/mg protein. Thrombin digestion was quenched by addition of 10 mm EDTA and 1 mm 4-(2-aminoethyl)benzenesulfonyl fluoride.

Protein Reconstitution

Reconstitution of GltPh was achieved using the process pioneered by Rigaud and co-workers (21). Pre-formed liposomes were partially solubilized with Triton X-100, and protein was added resulting in co-micellization of the constituents, and detergent was removed using polystyrene beads (Biobeads SM-2). After obtaining inconsistent transport rates, we thoroughly examined the variables involved and found that to obtain high activity proteoliposomes we needed to do the following: (a) add Triton X-100 from a 10% (w/v) solution of instead of adding from the 100% detergent stock, and (b) use the light scattering curve to determine the correct detergent ratio for each batch reconstitution rather than using a fixed and pre-determined Triton X-100/lipid ratio. A 3:1 ratio of E. coli polar lipid extract and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids) was mixed, dried, and resuspended to 10 mg/ml in Inside Buffer (20 mm Tris/HEPES, pH 7.4, 1 mm NaCl, and 199 mm KCl), unless indicated otherwise. The lipid suspension was freeze-thawed five times, extruded, and then diluted to 4 mg/ml. Aliquots of 10% Triton X-100 were added to the liposomes, and incorporation was monitored using absorbance at 540 nm. Upon saturation of the liposomes with Triton X-100, purified protein was added in a ratio of 3 μg of protein/mg of lipid. Detergent was removed by multiple additions of Biobeads SM-2 polystyrene beads (Bio-Rad). Liposomes were separated from Biobeads and collected by ultracentrifugation. Proteoliposomes were resuspended in Inside Buffer to a final concentration of 10 mg/ml (lipid content), snap-frozen, and stored at −80 °C.

Transport Assays

Proteoliposomes were thawed, extruded through a 400-nm filter, collected by ultracentrifugation, and resuspended to a final lipid concentration of 100 mg/ml. In a standard transport assay, the reaction was initiated by diluting proteoliposomes 150-fold into reaction buffer containing 20 mm Tris/HEPES, pH 7.4, 100 mm KCl, 100 mm NaCl, 1 μm valinomycin, and 100 nm l-[3H]Asp at 30 °C. 200-μl samples were taken periodically and quenched by addition of 2 ml of ice-cold quench buffer containing 20 mm Tris/HEPES, pH 7.4, 200 mm LiCl. The quenched reaction was applied to a nitrocellulose filter (Millipore) over a vacuum manifold and then washed with 2 ml of quench buffer. The nitrocellulose filters were dissolved with 3 ml of FilterCount liquid scintillation mixture (PerkinElmer Life Sciences), and radioactivity was counted using a TriLux beta counter (PerkinElmer Life Sciences). The solute counterflow assay was performed in the same way except the proteoliposomes were loaded with buffer containing 20 mm Tris/HEPES, pH 7.4, 100 mm NaCl, and 1 mm l-Asp by multiple freeze/thaw cycles and extrusion through a 400-nm filter. The reaction buffer contained 20 mm Tris/HEPES, pH 7.4, 100 mm NaCl, and 100 nm l-[3H]Asp.

Factor X Digestion

Purified GltPh variants were exchanged into Factor Xa digestion buffer (10 mm Tris/HEPES, pH 8, 5 mm CaCl2, 100 mm NaCl and 2 mm DDM). Factor X (New England Biolabs) was added in a ratio of 125 μg/1 mg of protein and incubated at 37 °C for 24 h. To discourage the stabilization of the IFS by disulfide formation between the cysteines introduced at positions 55 and 364 during the 24-h incubation, where applicable we added 1 mm l-Asp to the reaction. Factor X digestion was stopped by addition of 10 mm EDTA and 1 mm 4-(2-aminoethyl)benzenesulfonyl fluoride. Control samples that were not digested with Factor X were treated in an identical fashion.

Filter Binding Assays

Following purification by immobilized metal affinity chromatography and digestion by Factor X (both described previously), GltPhXa was further purified and exchanged into binding buffer (20 mm Tris/HEPES, pH 7.4, 200 mm choline chloride, 10 mm NaCl, 1 mm DDM) using size exclusion chromatography (Superdex 200 10/300 GL). 0.2 μm protein was incubated with a range of l-[3H]Asp concentrations (made up in the same buffer) for 2 h at room temperature. Binding was quenched, and protein was precipitated by addition of ice-cold 50% ammonium sulfate. Precipitated protein was applied to a nitrocellulose filter over a vacuum manifold and washed with 2 ml of 50% ammonium sulfate. The filters were dissolved in 3 ml of FilterCount liquid scintillation mixture (PerkinElmer Life Sciences), and radioactivity was counted using TriLux beta counter (PerkinElmer Life Sciences). Background binding of radiolabeled substrate was measured by performing the same experiment in the absence of protein. Binding curves are fit to a single site saturation model as shown in Equation 1,

equation image

Chemical Cross-linking

Protein was cross-linked with 1,1-methanediyl bismethanethiosulfonate (MTS-1-MTS, Toronto Research Chemicals) by first exchanging the protein into buffer containing 20 mm Tris/HEPES, pH 7.4, 5 mm EDT, and 2 mm DDM and then, unless stated otherwise, incubating a 10 μm protein solution with 50 μm cross-linker (dissolved DMSO). Uncross-linked controls were treated in the same way but with an equivalent volume of DMSO instead of MTS-1-MTS. The cross-linking reaction was incubated at 37 °C for 30 min and quenched by addition of 100 mm S-methyl methanethiosulfonate (MMTS, Sigma). The cross-linking time courses were performed at room temperature. Cross-linking time course data were fit to a single exponential model described by Equation 2,

equation image

where Y0 is the Y value at time 0; a is the amplitude of the curve, and k is the rate constant.

We first set out to explore the effects of 3L4 cleavage on protein conformational sampling by using Hg2+-based cross-linking, which is a well established method used successfully with GltPh (8, 9, 22). However, not only are false-positives an issue with Hg2+ cross-linking, wherein Hg2+-induced protein band shifts are observed when no cross-link is formed (8), but it is also difficult to quench the Hg2+ cross-linking reaction with commonly used quenching compounds, such as N-ethylmaleimide or MMTS. In the absence of a quenching reagent, when attempting to cross-link cleaved GltPh in detergent solution, we observed protein bands on SDS-polyacrylamide gels corresponding to cross-link formation between intra-protein fragments and also, surprisingly, inter-subunit fragments. We reasoned that unwanted cross-linking was occurring between unreacted cysteines and residual Hg2+ ions in the quasi-denatured environment of the SDS-polyacrylamide gel or sample buffer. This led to difficulties in differentiating genuine intramolecular cross-link products from intact protein and cross-linking artifacts. We therefore switched to using the homobifunctional thiol-reactive reagent, MTS-1-MTS (linker length ~5 Å), which we could effectively and rapidly quench with an excess of MMTS. Indeed, pre-treatment of detergent-solubilized GltPhXaC2 with MMTS prevented any cross-linking from taking place between the cysteines introduced at positions 55 and 364 even in intact protein.


Densitometric SDS-PAGE band analysis was performed using Alphaview software (Cell Biosciences). Each protein band was selected using identically sized boxes, and background values were obtained by selecting an identically sized box from a blank region of the gel directly below the band. Values were normalized to a control protein band of known amount.


Cleaving 3L4 Does Not Prevent GltPh from Sampling the Inward-facing Conformation

The observed reduction in transport activity by GltPh cleaved at residue 125 in the 3L4 may be due to a decrease in the protein's ability to sample particular states in the transport cycle, to changes in its ability to bind substrate or Na+, to changes in transition rates between two or more cycle states, or a combination thereof. We sought here to distinguish among these possibilities.

The transition of the GltPh transport domain between the outward- and inward-facing conformations is a major conformational rearrangement required for alternating access in this protein (9). To determine whether cleaving 3L4 restricts GltPh's access to one key state, the IFS, we introduced cysteines at positions known to form cross-links only in that state (9). If such cross-links form effectively after cleaving 3L4, GltPh must be able to sample the inward-facing conformation despite loop scission. Using a gel-based cross-linking assay, we monitored IFS formation in a purified, detergent-solubilized GltPh by introducing cysteines at positions 55 and 364 into a Cys-less background with a Factor X site at residue 125 (from now on referred to as GltPhXaC2, see Fig. 1A). Cysteines at these positions were first shown to form a disulfide bond during an electrophysiological characterization of EAAT1 (23). Subsequently, an x-ray structure of the cross-linked form of the equivalent GltPh mutant showed that cysteines in these positions are only in close proximity in the IFS (IFS Cα-Cα distance = 7.3 Å, OFS Cα-Cα distance = 27.6 Å) (9). Furthermore, stabilizing the IFS of GltPh by cross-linking residues 55 and 364 increases the protein's electrophoretic mobility, making it easily discernible from noncross-linked protein on a polyacrylamide gel (9). Here, cross-linking was performed in the absence of substrate, so the inward-facing state stabilized will be predominantly empty transporter (Fig. 1B, black box). Initial attempts to cross-link cleaved GltPhXaC2 with Hg2+ were complicated by extraneous reactions with the metal (see “Experimental Procedures”), so we developed an alternative approach based on the homobifunctional thiol-reactive reagent, MTS-1-MTS (linker length ~5 Å).

In the absence of Factor X treatment, the predominant protein band is a full-length and noncross-linked GltPhXaC2 (Fig. 1C, lane 1). A small population of cross-linked protein was also apparent, caused by oxidative disulfide formation during the 24-h incubation, a fact confirmed by the disappearance of this band after reduction with β-mercaptoethanol (β-ME) (Fig. 1C, lane 2). Treatment of GltPhXaC2 with Factor X produced two fragments (N- and C-terminal fragments) with no full-length protein remaining (Fig. 1C, lane 3). Minimal changes in electrophoretic migration of the two fragments upon reduction with β-ME indicate that the protein band positions are not caused by aberrant cross-linking events (Fig. 1C, lane 4). We observed small cross-link-independent differences in all protein band migration profiles in the presence of β-ME. Treating detergent-solubilized GltPhXaC2 with MTS-1-MTS alone led to increased electrophoretic mobility, indicative of IFS cross-link formation, and it was fully reversible with β-ME treatment (Fig. 1C, lanes 5 and 6). Cleaving GltPhXaC2 produces only N- and C-terminal fragments; however, if the fully cleaved protein is then treated with MTS-1-MTS, a third higher molecular weight protein band was also apparent, which is the product of cross-linking the N- and C-terminal fragments (Fig. 1C, lane 7). We confirmed that this band is formed by cross-linking between the proteolytic fragments because, upon reduction, we observed disappearance of the high molecular weight band and an intensification of the N- and C-terminal fragments (Fig. 1C, lane 8). Mutants containing the Factor X site and the single cysteine substitutions did not form this cross-linked band, indicating that both cysteines in the engineered cross-linking pair are required and that intermolecular cross-linking is not responsible (data not shown). This result demonstrates that, despite lacking an intact 3L4, GltPh is still able to sample the inward-facing conformation in detergent solution. In a related assay, where GltPhXaC2 is first locked into the IFS by treatment with MTS-1-MTS and then digested with Factor X, we observe full cleavage of 3L4, indicating that 3L4 is accessible to protease in the inward-facing conformation (data not shown).

To complement this work, we also made several attempts to stabilize the OFS using engineered cysteines; K55C/G280C, V51C/T275C, L212C/V274C, V216C/A391C, Q220C/I389C, V58C/P283C, and L66C/S300C. For all pairs attempted, the introduced cysteine pairs either did not cross-link using MTS-1-MTS (however, one of these examples, L66C/S300C, does cross-link robustly with Hg2+; its structure has been published recently (22)) or a disulfide would form during purification despite efforts to prevent it. These disulfide bonds could only be reduced under harsh conditions that would render the protein inactive.

Cleaved GltPh Has Na+-driven l-Asp Transport Activity

Having demonstrated that cleaving 3L4 does not prevent GltPh from accessing at least one conformation essential to the transport cycle, we reassessed the transport capabilities of cleaved GltPh. Following incubation of purified wild-type GltPh (GltPhWT) and GltPhXa (GltPh containing a Factor X recognition site at residue 125) in the presence and absence of Factor X, we reconstituted the treated proteins into liposomes using an optimized protocol (see “Experimental Procedures”). This protocol increased the substrate uptake ~5-fold, and thereby permitted detection of transport activity in the Factor Xa-cut GltPhXa, activity we could not detect with our previous methods (20). SDS-PAGE analysis of the proteins prior to reconstitution revealed that treatment of GltPhXa with Factor X resulted in complete digestion, but under identical conditions, GltPhWT remained intact (Fig. 2B). We monitored initial rates of l-[3H]Asp transport into proteoliposomes containing cleaved GltPh in the presence of an inwardly directed sodium gradient and, contrary to the negligible activity we previously reported, we observed reduced but still easily detectable activity (~30% compared with wild type). There were no apparent effects on the activity of GltPhWT after treatment with Factor X (Fig. 2A). Uncut GltPhXa has lower activity (~70%) than GltPhWT, which is likely due to the effects of the amino acid substitutions in 3L4 required to introduce the Factor X recognition site and, as demonstrated by the SDS-PAGE analysis, not from cleavage of the protein during expression and purification (Fig. 2B).

Reconstituted GltPh remains active after 3L4 cleavage. A, Na+-driven initial transport rates of l-[3H]Asp into proteoliposomes containing GltPhWT and GltPhXa reconstituted after incubation at 37 °C for 24 h in the presence (+) and absence (−) ...

The ability to support the transport of l-Asp, albeit with decreased efficacy, clearly demonstrates that even with a fully cleaved 3L4, GltPh can sample all the conformations necessary for transport. The reduced transport rates must therefore stem from either altered thermodynamic properties of one or more states in the cycle or from altered kinetic properties of one or more transitions in the cycle. We sought to establish which part of the transport cycle is compromised upon 3L4 cleavage by systematically isolating steps and transitions of the cycle and observing the impact of 3L4 cleavage at each stage.

Cleavage of 3L4 Minimally Affects Substrate Interaction

Closure of HP2, the outer hairpin, is thought to be an essential step in forming the GltPh substrate-binding site and allowing translocation of the transport domain. Given that 3L4 directly overlies the HP2 hairpin, we considered the possibility that the loop stabilizes the open state of the hairpin, thereby influencing substrate and Na+ binding (7, 9). If true, this hypothesis predicts that cleavage of 3L4 would substantially affect substrate binding. We tested this model by deriving the kinetic parameters of transport (Vmax and Km, see Table 1) using functional protein reconstituted into lipid vesicles. The l-Asp dose response reveals a modest decrease in the Km value of cleaved protein (69.5 ± 14.1 nm compared with 129.5 ± 16.8 nm for GltPhWT, see Fig. 3A and Table 1) and a large decrease in the Vmax value (9.2 ± 0.7 nmol/mg/min compared with 42.7 ± 4.5 nmol/mg/min for GltPhWT, see Fig. 3A and Table 1). We observed the same effects of cleaving 3L4 on the Na+ dependence of transport as follows: minimal difference to the Km values and a large decrease in the Vmax (Fig. 3B). As expected, treatment with Factor X had no effect on the Km or Vmax values for either l-Asp or Na+ of GltPhWT (Fig. 3, A and B, and Table 1). GltPhXa, in the absence of Factor X treatment, exhibits a lower Km value compared with wild type; this is likely due to the 4-amino acid substitution made to create the Factor X site in 3L4 (Table 1) (20).

Effects of cleaving 3L4 on the binding affinity kinetic parameters of transport
Substrate dependence of transport and substrate binding activity of cleaved and intact GltPh. Rate of l-[3H]Asp transport into proteoliposomes containing GltPhWT (circles) and GltPhXa (squares) reconstituted after incubation at 37 °C for 24 h ...

These data reveal that cleaving 3L4 does not substantially affect the Km value of GltPh for either l-Asp or Na+. If 3L4 cleavage had a major impact on substrate binding, KD, we would expect this to be reflected in the Km. The preservation of Km therefore indicates that the substrate binding/unbinding events during the transport cycle are at most minimally affected by 3L4 scission (Fig. 3B, inset, steps 1 and 3).

To corroborate these findings, we directly measured the binding of l-Asp to detergent-solubilized protein and calculated the dissociation constants (KD) for cleaved and intact GltPhXa. Attempts were made to assess l-Asp binding using both isothermal titration calorimetry, a technique recently used to great effect with GltPh (22), and equilibrium dialysis. Both methods proved unsuitable for different technical reasons; the former, due to the large amount of cleaved protein required (the amount of Factor X protease required being the limiting factor), and the latter, due to the inconsistent data presumably caused by the substrate interacting with the dialysis membrane. Ultimately, data obtained using a filter binding assay revealed robust aspartate binding by both intact and cleaved GltPhXa (Fig. 3C). We observed no substantial difference in the KD value between intact and cleaved protein (4.0 ± 0.1 and 1.4 ± 0.3 μm, respectively) indicating that substrate binding is essentially preserved after 3L4 loop scission. Using this method, we measure a KD of 1.0 ± 0.3 μm for GltPhWT (a value in good agreement with the GltPhWT KD obtained using isothermal titration calorimetry under similar conditions (22)) revealing that introduction of the Factor X site into the 3L4 loop of GltPh results in a slight decrease in affinity, a decrease that is reversed upon cleavage of the loop (Fig. 3C and Table 1). Thus, the observed decrease in transport activity is not a consequence of decreased affinity of binding rate but is due to a lower transport turnover rate, highlighting the possibility that cleaving 3L4 impedes other steps in the transport cycle.

Activation Energy of Transport Is Increased When 3L4 Is Cleaved

The activation energy, Ea, of a process reflects the relative height of the energetic barrier that must be hurdled for that process to occur. If the effects of 3L4 cleavage are due to alterations in a significant energy barrier in one of the rate-limiting transport cycle reactions, then we would expect cleavage to cause changes in the Ea of transport. These changes, in turn, should be reflected in the temperature dependence of transport.

Over a temperature range of 3–40 °C, we observed an ~16- and ~64-fold increase in the initial rates of l-[3H]Asp transport by intact and cleaved GltPhXa, respectively (Fig. 4A). Analyses of these data with an Arrhenius plot revealed a clear temperature dependence for the transport rate and corresponds to an Ea of 56.6 kJ·mol−1 and a temperature coefficient (Q10) of 2.13 for intact GltPhXa (Fig. 4B). The Q10 value and Ea for cleaved GltPhXa are ~1.5-fold higher than intact mutant (3.1 and 83.7 kJ·mol−1, respectively) indicating a higher energy barrier to at least one step in the transport cycle. The activation energy values are composites of the temperature dependence of various conformational transition rates during the transport cycle, but combined with our evidence that the binding reactions are minimally affected by 3L4 cleavage, these data point to other steps in the cycle, namely the closing/opening and translocation reactions of loaded and unloaded transport domains. Because our current experimental methods do not have the resolution to distinguish among these steps, we will henceforth collectively refer to them as the “transfer steps” because together they transfer the accessible substrate-binding sites from one face of the membrane to the other. These steps together compose step 2 (the loaded transfer) for the substrate-loaded transporter and step 4 (the apo-transfer) for the empty protein in our simplified kinetic scheme (Fig. 1B).

Temperature dependence of transport by cleaved and intact GltPh. A, effect of temperature on Na+-driven transport of l-[3H]Asp into empty liposomes (closed diamonds) or proteoliposomes containing GltPhXa reconstituted after incubation at 37 °C ...

Cleaving 3L4 Results in Severely Diminished Substrate Exchange

Thus, the transfer reactions are groups of conformational changes that alternately expose the substrate-binding site from one side of the membrane to the other; the loaded transfer step can be isolated from net transport by monitoring protein-facilitated exchange of substrate across the membrane. In an exchange experiment, equimolar concentrations of Na+ and l-Asp are introduced on either side of the membrane and then substrate is exchanged between the external and internal solutions at equilibrium as the substrate-binding site stochastically samples both sides of the membrane (24). By adding a small amount of l-[3H]Asp to the external solution, exchange was measured by monitoring l-[3H]Asp accumulation in the lumen of the proteoliposome. Despite several efforts to apply this method to GltPh-containing proteoliposomes, we could not measure appreciable radiolabel accumulation. However, we overcame this problem using a solute counterflow assay; here, proteoliposomes are loaded with excess unlabeled substrate (1 mm) and diluted into an external solution containing a trace amount of radiolabeled substrate (100 nm). Here, as in exchange mode, the alternating exposure of the substrate-binding site to both sides of the membrane will initially result in exchange of unlabeled substrate in the proteoliposome lumen for radiolabeled substrate in the external solution (Fig. 5, inset, steps 1–3). In counterflow, however, the relative concentration of radiolabeled and unlabeled substrate in the proteoliposome lumen essentially eliminates the likelihood of the accumulated radiolabeled substrate from rebinding and exiting back into the external solution. At first, this results in uptake of radiolabel by a process identical to exchange. Eventually, however, the accumulation of radiolabel in the proteoliposome lumen peaks, and the accumulated substrate effluxes from the proteoliposomes until the outwardly directed substrate gradient is dissipated (25). If the turnover rate of the transporter is slow, as it is for GltPh, then substrate exchange can be monitored separately from the efflux portion of counterflow.

Effects of cleaved 3L4 on the IFS-OFS transition. Rate of l-[3H]Asp accumulation in proteoliposomes containing GltPhXa reconstituted after incubation at 37 °C for 24 h in the presence (open symbols) and absence (closed symbols) of Factor X. Counterflow ...

Under these experimental conditions, we observe robust accumulation of l-[3H]Asp in proteoliposomes containing GltPhWT or intact GltPhXa as a function of time (Fig. 5). In contrast, we observed very slow accumulation of l-[3H]Asp in proteoliposomes containing cleaved GltPhXa; i.e. ~8-fold lower accumulation after 10 min compared with proteoliposomes containing intact GltPhXa (Fig. 5). Note that we do not continue these experiments long enough to observe the falling phase of the counterflow reaction. This experiment isolates substrate binding/unbinding events (Fig. 5, inset, steps 1 and 3) and the transfer of the substrate-loaded transport domain (Fig. 5, inset, step 2) from the rest of the transport cycle. Having already demonstrated that 3L4 cleavage causes minimal perturbation of substrate interaction, this result shows that loop scission substantially attenuates the substrate-loaded transfer reaction.

Efficient Transition between Substrate-loaded OFS and IFS Depends on an Intact 3L4

The counterflow experiments implicate 3L4 in the loaded transfer reaction but provide no information on whether 3L4 scission affects the equivalent transition of the apo and substrate-free transport domain (Fig. 5, inset, step 4). We therefore sought to compare the effects of loop scission on the transfer of the empty transport domain with those of the cleavage on the fully loaded form. Because transport measurements will not report on isolated transitions of substrate-free forms of the protein, we measured the effects of loop cleavage on the empty (Fig. 6C, left panel, step 4) and substrate-loaded (Fig. 6C, right panel, step 2) equilibria separately by monitoring the rate of IFS cross-link formation in the absence or presence of saturating substrate concentration, respectively. If the energetics of the transfer reactions are affected then the population of the cross-link-competent, inward-facing state will be altered and will be reflected as a change in the cross-linking rate.

Effects of cleaving 3L4 on the rate of IFS cross-linking. MTS-1-MTS cross-linking time course of cleaved and intact GltPhXa in the absence (left panel) and presence of 1 mm l-Asp and 100 mm NaCl (right panel). A, representative Coomassie-stained SDS-PAGE ...

We quantified the rate of IFS cross-link formation of cleaved and intact GltPhXa in the presence and absence of substrate using SDS-PAGE and densitometric analysis (Fig. 6, A and B). IFS cross-link formation was determined for both intact and cleaved protein by quantifying the intensity of the cross-linked band (labeled CL in Fig. 6A). For intact protein, the cross-linked band is reflected in a shift of the full-length protein band toward faster electrophoretic migration; for cleaved protein, a single cross-linked band is formed by the cross-linking of the two proteolytic fragments (e.g. Fig. 1C, lane 7). In the absence of substrate, we observed rapid cross-link formation for both intact and cleaved protein. Cleaved protein cross-links with a slightly faster rate than intact protein (rate constants of 1.4 and 0.78 min−1, respectively), although it reaches a lower absolute level of cross-linking (75% compared with ~100% for intact protein, Fig. 6, A and B, left panel). Under these conditions, we predominantly monitored cross-link formation of empty transporter in equilibrium between the OFS and IFS (Fig. 6C, left panel, black box). These results suggest that cleaving 3L4 has little effect on the equilibrium of empty GltPh between IFS and OFS (the apo-transfer reaction, Fig. 6C, left panel, step 4). This observation is strikingly different from the cross-linking behavior in the presence of saturating concentrations of both substrates. Here, although the rate of IFS cross-link formation for intact GltPh was similar to the cross-linking rate without substrate (0.81 min−1), the cross-linking is slowed to an immeasurable rate in the cleaved protein, with no more than 3% cross-linking over the 10-min course of the experiment. (Fig. 6, A and B, right panel). These results indicate that cleaving 3L4 results in lower occupancy in the cross-link-competent, inward-facing conformation when in the presence of substrate than in the apo-form of the protein. The greatly diminished cross-linking rate for cleaved GltPh demonstrates that loop scission specifically impedes the substrate-loaded transport domain from accessing the cross-link-competent IFS (Fig. 6C, right panel, step 2).

Curiously, during this experiment we observed that cross-linking of intact protein in the presence of substrate (Fig. 6B, left panel, closed squares) does not reach completion. This result suggests that the presence of substrate prevents a population of the GltPh (40%) from accessing the inward-facing cross-link-competent state; an unexpected result considering the irreversible nature of the cross-linking reaction. An alternative hypothesis is that the presence of substrate may make one or both of the cysteine residues more accessible to reaction with the cross-linking reagent. If this is the case, and if the rate of this reaction exceeds the rate of entry into the cross-link-competent state (OFS-IFS transition), each cysteine (Cys-55 and Cys-364) may react with different MTS-1-MTS molecules, thus preventing cross-link formation between the two cysteines via a single MTS-1-MTS molecule. We investigated whether this was the case by measuring cross-linking rates under conditions that would slow down the rate of the MTS reaction while leaving the rate of conformational change unaffected. Two parameters were varied that might result in the separation of these two events as follows: concentration of MTS-1-MTS and the pH of the reaction. In the absence of substrate, decreasing the concentration of cross-linker results in a decreased rate of cross-link formation, but the absolute amount of cross-link formation remains essentially the same (Fig. 7A). In the presence of substrate, decreased cross-linker concentration also results in a lower cross-linking rate; however, the absolute amount of cross-linking is greater when lower concentrations are used (Fig. 7B). This demonstrates that when the cross-linking rate is slower, more cross-linking can occur, which we interpret to be due to the protein accessing the cross-link-competent state before the cysteines react with one MTS-1-MTS each.

Effects of cross-linker concentration on the rate and absolute amount of cross-linking. SDS-PAGE (left) and densitometric analysis (right) of the MTS-1-MTS cross-linking rate in the absence (A) and presence (B) of saturating substrate concentrations upon ...

MTS reagents react predominantly with the ionized thiolate form of cysteine, which is more abundant at higher pH values, and therefore decreasing the pH of the reaction should decrease the rate of cross-linking. Conveniently, the transport rate of GltPh remains constant over a wide range of pH values indicating that transport, and any associated conformational shift, is insensitive to pH change (11). Cross-linking time courses were performed in the presence and absence of substrate at pH 5, 7, or 9. In the absence of substrate, decreasing the pH of the reaction decreased the rate of cross-linking; however, the absolute amount of cross-linking was the same regardless of the pH (data not shown). In the presence of substrate, decreasing the pH resulted in a lower cross-linking rate, but it resulted in a higher absolute amount of cross-linking compared with the cross-linking performed at higher pH values (data not shown). Together, these findings strongly suggest that the incomplete cross-linking we observe in our experiments is due to reactions of the two cysteines with separate MTS-1-MTS molecules. This phenomenon results in competition between the reaction of interest, cross-linking the cysteines together with one MTS-1-MTS molecule, and a side reaction, where each exposed cysteine reacts with a separate MTS-1-MTS molecule, preventing cross-link formation. However, the cross-linking rates themselves, which are the measurement of interest, are not compromised by the side reaction.


Here, we explored the mechanism by which the 3L4 influences the transport cycle in GltPh, using a combination of 3L4 proteolytic cleavage, chemical cross-linking, and transport measurements to specifically probe major components of the transport cycle, distinguishing substrate binding, loaded transfer, and apo-transfer reactions. In the context of a simplified kinetic scheme, which nonetheless captures the essential features of transport, we find strong evidence that the basic binding/unbinding reactions with substrate and Na+ are minimally affected by cutting 3L4 and, surprisingly, that the transfer of the empty transport domain is also preserved. Indeed, our experiments point to the loaded transfer, which includes opening and closing steps and the major translocation of the fully loaded and occluded transport domain across the membrane as the locus affected by cutting 3L4, primarily through effects on the activation energy of translocation. This finding implies that the structure of the unloaded transport domain is significantly different from that of the loaded domain, an idea strongly supported by a recent structure of an apo-form of a GltPh homolog (19).

The simplified model we have focused on to this point (Fig. 1B) distinguishes steps that can be isolated using our functional experiments. Clearly however, each of these reactions includes multiple substeps that we cannot identify functionally. By lumping the binding reactions of l-Asp and Na+, our kinetic scheme captures the general features of the binding portions of the transport cycle without requiring a specific binding order. Clearly, a more detailed model would include separate binding steps for l-Asp and Na+, ideally in a particular order (26), see Fig. 8 (beige reactions). But by working at zero or saturating substrate/Na+, we can safely ignore these details.

Model of transport modulation by 3L4. Schematic depicting conformational changes and predicted modulation of interaction between the transport domain (blue domain), the trimerization domain (gray domain), and 3L4 (black line). The simple model used to ...

As we have discussed, the transfer reaction must include multiple substates (8) as shown in the blue reactions in Fig. 8. The transfer steps in our model (Fig. 8, steps 2 and 4) each include three substeps as follows: between outward-open and outward-occluded, between outward-occluded and inward-occluded (the piston movement), and between inward-occluded and inward-open, as indicated in Fig. 8. At the level of our experiments, however, these detailed reactions would be difficult or impossible to isolate; our results do not distinguish which one (or more) of these substeps is affected by 3L4 cleavage in the substrate-loaded form of the transport domain. Our findings do, importantly, clearly and definitively distinguish between the behavior of the apo-transport domain and the loaded domain for the overall transition that captures these three experimentally indistinguishable substeps, with only the loaded domain affected by 3L4 cleavage (Fig. 8, blue shading).

Because of the position of 3L4, directly overlying the HP2 hairpin, an attractive proposition for its role is to stabilize one or more states of the hairpin, thereby modulating the binding of protein to substrate. Because opening of HP2, as observed in the l-Asp- and dl-threo-β-benzyloxyaspartic acid-bound structures, may bring it into more intimate contact with 3L4, we considered the possibility that 3L4 could be stabilizing that state, which would in turn affect the binding sites of both substrate and inhibitor. However, we eliminated this possibility after measuring the kinetic parameters for cleaved and intact GltPh (Fig. 3). Measurements of both Km and KD suggest that 3L4 cleavage has minimal effects on the substrate binding rates and affinities. Our results therefore focus attention on the kinetic properties of the transfer reactions, showing that the activation energy barrier for one part of this reaction is raised by 3L4 cleavage.

The strong temperature dependence of active transport reflects all the temperature-dependent reactions that occur during the transport process, including substrate binding and conformational changes. In the GltPh homolog EAAC1, the binding of substrate is associated with a low energy of activation and is diffusion-controlled; binding of substrate and any associated conformational changes do not significantly contribute to the temperature dependence of transport (27). Additionally, the Km value of wild-type GltPh for Na+ is stable between 30 and 40 °C, despite a large difference in the maximum transport rate (11). Together, these results suggest, at least for Na+, that the substrate binding event for GltPh is relatively temperature independent and support the conclusion that the difference in the temperature dependence between cleaved and intact GltPhXa primarily reflect the isolated transfer reactions.

What is the structural basis of transport modulation by 3L4? Cysteine-scanning mutagenesis of 3L4 revealed that many single amino acid substitutions result in altered transport activities (17), hinting that specific interactions between residues in 3L4 and another part of the protein are important for transport. Results reported here suggest a model in which the intact 3L4 interacts specifically with the loaded transport domain, thereby stabilizing a specific transition state in the translocation process (Fig. 8), a model supported by the protection of the loop from proteolysis in the presence of substrate (20). We speculate, based on the location of 3L4, that this stabilization might be mediated by interactions between 3L4 and HP2, which directly underlies the loop in the OFS structure. In order for 3L4 to discriminate between substrate-loaded and empty transport domain, as is demonstrated by our data, the transport domain must have an appreciably different form in the presence and absence of substrate. This hypothesis is supported by a newly published structure of a GltPh homolog in the apo-form, which shows subtle but clear changes in the disposition of HP2 (19). This implies a kind of asymmetry in the transport cycle, with the structure of the translocating unloaded domain detectably (to 3L4) different from that of the loaded domain, a possibility not captured in previous models of transport, which assume similar closed forms of the protein for both translocation steps (e.g. steps 2 and 4 in Fig. 1B). These observations offer the possibility of additional protein conformations in these transporters that might serve as targets for state-specific or subtype-specific drugs to modulate their function.


We thank Kenton Swartz and Jeff Diamond for critically reading the manuscript.

*This work was supported by the Intramural Research Program of the National Institutes of Health, NINDS.

2The abbreviations used are:

excitatory amino acid transporter
1,1-methanediyl bismethanethiosulfonate
n-dodecyl β-d-maltopyranoside
outward-facing state
inward-facing state.


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