JOURNAL OF BACTERIOLOGY, Apr. 2009, p. 2122–2132 Vol. 191, No. 70021-9193/09/$08.00�0 doi:10.1128/JB.00830-08Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Structural and Functional Importance of Transmembrane Domain 3(TM3) in the Aspartate:Alanine Antiporter AspT: Topology and

Function of the Residues of TM3 and Oligomerization of AspT�

Kei Nanatani,1† Peter C. Maloney,2 and Keietsu Abe1*Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan,1

and Department of Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland 212052

Received 13 June 2008/Accepted 21 January 2009

AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, a membrane protein of 543 amino acidswith 10 putative transmembrane (TM) helices, is the prototype of the aspartate:alanine exchanger (AAE)family of transporters. Because TM3 (isoleucine 64 to methionine 85) has many amino acid residues that areconserved among members of the AAE family and because TM3 contains two charged residues and four polarresidues, it is thought to be located near (or to form part of) the substrate translocation pathway that includesthe binding site for the substrates. To elucidate the role of TM3 in the transport process, we carried outcysteine-scanning mutagenesis. The substitutions of tyrosine 75 and serine 84 had the strongest inhibitoryeffects on transport (initial rates of L-aspartate transport were below 15% of the rate for cysteine-less AspT).Considerable but less-marked effects were observed upon the replacement of methionine 70, phenylalanine 71,glycine 74, arginine 76, serine 83, and methionine 85 (initial rates between 15% and 30% of the rate forcysteine-less AspT). Introduced cysteine residues at the cytoplasmic half of TM3 could be labeled with Oregongreen maleimide (OGM), whereas cysteines close to the periplasmic half (residues 64 to 75) were not labeled.These results suggest that TM3 has a hydrophobic core on the periplasmic half and that hydrophilic residueson the cytoplasmic half of TM3 participate in the formation of an aqueous cavity in membranes. Furthermore,the presence of L-aspartate protected the cysteine introduced at glycine 62 against a reaction with OGM. Incontrast, L-aspartate stimulated the reactivity of the cysteine introduced at proline 79 with OGM. These resultsdemonstrate that TM3 undergoes L-aspartate-induced conformational alterations. In addition, nonreducingsodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses and a glutaraldehyde cross-linking assaysuggest that functional AspT forms homo-oligomers as a functional unit.

In some strains of the lactic acid bacterium Tetragenococcushalophilus, a proton motive force (PMF) is generated by thecombined action of an intracellular L-aspartate decarboxyl-ation reaction catalyzed by an L-aspartate-4-decarboxylase(AspD [EC 4.1.1.12]) and an electrogenic aspartate1�:alanine0

exchange reaction catalyzed by an aspartate:alanine antiporter(AspT [TC# 2.A.81.1.1]): L-aspartate (out) � L-alanine (in)3L-aspartate (in) � L-alanine (out). The PMF generated is suf-ficiently high to drive ATP synthesis via the bacterial FoF1

ATPase. This combination of PMF and ATP synthesis hasbeen proposed as a proton motive metabolic cycle, and theprototype model is found in Oxalobacter formigenes (3, 9, 30).Such decarboxylation reactions are thought to be advanta-geous for cells because the reactions generate metabolicenergy and regulate the intracellular pH. In previous worksusing proteoliposomes, we found that the aspartate:alanineexchange catalyzed by AspT is electrogenic (1, 2). The bio-chemical features of substrate transport by AspT indicate thatthe protein can be classified as a conventional secondary trans-port protein and that it is an electrogenic antiporter similar to

the prototype precursor:product exchanger OxlT, an oxalate:formate antiporter that is a member of the major facilitatorsuperfamily, from O. formigenes (3, 9, 30, 39). AspT belongs tothe newly classified aspartate:alanine exchanger (AAE) family(TC# 2.A.81) of transporters in the transporter classificationsystem developed by Saier et al. (http://www.tcdb.org/index.php). Recently, the results of a BLAST (http://www.ncbi.nlm.nih.gov/BLAST/; 7) search of the nucleotide sequence of theaspT gene and the amino acid sequence of the AspT proteinagainst current nucleotide and protein databases have sug-gested that AAE family transporters are conserved in manybacterial species (10, 19). The putative broad distribution ofAspT orthologues and paralogues in bacteria suggests that anadditional biochemical study of AspT can be a valuable part ofthe ongoing investigation of membrane transport.

AspT is a membrane protein containing 543 amino acids(57.2 kDa). The membrane topology of AspT has been studiedby means of alkaline phosphatase and �-lactamase fusionmethods (33); it has also been studied by the substituted-cysteine accessibility method (SCAM) (6), which uses theimpermeant, fluorescent thiol-specific probe OGM and theimpermeant, nonfluorescent thiol-specific probe [2-(trimethyl-ammonium)ethyl]methanethiosulfonate bromide (34). Theseanalyses revealed that AspT has a unique topology: the proteinhas 10 transmembrane helices (TMs), a large hydrophilic cy-toplasmic loop (about 180 amino acids) between TM5 andTM6, and N and C termini located at the periplasm. TM3

* Corresponding author. Mailing address: Department of Molecularand Cell Biology, Graduate School of Agricultural Science, TohokuUniversity, Sendai 981-8555, Japan. Phone: 81-22-717-8777. Fax: 81-22-717-8778. E-mail: kabe@biochem.tohoku.ac.jp.

† Present address: Department of Physiology, Johns Hopkins Schoolof Medicine, Baltimore, MD 21205.

� Published ahead of print on 30 January 2009.

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contains amino acid residues that are well conserved amongmembers of the AAE family. Moreover, our topological anal-ysis indicated that there are isolated charged residues (aspar-tate 67 and arginine 76) in the middle of TM3. For the trans-porters of polar molecules such as aspartate, the substratetransport pathway can be expected to be enriched with resi-dues that are more hydrophilic than residues found elsewherein the TMs.

In the present study, we applied SCAM to the TM3 of AspTto further elucidate the role of TM3 in the transport process.An analysis of the effects of the amino acid substitutions ontransporter function identified amino acids that are crucial fortransport. Furthermore, our SCAM results suggest that TM3participates in the formation of a hydrophilic cleft in the mem-brane and implicate the TM in ligand-induced conformationalalterations. In addition, nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analyses ofpurified AspT showed that some single-cysteine variants formS-S-linked homodimers in membranes. We speculated thatAspT forms oligomers in the membrane and that the TM3s arelocated close to each other, as shown in the similar case of themultidrug exporter AcrB, in which the extramembrane centralpore �-helices of each AcrB protomer are close to each otherin the trimer formation (32). To confirm the homo-oligomerformation of AspT, we developed a solubilization and purifi-cation scheme using n-dodecyl-�-D-maltoside (DDM), and westudied the oligomerization of AspT by means of a glutaralde-hyde cross-linking assay.

MATERIALS AND METHODS

Chemicals, cells, and expression plasmids. L-[2,3-3H]aspartic acid (1.07 GBq/mmol) was purchased from Amersham-Pharmacia Biotech (Piscataway, NJ).1-O-n-Octyl-�-D-glucopyranoside (OG) and DDM were obtained from NacalaiTesque (Kyoto, Japan). Escherichia coli phospholipid was provided by AvantiPolar Lipids (Alabaster, AL) (8). OGM was purchased from Invitrogen Co.(Carlsbad, CA). Escherichia coli strain XL1-Blue harboring pMS421 (Spcr

LacIq)—referred to as strain XL3 (3)—was used for the expression of the aspoperon with pTrc99A (Amersham-Pharmacia Biotech).

Site-directed mutagenesis. Single-cysteine variants were constructed by theoligodeoxyribonucleotide-directed dual amber mutagenesis method (Takara Bio,Tokyo, Japan) (21). The pKF 19k/18k vector (Takara Bio) harboring the gene forcysteine-less AspT-(His)6 was used as a DNA template for the mutagenesismethod. DNA fragments encoding AspT in which a single cysteine had beenintroduced were ligated back into the corresponding site of the pBlue cysteine-less AspHis. DNA fragments encoding single-cysteine AspT-(His)6 were clonedinto pTrcAsp instead of wild-type AspT. The DNA sequences of all the mu-tagenized AspT proteins were verified by DNA sequence analysis, as describedpreviously (2).

Production of single-cysteine AspT-(His)6. A preculture of E. coli XL3 carry-ing pTrc single-cysteine AspT-His or pTrc99A was diluted 100-fold in freshLuria-Bertani (LB) medium containing 30 mM D-glucose, 30 �g/ml carbenicillin,and 30 �g/ml spectinomycin. These cells were grown for 2.5 h at 37°C withshaking to an optical density at 650 nm of 0.5 and were then diluted twofold infresh LB broth containing 30 mM D-glucose, 60 mM L-aspartate, and 1 mMpyridoxal 5�-phosphate. The cell suspensions were incubated statically for 1 h at37°C. Afterward, 200 �M (final concentration) isopropyl-�-D-thiogalactoside wasadded to each culture, and the static inductions of the AspT variants wereallowed to proceed for 12 h at 37°C.

Solubilization, reconstitution, and transport assay of AspT variants. Thepreparation of the AspT variant proteoliposomes was carried out as previouslydescribed (34). In brief, membrane ghosts were prepared by an osmotic shockprocedure (8). The membrane ghosts were solubilized with 1.25% (wt/vol) OG inthe presence of 0.4% (wt/vol) E. coli phospholipid, 100 mM KH2PO4 (pH 7), and20% glycerol (8). Control extracts were prepared in the same way but withoutadded protein. These solubilized membrane proteins were reconstituted in a finalvolume of 1 ml with 800 �l of detergent extracts (1.2 mg of protein) (or control

lipid extract), 130 �l of bath-sonicated liposomes (5.9 mg of E. coli phospho-lipid), and 18 �l of 15% OG, with the balance made up by 100 mM KH2PO4 (pH7). After incubation of the mixture for 20 min on ice, proteoliposomes (or controlliposomes) were formed at room temperature (R.T.) by rapid injection into 20 mlof a loading buffer containing 100 mM KH2PO4 (pH 7) and 100 mM L-aspartateas the potassium salt. The substrate-loaded proteoliposomes (or liposomes) werekept at R.T. for 20 min.

Unless otherwise noted, the initial rates of L-[2,3-3H]aspartate incorporationwere measured in duplicate at 25°C by means of a filtration assay (34, 45, 51).Proteoliposomes were applied directly to the center of a 0.22-�m-pore-sizeGSTF Millipore filter (Millipore Co., Billerica, MA) and washed twice with 5 mlof chilled assay buffer (100 mM KH2PO4 [pH 7], 100 mM K2SO4). Upon releaseof the vacuum, proteoliposomes were covered with preincubated assay buffercontaining 0.1 mM L-[2,3-3H]aspartate, and the reaction was terminated after 1min by filtration and washing. AspT function is usually reported as relativespecific activity by the normalization of observed rates to levels of AspT produc-tion as determined by immunoblot analysis (described below).

Immunoblot analysis. The detergent extracts of the membrane ghosts of eachof the single-cysteine variants and the cysteine-less parent were analyzed byreducing SDS-PAGE. For the SDS-PAGE, 45 �g of proteins was used, and afterelectrophoresis, the proteins were transferred to a polyvinylidene difluoridemembrane (Nippon Genetics, Tokyo, Japan) by semidry electrophoretic blotting(Bio-Rad Laboratories, Hercules, CA) and probed with an anti-AspT rabbitpolyclonal antibody (Operon Biotechnologies, Tokyo, Japan). Rabbits were in-jected with two different synthetic polypeptides (SKLPISDHLKTLYSNQ andNDVSERVGSDASPF) as antigens with adjuvant to elicit an immune responseto AspT peptides. AspT production was detected by chemiluminescence with aLAS-3000 imaging system (Fujifilm, Tokyo, Japan), and signals were quantifiedwith NIH Image software (v. 1.63). Antisera were used at the following dilutions:anti-AspT rabbit polyclonal antibody, 1:2,000, and anti-rabbit immunoglobulin Ggoat polyclonal antibody-horseradish peroxidase conjugate (StressGen Biore-agents Co., Victoria, Canada), 1:2,000. The production of each AspT variant wasnormalized to that of the cysteine-less parental control found on the same gel.

Site-directed fluorescence labeling. The exposure of TM3 positions to theaqueous environment (the extracellular medium or the cytosol) was assessed inthe single-cysteine variants. The membrane ghosts (prepared as described above)were resuspended in 20 mM potassium phosphate (pH 8) or 20 mM potassiumphosphate (pH 8) containing 100 mM L-aspartate and incubated for 20 min at25°C with 40 �M OGM, an impermeable thiol-active agent (50). The reactionwas quenched by the addition of 6 mM �-mercaptoethanol and three cycles ofwashing with distilled water. The protein was solubilized by resuspending themembrane vesicles in 1 ml of solubilization buffer (50 mM Tris-HCl [pH 7], 0.75mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 0.1% SDS). After themixture was incubated at 4°C for 2 h on a rotary platform shaker, the insolubledebris was removed by centrifugation at 4°C (17,500 � g for 30 min), and AspTwas purified in a one-step affinity procedure (17, 34). In brief, six-histidine-taggedAspT was precipitated with 50 �l of Ni-nitrilotriacetic acid (NTA) Superflowresin (Qiagen, Valencia, CA) by overnight batch incubation at 4°C on a rotaryplatform shaker. The resin, with bound AspT, was washed on ice with a total of3 ml of wash buffer (solubilization buffer supplemented with 200 mM sodiumfluoride and 25 mM imidazole). AspT was eluted by a brief centrifugation at 4°Cwith 60 �l of elution buffer (50 mM Tris-HCl [pH 7], 2% SDS, and 0.5 Mimidazole).

To label cysteines exposed at the extracellular surface, intact cells were har-vested by centrifugation (6,000 � g for 30 min) and suspended in buffer A (100mM K2SO4, 50 mM KH2PO4 [pH 8]), and the absorbance at 530 nm was adjustedto 8.5. OGM (40 �M final concentration) was added to 5 ml of the cell suspen-sion, and the mixture was incubated for 20 min at 25°C. The labeling reaction wasquenched by the addition of 6 mM (final concentration) �-mercaptoethanol. Thecells were collected immediately and washed three times with buffer B [100 mMK2SO4, 50 mM 3-(N-morpholino)propanesulfonic acid (pH 7) as the potassiumsalt]. The membrane ghosts were prepared from labeled cells, and these mem-branes served as the source of AspT for solubilization and purification as de-scribed above.

Detection of OGM-labeled protein. The protein was subjected to SDS-PAGEwith a 10% polyacrylamide gel matrix. For the SDS-PAGE, 10 �l of elutionsample was used, and after electrophoresis, the gel was rinsed briefly with adestaining solution (10% glacial acetic acid, 15% methanol). Fluorescence pro-files were recorded with a LAS-3000 imaging system. After the fluorescenceprofiles were recorded, the protein content of each lane was evaluated by stainingthe same gel with Coomassie brilliant blue (CBB).

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Expression, solubilization, and purification of wild-type AspT-His [AspT(WT)-His] for analysis of oligomerization. A preculture of E. coli XL3 carrying pTrcAspT(WT)-His was diluted 100-fold in fresh LB medium containing 30 mMD-glucose, 30 �g/ml carbenicillin, and 30 �g/ml spectinomycin. These cells weregrown for 2.5 h at 37°C with shaking to an optical density at 650 nm of 0.5 andwere then diluted twofold in fresh LB broth containing 30 mM D-glucose, 60 mML-aspartate, and 1 mM pyridoxal 5�-phosphate. Afterward, 200 �M (final con-centration) isopropyl-�-D-thiogalactoside was added to the cultures, and theinduction of AspT(WT)-His by static culture was allowed to proceed for 12 h at37°C. The membrane ghosts were prepared by an osmotic shock procedure (8).The cells harvested from each liter of culture solution were suspended in 7.5 mlof a lysis solution (500 �g/ml lysozyme [Seikagaku Co., Tokyo, Japan], 40 �g/mlDNase I [Sigma, St. Louis, MO], 10 mM Tris-HCl [pH 7.5], 1 mM phenylmeth-ylsulfonyl fluoride) and incubated at 37°C for 30 min. The cells were disrupted bya 10-fold dilution into 45 ml of iced distilled water. After the cells were disrupted,the cytoplasmic proteins released were removed by two cycles of washing withiced distilled water and centrifugation (44). The membrane ghosts were solubi-lized (8) at 4°C for 6 h with 1.5% (wt/vol) DDM in the presence of 200 mML-aspartate, 100 mM KH2PO4 (pH 7), and 20% glycerol. After centrifugation at12,000 � g for 60 min, the supernatant was incubated with a Ni-NTA affinitycolumn (375-�l bed volume for a 1-liter culture) at 4°C for 6 h. The column waswashed on ice with a total of 7.5 ml/1-liter culture of wash buffer (200 mML-aspartate and 20 mM KH2PO4 [pH 7], 20% glycerol, 0.05% DDM, and 25 mMimidazole). Then, AspT(WT)-His was eluted by a brief centrifugation in the coldwith elution buffer (200 mM L-aspartate and 20 mM KH2PO4 [pH 7], 20%glycerol, 0.05% DDM, and 0.5 M imidazole) at 375 �l/1 liter of culture.

Reconstitution and transport assay of purified AspT(WT)-His. The solubi-lized membrane proteins were reconstituted in a final volume of 1 ml with 800 �lof detergent extracts (10 �g of protein) (or control lipid extract), 130 �l ofbath-sonicated liposomes (5.9 mg of E. coli phospholipid), and 18 �l of 15% OG,with the balance made up by 100 mM KH2PO4 (pH 7). After incubation for 20min on ice, proteoliposomes (or control liposomes) were formed at R.T. by rapidinjection of the mixtures into 20 ml of a loading buffer containing 100 mMKH2PO4 (pH 7) and 100 mM L-aspartate as the potassium salt. The substrate-loaded proteoliposomes (or liposomes) were kept at R.T. for 20 min. To assay forL-aspartate transport by L-[2,3-3H]aspartate-loaded particles, proteoliposomeswere diluted 20-fold from the concentrated stock preparation into an appropri-ate volume of assay buffer (100 mM KH2PO4 [pH 7] and 100 mM K2SO4). After1 to 3 min of preincubation at 25°C, L-[2,3-3H]aspartate was added to a finalconcentration of 100 �M; at various times, 50- to 100-�l aliquots were removedfor membrane filtration (0.22-�m-pore-size GSTF Millipore filters). The mem-brane filters were followed by two washes with 5 ml of assay buffer (8).

Glutaraldehyde cross-linking. Aliquots (0.4 �g) of the purified AspT(WT)-His (0.01 mg/ml in wash buffer containing either 0.05% DDM or 1% SDS, forcross-linking in native or denaturing conditions, respectively) were subjected toin vitro cross-linking by incubation with 1 to 100 mM glutaraldehyde at 25°C for30 min. The reaction was terminated by the addition of gel sample buffercontaining 4% SDS, 125 mM Tris-HCl (pH 6.8), and 10% �-mercaptoethanol,and the samples were analyzed by SDS-PAGE (7.5% polyacrylamide gel matrix).The gels were silver stained and optically scanned using ImageJ (National Insti-tutes of Health [http://rsb.info.nih.gov/ij/]).

RESULTS

Transport activities of single-cysteine variants of TM3 in afunctional AspT. We performed a multiple alignment of 10AAE family transporters to identify conserved amino acids inthe AspT proteins. The alignment showed that TM3 has manyamino acid residues that are conserved among members of theAAE family (Fig. 1). To clarify the role of TM3 in L-aspartatetransport, we performed a complete cysteine-scanning mu-tagenesis of TM3. In the first step, each amino acid fromthreonine 59 to phenylalanine 88, including TM3 (isoleucine64 to methionine 85), was individually replaced with cysteine ina functional AspT molecule devoid of all three native cysteineresidues (AspT cysteine-less). The level of active transport wasmeasured by using L-aspartate-loaded proteoliposomes inwhich each variant of AspT was reconstituted. Because Abe etal. (2) demonstrated that E. coli crude membranes reconsti-

tuted in proteoliposomes possess background aspartate:aspar-tate self-exchange activities, we measured the background L-aspartate self-exchange activity of membranes prepared fromE. coli harboring the empty vector pTrc99A. We found that theresultant background L-aspartate self-exchange activity was11.7% of that of the AspT cysteine-less variant (Table 1).Given the background activity of E. coli membranes, the sub-stitutions of tyrosine 75 and serine 84 had the strongest inhib-itory effects on transport; the initial rates of L-aspartate trans-port were below 15% of the rate for cysteine-less AspT (Table1). Considerable but less-marked effects were observed uponthe replacement of methionine 70, phenylalanine 71, glycine74, arginine 76, serine 83, and methionine 85 (initial ratesbetween 15% and 30% of the rate for cysteine-less AspT). Incontrast, the replacement of amino acids in the periplasmichalf of TM3 (isoleucine 64 to phenylalanine 69) had little or noeffect on AspT function.

Definition of the hydrophobic core region and water-filledcavity of TM3. To obtain a comprehensive picture of the ac-cessibility of the cysteines at the various positions of TM3, weemployed a labeling approach specific for each artificially in-troduced cysteine. Randomly oriented membrane ghosts con-taining the corresponding single-cysteine AspT variants werelabeled with the hydrophilic fluorescent probe OGM. Studiesof OxlT have shown that cysteine residues exposed to theaqueous phase can be identified by their accessibility to OGM(18, 50, 51), which is known to be membrane impermeantunder the conditions used here (34, 50). After membrane

FIG. 1. Multiple sequence alignment of members of the AAE fam-ily of transporters. A multiple alignment was generated with ClustalW2(version 1.83) with sequences obtained from a BLASTP search (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) against AspT of T. halophilus(accession number Q8L3K8) at the European Bioinformatics Instituteserver (http://www.ebi.ac.uk/Tools/clustalw2/index.html) (35, 36). Thechosen matrix was BLOSUM; penalties were 10 (open gap), 0.05(extending gap), and 10 (gap distance). The resulting alignment wasoptically improved with the Boxshade 3.31 program (http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html); conserved residues arehighlighted in black (identical to consensus) or gray (similar to con-sensus). The term AspT refers to the homology with AspT of T.halophilus (Thal). The bacterial host strains and accession numbers forthe AspT homologs are as follows: Lactobacillus reuteri (Lreu),ABQ82551; Lactobacillus acidophilus (Laci), AAV43508; Parabacte-roides distasonis (Pdis), ABR42837; Ralstonia metallidurans (Rmet),ABF08864; Bordetella bronchiseptica (Bbro), CAE32035; Bordetellaparapertussis (Bpar), CAE37441; Francisella tularensis (Ftul), ABK89250;Bradyrhizobium japonicum (Bjap), BAC48740; and Comamonas testos-teroni (Ctes), BAC65228. Experimental evidence for aspartate:alanineantiporter activity exists only for T. halophilus and C. testosteroni.Numbers indicate the position in the primary sequence and refer to thefirst amino acid of the alignment.

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ghosts labeling, the AspT variants were solubilized from themembranes, purified by Ni-NTA affinity chromatography, andsubjected to SDS-PAGE. The fluorescence of each AspT vari-ant labeled with OGM was detected by the UV irradiation ofthe gels (Fig. 2A, bottom panel). The intensities of the fluo-rescence and CBB were normalized to the corresponding in-tensities of the F88C variant, whose mutation is located in theintracellular hydrophilic loop. The labeling efficiency of thecysteine in each variant was assessed as the ratio of the inten-sities of the fluorescent and CBB bands (Fig. 3A, black bars).

Despite the fact that amino acids isoleucine 64 to methio-nine 85 are predicted to form a membrane-spanning domain(TM3), cysteines placed at several positions within this regionwere modified by OGM (Fig. 2A, bottom panel). Introducedcysteine residues corresponding to the positions of glycine 78,serine 80, and serine 83 were particularly accessible (�0.8relative to phenylalanine 88) to OGM (Fig. 2A, bottom panel,and Fig. 3A, black bars). This region of the protein musttherefore be exposed to the aqueous environment. The inter-mediate accessibility (�0.8 but �0.3 relative to phenylalanine

88) was observed for the cysteine residues introduced in placeof arginine 76, proline 79, and methionine 85. A negativeresponse (�0.3 relative to phenylalanine 88) was found at the12 cysteines close to the periplasmic half of TM3 (from iso-leucine 64 to tyrosine 75), valine 77, phenylalanine 81, isoleu-cine 82, and serine 84 (Fig. 2A, bottom panel, and Fig. 3A,black bars). On the whole, positions in the C-terminal (cyto-plasmic) half of TM3 showed higher accessibility than posi-tions in the N-terminal (periplasmic) half of the TM. To studythe accessibility of introduced cysteine residues at the C-ter-minal (cytoplasmic) half of TM3 from the periplasmic side, weused whole-cell OGM labeling for six variants (G62C, D63C,G78C, S80C, S83C, and K87C) that showed high accessibilityto OGM in membrane ghost labeling (Fig. 2A, bottom panel,and Fig. 3A, black bars). G62C and D63C, which are predictedto be located at the periplasmic side, maintained their goodaccessibility to OGM in whole-cell labeling, whereas G78C,S80C, S83C, and K87C showed remarkable defects in theiraccessibility to OGM in whole-cell labeling (Fig. 2C).

Influence of ligand binding on cysteine accessibility. Tofurther explore the role of TM3 in AspT function, we exam-ined the influence of a native ligand (L-aspartate) on the ac-cessibility of introduced cysteine residues in single-cysteinevariants to OGM. Membrane ghosts containing the single-cysteine AspT variants were labeled after incubation with 100mM L-aspartate. Subsequently, the AspT variants were iso-lated, and fluorescence was detected as described above (Fig.2B, bottom panel). The analysis revealed four groups of single-cysteine AspT variants with the following characteristics (Fig.2A and B, bottom panels, and Fig. 3A). (i) Cysteines in thepositions of leucine 61, aspartic acid 63, arginine 76, glycine 78,serine 80, serine 83, methionine 85, lysine 86, lysine 87, andphenylalanine 88 were accessible to OGM (�0.3 relative tophenylalanine 88), and the labeling reaction was not markedlyinfluenced by the presence of L-aspartate. (ii) Cysteines intro-duced at threonine 59, from isoleucine 64 to tyrosine 75, or atvaline 77, phenylalanine 81, isoleucine 82, or serine 84 showedonly low reactivity toward OGM (�0.3 relative to phenylala-nine 88), and the addition of L-aspartate did not stimulatecysteine reactivity. (iii) The cysteine residue introduced at gly-cine 62 was labeled by OGM, and the labeling reaction wasinhibited by L-aspartate. (iv) L-Aspartate stimulated the reac-tivity of cysteine at proline 79. The observed substrate protec-tion can be explained by direct steric hindrance; by ligand-induced conformational alterations, which either bury thecorresponding residue within the protein or move it from anaqueous environment into an apolar environment; or by bothsteric hindrance and conformational alterations.

Oligomerization of purified AspT. Nonreducing SDS-PAGEanalysis indicated that 12 of the single-cysteine variants formedS-S-linked homodimers (�20% of purified single-cysteineAspT) in the native E. coli membrane (Fig. 2A, top panel, andFig. 3B, black bars). This result suggests that AspT may formhomo-oligomers in the membrane and that the TM3s of theindividual protomers are close to each other. To confirm thehomo-oligomer formation of AspT by means of a glutaralde-hyde cross-linking assay, we developed a solubilization andpurification scheme under DDM-solubilized conditions.

An AspT variant with a six-histidine tag inserted into thelarge hydrophilic loop, AspT(WT)-His (34), was expressed in

TABLE 1. Production levels and specific activities of single-cysteinevariants relative to those of cysteine-less AspT

Variant Production (%)a Sp act (%)b

—c — 11.7 1.24Cysteine-less 100.0 100.0T59C 111.0 1.0 110.0 21.3L60C 139.2 1.29 49.1 2.3L61C 154.2 � 0.35 121.6 18.3G62C 79.2 � 0.76 259.6 25.4D63C 136.0 0.92 75.2 4.04I64C 191.5 � 0.91 101.1 2.66F65C 56.9 � 2.04 50.1 2.91F66C 54.5 � 2.68 38.3 0.29D67C 89.3 1.8 45.5 3.46F68C 52.3 � 0.81 101.2 12.3F69C 48.4 � 2.04 59.0 2.99M70C 72.2 1.61 26.1 1.26F71C 51.7 0.53 27.8 0.71A72C 55.2 0.67 54.3 7.67I73C 63.2 1.51 37.3 7.55G74C 30.6 1.17 17.2 3.69Y75C 53.1 0.3 11.3 8.6R76C 24.9 � 0.95 22.9 6.3V77C 45.9 2.37 71.4 10.0G78C 27.8 4.38 28.1 1.72P79C 36.5 � 3.88 34.1 3.9S80C 64.6 2.45 70.2 3.76F81C 31.0 4.96 33.7 0.71I82C 42.2 � 4.4 65.6 � 5.58S83C 107.9 2.97 18.7 1.79S84C 101.1 2.42 8.7 1.51M85C 63.3 � 2.5 28.1 10.2K86C 75.8 1.6 40.6 6.53K87C 79.2 0.44 35.6 2.07F88C 144.3 5.82 14.8 1.41

a Production is given relative to that of the cysteine-less parent (mean standard deviation).

b Initial rates of L-2,3-3H�aspartate transport, normalized for the levels ofAspT production, are given relative to the rate for the cysteine-less parent, whoseactivity was 4.24 nmol min�1 mg�1 of protein.

c Membrane ghosts from control cells (without AspT expression) were usedfor control reconstitution and the transport assay. Data reflect mean values standard deviations found in three independent trials. For each single-cysteinevariant, an equal amount of protein was used for reconstitution in L-aspartate-loaded proteoliposomes.

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E. coli, solubilized in detergent (DDM), and purified by aconventional one-step procedure employing Ni-NTA chroma-tography (Fig. 4A). We observed a single band on an SDS-PAGE gel at a position lower than that expected from thepolypeptide sequence (57.2 kDa) of the AspT variant; similarresults have been observed for other membrane proteins (3,13). Then we reconstituted the purified AspT variant intoproteoliposomes and confirmed that it catalyzed the L-aspar-tate self-exchange reaction. The proteoliposomes containingthe purified AspT variant were loaded with 100 mM potassiumL-aspartate. Then the proteoliposomes were resuspended in

0.1 M potassium phosphate buffer (pH 7), and L-aspartateexchange reactions were started by the addition of 100 �M(final concentration) external L-[3H]aspartate. L-[3H]aspartatewas incorporated into proteoliposomes by L-aspartate self-ex-change. The steady-state incorporation of L-[3H]aspartate was ap-proximately 3,300 nmol/mg of protein (Fig. 4B). Moreover, accumu-lated L-[3H]aspartate was released by the addition of excessunlabeled L-aspartate, suggesting that we succeeded in purifying theAspT, while completely maintaining its transport activity.

To confirm the oligomer formation of the purified protein,we carried out a glutaraldehyde cross-linking assay. Directed at

FIG. 2. OGM binding to single-cysteine variants of TM3. The hydrophobic core of TM3 was defined experimentally by OGM labeling of theindicated single-cysteine variants spanning the entire transmembrane segment. (A and B) Membrane ghosts of each variant were exposed to OGMin the absence (A) or presence (B) of L-aspartate prior to protein solubilization, purification under denaturing conditions using solubilization with1% Triton X-100 and 0.1% SDS and elution with 2% SDS, and analysis using nonreducing SDS-PAGE (10% polyacrylamide gel matrix).(C) Whole-cell OGM labeling (34) was applied to six single-cysteine variants that showed high accessibility to OGM in membrane ghost labeling.E. coli cells that expressed each variant were exposed to OGM in the absence of L-aspartate. Purified proteins from OGM-exposed E. coli cellswere analyzed using nonreducing SDS-PAGE as described above. A single gel containing all samples was used to record the fluorescence signalwith a LAS-3000 imaging system (bottom panel) before staining with CBB to visualize protein (top panel).

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surface-exposed amino groups, glutaraldehyde has been usedto analyze the quaternary structures of purified multisubunitmembrane proteins (13, 26, 28, 38, 40, 52). The treatment ofpurified AspT protein with glutaraldehyde showed shifts of themonomer band (at �50 kDa on a denaturing SDS gel) to theposition (100 kDa) expected for homo-dimers (Fig. 4C). More-over, cross-linker treatment in a denaturing detergent (SDS)failed to shift the monomer band. This result supports the ideathat the band shifts were caused by intermolecular cross-link-ing. The glutaraldehyde-treated samples, whether cross-linkedor not, ran as fuzzy bands, as expected from the adduct heter-ogeneity derived from the different extents of glutaraldehydemodification in the individual monomers and dimers by thisreaction. The results of the glutaraldehyde cross-linking assaysuggest that functional AspT formed homo-oligomers underDDM-solubilized conditions.

DISCUSSION

Identification of sites involved in both substrate binding andtranslocation is a central goal of ongoing studies of AAE family

transporters. Solute transporters such as AspT and OxlT havea network of key amino acid residues that facilitate substratemovement into and out of an appropriate binding site, therebydefining a substrate translocation pathway through the protein(48, 49). For transporters of polar molecules like aspartate, thispathway is assumed to be enriched in residues of a morehydrophilic character than found elsewhere in the transmem-brane helices, as is the case for the substrate translocationpathways found in other transporters (12, 20, 25, 29, 49). Forthese reasons, because TM3 is enriched with hydrophilic aminoacid residues, including aspartate 67 and arginine 76, and be-cause these are the only charged residues in the TMs of AspT,TM3 deserves attention. Therefore, residues on the same he-lical face as aspartate 67 or arginine 76 might also be expectedto be involved in the substrate translocation pathway. To in-vestigate the role of TM3, we performed a complete cysteine-scanning mutagenesis study of TM3 in the presence and ab-sence of L-aspartate to learn more about the membranetopology, possible ligand-binding sites, and the functional dy-namics of AspT.

FIG. 3. Conformational alteration induced by L-aspartate and disulfide dimer formation of single-cysteine variants in the cell membrane.(A) The levels of fluorescence intensity and CBB staining in nonreducing SDS-PAGE (Fig. 2A and B) were normalized to the corresponding levelsof the F88C variant, whose mutation is located in an intracellular hydrophilic loop. The labeling efficiency of cysteine in each variant is shown asthe ratio of the normalized levels of fluorescence intensity and CBB staining with black bars (absence of L-aspartate) and gray bars (presence ofL-aspartate). The asterisk indicates that L60C showed strong disulfide dimer formation; the amount of monomer was too small to normalize thestrength of the fluorescence. (B) The bands representing monomeric and dimeric forms were quantified by nonreducing SDS-PAGE analysis (Fig.2A, top panel). The efficiency of the disulfide bond formation of each single-cysteine variant is shown as the ratio of dimer to total protein (blackbars). The specific activity of each variant is shown by the gray bars.

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Impacts of cysteine substitution. Cysteine scanning of TM3revealed that the replacements of tyrosine 75 and serine 84 hadthe strongest inhibitory effects on transport (initial rates ofL-aspartate transport were below 15% of the rate for cysteine-less AspT), and the alteration of 9 of the 22 amino acid (iso-leucine 64 to methionine 85) positions tested reduced AspTfunction (initial rates of L-aspartate transport were below 30%of the rate for cysteine-less AspT; Table 1). The results indi-cated that three groups of amino acid residues played impor-tant roles in L-aspartate transport processes: (i) amino acidslocated at the hydrophilic face in the hydrophobic core (me-thionine 70 and phenylalanine 71), (ii) the amino acids of theGxxxG motif (glycine 74, tyrosine 75, arginine 76, valine 77,and glycine 78), and (iii) amino acids located at the C-terminalend of the helix (serine 83, serine 84, and methionine 85). Inthe first group, phenylalanine 71 is well conserved as an aro-matic amino acid (tyrosine or phenylalanine) within the AAEfamily (Fig. 1). Methionine 70 is not conserved within thefamily, but the substitution of methionine 70 with cysteine may

cause local structural perturbations affecting the adjacent func-tionally important region around phenylalanine 71, therebyexplaining the reduced transport activity of the correspondingvariant. Therefore, we speculated that methionine 70 and phe-nylalanine 71 are located on the hydrophilic face of the hydro-phobic core of TM3 (Fig. 5B, top panel). In the second group,glycine 74 and glycine 78 are completely conserved within thefamily. Tyrosine 75 is well conserved as an aromatic amino acid(tyrosine or phenylalanine). Arginine 76 of TM3 is not con-served within the AAE family, but a charged or polar aminoacid is found at this position in other members of the family(Fig. 1). Therefore, we speculated that arginine 76 is located inthe hydrophilic water-filled cavity, and this speculation is sup-ported by the fact that this residue was accessible to sulfhydrylreagents (Fig. 2A and B and 3A; see also Discussion below).Glycine 74 and glycine 78 may be important for the structureor conformational flexibility of TM3. A similar role has beenreported for specific glycine residues in the lactose permeaseLacY of E. coli (4, 24, 47). In fact, our results indicate that

FIG. 4. Oligomerization of AspT. (A) Purification of AspT(WT)-His. SDS-PAGE analysis with a 10% polyacrylamide gel matrix of purifiedAspT(WT)-His under nondenaturing conditions using solubilization with 1.5% DDM and elution with 0.05% DDM. (B) L-Aspartate transportassay with proteoliposomes containing purified AspT(WT)-His. Proteoliposomes loaded with 100 mM L-aspartate and 100 mM potassiumphosphate (pH 7.0) were placed in assay buffer (100 mM potassium phosphate [pH 7], 100 mM potassium sulfate) at 10 �g of protein/ml alongwith 100 �M L-[3H]aspartate. The uptake of L-[3H]aspartate by the proteoliposomes containing purified AspT(WT)-His is shown (�). Proteoli-posomes were allowed to take up L-[3H]aspartate for 7.5 min. At the time indicated by the arrow, L-aspartate was added to achieve a finalconcentration of 15 mM (f). Samples were removed, filtered, and washed at the times indicated. (C) Glutaraldehyde cross-linking of the purifiedAspT(WT)-His. Image of silver-stained SDS-PAGE gel (7.5% polyacrylamide gel matrix) of AspT(WT)-His after 1 to 100 mM glutaraldehyde(GA) cross-linking in 0.05% DDM or 1% SDS (left panel) and densitometric scans of silver-stained SDS-PAGE gels (right panel) of AspT after100 mM glutaraldehyde cross-linking in 0.05% DDM.

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TM3 of AspT is involved in ligand-induced conformationalalterations, as described below. Because cysteine substitutionvariants at phenylalanine 71 and tyrosine 75 (groups 1 and 2,respectively) showed high frequencies of disulfide bond forma-tion on nonreducing SDS-PAGE, disulfide bond formationmay decrease the flexibility of TM3, which may in turn de-crease the transport activities. In group 3, serine 84 is wellconserved (but not completely) as a small amino acid (serine,glycine, or alanine). The substitution of serine 83 or methio-nine 85 with cysteine may cause local structural perturbationsaffecting the adjacent functionally important region aroundserine 84, thereby explaining the reduced transport activities ofthe corresponding variants. Taken together, the results of theactivity measurements confirmed the particular functional sig-nificance of TM3 in the transport process.

Assignment of the hydrophobic core and water-filled cavity.To obtain a comprehensive picture of the accessibility of cys-teines at the various positions of TM3, randomly orientedmembrane ghosts containing single-cysteine AspT variants

were labeled with the hydrophilic fluorescent probe OGM. Thelabeling experiments (Fig. 2A) revealed a striking discontinuityin OGM accessibility along TM3. Thus, when AspT was la-beled in situ, OGM failed to react with cysteines within theN-terminal 12-residue segment (residues 64 to 75), whereasinserted cysteines at the C-terminal segment yielded fluores-cent products (Fig. 2A). These results indicate that residues 64to 75 form the hydrophobic core of TM3. The existence of ahydrophobic core within the membrane has recently also beenreported for OxlT (18, 51). There are two possible generalexplanations for such findings. The first possibility is that theregion of low OGM reactivity (positions 64 to 75) is within thelipid bilayer and hence inaccessible to the impermeant probe.Once OGM has modified its target, the OGM carboxylate liesabout 8 to 10 Å from the target cysteinyl sulfur; therefore,cysteines that react with OGM can be expected to be within 8to 10 Å of the external or internal aqueous phase. If TM3forms a transmembrane �-helix with 20 to 25 residues thatspan the 30- to 40-Å bilayer, a central core of some 10 residues

FIG. 5. Integrated view of AspT TM3. This figure summarizes the cysteine accessibility data shown in Table 1 and Fig. 2 and 3. (A) Side viewof TM3. The residues in black circles are highly accessible to OGM (�0.8 relative to F88C), the residues in gray circles show an intermediateaccessibility (�0.8 but �0.3 relative to F88C), and the residues in unshaded circles are not accessible or only slightly accessible (�0.3 relative toF88C). The reactivity of the cysteine at the amino acid position shown by the black square was stimulated by L-aspartate; the amino acid at theposition indicated by the black triangle was protected by L-aspartate. The shaded area demarcates the water-filled cavity of TM3, which is accessibleto OGM (Fig. 2A and B). (B) Helical-wheel projection of the hydrophobic core (isoleucine 64 to tyrosine 75; top panel) and the water-filled cavity(arginine 76 to methionine 85; bottom panel) with specific activities; symbols are the same as described for panel A. Specific activities are shownin squares: black squares, �50% of that of cysteine-less AspT; dark gray squares, �50%, �30%; light gray squares, �30%, �15%; and unshadedsquares, �15%) (Table 1). Asterisks within the helical wheel indicate cysteine substitutions that show clear disulfide dimer formation innonreducing SDS-PAGE (Fig. 2 and 3).

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(e.g., residues 64 to 75) can be expected to be inaccessible toOGM for purely geometric reasons. The second possible ex-planation is that cysteines in this core are unreactive for somereasons having to do with their chemical environment. Cys-teines in a nonpolar (i.e., lipid) environment are generallythought to have high pKa values (pKa 14) characteristic ofthe side chain of cysteine (18). In the second explanation, thereactive sulfide (�S1�) would not be present at a sufficientlyhigh concentration to permit its chemical modification withOGM. We caution, however, that these two explanations arenot mutually exclusive. A transmembrane helix might havepositions that face other helices or the hydrophilic transloca-tion pathway (e.g., see the work of Goswitz and Brooker [20]);these positions might be inaccessible but chemically reactive.In contrast, there might be positions that face the membranelipid, and these positions might be accessible but chemicallyunreactive.

In addition, it is noteworthy that most positions (6 of 10residues [arginine 76 to methionine 85]) located in the cyto-plasmic half of TM3 showed high reactivities toward OGM(Fig. 2A and B). The data indicate that the C-terminal half ofthe putative �-helix is exposed to an aqueous cavity that isopen to the cytoplasmic side of the membrane. This cavitymost likely extends from the cytoplasmic end of TM3 to themiddle of the domain (residues 76 to 85). To study the acces-sibility of the water-filled cavity at the C-terminal (cytoplasmic)half of TM3 from the periplasmic side, we applied whole-cellOGM labeling for six variants (G62C, D63C, G78C, S80C,S83C, and K87C) that showed high accessibility to OGM inmembrane ghost labeling (Fig. 2A). G62C and D63C, whichare predicted to be located on the periplasmic side of themembrane, maintained their good accessibility to OGM inwhole-cell labeling. In contrast, G78C, S80C, S83C, and K87Cshowed remarkable defects in their accessibility to OGM inwhole-cell labeling (Fig. 2C). This result suggests that aminoacid residues located in the C-terminal half of TM3 are inac-cessible from the periplasmic side and that the water-filledcavity in the C-terminal half of TM3 is open to the cytoplasmicside.

The probable side view of TM3 (helical cylinder) predictedfrom the results of the OGM labeling assay is shown in Fig. 5A.The N-terminal half of TM3 (isoleucine 64 to tyrosine 75) isenriched with hydrophobic amino acids (such as phenylalanine,isoleucine, methionine, and alanine), and cysteine substitutionof the hydrophobic sector was less inhibitory to the transportactivities of the variants. Moreover, many single-cysteine vari-ants in the hydrophobic sector were labeled with OGM only toa small extent. In contrast, the C-terminal half (arginine 76 tomethionine 85) of TM3 includes many hydrophilic amino acidresidues (such as arginine and serine), and cysteine substitu-tion caused a loss of transport function. Many of the cysteine-substituted variants in the hydrophilic sector were well labeledwith OGM. Taken together, the results indicate that the localenvironment around the N-terminal half of TM3 differs fromthat around the C-terminal half.

The center of TM3 contains a proline residue (position 79)and glycine residues (positions 74 and 78) that may be involvedin the formation of kinks and bends, thereby distorting theregular �-helical structure. This possibility is implied by thecrystal structure of LacY, in which only 3 of 12 helices appear

to be straight; all the others are arched, kinked, or S-shaped(4). Therefore, we used helical-wheel analysis to separatelyexamine the N-terminal half forming a hydrophobic core (iso-leucine 64 to tyrosine 75) and the C-terminal half forming awater-filled cavity (arginine 76 to tyrosine 75) (Fig. 5B).

A display of the hydrophobic core (isoleucine 64 to tyrosine75) as a helical wheel (Fig. 5B, top panel) clearly showed thatthe attributed TM3 residues are asymmetrical. Thus, one he-lical face was enriched in residues whose substitution by cys-teine was usually without marked function loss (except forY75C). In contrast, at the other helical face, cysteine-scanningmutagenesis resulted in larger function loss; note that thislatter face includes the charged residue aspartate 67, which isthe only charged residue located in the hydrophobic core. Thesubstitution of aspartate 67 with cysteine resulted in a moder-ate loss of transport activity (45.5% of the initial transport ratioof cysteine-less AspT). In addition, aspartate 67 is not con-served within the AAE family (Fig. 1). These results suggestthat aspartate 67 does not play crucial roles in AspT function,but the location of aspartate 67 supports the idea that the latterhelical face is exposed to hydrophilic environments. Despitethe fact that tyrosine 75 seems to be located in the hydrophobicsector, the significant loss of function observed in the Y75Cvariant might be attributable to the GxxxG motif; this motifincludes tyrosine 75, and its function was affected by the sub-stitution, as described below. A display of the cytoplasmic halfof TM3 (arginine 76 to methionine 85) as a helical wheel (Fig.5B, bottom panel) showed that many of the cysteine-substi-tuted variants in the segment were OGM labeled and showedfunction loss. In particular, on the face that includes arginine76, the three residues proline 79, serine 80, and serine 83 werehighly accessible to OGM. We therefore propose that thecytoplasmic half of TM3 is located in (or forms a part of) thehydrophilic water-filled cavity and plays an important role inthe substrate transport of AspT.

L-Aspartate-induced conformational alteration. In TM3,some positions showed variable accessibility to OGM depen-dent on whether or not L-aspartate was present (Fig. 2A and B,bottom panels, and Fig. 3A). This phenomenon has been ex-plained by an L-aspartate-induced conformational alterationthat makes these positions accessible or inaccessible to theaqueous phase and leads to L-aspartate binding at, or close to,these residues.

In the case of the cysteine introduced at proline 79, which isin a cytoplasmic cavity, the reactivity of cysteine was markedlystimulated in the presence of L-aspartate. Although the pres-ence of L-aspartate inhibited the reactivity of the cysteine in-troduced at glycine 62, which is in a periplasmic loop, position62 exhibited high accessibility to OGM only in the absence ofL-aspartate (Fig. 2A and B, lanes G62C and P79C). The L-aspartate-dependent protection of G62C against OGM label-ing may be achieved by direct steric hindrance derived fromL-aspartate binding to the positions close to glycine 62, but thisreason does not explain the stimulatory effect of L-aspartate onthe OGM labeling of P79C. A second possibility is that theremay be an L-aspartate-induced conformational alteration thatburies or exposes the residues within the protein. In brief, inthe absence of substrate, glycine 62 is exposed to the periplas-mic surface, and proline 79 is located at the cytoplasmic end ofthe hydrophobic core. Substrate binding induces a structural

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conformation change, and those residues (glycine 62 and pro-line 79) move to the periplasmic end of the hydrophobic coreand the cytoplasmic water-filled cavity, respectively. This hy-pothesis clearly explains the reasons for the protective effectand stimulatory effect of OGM labeling by substrate binding.Similar substrate-induced conformational alterations havebeen shown by means of the site-directed chemical labeling ofOxlT, LacY, and the Na�/proline transporter PutP of E. coli(16, 37, 46).

Role of TM3 in AspT function. Nonreducing SDS-PAGEanalyses of purified single-cysteine AspT showed that somesingle-cysteine variants formed S-S-linked homodimers inmembranes (Fig. 2A, top panel, and Fig. 3B, black bars).Moreover, a glutaraldehyde cross-linking assay suggested thatfunctional AspT formed homo-oligomers under DDM-solubi-lized conditions (Fig. 4C). AspT solubilized only with DDMshowed transport activity after reconstitution in proteolipo-somes (Fig. 4B); this result suggests that DDM-solubilizedAspT molecules probably kept active oligomer forms. Becausethese experiments do not show functional subunit stoichiome-try within a protein complex in the native membrane, it isdifficult to determine the oligomeric stoichiometry of the AspTcomplex from these experiments. However, these results dosuggest that AspT formed homo-oligomers in the membraneand that the TM3s of the individual protomers are close toeach other. In many membrane proteins, the GxxxG motif (twoglycine residues separated by any three residues) is often foundto be important for mediating the interaction of TM helices(11, 42). Early studies (including mutagenesis, computationalmodeling, and thermodynamic characterization) on glyco-phorin, a TM dimer, showed the central role of GxxxG (5, 15,27) for TM interaction. For secondary transporters, the humanserotonin transporter and the osmosensor and osmoprotectanttransporter of E. coli have recently been reported, and GxxxGmotifs in their TMs play an important role in their oligomer-ization and helix packing (14, 23). Interestingly, in the AAEfamily transporters, we found highly conserved GxxxG motifsin the hinge region (GYxxGP) that connects the N- and C-terminal halves of TM3 (Fig. 1). As a predictable role of theGxxxG motif in TM3 of an AspT protomer, the motif mightcontribute to the oligomerization of AspT by means of helixpacking through the proximity of the individual TM3 in eachAspT protomer.

The 10 single-cysteine variants of sodium:proton antiporterNhaA TM9 are known to form dimers without cross-linkingreagents, and the positions forming dimers are located at theN-terminal half of NhaA TM9 (43). Pulsed electron paramag-netic resonance distance measurements of NhaA demon-strated that the TM9s of each protomer of NhaA are close toeach other (22). Such spontaneous disulfide bond formationfound in single-cysteine variants of a TM is generally thoughtto reflect the proximity of the TM in one protomer to that inthe other protomer in its three-dimensional structure. Becausesix single-cysteine variants with substitutions located in theN-terminal half of AspT TM3 spontaneously formed a dimerby disulfide bonding under nonreducing conditions, we pre-dicted that the N-terminal half of TM3 in one protomer is closeto that of TM3 in the other protomer. Notably, five phenylal-anine residues and one tyrosine residue are predicted to existin the hydrophobic core (Fig. 5A). Aromatic amino acid resi-

dues have been shown to mediate the self-assembly of severalsoluble proteins through �-� interaction between aromaticrings (31, 41). Very recently, aromatic amino acid residues inthe TMs of membrane proteins have been shown to promoteoligomerization (41). It is also plausible that the aromaticamino acid residues in the hydrophobic core of AspT TM3are involved in oligomerization. The single-cysteine variants(F66C, I73C, I64C, F71C, and Y75C) that formed an S-S-linked dimer in the hydrophobic core are clustered at thehydrophobic face (Fig. 5B, top panel). However, the single-cysteine variants in the probable substrate translocation path-way showed lower transport activities than the wild type, andthese variants also showed low frequencies of disulfide bondformation; this result suggests that the positions of TM3 in oneprotomer are not close to the corresponding positions of theTM3s in other protomers. Therefore, we presume that theTM3 hydrophobic core consists of one face that is involved inoligomerization and another face that forms the substratetranslocation pathway.

Recently, structural studies of the potassium channel andCa2�-ATPase revealed that the small side chains of the aminoacid residues found in the GxxxG motifs of these proteins playan important role in the stability and conformational changesof the proteins during substrate transport (11). For AspT,cysteine substitutions for highly conserved GxxxG motifs de-creased L-aspartate transport activities (Table 1). Moreover,we found L-aspartate-induced conformational alterations inTM3, and the most drastic alterations of the reactivity of sub-stituted cysteine residues toward OGM were observed at pro-line 79, which is located next to the GxxxG motif (Fig. 2A andB). Therefore, contribution to the flexibility of TM3 duringsubstrate transport might be another potential role for theGxxxG motif in TM3 of AspT. To determine the substratetransport mechanism of AspT, ongoing studies are focusing onthe GxxxG motif of TM3 and other TMs that form putativesubstrate translocation pathways.

ACKNOWLEDGMENTS

This work was supported by a research fellowship for young scien-tists from the Japan Society for the Promotion of Science. K.N. is aresearch fellow of the Japan Society for the Promotion of Science.

We thank Di (Cody) Kang (Department of Physiology, the JohnsHopkins School of Medicine Institute) for helpful comments concern-ing protein purifications. We thank the Kikkoman Corporation fortheir gift of the T. halophilus asp operon.

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