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J. Biol. Chem., Vol. 281, Issue 40, 29817-29829, October 6, 2006
Structural and Functional Characterization of Transmembrane Segment VII of the Na+/H+ Exchanger Isoform 1*
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| ABSTRACT |
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-helical, with a break in the helix at the functionally critical residues Gly261Glu262. The relative positions and orientations of the N- and C-terminal helical segments are seen to vary about this extended segment in the ensemble of NMR structures. Our results show that TM VII is a critical transmembrane segment structured as an interrupted helix, with several residues that are essential to both protein function and sensitivity to inhibition. | INTRODUCTION |
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NHE1 is composed of two domains as follows: an N-terminal membrane domain of
500 amino acids and a C-terminal regulatory domain of
315 amino acids (1, 6). The N-terminal membrane domain is responsible for ion movement and has 12 transmembrane segments and 3 membrane-associated segments (11) (Fig. 1A). How this domain binds and transports Na+ ions and protons is only recently starting to be elucidated. We have recently analyzed TM IV of the NHE1 isoform of the Na+/H+ exchanger. We showed that prolines 167 and 168 are critical to NHE1 function, targeting, and expression (12). Phe161 was shown to be a pore-lining residue critical to transport, and the structure of TM IV was shown to be atypical of TM proteins, being composed of one region of
-turns, an extended middle region, including Pro167Pro168, plus a region helical in character (13).
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-helix. We identify residues critical in transport and those that modify inhibitor resistance. TM VII is distinctly different from TM IV in both its structure and in functional aspects. | EXPERIMENTAL PROCEDURES |
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Site-directed MutagenesisTo examine and characterize critical amino acids of TM VII of the Na+/H+ exchanger, mutations were made to an expression plasmid containing a hemagglutinin (HA)-tagged human NHE1 isoform of the Na+/H+ exchanger. The plasmid pYN4+ contains the cDNA of the entire coding region of the Na+/H+ exchanger (12). Two series of mutants were made (Table 1). One series of mutants was made in which all the residues of TM VII were mutated to alanine. A second series was for insertional mutagenesis, whereby alanine residues were inserted at critical locations between residues of TM VII in the wild type pYN4+. Two alanine insertional mutants were made, one inserting an alanine between Gly261 and Glu262, and a second inserting an alanine between Leu264 and Leu265. A third insertional mutant had two mutations, a glutamate inserted between Gly261 and Glu262 plus an N266D mutation. Site-directed mutagenesis using amplification with PWO DNA polymerase (Roche Applied Science) was followed by using the Stratagene (La Jolla, CA) QuikChangeTM site-directed mutagenesis kit. Mutations created a new restriction enzyme site for use in screening transformants. DNA sequencing confirmed the mutations and fidelity of PCR.
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SDS-PAGE and ImmunoblottingTo confirm NHE1 expression, cell lysates were made from AP-1 cells as described earlier (12). For Western blot analysis, equal amounts of up to 100 µg of each sample were resolved on 10% SDS-polyacrylamide gels. Nitrocellulose transfers were immunostained using anti-HA monoclonal antibody (Roche Applied Science) and peroxidase-conjugated goat anti-mouse antibody (Bio/Can, Mississauga, Ontario, Canada). The enhanced chemiluminescence Western blotting and detection system (Amersham Biosciences) was used to visualize immunoreactive proteins. Densitometric analysis of x-ray films was using NIH Image 1.63 software (National Institutes of Health, Bethesda).
Cell Surface ExpressionCell surface expression was measured with sulfo-NHS-SS-biotin (Pierce) essentially as described earlier (12). Briefly, the cell surface was labeled with sulfo-NHS-SS-biotin, and immobilized streptavidin resin was used to remove plasma membrane Na+/H+ exchanger. Equivalent amounts of the total and unbound proteins were analyzed by SDS-PAGE followed by Western blotting and densitometry as described above. The relative amount of NHE1 on the cell surface was calculated by comparing both the 110- and the 95-kDa HA-immunoreactive species in Western blots of the total and unbound fractions.
Na+/H+ Exchange ActivityNa+/H+ exchange activity was measured using a PTI Deltascan spectrofluorometer. The initial rate of Na+-induced recovery of cytosolic pH (pHi) was measured after ammonium chloride-induced acute acid load using 2',7'-bis(carboxyethyl)-5,6-carboxyfluorescein-AM (Molecular Probes Inc., Eugene, OR). Recovery was in the presence of 135 mM NaCl and was measured as described previously (13). There was no difference in the buffering capacities of stable cell lines as indicated by the degree of acidification induced by ammonium chloride. For some experiments cells were treated with EMD87580 of varying concentrations. EMD87580 was dissolved in water, and the inhibitory effect of EMD87580 was documented using a two-pulse acidification assay. Cells were treated with ammonium chloride two times and allowed to recover in NaCl-containing medium. One pulse was in the absence of EMD87580 and one in the presence of inhibitor. The rate of recovery from acid load was compared ± inhibitor. Where indicated, the activity of the Na+/H+ exchanger mutants was corrected for the level of protein expression and for the targeting of the protein to the cell surface. Results are shown as mean ± S.E., and statistical significance was determined using the Mann-Whitney U test.
Peptide Synthesis and PurificationTM VII peptides (sequence, HINELLHILVFGESLLNDAVTVVLYKK; free N terminus, amide-capped C terminus) with and without selective 15N labels were synthesized and purified using previously published t-Boc solid-phase techniques optimized for hydrophobic membrane-spanning peptides (25), with the difference that purification was carried out using a Zorbax 300 SB-C3 9.4-mm x 25-cm HPLC column (Agilent Technologies, Palo Alto, CA). Peptide identity was confirmed by matrix-assisted laser desorption ionization mass spectrometry and by amino acid analysis.
NMR Spectroscopy and Structure CalculationSamples for structural study were obtained by dissolving
1mM synthetic TM VII peptide in 90% H2O, 10% D2O solution containing
75 mM DPC-d38. Chemical shifts were referenced to 2,2-dimethyl-2-silapentane-5-sulfonic acid at 1.0 mM, with indirect referencing employed for 15N (26). Solution pH was adjusted to 4.8 (deuterium isotope effects not taken into account), and all experiments were carried out at 30 °C. One-dimensional 1H, natural abundance gradient-enhanced 1H-13C HSQC, TOCSY (60-ms mix; DIPSI spin lock), and NOESY (225250-ms mix) experiments were acquired on the Canadian National High Field NMR Centre Varian INOVA 800-MHz spectrometer for each sample. With the selectively 15N-labeled peptide, additional three-dimensional 15N-edited NOESY-HSQC (250-ms mix) and TOCSY-HSQC (57-ms mix, DIPSI spin lock) experiments were acquired at 500-MHz on a Varian Inova spectrometer. All experiments were used as configured within the Varian BioPack software package. Spectra were processed using NMRPipe (27) and analyzed using Sparky 3 (T. D. Goddard and D. G. Kneller, University of California, San Francisco).
Structure calculation was carried out in the python scripting interface of XPLOR-NIH version 2.13 (28) using NOE restraints derived from the 225- and 250-ms mixing time experiments at 800 MHz. Homonuclear NOESY peaks were manually picked in Sparky, and volumes were calculated using Gaussian fits, with motion of the peak center generally allowed; in some cases (
1.5%) in the NOESY spectra, Sparky's gaussian fit algorithm did not find a convergent solution, and a summed signal intensity was used instead over a manually specified region. Initial NOE calibration was carried out empirically from peak volumes to provide a value in the range of 1.86.0 Å; this was carried out separately for each spectrum in order to normalize for mixing time. These estimates were used to bin each restraint into one of strong (1.82.8 Å), medium (1.83.6 Å), weak (1.85.0 Å), or very weak (1.86.0 Å). Ambiguous assignments were handled using the XPLOR-NIH "or" statement, with the "sum" averaging option employed and the "number of monomers" parameter set to 1. The NOE term used the hard (square well) potential with a scaling factor of 20 for the high temperature stage and a ramped scaling factor over the range 130 for the cooling stage. The dihedral angle potential used a constant scaling factor of 5 (rounds 18) or 25 (rounds 910) throughout the annealing protocol. Families of structures were generated using simulated annealing with a high temperature stage at 3500 K of length 20 ps and a slow cooling stage going from 3500 to 100 K in 25 K temperature steps for 2-ps stages. Time steps of 10 fs were used in each case.
Structure calculations were carried out in two different manners. In one, a single extended polypeptide was generated and subjected to simulated annealing. In the other, two extended polypeptides with identical TM VII primary sequence were generated. In this case, each intra-residue NOE was doubled to apply to each conformer. All other NOEs were made ambiguous, allowing satisfaction through the XPLOR-NIH summed average by any combination of intra-polypeptide and inter-polypeptide NOE restraints. To handle the multiple conformations of the TM VII peptide being produced and to allow practical generation and analysis of numerous ambiguous restraints, an in-house tcl/tk script (freely available upon request) was used to iteratively refine the NOE restraints. As will be discussed below, use of two conformations allowed satisfaction of all NOE restraints, whereas a single conformation required significant pruning of the family of NOE restraints. Analysis and NOE refinement are therefore only described for the two-conformer calculation. Families of 50200 structures were generated, and NOE violations were analyzed over each ensemble of structures. A series of NOE restraint refinements was carried out. Initially, violations >0.5 Å in >50% of structures were lengthened by one category; over subsequent rounds, the violation threshold was subsequently decreased incrementally to 0.05 Å and the number of violators to >10%. After 8 cycles of simulated annealing and NOE refinement, calculated XPLOR-NIH structure energies contained minimal contributions from NOE violations; violations were not observed in >10% of the ensemble for any NOEs, and magnitudes of all observed violations were minimal. Two further cycles of simulated annealing were carried out with increased weighting on the dihedral angle restraints with further, very minor, NOE restraint refinements carried out using the most stringent bounds given above between rounds 9 and 10. From this ensemble of 60 two-conformer structures, the lowest energy 33 ensemble members (selected based upon an arbitrary cutoff of 60 kcal/mol in XPLOR-NIH total energy values) containing 66 polypeptide conformers were retained for further analysis. The final sets of restraints have been deposited in the Protein Data Bank (entry 2HTG) along with this ensemble of structures.
| RESULTS |
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We have shown earlier (13) that mutation of amino acids of transmembrane segments can affect surface targeting of the Na+/H+ exchanger. Therefore, we examined intracellular targeting of the NHE1 expressing cell lines within AP-1 cells. Cells were treated with sulfo-NHS-SS-biotin and then lysed and solubilized, and labeled proteins were bound to streptavidin-agarose beads. Equal amounts of total cell lysates and unbound lysates were separated by size using SDS-PAGE, and Western blotting with anti-HA antibody identified the tagged NHE1 protein. Fig. 3 (first 24 panels) illustrates examples of the results and a summary of quantification of at least six experiments. Both the 110- and 95-kDa bands were included in the analysis. The Glu262 mutant was found principally in intracellular compartments. Mostly this was as the 95-kDa unglycosylated form of the protein. Nonspecific binding of NHE1 protein to streptavidin-agarose beads was
16%, so the values shown overestimate the level of surface protein.
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Insertional MutagenesisAlanine insertional mutagenesis within a transmembrane segment has been used to scan membrane domains of lactose permease (16), the Escherichia coli F1F0-ATP synthase (32), and other proteins (3335). Two mutants were made with alanine insertions. Alanines were inserted between amino acids 261 and 262 (Ins261A), and a different mutant had an alanine inserted between amino acids 264 and 265 (Ins264A). A third related mutant had asparagine 266 mutated to aspartic acid plus a glutamic acid inserted between amino acids 261 and 262 (N266DIns261E). The reasoning behind the mutation was that if the positions of acidic residues in TM VII were critical, an insertion of glutamic acid between Gly261 and Glu262 might conserve a required charge at this position. In addition, mutation of Asn266 to an aspartic acid might, in effect, result in replacement of Asp267 with an aspartic acid that is shifted into the same position that was formerly occupied by Asp267. For all the insertional mutants, expression of the protein was greatly decreased (Fig. 2D). Expression was from 28 to 39% of the control levels. In addition, in all cases the majority of the protein expressed was as a deglycosylated 95-kDa protein. In the double mutant there was almost no 110-kDa protein, whereas in the insertions after amino acids 261 and 264 there was relatively more 110-kDa protein. The pattern of expression of mostly 95-kDa protein was similar to that obtained for substitution of Glu262 with alanine (Fig. 2B). Surface expression of the insertional mutants was also greatly compromised. Ins261A and the double mutant were both
80% intracellular in location. The Ins264A mutant was
60% intracellular.
The activity of insertional mutants was assayed as described for alanine scanning mutations. The Ins264A mutant was virtually totally inactive, even after correction for targeting and expression levels. The Ins261A mutant retained
25% activity after corrections. Despite the apparent lack of expression of the 110-kDa protein, the double mutant (N266DIns261E) retained significantly more raw activity than either of the single insertional mutants. In addition, after correction for targeting and expression levels, the mutant was as active as the wild type.
Peptide Design and Conditions for NMR SpectroscopyPairs of cationic residues at the N and C termini of extremely hydrophobic peptides such as 24-mers of leucines have been shown to aid in peptide purification and handling (36). Therefore, we chose to add a pair of lysines to the C terminus of the sequence following Tyr274. The N terminus of the segment was chosen to be the basic His250 residue, and we opted to keep a free N-terminal amine group; therefore, no additional cationic residues were added at the N terminus. Although there is no biological relevance to the numbering, the pair of lysine residues at the C terminus are referred to herein as Lys275 and Lys276. A number of TM VII peptides were prepared, either by fusion in the GB1 system (13, 37) or by chemical synthesis. In the former case, the yield of purified peptide upon cyanogen bromide cleavage was extremely low. All high resolution structural studies were therefore carried out using two different synthetic peptides with identical sequences, one of which had no isotope labels and one selectively 15N-labeled at residues Leu254, Leu258, Gly261, Leu264, Ala268, and Leu273.
A number of organic solvent conditions were initially tried as membrane mimetics for the TM VII peptides: a methanol/chloroform/water (4:4:1 v/v) mixture, dimethyl sulfoxide, acetonitrile, chloroform, and mixtures of acetonitrile and hexafluoropropanol. Note that the first two conditions were previously found to provide stable solubilization of the TM IV segment of NHE1 (13). SDS micelles (pH
5) also failed to solubilize TM VII. In many cases, promising one-dimensional 1H NMR spectra were obtained, but the peptide would come out of solution after
424 h. These were generally precipitates that could be readily resuspended in solution, as opposed to irreversible aggregates. The same phenomenon was noticed in fractions containing the TM VII peptide collected during HPLC purification in 0.5% trifluoroacetic acid/isopropyl alcohol/water mixtures. Conversely, DPC micelles containing TM VII stayed in solution for weeks at ambient temperature. Sample components were
1mM peptide,
75 mM deuterated DPC, and 1 mM 2,2-dimethyl-2-silapentane-5-sulfonic acid (as a chemical shift standard) in 90% H2O, 10% D2O adjusted to pH
4.8 and studied at 30 °C. Note that this temperature is lower than temperatures often employed for DPC micelle studies, allowing use of the cryogenically cooled triple-resonance probe on the 800-MHz Canadian National High Field NMR Centre spectrometer but still providing extended stability of the samples and retention of good spectral characteristics. This combination of factors allowed determination of the structure of TM VII in DPC micelles.
Resonance Assignment and Structure CalculationSequential chemical shift assignments were carried out using TOCSY experiments, including 15N-edited three-dimensional 1H-15N TOCSY-HSQC experiments for the isotope-labeled TM VII peptide, natural abundance 1H-13C HSQC experiments, and two-dimensional NOESY experiments (38, 39). Natural abundance 1H-15N HSQC was not feasible because of low signal-to-noise arising from the tumbling rate of the TM VII micelles. Poor coherence transfer from HN protons, characteristic of JHN
in
-helices (40), made TOCSY and 15N-edited experiments less efficient and full unambiguous assignment difficult because of H
overlap. Despite these difficulties, we were able to unambiguously assign all backbone HN and H
resonances (excluding the N-terminal
) and the vast majority of side chain protons. (Unambiguous assignment of all Leu H
and H
resonances was not possible; ambiguous NOE assignments were frequently employed in these cases.) Coupling from 15N nuclei in the labeled sample in the either the indirect or both dimensions served to aid in assignment of ambiguous 1H resonances. C
and C
(where applicable) chemical shifts were also assigned for all residues. Resonance assignments have been deposited in the BioMagResBank.
NOE build-up experiments carried out at 500 MHz over the range of mixing times from 75 to 350 ms indicated an optimal mixing time of 225250 ms (results not shown). 1H-1H NOE restraints were assigned using homonuclear spectra acquired at 800 MHz and pooled for the unlabeled and 15N-selective labeled samples. As with resonance assignment, comparison of 15N-1H coupled versus decoupled spectra with the 15N-labeled sample proved extremely useful in assignment of some ambiguous restraints. As detailed in the Supplemental Material, structure calculation made use of pairs of TM VII polypeptides. Each inter-residue restraint was made ambiguous, in that it could be satisfied either within a given polypeptide chain or between chains. Furthermore, through distance averaging any restraint could be satisfied in a single conformer or through dimerization. After refinement, a total of 1311 unique NOE restraints (Table 2) were used for calculation of the two-conformer TM VII structure. These are summarized graphically in terms of the standard connectivities examined for secondary structure characterization and in terms of the number of unique restraints per residue in Fig. 6. Chemical shift analysis indicates a negative deviation for H
from random coil over residues Asn252Lys276 alongside a positive deviation from random coil for C
and a negative deviation for C
over residues His250Lys275, as illustrated in Fig. 7 (random coil values from Ref. 41). Deviation of HN chemical shift from temperature-corrected (42) random coil shifts (41) displays a periodic character over 45-residue stretches, and actual chemical shifts show a general upfield shift from the N to C terminus (not shown). As a whole, chemical shift data over residues Asn252Lys275 for H
, C
, and C
(43) and for HN (44, 45) are strongly indicative of
-helical secondary structure, including surpassing the chemical shift index cutoffs (dashed lines in Fig. 7, A and B) for both H
(46) and C
(47). Therefore, restraints of
=60 ± 30 and
= 40 ± 40 were included over residues Asn252Lys275, where all chemical shifts differences relative to random coil and HN periodicity characteristics indicated helical character. Hydrogen bond restraints were not employed as we feel that these would too strongly bias the structure toward an ideal
-helix rather than allowing combined satisfaction of the dihedral angles indicated by chemical shift data and of the observed NOE restraints. NOE restraint violations in the final ensemble of 66 retained structures are given in Table 2, and a Ramachandran plot for the ensemble of retained structures demonstrating the general agreement with
and
restraints is shown in Fig. 8.
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| DISCUSSION |
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Initial experiments substituted each of the amino acids of TM VII with alanine residues. Alanine 268 was left unchanged. We found that mutation to alanine caused varying effects on NHE1 activity and expression and targeting. Between amino acids 255 and 262 most mutants lost
50% of their activity. The effect on activity of mutant Glu262, Leu254, Leu255, Val269, and Leu273 was accounted for, in part, by effects on targeting and expression levels. For mutant E262A, we observed that a large portion of the protein was present as a partial or de-glycosylated form. This correlated with aberrant targeting of the protein, which we have seen earlier in NHE1 (12, 13). Mutations to amino acids 266 and 267 resulted in mostly inactive protein, even after correcting for expression and targeting. We previously showed that a negative charge at amino acid 267 is critical for activity. Mutation of this residue to Asn caused loss of activity, whereas mutation to Glu retained normal activity (14). Our present results confirm this observation and show that the smaller Ala residue also cannot substitute for a charged amino acid.
Although we found many cases of reduced activity of NHE1 via substitution with Ala, including residues Leu254, Leu255, His256, Ile257, Val259, Phe260, Gly261, Glu262, Asn266, Asp267, Thr270, Val271, and Val272, there were actually few residues in which activity was extremely reduced. This is in contrast to what was observed earlier with TM IV, in which substitution to Cys results in a nearly inactive protein in many cases. The difference between these results could be due to a difference in the transmembrane segments themselves. For example TM XI of the lactose permease was very sensitive to mutation (50), whereas TM XII was not (51). However, in this study, the replacements in TM VII of NHE1 were done with Ala as opposed to Cys replacements of TM IV in our earlier study (13). As this segment was found to be predominantly helical in character, small helix-forming alanine may be less disruptive in this transmembrane segment than a Cys residue was in TM IV (13). Alanine may better preserve the overall character of TM VII and be a better choice for examining the importance of side chains and helical character, as compared with insertion of a Cys residue because Cys has a much lower propensity than Ala for
-helix formation in a TM region (52, 53). The results suggest that many of the side chains of the amino acids do not appear to be especially critical for activity, although they sometimes influenced expression levels and targeting. When considering corrections for expression levels and targeting, the subgroup that had activity reduced 50% or more included only Leu255, Ile257, Val259, Phe260, Gly261, Asn266, Asp267, and Thr270. The E262A mutation caused a very large decrease in activity, although much of this was because of aberrant targeting and expression, and after these corrections activity was slightly over 50% of control.
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-helix, the helix might shift such that amino acid Asn266 was in the position of Asp267. Mutation of Asn266 to Asp might return a critical acidic residue to this position. In addition, the glutamic acid insertion after Gly261 might substitute for Glu262. In fact, we found that this double mutant retained much more activity than simple insertion of alanine after 261. Upon correction for defective targeting and expression, the activity was equivalent to that of the controls (Fig. 4B). This was somewhat surprising because the protein was even more poorly glycosylated than the other insertional mutants (Fig. 2D); however, we have previously shown that glycosylation is not essential to NHE1 function (29). Although having two glutamate residues following one another in the mutant would not be conducive to
-helix formation (52, 54), this region is extended rather than helical in the structure of TM VII that we have solved. An important characteristic of the NHE1 protein is its sensitivity to inhibition by benzoyl guanidine type of inhibitors. Sites in TM IV (55) and TM IX (5658) alter sensitivity to inhibition. We reasoned that because of the critical nature of this transmembrane segment, it might also affect sensitivity to inhibition. Several of the residues altered the sensitivity. The maximum changes were a 10-fold increase in sensitivity to inhibition with mutation of L265A and a 5-fold increase in resistance with the V272A mutation. These changes are not as large as some reported earlier (58), but nonetheless they altered the inhibitor efficacy significantly. Other mutations have reported significant effects on NHE inhibitor resistance but no effects on Na+ affinity (59), suggesting that the inhibitor-binding site may be physically distinct but closely related to the Na+-binding site (60). The contribution of many regions of the NHE1 protein to inhibitor resistance, shown in this and other studies, suggests that a number of different regions of the protein likely come together to influence the protein structure and thereby influence the NHE inhibitor-binding site. Likely, alterations in many amino acids and transmembrane segments that affect the structure and function of the protein affect inhibitor binding. However, we did find that the effects were specific. Amino acids Leu265, Leu255, Ile251, and Val272 had significant effects on NHE1 inhibitor resistance whereas others did not.
Structural Analysis of TM VIIAttempts to calculate a single conformer in agreement with the assigned NOE data required removal of a high proportion (34.4%) of the NOE restraint data to allow production of an ensemble of structures with low violation statistics (data not shown). Two possible reasons for the inability to satisfy the NMR data were that the TM VII peptide was sampling a number of conformations, as is frequently observed with peptides or unstructured proteins, or that oligomerization of the TM VI peptide was taking place. In either case, NOE restraints would be observed that are not satisfied by a single conformation. Interestingly, we found that simultaneous calculation of two conformers satisfied the NOE data set without significant dimer formation suggesting that sampling of multiple conformations rather than dimerization is responsible for reducing restraint violations. A similar result, but without the ability to test for dimerization, could likely be achieved through ensemble-average structure calculation (6164). Further details are supplied in the Supplemental Material.
An ensemble of 66 TM VII structures (33 dual conformer pairs) was obtained that satisfy the vast majority of observed NOE and chemical shift-derived
and
dihedral angle restraints equally well (Table 2; Fig. 8). Despite strong chemical shift evidence (Fig. 7; values deposited in the BioMagResBank), NOE connectivities (Table 2 and Fig. 6; restraints deposited in the Protein Data Bank code 2HTG and RCSB code RCSB038740) do not result in an uninterrupted helix over residues Asn252Lys275. Superposition of all members of the ensemble over the full length of the peptide is not possible. Rather, two distinct portions of the peptide show strong structural convergence, as demonstrated by superposition of the polypeptide backbone over the ensemble of structures. The break point between these converged segments of TM VII is at Gly261Glu262. Minor variability in backbone structure is also observed over the ensemble of structures at Leu254Leu255, Leu265Asn266, and Thr270Val271, requiring separate superpositions for optimal root mean square deviation, as detailed in the Supplemental Material. Residues highlighted in gray in Fig. 8 with greater than usual dispersion of (
,
) angle are Ile251 (corresponding to flexibility at the N terminus), Gly261 (corresponding to major break between helical segments), and Val271 (corresponding to minor variability in positioning of the C terminus relative to N terminus of helical segment
Ser264Leu273). Using the Kabsch-Sander secondary structure assignment method (65) as implemented in PROMOTIF (66), helical structure predominates over the converged segments N- and C-terminal to Gly261. In the N terminus, helical structure predominates from Leu255Phe260 and in the C terminus from Leu264Val272 (detailed analysis in the Supplemental Material). In a given two-conformer structure in agreement with the experimental data, the relative positions and orientations of the two helical segments about Gly261Glu262 tend to differ.
The structure of TM VII in DPC micelles is therefore an interrupted helix. A representative conformer from the ensemble of structures is shown in Fig. 9. The relative positioning and orientation of the N- and C-terminal helical stretches are quite variable about Gly261 in the isolated TM segment. However, in the protein environment this would likely be a well defined kink, with strong potential for an interruption in helicity over the range Phe260Ser263. It should be noted that in the prokaryotic Na+/H+ exchanger NhaA (67), as well as a number of other membrane protein structures, kinked and interrupted helices are thought to play crucial roles in function. The inherent flexibility of the TM VII segment about Gly261 also suggests the potential for structural change in response to pH, as has been hypothesized to be take place with the kinked and interrupted helical transmembrane segments IV and XI of NhaA (67). The exact role of TM VII in ion transport should become more apparent as the pH sensor mechanism of NHE1 becomes better understood.
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Ala mutant is actually highly conservative because Ala and Ser have very similar packing characteristics (68). Replacement of the subsequent Leu264 or Leu265 with Ala did not greatly inhibit activity, after correction for expression and targeting was taken into account. Therefore, it seems that the local structure rather than the chemical character of side chains over Ser263Leu265 is important for function, with the good possibility that substitution of Ser263 with a residue of lower helical packing capability would affect overall NHE1 structure.
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-helical nature of the TM VII segment over the range including Asn266, Asp267, and Thr270 means that all three side chains fall on the same face of the segment (for example see their positions in Fig. 9). Negatively charged amino acids have been reported to be present in the funnel region of the prokaryotic Na+/H+ exchanger NhaA (67), and Asp267 could play a similar role in NHE1. Along these lines, Thr270 may have an analogous function to Thr132 of NhaA, which serves an important, although not essential, role in Na+ binding (67). Therefore, it is possible that the side chains of these three residues are all involved in a cytoplasmic side ion funnel of NHE1 similar to that proposed for NhaA. Alternatively, the Asp267 side chain may form a critical salt bridge for functional protein structure. As with Ser, Thr is proposed to allow close packing of TM segments in membranes (68), meaning that Thr270 may readily have a crucial packing interaction with the same neighboring segment that would be disrupted by replacement with the much smaller Ala side chain. Insertion of an Ala between Leu264 and Leu265 would disrupt either role of these critical residues by shifting the register of the entire helix off by one residue, and this insertional mutant indeed showed strongly perturbed expression, targeting, and activity.
Our study gives a detailed structural and full functional picture of TM VII. TM VII is a transmembrane segment that is critical for NHE1 function. We demonstrate that 13 of 22 residues were sensitive to mutation to alanine and that mutation of 5 residues altered sensitivity to inhibition by EMD87580. In contrast to TM IV of NHE1, TM VII is predominantly
-helical. However, it has a pronounced break in helicity in its central region, which includes the functionally essential acidic Glu262 residue. The helical nature of the C terminus of this segment positions three critical residues (Asn266, Asp267, and Thr270) on the same face of the segment. If these are determined to be involved in ion transport rather than structural stabilization of NHE1, this result provides a starting point for mechanistic elucidation of ion funneling and transport. Future experiments may both further elaborate the role of TM VII in ion exchange and examine the structure-function relationship for other TM segments of the NHE1 isoform of the Na+/H+ exchanger.
| FOOTNOTES |
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The atomic coordinates and structure factors (code 2HTG) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/). ![]()
The on-line version of this article (available at http://www.jbc.org) contains supplemental text, Figs. S1 and S2, and supplemental Refs. 110. ![]()
1 Both authors contributed equally to this work. ![]()
2 Supported by Alberta Heritage Foundation for Medical Research and the Canadian Institutes of Health Research Strategic Training Institute in Membrane Proteins and Cardiovascular Disease. ![]()
3 Recipient of postdoctoral fellowships from the Natural Sciences and Engineering Research Council of Canada, the Alberta Heritage Foundation for Medical Research, and the Canadian Institutes of Health Research Strategic Training Institute in Membrane Proteins and Cardiovascular Disease. ![]()
4 Recipient of support as a Canada Research Chair in Structural Biology. ![]()
5 Supported by a grant from the Canadian Institutes of Health Research and a Scientist Award from Alberta Heritage Foundation for Medical Research. To whom correspondence should be addressed: Dept. of Biochemistry, 347 Medical Science Bldg., University of Alberta, Edmonton, Alberta T6G 2H7, Canada. Tel.: 780-492-1848; Fax: 780-492-0886; E-mail: lfliegel{at}ualberta.ca.
6 The abbreviations used are: NHE1, Na+/H+ exchanger isoform 1; DIPSI, decoupling in the presence of scalar interactions; DPC, dodecylphosphocholine; DPC-d38, deuterated DPC; HA, hemagglutinin; HSQC, heteronuclear single quantum coherence spectroscopy; NOE, nuclear Overhauser effect; NOESY, NOE spectroscopy; PBS, phosphate-buffered saline; TM, transmembrane (segment); TOCSY, total correlation spectroscopy; HPLC, high pressure liquid chromatography; t-Boc, tert-butyloxycarbonyl. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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