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J. Biol. Chem., Vol. 280, Issue 15, 14499-14506, April 15, 2005
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From the
Adolf-Butenandt-Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München, 81377 München, Germany,
Institut für Humangenetik, GSF Forschungszentrum für Umwelt und Gesundheit, 85764 Neuherberg, Germany, ¶Botanisches Institut, Ludwig-Maximilians-Universität München, 80638 München, Germany, ||Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada, and **Abteilung Biophysik, Biologisches Institut, Universität Stuttgart, 70550 Stuttgart, Germany
Received for publication, December 3, 2004 , and in revised form, February 7, 2005.
| ABSTRACT |
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| INTRODUCTION |
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Studies on the isolated TOM complex from Neurospora crassa and Saccharomyces cerevisiae have provided detailed information about the structure and function of this translocase (712). The holocomplex consists of two receptor subunits, Tom70 and Tom20, and the proteins Tom40, Tom22, Tom7, and Tom6. The receptor subunits recognize different subsets of mitochondrial precursor proteins, whereas the other components form the protein-conducting channel complex (1317). The TOM core complex consists of the subunits Tom40, Tom22, Tom7, and Tom6 (8).
An additional small subunit of the TOM complex, Tom5, was identified in S. cerevisiae (18). This protein is associated with the protein-conducting channel. Yeast mitochondria lacking Tom5 were reported to have severe defects in the import of proteins destined for the outer membrane (19), intermembrane space (20), inner membrane, and matrix compartment (18). This was taken to suggest that Tom5 is crucial for protein import to all mitochondrial subcompartments.
In yeast mitochondria, Tom5 is anchored in the outer membrane by a single transmembrane segment. Its primary structure revealed a cytosolic domain that carries a net negative charge. This feature led to the hypothesis that Tom5 guides positively charged mitochondrial targeting sequences from the surface receptors to the protein-conducting channel (18). A detailed structural analysis of the cytosolic domain of yeast Tom5 was performed using nuclear magnetic resonance spectroscopy. The cytosolic domain was found to exhibit an
-helical fold with alternating positive and negative charges (21). The charge topology did not present a pattern complementary to typical amino-terminal mitochondrial presequences. In addition, the structure did not provide a hydrophobic surface that could favorably interact with the hydrophobic face of amphiphilic mitochondrial presequences.
In view of the different concepts derived from functional and structural studies we decided to investigate the role of Tom5 in mitochondrial protein import in Neurospora and yeast. We cloned the Neurospora gene and tested whether Tom5 is interchangeable between S. cerevisiae and N. crassa. Although the amino acid sequence of Neurospora Tom5 shares only moderate sequence similarity with the yeast protein, it could substitute for its counterpart in yeast. In contrast to what was observed in yeast, Neurospora Tom5 deletion strains did not exhibit any growth defect. In line with this finding, mitochondria isolated from a N. crassa strain with an inactivated tom5 gene were unimpaired in their capacity to import mitochondrial preproteins.
A role of Tom5 as a preprotein receptor was not observed in either organism. Rather our results point to a non-essential structural role of Tom5 in the TOM complex of Neurospora. In yeast, Tom5 appears to be required for maintaining the stability of the TOM complex at higher temperatures. This in turn is a prerequisite for functionality of preprotein import of the mitochondrial outer membrane protein translocation machinery.
| MATERIALS AND METHODS |
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Isolation of Mitochondria and Outer Membrane VesiclesThe preparations of mitochondria and mitochondrial outer membrane vesicles from S. cerevisiae and N. crassa were carried out as described previously (7, 23). Mitochondria used for protein import studies were isolated from the N. crassa wild-type strain 74A, the N. crassa tom5RIP mutant strain, the S. cerevisiae wild-type strain YPH499, the S. cerevisiae tom5
mutant strain (a kind gift from Dr. N. Pfanner, University of Freiburg, Freiburg, Germany) and the S. cerevisiae tom5
strain rescued by a plasmid carrying the sequence information for a Fis1-Tom5C fusion protein (24).
Isolation of the TOM Core ComplexLarge scale purification of TOM core complex was performed according to Ahting et al. (8) from N. crassa strain GR-107 that carries a hexahistidinyl-tagged tom22 gene instead of the wild-type copy (7). Mitochondrial membranes were solubilized for 30 min at 4 °C in 1% n-dodecyl
-maltoside (Glycon Biochemicals), 50 mM potassium acetate, 10 mM MOPS,1 pH 7.2, 10% glycerol. After a clarifying by centrifugation the supernatant was passed through a Ni2+-nitrilotriacetic acid column (Qiagen), and the resin was washed with 40 mM imidazole. Specifically bound material was eluted with 300 mM imidazole, 50 mM potassium acetate, 10 mM MOPS, pH 7.2. For further purification, the TOM complex-containing fractions were pooled and transferred to a Resource Q anion exchange column (Amersham Biosciences) equilibrated with 50 mM potassium acetate, 10 mM MOPS, pH 7.2, 10% glycerol, 0.1% n-dodecyl
-maltoside. TOM core complex was then eluted by a linear 0500 mM KCl gradient. The protein solution was stored at 4 °C at a concentration between 2 and 5 mg/ml.
Mass SpectrometryIndividual subunits of isolated TOM core complex were separated by SDS-polyacrylamide gel electrophoresis. Tom5 was prepared for mass spectrometry by in-gel digestion according to procedures described previously (2527). Peptides were dried and stored at 20 °C. Salts and detergents were removed by Zip-TipTM chromatography (C18 reverse phase, Millipore). Wetting, equilibration of the column, peptide binding, washing, and elution of the peptides were performed as described in the Zip-TipTM user's manual.
All mass spectrometric analyzes were carried out on a MicromassTM Q-TOF-1.5 hybrid mass spectrometer (Micromass, UK). The instrument was equipped with a z-electrospray ionization source and a quadrupole and a time-of-flight (TOF) mass analyzer as well as a hexapole collision cell. All spectra were acquired in electrospray positive ion mode. For sample introduction, a "medium" nanoelectrospray capillary was used (Micromass Q-TOF, Protana, Denmark). No electrospray ionization gas (nitrogen) or desolvation gas was applied to the capillary. The flow rate was regulated by alteration of the capillary voltage. The quadrupole was set in wide bandpass mode to 3001500 m/z. Data were acquired in continuum mode. Duration of data collection was about 1 min. 25 scans were averaged at a rate of 2.0 s/scan. For electrospray MS/MS experiments, argon was used as collision gas, and the collision energy varied between 16 and 42 eV depending on the peptide analyzed. For representative spectra, data from 2550 scans were summed. For optimized spectra the following conditions were applied: electrospray capillary voltage was set to 650850 V; cone voltage was set to 45 V, and the microchannel plate was set to 2700 V when collecting MS data and to 2850 V for collecting MS/MS data. At first, the MS1 resolution was set to 10 to obtain optimal resolution. In later measurements the resolution was set to 15.
MS1 and MS2 were maintained as recommended in the user's guide. Acquired mass spectra were processed using software Mass-Lynx versions 3.4 and 3.5. For calibration, standard solutions of sodium iodide (2 µg/µl) and rubidium iodide (0.05 µg/µl) were dissolved in 50% propan-2-ol (Q-TOF user's guide). Calibration data were acquired over a mass range from 50 to 2000 m/z.
Cloning of N. crassa tom5Based on parts of the Tom5 amino acid sequence, a 153-base genomic sequence was identified from the White-head Institute Neurospora crassa sequence data base (Cambridge, MA; N. crassa contig 3.132). A cDNA version of the N. crassa tom5 gene was amplified from a
Bluescript cDNA library by the PCR using T5up (5'-CGCGGATCCCGACTTCCATATCAAAATGTTCGG-3') and T5low (5'-CCCAAGCTTCGAATATTTAGAGAACCTTGCTAACGGC-3') as primers and cloned into pGEM-T (Promega). The PCR was performed using Pfu DNA polymerase (Promega) according to the manufacturer's instructions. DNA sequencing was performed using automated fluorescent sequencing technology (MediGenomix).
To improve the detection of [35S]methionine-labeled Tom5 by auto-radiography, a tom5 gene encoding two additional methionine residues at the carboxyl terminus was cloned in pGEM-T with its expression under the control of the T7 promoter. The PCRs were carried out using T5up and T5lowMM (5'-CCCAAGCTTTTACATCATGAGAACCTTGCTAACGGCGTCGATAACGAA-3') as primers. For expression of N. crassa Tom5 in S. cerevisiae, N. crassa tom5 was cloned into the EcoRI/XhoI sites of pYX132 under the control of the constitutively active triose-phosphate isomerase promoter (Novagen). The construct and empty vector were transformed into yeast tom5
cells that were derived from the isogenic wild-type strain YPH-501 (18).
AntibodiesAntibodies against Tom5 were raised in rabbits using an oligopeptide corresponding to 20 amino-terminal amino acid residues of Tom5 as the antigen (NH2-FQPPALSREELQAAEAEATF-COOH coupled to keyhole limpet hemocyanin; Pineda Antikörper Service, Berlin, Germany).
Construction of an N. crassa Strain Deficient in Tom5The report of a severe phenotype in tom5 mutants of S. cerevisiae (18) suggested that inactivation of tom5 in N. crassa might also cause severe import and growth defects. For this reason, we chose to inactivate the gene using the procedure of "sheltered repeat-induced point mutation (RIP)." This procedure utilizes the natural phenomenon of RIP to inactivate genes in N. crassa (28) and also allows for the maintenance of nuclei containing non-functional alleles of an essential gene in a heterokaryon that also contains nuclei with a wild-type copy of the gene. The rationale and methodology of the procedure have been described previously (29). The tom5 gene was found on chromosome I by examination of the sequence at the N. crassa genome sequencing website (www-genome.wi.mit.edu/annota-tion/fungi/neurospora). A duplication of tom5 was created in the Host I strain by transformation with plasmid pTom5RIPhyg, which contains a 2.5-kb PCR product of the tom5 region of the genome cloned into the hygromycin resistance vector pCSN44. The sheltered RIP cross-yielded several heterokaryotic strains. DNA from these strains was subjected to the PCR using primers specific for the tom5 gene. Heterokaryon Tom5RIPed-35 was chosen as a strain that contained mutations characteristic of RIP in the tom5 gene. Conidiospores from the heterokaryon were streaked onto medium containing all the requirements of the two nuclei that were components of the heterokaryon. Individual colonies were isolated and tested for nutritional requirements. Surprisingly many robust cultures were found to be nicotinamide-requiring, a trait that was diagnostic for the nucleus predicted to carry tom5 genes that had been inactivated by RIP. Analysis of these cultures with antiserum raised against Tom5 revealed a total absence of the protein. Strain Tom5RIPed-35-5 (abbreviated tom5RIP) was chosen for further work.
Cross-linkingFor cross-linking experiments outer membrane vesicles (50 µg) and purified TOM core complex (1.5 µg) were suspended in 25 µl of 50 mM HEPES, pH 7.2, and incubated with 0.10.4% (v/v) freshly prepared paraformaldehyde at 25 °C for 2040 min. Aliquots were removed before and after the addition of the cross-linking reagent. Proteins were directly analyzed by SDS-PAGE and Western blotting.
Size Exclusion ChromatographyOuter membrane vesicles (100 µg) isolated from wild-type and tom5RIP mitochondria were solubilized in 0.2% n-dodecyl
-maltoside with 50 mM potassium acetate, 10 mM MOPS (pH 7.2), 10% glycerol. After clarifying by centrifugation, detergent-solubilized proteins were loaded onto a Superose 6 PC 3.2/20 size exclusion column (Amersham Biosciences) equilibrated with the solubilization buffer using the Ettan-LC chromatography system (Amersham Biosciences). Protein was eluted at room temperature at a flow rate of 0.04 ml min1. Individual fractions were analyzed by SDS-PAGE and immunoblotting. The molecular masses of TOM complexes were calculated using UV spectra of chromatographs of thyroglobulin (669 kDa), apoferritin (443 kDa), alcohol dehydrogenase (155 kDa), and carbonic anhydrase (29 kDa) as protein standards.
StoichiometryFor the determination of the stoichiometry of Tom5, Tom6, and Tom7, the TOM core complex was isolated from strain GR-107 that had been grown in the presence of [35S]sulfate as described previously (8). The purified TOM core complex was subjected to high Tris/urea SDS-polyacrylamide gel electrophoresis. Radiolabeled proteins were extracted from the gel by incubation of 1-mm gel slices in 10% SDS and quantified by scintillation counting (Tri-Carb 2100TR liquid scintillation analyzer, Canberra-Packard GmbH). The molar ratio between the individual subunits of the TOM complex was calculated based on their number of methionine and cysteine residues.
Import of Preproteins into Isolated MitochondriaPreproteins were synthesized using the TNT® T7/SP6 coupled reticulocyte lysate transcription/translation system (Promega) in the presence of [35S]methionine. In vitro transcription from pGEM4 vectors containing the gene of interest was performed with SP6 polymerase. Radiolabeled precursor proteins (2% reticulocyte lysate) were incubated at room temperature with 50 µg of Neurospora or S. cerevisiae mitochondria in 250 mM sucrose, 80 mM KCl, 5 mM MgCl2, 13 mM ATP, 4.4 mM NADH, 3% (w/v) bovine serum albumin, 10 mM MOPS-KOH, pH 7.2, for 110 min. Import reactions were stopped by addition of ice-cold SEM buffer (250 mM sucrose, 1 mM EDTA, 10 mM MOPS-KOH, pH 7.2). Mitochondria were reisolated by centrifugation for 10 min at 12,500 x g, resuspended in SEM buffer, and incubated with proteinase K for 15 min on ice followed by addition of 2 mM phenylmethylsulfonyl fluoride. Import was analyzed by SDS-PAGE and blotting to nitrocellulose membranes. Alternatively reisolated mitochondria were solubilized in 20 mM Tris, pH 7.2, 0.25% (w/v) n-dodecyl
-maltoside at 4 °C, subjected to blue native (BN)-PAGE and blotted to polyvinylidene difluoride (PVDF) membranes.
Gel ElectrophoresisBN-PAGE was carried out essentially as described previously (30). Mitochondria (50 µg) were solubilized in 100 mM bis-Tris, pH 7.2, 0.25% (w/v) n-dodecyl
-maltoside. After clarifying by centrifugation, the supernatants (40 µl) were supplemented with 5 µl of sample buffer (5% (w/v) Coomassie Brilliant Blue G-250, 0.5 M
-amino-n-caproic acid, 100 mM bis-Tris, pH 7.0) and electrophoresed through 613% polyacrylamide gradient gels. The cathode and anode buffers for performing the electrophoresis were as described previously (30).
SDS-polyacrylamide gel electrophoresis and blotting were performed according to standard procedures. To achieve a higher resolution of the smaller TOM components high Tris/urea gels were used (7). The chemiluminescence ECL detection system (Amersham Biosciences) and goat anti-rabbit antibodies conjugated to horseradish peroxidase were used for immunostaining. Radiolabeled precursor proteins were detected by autoradiography and quantified using the TINA software of the BAS 1500 phosphorimaging system (Fuji Medical Systems).
| RESULTS |
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5-kDa molecular mass (Fig. 1A). To determine its amino acid sequence the protein was extracted from the gel and sequenced by mass spectrometry. Using parts of the amino acid sequence as queries, the genomic sequence encoding the protein was identified in the N. crassa nucleotide sequence data base (Fig. 1B). The tom5 gene contains two introns and encodes a protein consisting of 50 amino acid residues. The Tom5 sequence can be viewed in GenBankTM under accession number CAE76411
[GenBank]
The protein shares 34% sequence identity with Tom5 of S. cerevisiae and 44% sequence identity with an open reading frame of the fungus Botryotinia fuckeliana. The amino acid sequence of Tom5 exhibits a hydropathy profile with one predicted transmembrane segment near the carboxyl terminus, a feature conserved in the proteins of B. fuckeliana and S. cerevisiae (Fig. 1C). The amino-terminal domain of Neurospora Tom5 contains four negatively charged amino acid residues. However, the positions of only two of them are conserved among the three organisms mentioned above.
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To confirm that the newly identified protein is a real subunit of the TOM complex radiolabeled Tom5 was imported into mitochondria isolated from Neurospora. As controls, we studied the integration of the radiolabeled precursors of Tom7, Tom22, and Tom40 into the TOM complex. Imported Tom5 was shown to be present in the mature 400-kDa TOM core complex (Fig. 2E). In contrast to imported Tom40 no low molecular mass import intermediate was observed indicating that Tom5 inserted into a largely assembled TOM complex.
Neurospora Tom5 Is a Functional Homolog of Yeast Tom5To test whether Neurospora Tom5 can substitute for yeast Tom5 we transformed the Neurospora tom5 cDNA into a yeast TOM5 deletion mutant that was described to exhibit a characteristic temperature-sensitive growth defect (18). Yeast cells lacking tom5 stopped growing when the temperature was raised from 30 to 37 °C (Fig. 3). Expression of Neurospora Tom5 in these cells restored growth. This indicated that the Tom5 proteins in the two fungi are functional equivalents.
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Depletion of Tom5 in Neurospora Has No Effect on Import of Mitochondrial PreproteinsTo assess whether Tom5 functions as a receptor for mitochondrial preproteins, in vitro synthesized mitochondrial preproteins labeled with [35S]methionine were imported into mitochondria isolated from tom5RIP cells. Fig. 5 (AD) shows the import kinetics of the mitochondrial outer membrane protein Tom40, the intermembrane space protein Tim9, the inner membrane protein Tim23, and the matrix-targeted protein pSu9-DHFR, consisting of the presequence of subunit 9 (Su9) of the F0-ATPase and dihydrofolate reductase (DHFR). No significant differences were observed in the import kinetics of these precursors between mitochondria isolated from wild-type cells and cells lacking Tom5. The assembly of Tom40 into the TOM complex was not affected in Tom5-deficient mitochondria (Fig. 5E). We conclude that Tom5 has no direct role in the import of mitochondrial preproteins or in the biogenesis of the TOM complex in N. crassa.
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To compare the stability of yeast and Neurospora TOM complexes mitochondria from both organisms were solubilized in the presence of increasing concentrations of the non-ionic detergent n-dodecyl
-maltoside (Fig. 6, C and D). The TOM complex of Neurospora was stable up to 0.4% (w/v) n-dodecyl
-maltoside irrespective of the presence or absence of Tom5 (Fig. 6D). The TOM complex of S. cerevisiae, however, was found to dissociate into a subcomplex with a molecular mass of
100 kDa (Fig. 6C). In the absence of yeast Tom5, the TOM complex was completely unstable. Most of its components aggregated even at higher detergent concentrations.
There was no difference between the apparent molecular mass of the TOM complex lacking Tom5 compared with the wild-type complex in Neurospora (see Figs. 4B and 6A, upper panel). In addition, the stability of the Tom5-deficient complex when exposed to increasing concentrations of n-dodecyl
-maltoside did not differ from that of wild-type complex (Fig. 6D). In electrophysiological analysis and electron microscopic studies of the isolated Tom5-deficient complex no differences were found in comparison with the wild-type complex (data not shown). In conclusion, in the absence of Tom5 the overall architecture of the Neurospora TOM complex remains unaltered.
The Carboxyl-terminal Segment of Tom5 Rescues the Protein Import in S. cerevisiae tom5
CellsFinally we asked whether the transmembrane segment of yeast Tom5 can complement the temperature-sensitive growth defect of yeast cells lacking Tom5 and restore the ability of tom5
mitochondria to import proteins. As a model protein we used the chimeric protein Fis1-Tom5C (24). Protein import studies were performed using in vitro synthesized mitochondrial preproteins labeled with [35S]methionine and mitochondria isolated from wild-type, tom5
, and tom5
cells expressing Fis1-Tom5C.
Fig. 7 (AC) shows the import kinetics of the outer membrane protein mitochondrial porin (voltage-dependent anion channel), the intermembrane space protein cytochrome c hemelyase, and the inner membrane protein Tim23. Expression of Fis1-Tom5C largely restored protein import into mitochondria. According to this the temperature-sensitive phenotype of tom5
cells was efficiently complemented by expression of Fis1-Tom5C (Fig. 3).
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| DISCUSSION |
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5 kDa was co-immunoprecipitated with antibodies against Tom40 of rat (34). Therefore, a homolog to yeast and Neurospora Tom5 might be present in mammalian TOM complexes. Several proteins of low molecular mass associated with the TOM complex were detected in plants, but none has yet been identified as a Tom5 homolog (1, 35). For yeast Tom5 a role as a general import receptor in protein import has been proposed (18). However, unlike in yeast, all tested precursor proteins of the various mitochondrial subcompartments were imported into Neurospora mitochondria deficient in Tom5 as effectively as into wild-type mitochondria. A role of yeast Tom5 in assembly of Tom40 into the TOM complex in vitro has also been reported (16). In the absence of Tom5 a radiolabeled Tom40 precursor accumulated in a 250-kDa assembly intermediate containing Tob55, and the maturation into the 400-kDa TOM complex was impaired (6, 16). In contrast, in a tom5RIP strain of Neurospora we did not detect any defects in the assembly pathway of Tom40. Furthermore TOM5 is not an essential gene in yeast, and endogenous protein levels of Tom40 were not altered either in a yeast (18) or in a Neurospora Tom5 deletion strain. A receptor-like function of Tom5 would be expected to reside in its cytosolic domain. However, a fusion protein consisting of the transmembrane region of yeast Tom5 with the unrelated protein Fis1 replacing the cytosolic domain is sufficient to rescue the growth phenotype and the mitochondrial protein import defect of the yeast Tom5 deletion mutant (24, 33). This makes a receptor-like function of Tom5 unlikely.
As our findings did not agree with a receptor-like function of Tom5 we asked whether Tom5 rather has a structural role. The yeast TOM complex lacking Tom5 exhibited a decreased stability as compared with the complex from wild-type cells. Exposure of the yeast TOM complex to mild detergent caused it to disassemble to a 100-kDa species. In the Tom5 deletion mutant this species was absent, and most of the protein seemed to be aggregated. Integration of Neurospora Tom5 into the Tom5-deficient yeast TOM complex restored its stability. A structural role of Tom5 was also suggested by an altered electrophoretic behavior of the TOM complex from Tom5-lacking cells. Again this could be cured by integration of Neurospora Tom5 or likewise the expression of a fusion protein consisting of the cytosolic domain of Fis1 and the transmembrane segment of yeast Tom5. In Neurospora we did not observe differences in the electrophoretic mobility after heat treatment or upon exposure to detergent. We conclude that Neurospora TOM complex is more stable than its yeast counterpart and does not depend on the function of Tom5 under the conditions analyzed.
We suggest that the membrane-spanning segment of Tom5 is responsible for its structural function. This is supported by the finding that the transmembrane region of Tom5 is sufficient to rescue the growth phenotype of the yeast Tom5 deletion mutant (24, 33). A proline residue within the transmembrane segment that was shown to be part of a targeting signal of Tom5 is conserved among the Tom5 proteins so far identified (33). In addition, a proline residue can be found in the transmembrane region of the Tom6, Tom7, and Tom22 proteins. This led to the hypothesis that it is essential for the interaction of these tail-anchored components of the TOM complex with the pore-forming protein Tom40 (24, 36). In conclusion Tom5 plays a role in maintaining the structural integrity of the TOM complex but has no apparent role as a presequence-recognizing receptor component.
| FOOTNOTES |
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To whom correspondence should be addressed: Biologisches Institut, Abteilung Biophysik, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany. Tel.: 49-711-685-5002; Fax: 49-711-685-5090; E-mail: nussberger{at}bio.uni-stuttgart.de.
1 The abbreviations used are: MOPS, 4-morpholinepropanesulfonic acid; Q-TOF, quadrupole time-of-flight; MS, mass spectrometry; RIP, repeat-induced point mutation; BN, blue native; PVDF, polyvinylidene difluoride; bis-Tris, 2-[bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)-propane-1,3-diol; Su9, subunit 9; DHFR, dihydrofolate reductase; TIM, translocase of the inner mitochondrial membrane; TOM, translocase of the outer mitochondrial membrane; TOB, protein complex essential for the topogenesis of mitochondrial outer membrane
-barrel proteins. ![]()
| ACKNOWLEDGMENTS |
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(YPH-501). | REFERENCES |
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