2. Protein structure and membrane interaction of BamB is mediated by negatively
2.4 Results
2.4.4 Fluorescence studies confirm binding of BamB to the lipid membrane
functional secondary structure which was comparable to the available crystal structure data. In this study, ProBamB was used to examine the interaction to the lipid membrane with different preparations of LUVs (DLPE/DLPG (4:1) or DLPG). Since BamB developed distinct structures depending on the lipid membrane environment, it was investigated if this is correlated to the binding of BamB to the lipid membrane.
To examine the interaction of BamB with the lipid membrane, fluorescence spectroscopy was used to excite the intrinsic fluorescence of tryptophan residues, naturally occurring in the protein. The fluorescence of tryptophan is highly sensitive to its (local) environment and changes in the wavelength of the fluorescence maximum as well as in the fluorescence intensity result from conformational changes in BamB or binding to membranes or both. A shift of the fluorescence maximum to shorter wavelengths (blue-shift) can occur upon binding to the lipid bilayer, which is less polar. A decrease of the quantum yield of the fluorescence is observed, when the tryptophan residues are exposed to water molecules that can deactivate the excited state of the fluorophore by collision. Wt-BamB contains nine tryptophan residues which are evenly distributed in the protein and can be used as an indicator for protein-lipid interactions (Fig. 2.7).
Unfortunately, the substitution of eight tryptophan residues to phenylalanine resulted in a loss of secondary structure of BamB (Fig. A1). The only tryptophan residue of BamB that could be substituted to phenylalanine without losing β-structure was the tryptophan at amino acid position W103, located in loop1 (Fig. 2.7). Based on protein sequence alignment, this tryptophan is the least conserved one in E. coli BamB as compared to various homologs from Y. pestis, V. cholerae stereotype 1, P. aeruginosa, B. pertussis and S. typhimurium (Fig. A2).
Consequently, site-specific interaction between BamB and the lipid membrane could not be investigated with tryptophan.
1 48 93 138 182 226 271 316 360
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTA WSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEI WSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTS DGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAV KWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQ MIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVFALAYNGNLTAL DLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVT LWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQ QKVDSSGFQTEPVAADGKLLIQAKDGTVYSITRLEHHHHHH*
47 92 137 181 225 270 315 259 400
Fig. 2.7 Position of native tryptophan residues in wt-BamB. Wt-BamB contains a signal sequence (amino acids 1 - 19, underlined) and the native cysteine at amino acid position 20 (C20, green) at the N-terminus. The tryptophan residues are given in red together with the number showing the exact position of the amino acid within the sequence. The protein was purified upon the His-tag (blue) at the C-terminus. (A) Lateral view of wt-BamB showing all nine native tryptophan residues in red. (B) BamB was rotated 90° around the x-axis demonstrating that the tryptophan residues are evenly distributed in the protein with one tryptophan localized in each β-blade (numbered 1 - 8) and one tryptophan (W103) in loop1. Amino acid side chains are shown in spheres for better illustration. The configurated figure is based on PDB structure 2yh3 (Albrecht and Zeth, 2011) and was created with PyMol 1.8.0.7 for macOS.
BamB, isolated in unfolded form in solutions of 8 M urea, was refolded by dilution of urea in aqueous solution both in the absence and in the presence of lipid bilayers. The fluorescence intensity of all nine tryptophan residues of BamB was measured to investigate binding of the protein to the lipid membrane. The fluorescence intensity increased after vesicles of the lipid compositions DLPE/DLPG (4:1) or of DLPG were added, indicating binding of BamB to these lipid bilayers (Fig. 2.8). BamB showed a significant increase in the fluorescence intensity up to 28 % in the presence of DLPG and the fluorescence maximum was shifted from 333 nm to 335 nm (Fig. 2.8, A). On the other hand, the addition of DLPE/DLPG (4:1) showed only a minor effect with an increase in the fluorescence intensity of 5 % and a shift of the wavelength of the fluorescence maximum λmax was not observed in these bilayers.
To analyze the binding of BamB to lipid bilayers specifically at its N-terminal region, the native cysteine of BamB (C20) was spectroscopically labeled with an organic fluorophore, either
B
90°
1 2 3 4
5
6
7 8
W103
W103 W48
W93 W143 W183
W228
W279
W317 W348
A
IAEDANS or IANBD. As for tryptophan, the fluorescence emissions of these organic fluorophores are sensitive to changes in polarity and mobility of the environment. The fluorescence emission of C20 labeled with IANBD had a fluorescence maximum at 541 nm in aqueous solution with a relative fluorescence of F541 = 0.32 Mcps. The addition of DLPG increased the fluorescence intensity up to 161 % (F541 = 0.83 Mcps) displaying a clear blue-shift in λmax from 555 nm in the absence to 540 nm in the presence of DLPG (Fig. 2.8, B).
Fig. 2.8 Fluorescence spectra indicate that the binding of BamB to lipid bilayers depends on bilayer properties. All spectra were recorded for 0.5 μΜ BamB in glycine buffer (10 mM, 2 mM EDTA, pH 8.0) at 25°C either in the absence or presence of lipid membranes (500 mM), either composed of DLPE/DLPG (4:1) or of DLPG. (A) The nine native tryptophan residues of ProBamB were excited at 295 nm and the emission spectra were recorded over the wavelength range from 310 nm to 400 nm. (B) The native cysteine of ProBamB (C20) was labeled with IANBD and excited at 478 nm. The fluorescence spectra were recorded in the wavelength range from 490 nm to 700 nm. (C) The C20 residue of ProBamB was labeled with IAEDANS, excited at 336 nm and the fluorescence spectra were recorded from 410 nm to 650 nm.
In the presence of DLPE/DLPG (4:1) λmax was blue-shifted by 3 nm and the fluorescence intensity slightly increased to F541 = 0.36 Mcps (15 %) indicating binding of C20 to both lipid membrane types with different affinities. The same experiment was performed with IAEDANS-labeled C20 (Fig. 2.8, C). Surprisingly, the addition of lipid vesicles composed of DLPE/DLPG (4:1) or DLPG did not show any significant changes of the fluorescence signal indicating that BamB did not bind to the membrane as demonstrated by overlapping fluorescence emission curves. Presumably caused by repulsion of its negative charge, IAEDANS is obviously not suitable as a fluorophore for the investigations of BamB with membranes containing negatively charged PG. For that reason, all other binding experiments were performed with BamB labeled at the native C20 with IANBD and the non-labeled BamB.
To determine the stoichiometry by which BamB binds to lipids, different samples were prepared containing 0.5 μM BamB and either DLPE/DLPG (4:1) or DLPG membranes at a lipid/BamB ratio ranging from 0 to 800 (Fig. 2.9). Tryptophan fluorescence spectra of BamB
were recorded by selective excitation at 295 nm. While the fluorescence intensity of BamB did not increase much in the presence of bilayers composed of DLPE/DLPG (4:1), it increased in bilayers of pure DLPG up to 28 % at a L/P ratio of 200 (Fig. 2.9, A and C).
The fluorescence intensity at 330 nm was plotted as a function of the L/P ratios (Fig. 2.10, A and B). By fitting equation 2.2 (section 2.3.7) to the experimental data a binding stoichiometry of 42 ± 9 was determined suggesting that 42 DLPG lipids were necessary to bind all of BamB to the membrane.
Fig. 2.9 Fluorescence spectra of native tryptophans of BamB and of IANBD linked to C20 of BamB depend on the lipid/BamB ratio. The spectra were used to determine the lipid/BamB stoichiometry. 0.5 μΜ ProBamB was either excited at the tryptophan wavelength of 295 nm (A and C) or at the IANBD wavelength of 541 nm in glycine buffer (10 mM, 2 mM EDTA, pH 8.0) at 25 °C (B and D). The fluorescence spectra of BamB were recorded at various molar L/P ratios, ranging from 0 (dashed black lines) to a 1000-fold molar excess (colored dotted lines and solid black line) of DLPE/DLPG (4:1) (A and B) or DLPG (C and D) over BamB.
Fig. 2.10 Determination of the lipid/BamB stoichiometry. The fluorescence measurements were performed in the presence of bilayers of either DLPE/DLPG (4:1) (A) or of pure DLPG (B) at various L/P ratios. The fluorescence intensities at 330 nm or 541 nm of wt-BamB (trp) or of the IANBD-labeled ProBamB, respectively were plotted as a function of the lipid/BamB ratios. The stoichiometry was obtained by fitting equation 2.2 to the experimental data (see section 2.3.7).
Beside the excitation of tryptophan in wt-BamB, the IANBD-labeled C20 was used to monitor the interactions of BamB with LUVs composed of DLPE/DLPG (4:1) or DLPG at various molar L/P ratios ranging from 0 to 1000. The IANBD-labeled protein was excited at 478 nm resulting in F541 = 0.32 Mcps in the absence of lipid (Fig. 2.9, B and D). The fluorescence emission spectra of IANBD displayed a blue-shift from 555 nm to 552 nm in the presence of DLPE/DLPG (4:1) bilayers (at L/P ranging from 100 to 1000) with a maximal fluorescence intensity of F541 = 0.36 Mcps, corresponding to a 15 % increase (Fig. 2.9, B). The fluorescence intensity at 541 nm was plotted as a function of the corresponding lipid/BamB molar ratio (Fig. 2.10, A). The binding stoichiometry of DLPE/DLPG (4:1)/BamB could not be
determined, as within error margins, no binding was observed. In the presence of DLPG the fluorescence spectra displayed a massive increase in the fluorescence intensity starting at L/P = 25 with F541 = 0.54 Mcps and leveling off at L/P = 400 with F541 = 0.83 Mcps, which was
~ 161 % greater than the intensity in the absence of lipid (Fig. 2.9, D). The increase of the intensity upon binding to DLPG bilayers was consistent with a blue-shift of the fluorescence of IANBD, from λmax ~ 555 nm in the absence of DLPG (L/P = 0) to λmax ~ 541 nm in the presence of DLPG bilayers (L/P = 200). The result from the fluorescence measurements was further analyzed by fitting equation 2.2 to the experimental data (Fig. 2.10, B). A binding stoichiometry of 35 ± 5 DLPG molecules per BamB molecule was obtained for the interactions of BamB with DLPG bilayers.
2.4.5 Confirmation of the native secondary structure in mutants of BamB by CD spectroscopy
The secondary structure of all designed single cysteine mutants of BamB (see 2.2 for details) was analyzed by CD spectroscopy to ensure that the substitutions of the selected amino acids to cysteines do not interfere with the correct folding of the protein. For comparisons, the recorded CD spectra of all single cysteine mutants of BamB were superimposed to the CD spectrum of wt-BamB (Fig. 2.11). All CD spectra displayed a similar line shape indicating comparable secondary structures dominated by β-sheets. The BamB mutants had secondary structures composed of 56 - 58 % β-sheets, 8 % α-helices and 35 - 38 % random coil as determined by deconvolution analyses with the algorithms CDSSTR (Sreerama and Woody, 2000) and CONTIN (Provencher and Glockner, 1981) (Table A1, A and B). As the secondary structures of the single cysteine mutants of BamB compared well to the structure of wt-BamB, all mutants were used in fluorescence studies.
Fig. 2.11 CD spectra of wt-BamB in comparison with single cysteine mutants of BamB. 12 μM of protein was measured in glycine buffer (pH 8.0) at room temperature. CD spectra were recorded in the range from 185 nm to 260 nm. The mean residue molar ellipticity [Θ](λ) was plotted as a function of the wavelength λ. The normalized spectra were analyzed to determine the secondary structure of the proteins to detect potential differences in their structures caused by the mutation (Table A1, A and B).
2.4.6 Studies on the site-specific interaction of IANBD-labeled single cysteine mutants of BamB with the lipid membrane
As demonstrated in previous experiments (see section 2.4.4), the binding of BamB to the lipid bilayer was not exclusively mediated by the signal peptide or the lipid anchor. Additional surface-exposed regions of BamB have to be involved in the interaction with the lipid bilayer.
To monitor the exact orientation of BamB to the lipid membrane, the single cysteine mutants described in sections 2.2 and 2.4.5 were used (Fig. 2.1). The interactions between IANBD-labeled BamB mutants and various lipid bilayers, composed of DLPG, DLPE/DLPG (4:1) or DLPC, were investigated in fluorescence studies.
All labeled single cysteine mutants of BamB were first measured in aqueous solution. The wavelengths of the maxima of the fluorescence emission (λmax) were different for the various BamB mutants and λmax ranged from λmax = 550 nm for the BamB mutants A47C and A203C to λmax = 557 nm for V181C (Table 2.6). Surprisingly, in the presence of lipid bilayers, all 13 single cysteine mutants of BamB and BamB C20 displayed increased fluorescence intensities and a blue-shift of λmax of different extents (Fig. 2.12). The λmax of the IANBD-labeled mutants of BamB and their changes Δλmax upon binding to lipid membranes are summarized in table 2.6 while changes in the fluorescence intensities are shown in table A2. For an overview, all measured single cysteine mutants of BamB were plotted as a function of the differencein the maximum wavelength of IANBD emission (∆λmax) and against the ratio of the fluorescence intensities either in the presence or in the absence of lipid (Fig. 2.13, A and B).An increased
fluorescence intensity in combination with a blue-shift of λmax identified specific binding regions of labeled BamB mutants to the lipid membrane or structural changes within BamB.
The BamB mutants with distinct changes in λmax and in the fluorescence intensity are shown by filled markers. Comparable to the fluorescence results in section 2.4.4, the fluorescence intensities of BamB mutants in the presence of neutral (DLPC) or mainly neutral (DLPE/DLPG (4:1)) lipid membranes were slightly increased, suggesting low affinity to these membranes (Fig. 2.12).
In the presence of DLPC, the largest blue-shift in λmax was displayed for the BamB mutant V181C with ∆λmax = –8 nm, from 557 nm in the absence to 549 nm in the presence of DLPC (Fig. 2.12, Table 2.6). This result was consistent with the observed increase of the fluorescence intensity by 15 % in the presence of DLPC (Fig. 2.12, Table A2). For the BamB mutants G102C, W103C and G120C, ∆λmax was ~ –6 nm, with G120C showing the highest increase of the fluorescence intensity by 9 % in the presence of DLPC. The mutations G102C, W103C, G120C and V181C were located near the N-terminus of the protein at the bottom (G120C, V181C) or the top (G102C, W103C) region and were all surface exposed. The amino acid residues S126C, A203C and A269C represented the single cysteine mutants of BamB in which the labeled cysteines were oriented towards the centered cavity of the protein and are shown in red in Fig. 2.13. All mutants facing the interior of the protein displayed a slight increase in the fluorescence intensity and a blue-shift in λmax with ∆λmax = –4 nm in case of S126C and ∆λmax
= –5 nm for A203C and A296C indicating an orientation of the fluorophore towards a hydrophobic environment.
Fig. 2.12 Site-specific interaction of labeled single cysteine mutants of BamB with the lipid bilayer. Single cysteine mutants of BamB were constructed as described in section 2.2 and labeled with the fluorophore IANBD. 0.5 μM protein was excited at the IANBD wavelength of 478 nm in glycine buffer (10 mM, 2 mM EDTA, pH 8.0) at 25 °C. The fluorescence spectra of BamB were recorded in the absence and in the presence of LUVs composed of DLPE/DLPG (4:1), DLPG and DLPC. Lipids were added in a 600-fold molar excess to the protein. The fluorescence (in Mcps) is plotted as a function of the wavelength (in nm).
Interestingly, the fluorescence of all BamB mutants showed a small increase and the λmax were shifted in the presence of DLPE/DLPG (4:1), both indicating binding of BamB to the lipid bilayer. By plotting the shifts ∆λmax against the position of the label in the BamB mutants a characteristic dependence was obtained. The pattern of this dependence was nearly identical
for BamB mutants in bilayers of either DLPC or of DLPE/DLPG (4:1), with approx. +/–1 nm difference in λmax (Fig. 2.13, A). Distinct changes in ∆λmax were again identified for the mutants V181C, G102C, W103C and G120C. G102C displayed the largest shift in the fluorescence maximum with ∆λmax = –6 nm, from 551 nm in the absence to 545 nm in the presence of DLPE/DLPG (4:1). In regard to these two lipid bilayers, relative differences in the ∆λmax of the fluorescence emissions of the labeled mutants of BamB were largest for those of C20, V181C and A203C. λmax of C20 displayed a small blue-shift, from 551 nm in the absence of lipids to 548 nm in the presence of DLPC bilayers with Δλmax = –3 nm but λmax changed in the presence of DLPE/PG (4:1) to 552 nm, representing a red shift with Δλmax = +1 nm. A203C was orientated to the interior of the protein and a change in the composition of the lipid bilayer from DLPC to DLPE/DLPG (4:1) resulted in a reduced blue shift of λmax compared to measurements in the absence of lipid with Δλmax = –2 nm.
Table 2.6 Fluorescence emission maximum (λmax) of IANBD-labeled single cysteine mutants of BamB in the presence of various dilauroylglycerophospho (DLP)-lipids a.
BamB
mutant λmax
(nm) (buffer)
λmax (nm)
(DLPE/DLPGb) λmax (nm)
(DLPG) λmax (nm)
(DLPC) Δλmaxc (nm) (DLPE/DLPGb)
Δλmax
(nm) (DLPG)
Δλmax
(nm) (DLPC)
C20 551 552 540 548 +1 –11 –3
A47C 550 547 542 548 –3 – 8 –2
S54C 554 550 543 549 –4 –11 –5
G102C 551 545 538 545 –6 –13 –6
W103C 555 550 541 549 –5 –14 –6
G120C 555 550 543 549 –5 –12 –6
S126C 548 545 540 544 –3 – 8 –4
V181C 557 552 541 549 –5 –16 –8
S191C 547 545 538 545 –2 – 9 –2
A203C 550 548 540 545 –2 –10 –5
A269C 555 551 544 550 –4 –11 –5
Q301C 553 549 543 548 –4 –10 –5
S364C 549 547 539 545 –2 –10 –4
A374C 549 547 539 545 –2 –10 –4
a A 600-fold molar excess of lipid to BamB was used. bThe phospholipids DLPE and DLPG were used in ratio of 4:1. c Difference in the maximum wavelength of IANBD emission (λmax in the presence of lipid – λmax in buffer).
Independent of the localization of the cysteine, the presence of the negatively charged DLPG had the highest impact on the fluorescence intensity and on λmax of the fluorescence of BamB mutants with Δλmax ranging from –8 nm in A47C and S126C to –16 nm in V181C (Fig. 2.13, Table 2.6, Table A2) indicating an orientation of the fluorophore towards a hydrophobic environment. Again, the BamB mutants G102C, W103C, G120C and V181C displayed distinct changes in their fluorescence intensity as well as in λmax. The highest increase in the fluorescence intensity was observed for G102C with F541 = 0.51 Mcps in the absence of lipid to F541 = 1.98 Mcps in the presence of DLPG resulting in a calculated fluorescence intensity
ratio of 3.88 (Fig. 2.13, B). BamB mutant W103C showed a comparable increase with F541 = 0.27 Mcps in the absence of lipid to F541 = 0.91 Mcps in the presence of DLPG resulting in a ratio of 3.39. For the mutants G102C, W103C, G120C and V181C ∆λmax values of –13 nm, –14 nm, –12 nm and –16 nm, respectively, were observed, representing large shifts in λmax that were consistent with observed increases in the fluorescence intensities. Additionally, BamB mutant S54C displayed a blue-shift from 554 nm in the absence of lipid to 543 nm in the presence of DLPG with ∆λmax = –11 nm.
The identified shifts in the fluorescence maximum wavelengths ∆λmax of all BamB mutants followed a pattern that was dependent on the composition of the lipid bilayers added to which BamB was bound, as plotted in Fig. 2.13. It is quite remarkable that the ∆λmax still showed very similar relative position-dependence for bilayers of DLPE/DLPG (4:1) in comparison to bilayers of pure DLPG, although the absolute ∆λmax were much larger for DLPG. These results were consistent with the changes in fluorescence intensity upon binding to the lipid membranes.
The surface exposed BamB mutants S54C, G102C, W103C, G120C and V181C located closely to the N-terminus of the protein and the amino acid positions were identified as potential binding regions between BamB and the lipid membrane.
Fig. 2.13 Single cysteine mutants of BamB, covalently labeled with fluorescent IANBD at the cysteine, display changes in the wavelength and in the intensity of the fluorescence maximum of IANBD upon binding to preformed lipid bilayers (A) Difference of the wavelengths of the fluorescence maxima (∆λmax) of IANBD-labeled BamB in lipid bilayers and in buffer, plotted vs. the position of the cysteine. The λmax were calculated from the fluorescence spectra shown in Fig. 2.12. (B) The ratio between the fluorescence intensities in the presence and in the absence of lipids was plotted as a function of the position of the labeled cysteine in the BamB mutants.
Different marker shapes were used to distinguish between the lipid type. Surface exposed BamB mutants are shown in black and BamB mutants facing the interior of the protein are shown in red. Potential binding regions between BamB and the lipid bilayer are shown as filled markers and are marked with X on the x-axis.
2.4.7 Quenching experiments of IANBD-labeled single cysteine mutants of BamB