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The light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum is tightly regulated by the [H+] gradient and transmembrane potential. BR exhibits optoelectric properties, since spectral changes during the photocycle are kinetically controlled by voltage, which predestines BR for optical storage or processing devices. BR mutants with prolonged lifetime of the blue-shifted M intermediate would be advantageous, but the optoelectric properties of such mutants are still elusive. Using expression in Xenopus oocytes and two-electrode voltage-clamping, we analyzed photocurrents of BR mutants with kinetically destabilized (F171C, F219L) or stabilized (D96N, D96G) M intermediate in response to green light (to probe H+ pumping) and blue laser flashes (to probe accumulation/decay of M). These mutants have divergent M lifetimes. As for BR-WT, this strictly correlates with the voltage dependence of H+ pumping. BR-F171C and BR-F219L showed photocurrents similar to BR-WT. Yet, BR-F171C showed a weaker voltage dependence of proton pumping. For both mutants, blue laser flashes applied during and after green-light illumination showed reduced M accumulation and shorter M lifetime. In contrast, BR-D96G and BR-D96N exhibited small photocurrents, with nonlinear current-voltage curves, which increased strongly in the presence of azide. Blue laser flashes showed heavy M accumulation and prolonged M lifetime, which accounts for the strongly reduced H+ pumping rate. Hyperpolarizing potentials augmented these effects. The combination of M-stabilizing and -destabilizing mutations in BR-D96G/F171C/F219L (BR-tri) shows that disruption of the primary proton donor Asp-96 is fatal for BR as a proton pump. Mechanistically, M destabilizing mutations cannot compensate for the disruption of Asp-96. Accordingly, BR-tri and BR-D96G photocurrents were similar. However, BR-tri showed negative blue laser flash-induced currents even without actinic green light, indicating that Schiff base deprotonation in BR-tri exists in the dark, in line with previous spectroscopic investigations. Thus, M-stabilizing mutations, including the triple mutation, drastically interfere with electrochemical H+ gradient generation.
Identification of the intermediates and determination of their structures in the reduction of dioxygen to water by cytochrome c oxidase (CcO) are particularly important to understanding both O2 activation and proton pumping by the enzyme. In this work, we report the products of the rapid reaction of O2 with the mixed valence form (CuA(2+), heme a(3+), heme a3(2+)-CuB(1+)) of the enzyme. The resonance Raman results show the formation of two ferryl-oxo species with characteristic Fe(IV)=O stretching modes at 790 and 804 cm(-1) at the peroxy oxidation level (PM). Density functional theory calculations show that the protein environment of the proximal H-bonded His-411 determines the strength of the distal Fe(IV)=O bond. In contrast to previous proposals, the PM intermediate is also formed in the reaction of Y167F with O2. These results suggest that in the fully reduced enzyme, the proton pumping ν(Fe(IV)=O) = 804 cm(-1) to ν(Fe(IV)=O) = 790 cm(-1) transition (P→F, where P is peroxy and F is ferryl) is triggered not only by electron transfer from heme a to heme a3 but also by the formation of the H-bonded form of the His-411-Fe(IV)=O conformer in the proximal site of heme a3. The implications of these results with respect to the role of an O=Fe(IV)-His-411-H-bonded form to the ring A propionate of heme a3-Asp-399-H2O site and, thus, to the exit/output proton channel (H2O) pool during the proton pumping P→F transition are discussed. We propose that the environment proximal to the heme a3 controls the spectroscopic properties of the ferryl intermediates in cytochrome oxidases.
Background: Understanding the coupling of O2 reduction to proton pumping by CcO requires detection of reaction intermediates.
Results: We have detected two oxoferryl intermediates at the PM oxidation state.
Conclusion: The H-bonding properties of the proximal heme a3 His ligand control the strength of the oxoferryl species.
Significance: The role of His-411, Thr-389, Gly-386, and Asp-399 residues in the proton pumping P→F transition is outlined.
The TolC-like protein HgdD of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 is part of multiple three-component "AB-D" systems spanning the inner and outer membranes and is involved in secretion of various compounds, including lipids, metabolites, antibiotics, and proteins. Several components of HgdD-dependent tripartite transport systems have been identified, but the diversity of inner membrane energizing systems is still unknown. Here we identified six putative resistance-nodulation-cell division (RND) type factors. Four of them are expressed during late exponential and stationary growth phase under normal growth conditions, whereas the other two are induced upon incubation with erythromycin or ethidium bromide. The constitutively expressed RND component Alr4267 has an atypical predicted topology, and a mutant strain (I-alr4267) shows a reduction in the content of monogalactosyldiacylglycerol as well as an altered filament shape. An insertion mutant of the ethidium bromide-induced all7631 did not show any significant phenotypic alteration under the conditions tested. Mutants of the constitutively expressed all3143 and alr1656 exhibited a Fox(-) phenotype. The phenotype of the insertion mutant I-all3143 parallels that of the I-hgdD mutant with respect to antibiotic sensitivity, lipid profile, and ethidium efflux. In addition, expression of the RND genes all3143 and all3144 partially complements the capability of Escherichia coli ΔacrAB to transport ethidium. We postulate that the RND transporter All3143 and the predicted membrane fusion protein All3144, as homologs of E. coli AcrB and AcrA, respectively, are major players for antibiotic resistance in Anabaena sp. PCC 7120.
The crystal structure of the title salt, [Li(CH3CN)4][B(NCS)4], is composed of discrete cations and anions. Both the Li and B atoms show a tetrahedral coordination by four equal ligands. The acetonitrile and isothiocyanate ligands are linear. The bond angles at the B atom are close to the ideal tetrahedral value [108.92 (18)–109.94 (16)°], but the bond angles at the Li atom show larger deviations [106.15 (17)–113.70 (17)°].
Synthese, Reaktivität und strukturelle Vielfalt im Festkörper von Ferrocenylboranen und -boraten
(2013)
The inner structural Gag proteins and the envelope (Env) glycoproteins of human immunodeficiency virus (HIV-1) traffic independently to the plasma membrane, where they assemble the nascent virion. HIV-1 carries a relatively low number of glycoproteins in its membrane, and the mechanism of Env recruitment and virus incorporation is incompletely understood. We employed dual-color super-resolution microscopy visualizing Gag assembly sites and HIV-1 Env proteins in virus-producing and in Env expressing cells. Distinctive HIV-1 Gag assembly sites were readily detected and were associated with Env clusters that always extended beyond the actual Gag assembly site and often showed enrichment at the periphery and surrounding the assembly site. Formation of these Env clusters depended on the presence of other HIV-1 proteins and on the long cytoplasmic tail (CT) of Env. CT deletion, a matrix mutation affecting Env incorporation or Env expression in the absence of other HIV-1 proteins led to much smaller Env clusters, which were not enriched at viral assembly sites. These results show that Env is recruited to HIV-1 assembly sites in a CT-dependent manner, while Env(ΔCT) appears to be randomly incorporated. The observed Env accumulation surrounding Gag assemblies, with a lower density on the actual bud, could facilitate viral spread . Keeping Env molecules on the nascent virus low may be important for escape from the humoral immune response, while cell-cell contacts mediated by surrounding Env molecules could promote HIV-1 transmission through the virological synapse.
Channelrhodopsin-2 (ChR2) is a light-gated cation selective channel from the unicellular alga Chlamydomonas reinhardtii, which is involved in phototaxis and photophobic responses. As other rhodopsins, ChR2 comprises a seven-transmembrane helix (TMH) motif and a retinal as the light-sensitive chromophore. The chromophore is covalently attached via a protonated Schiff base to the conserved lysine residue Lys257 located in TMH7. Based on its primary sequence and the all-trans configuration of the retinal in the ground state, ChR2 is assigned to the type I rhodopsins, also referred to as microbial-type rhodopsins. Upon light activation, the retinal isomerizes from the all-trans to the 13-cis form. This photoisomerization, which is accompanied by conformational changes of the protein, eventually leads to the opening of the channel and cation translocation. Cation flux during the conductive state leads to depolarization of the cell membrane and subsequent triggering of action potentials when expressed in neurons. Therefore, ChR2 has become the most versatile optogenetic tool, enabling a non-invasive investigation of neural circuits at high spatial and temporal resolution. With the rapidly increasing importance of ChR2 as a tool in neurobiology and cell biology, structural information is the prerequisite to an unambiguous understanding of the molecular mechanisms of this unique light-activated ion channel. The coupling between isomerization and structural alterations is well understood for other microbial-type rhodopsins, like bacteriorhodopsin (bR), halorhodopsin (HR) and sensory rhodopsin II (SRII). In case of ChR2, the first data on light-induced conformational changes came from spectroscopic studies and structural information is still missing. However, in order to fully understand the mechanism of light transduction by ChR2, it is necessary to determine the changes in the protein structure at specific steps in the photocycle.
By the time I started my PhD thesis, there was no structural information of ChR2 available. Therefore, the objective of this thesis was to obtain structural information of the transmembrane domain containing the first 315 amino acids of ChR2 by cryo electron crystallography. Besides revealing the structure of membrane proteins, cryo-EM of two-dimensional (2D) crystals is ideal for investigating conformational changes in membrane proteins induced by different stimuli. Therefore, the second objective of my thesis was the investigation of light-induced conformational changes in the slow C128T ChR2 mutant. The ~1,000 times longer lifetime of the open state of the C128T mutant compared to the wild-type allowed to trap different intermediates that accumulate during the photocycle.
In 2012, the X-ray structure of a channelrhodopsin-1/channelrhodopsin-2 chimaera (C1C2) at 2.3 Å resolution in the closed dark-adapted state was published (Kato et al., 2012). The structure revealed the essential molecular architecture of C1C2, including the retinal-binding pocket and the putative cation conduction pathway. Together with biochemical, spectroscopic, mutagenesis experiments, and the high-resolution model, some functionally important residues of ChR2 have been identified. However, unambiguous explanation of the molecular determinants that contribute to activation (gating) and transport were still mostly unknown.
RESULTS AND CONCLUSIONS
The first half of my theses dealt with 2D crystallization of ChR2. I succeeded in obtaining 2D crystals of ChR2 of four different types, which differed in size, crystal packing, crystal contacts and resolution, yielding structure factors up to 6 Å resolution. The crystals were grown by reconstituting the protein with different lipids at various lipid-to-protein ratios. The best crystals formed with the synthetic lipid DMPC and EPL upon detergent removal by dialysis. The projection maps calculated from these crystals revealed the overall structure of C128T ChR2 at 6 Å resolution and were published in 2011 (Müller et al., 2011). Surprisingly, ChR2 was found to be a dimer in all crystal types. The ChR2 dimer was stable both in detergent solution and in the presence of lipids for 2D crystallization. The monomers clearly showed the expected densities for the seven TMHs.
The arrangement of the ChR2 dimers on the four 2D lattices was different. However, comparison of the individual rojection maps revealed no significant differences within the ChR2 interface in the four crystal forms. The observation that the structure of the dimer was the same in all four crystal forms and in different lipids suggested strong specific contacts between the two protomers and implied that the protein was also dimeric in the native membrane. These findings were in agreement with Western blot analysis of plasma membranes from oocytes expressing ChR2 and laser-induced liquid bead ion desorption mass spectrometry, which both showed ChR2 as a dimer. The unusual stability of the ChR2 dimer contrasts with other microbial rhodopsins, which exist in different oligomeric states, i.e. monomers, trimers or dimers. These observations raised the question whether the functional unit is the monomer or the dimer.
The comparison of the projection map of the light-driven proton pump bR at the same resolution showed similar overall dimensions. Based on this comparison, the densities which became evident in the ChR2 projection maps could be assigned to the corresponding seven densities in bR. The shape of the densities near the dimer interface suggested that TMHs 2, 3, and 4 are oriented more or less perpendicular to the membrane plane, while the other four helices appear to be more tilted, as in bR.
Based on the high-resolution bR structure and the projection structures obtained, I have built a homology model. On the basis of this homology model, several residues found in the dimer interface were selected for mutational studies in order to disrupt the dimer interface.
The investigation of light-induced conformational changes in C128T ChR2 was the second part of my thesis. I designed an experimental setup for trapping light-induced conformational changes in C128T ChR2. In addition, I optimized the sample preparation in a way that the different illumination conditions did not alter the quality of the crystals. I have trapped two different functional states, namely the conductive open state and the non-conductive closed dark-adapted state.
In order to visualize the location and the extent of conformational changes, projection difference maps were calculated between the open and the closed state. Visual inspection of the difference maps between the open and the two closed states revealed three difference peaks that map to the TMHs 2, 6, and 7, indicating significant and specific rearrangements of these helices. The strong pair of positive/negative peaks at TMH6 suggests an outward tilt movement of approximately 2 Å. Close comparison of similar work on bR revealed that this movement is likely to occur at the cytoplasmic end of TMH6. A second highly significant negative peak is observed at TMH7, indicating a less pronounced tilt compared to TMH6. The third negative peak at TMH2 indicates a loss of density in this region. No significant differences were recorded at the TMH1, 5 and at the dimer interface formed by TMH3 and 4.
I succeeded in trapping and characterizing the open and closed state in the photocycle of ChR2 and could demonstrate that the transition from the closed to the open state is linked to significant light-induced tilt movements of TMH6 and 7, plus a loss of order in TMH2. These conformational changes are likely to create a large water-filled conducting pore, which seems to be required for the conductance of up to 2,000 ions per photocycle. The previously mentioned spectroscopic studies support the difference structures I obtained. This approach sets the stage for studying structural changes accompanying the formation and decay of other photocycle intermediates in ChR2. Future studies will aim at three-dimensional maps of the open and closed state at higher resolution.
Structural determinants for substrate specificity of the promiscuous multidrug efflux pump AcrB
(2013)
Opportunistic Gram-negative pathogens such as Escherichia coli, Klebsiella pneumoniae, Acinetobacter Baumanii and Pseudomonas aeruginosa are becoming more and more multiresistant against many commonly available antibiotics [39, 40]. An important resistance mechanism of Gram-negative bacteria is the efflux of noxious compounds by tripartite systems [39, 41-44]. The best studied and most clinically relevant tripartite system is the AcrA-AcrB-TolC system of Escherichia coli, where substrate recognition and energy transduction takes place in the inner membrane protein AcrB. AcrB has a remarkably huge substrate spectrum and can recognize structurally diverse molecules, such as hexan in contrast to erythromycin, as its substrates [45]. Therefore, overproduction of the tripartite system can render a Gram-negative pathogen resistant against multiple antibiotics at once. The mechanisms of how AcrB is able to recognize such an enormous spectrum of molecules as substrates, without compromising its specificity (e.g. by neglecting essential compounds like lipids or gluclose as its susbtates), remained puzzling. Structural insight into substrate specificity was so far limited to two co-crystal structures of AcrB, where minocycline and doxorubicin, respectively, were identified bound to an internal binding pocket of AcrB. This binding pocket is particularly deeply buried into internal parts of the T monomer of AcrB and was, therefore, denoted deep binding pocket (DBP). Analysis of several AcrB co-crystal structures with substrate molecules bound to the DBP [4, 23, 25] indicated that the substrate promiscuity involved multisite binding modes within the DBP. Multisite binding modes, where different substrate molecules can bind to slightly different positions and orientations to the same binding pocket, is a common feature of multidrug recognizing proteins such as QacR or BmrR [27-29]. Nevertheless, AcrB's substrate spectrum is much broader than substrate spectra of most other multidrug recognizing proteins. Therefore, it is likely that additional mechanisms are involved in mediating the observed high substrate promiscuity of AcrB. In our recently published high-resolution AcrB/doxorubicin co-crystal structure (pdb entry: 4DX7 [23]) we were able to identify two additional substrate binding pockets in the L monomer of AcrB: i) the access pocket (AP), with an opening towards the periplasm, and ii) a putative binding site in a groove between transmembrane helices 8 and 9 (TM8/TM9 groove), accessible from the lipid layer of the inner membrane. Both binding pockets are likely to be access sites for substrates towards AcrB. Furthermore, each of the binding pockets are possibly specialized to recognize a specific subset of the entire substrate spectrum of AcrB, i.e. highly hydrophobic substrates (e.g. n-dodecyl-ß-d-maltoside or sodium dodecylsulfate) might access AcrB towards the TM8/TM9 groove and water soluble substrates (e.g. berberine) might access AcrB towards the AP. Since substrates will accumulate in the membrane or the periplasm according to their hydrophilic or hydrophobic nature, substrates will be "pre-selected" by the medium, rather than by the protein itself, and guided to their appropriate access site. This process is proposed to be called "medium- mediated pre-selection". The AcrB/doxorubicin co-crystal structure (pdb entry: 4DX7 [23]) furthermore revealed that the AP and DBP are in next neighborhood to each other and are separated by a switch loop. This switch loop adopts distinct conformations in the L, T and O monomers. Specific switch loop conformations are strongly involved in coordinating the selective occupation of both binding pockets, the AP and the DBP. The conformation of the switch loop in the L monomer (L-switch loop) opens the AP and closes the DBP, whereas the conformation of the switch loop in the T monomer (T-switch Loop) opens the DBP and closes the AP. An analysis of all asymmetric AcrB structures indicated that the L-switch loop is able to adopt multiple distinct conformations, whereas the conformation of T-switch loop remained largely congruent in all crystal structures. Moreover, each distinct switch loop conformation, observed in co-crystal structures of AcrB with occupied AP [4, 23], was perfectly adapted to the bound substrate molecule. Therefore, the putatively flexible switch loop is likely to act as an adaptive module and mediates a high binding pocket plasticity without altering the global protein structure. This binding mode is called adaptor-mediated binding mechanism, where an flexible adaptive module (like the switch loop) is able to adapt the surface shape of an binding pocket to different substrate molecules. Furthermore, structural and biochemical analyses of an AcrB G616N variant, revealed the involvement of specific switch loop conformations in the substrate specificity of AcrB. A substitution of G616, located on the switch loop, to N616 was able to alter the conformation of the switch loop exclusively in the L monomers of AcrB, whereas the switch loop conformations in T and O monomers remained congruent to the conformations observed in crystal structures of wildtype AcrB. Moreover, cells producing the AcrB G616N and MexB, both bearing the G616N amino acid substitution, exhibited a reduced resistance against certain substrates, whereas the resistance against most other substrates remained on the level of wildtype AcrB. Correlations of the phenotypes with minimal projection areas, a novel 2-spatiodimensional parameter which approximates the size of a substrate molecule, revealed that AcrB variants with a G616N substitution have a reduced efflux activity for exclusively large substrate molecules. The rejection of large substrates is most likely connected with altered L-switch loop conformations....
Split intein enabled protein trans-splicing (PTS) is a powerful method for the ligation of two protein fragments, thereby paving the way for various protein modification or protein function control applications. PTS activity is strongly influenced by the amino acids directly flanking the splice junctions. However, to date no reliable prediction can be made whether or not a split intein is active in a particular foreign extein context. Here we describe SPLICEFINDER, a PCR-based method, allowing fast and easy screening for active split intein insertions in any target protein. Furthermore we demonstrate the applicability of SPLICEFINDER for segmental isotopic labeling as well as for the generation of multi-domain and enzymatically active proteins.