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The mitophagy receptor Nix interacts with LC3/GABARAP proteins, targeting mitochondria into autophagosomes for degradation. Here we present evidence for phosphorylation-driven regulation of the Nix:LC3B interaction. Isothermal titration calorimetry and NMR indicate a ~100 fold enhanced affinity of the serine 34/35-phosphorylated Nix LC3-interacting region (LIR) to LC3B and formation of a very rigid complex compared to the non-phosphorylated sequence. Moreover, the crystal structure of LC3B in complex with the Nix LIR peptide containing glutamic acids as phosphomimetic residues and NMR experiments revealed that LIR phosphorylation stabilizes the Nix:LC3B complex via formation of two additional hydrogen bonds between phosphorylated serines of Nix LIR and Arg11, Lys49 and Lys51 in LC3B. Substitution of Lys51 to Ala in LC3B abrogates binding of a phosphomimetic Nix mutant. Functionally, serine 34/35 phosphorylation enhances autophagosome recruitment to mitochondria in HeLa cells. Together, this study provides cellular, biochemical and biophysical evidence that phosphorylation of the LIR domain of Nix enhances mitophagy receptor engagement.
Denisovite is a rare mineral occurring as aggregates of fibres typically 200–500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have remained incompletely known since then. Recently obtained results from studies using microprobe analysis, X-ray powder diffraction (XRPD), electron crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT). A structural model of denisovite was developed from HAADF images and later completed on the basis of quasi-kinematic EDT data by ab initio structure solution using direct methods and least-squares refinement. The model was confirmed by Rietveld refinement. The lattice parameters are a = 31.024 (1), b = 19.554 (1) and c = 7.1441 (5) Å, β = 95.99 (3)°, V = 4310.1 (5) Å3 and space group P12/a1. The structure consists of three topologically distinct dreier silicate chains, viz. two xonotlite-like dreier double chains, [Si6O17]10−, and a tubular loop-branched dreier triple chain, [Si12O30]12−. The silicate chains occur between three walls of edge-sharing (Ca,Na) octahedra. The chains of silicate tetrahedra and the octahedra walls extend parallel to the z axis and form a layer parallel to (100). Water molecules and K+ cations are located at the centre of the tubular silicate chain. The latter also occupy positions close to the centres of eight-membered rings in the silicate chains. The silicate chains are geometrically constrained by neighbouring octahedra walls and present an ambiguity with respect to their z position along these walls, with displacements between neighbouring layers being either Δz = c/4 or −c/4. Such behaviour is typical for polytypic sequences and leads to disorder along [100]. In fact, the diffraction pattern does not show any sharp reflections with l odd, but continuous diffuse streaks parallel to a* instead. Only reflections with l even are sharp. The diffuse scattering is caused by (100) nanolamellae separated by stacking faults and twin boundaries. The structure can be described according to the order–disorder (OD) theory as a stacking of layers parallel to (100).
Glial cell line-derived neurotrophic factor (GDNF) is a ligand that activates, through co-receptor GDNF family receptor alpha-1 (GFRα1) and receptor tyrosine kinase “RET”, several signaling pathways crucial in the development and sustainment of multiple neuronal populations. We decided to study whether non-mammalian orthologs of these three proteins have conserved their function: can they activate the human counterparts? Using the baculovirus expression system, we expressed and purified Danio rerio RET, and its binding partners GFRα1 and GDNF, and Drosophila melanogaster RET and two isoforms of co-receptor GDNF receptor-like. Our results report high-level insect cell expression of post-translationally modified and dimerized zebrafish RET and its binding partners. We also found that zebrafish GFRα1 and GDNF are comparably active as mammalian cell-produced ones. We also report the first measurements of the affinity of the complex to RET in solution: at least for zebrafish, the Kd for GFRα1-GDNF binding RET is 5.9 μM. Surprisingly, we also found that zebrafish GDNF as well as zebrafish GFRα1 robustly activated human RET signaling and promoted the survival of cultured mouse dopaminergic neurons with comparable efficiency to mammalian GDNF, unlike E. coli-produced human proteins. These results contradict previous studies suggesting that mammalian GFRα1 and GDNF cannot bind and activate non-mammalian RET and vice versa.
Biogenesis of mitochondrial cytochrome c oxidase (COX) is a complex process involving the coordinate expression and assembly of numerous subunits (SU) of dual genetic origin. Moreover, several auxiliary factors are required to recruit and insert the redox-active metal compounds, which in most cases are buried in their protein scaffold deep inside the membrane. Here we used a combination of gel electrophoresis and pull-down assay techniques in conjunction with immunostaining as well as complexome profiling to identify and analyze the composition of assembly intermediates in solubilized membranes of the bacterium Paracoccus denitrificans. Our results show that the central SUI passes through at least three intermediate complexes with distinct subunit and cofactor composition before formation of the holoenzyme and its subsequent integration into supercomplexes. We propose a model for COX biogenesis in which maturation of newly translated COX SUI is initially assisted by CtaG, a chaperone implicated in CuB site metallation, followed by the interaction with the heme chaperone Surf1c to populate the redox-active metal-heme centers in SUI. Only then the remaining smaller subunits are recruited to form the mature enzyme which ultimately associates with respiratory complexes I and III into supercomplexes.
Bacteria are highly organized organisms which are able to adapt to and propagate under a multitude of environmental conditions. Propagation hereby requires reliable chromosome replication and segregation which has to occur cooperatively with other cellular processes such as transcription, translation or signaling. Several mechanisms were proposed for segregation of the Escherichia coli (E. coli) chromosome, for example a mitotic-like active segregation model or entropy-based passive chromosome segregation. Another segregation model suggests coupled transcription, translation and insertion of membrane proteins (termed "transertion"), which links the replicating chromosome (nucleoid) to the growing cell cylinder.
Fluorescence microscopy was widely used to provide evidence for a distinct segregation model. However, the dynamic nature of bacterial chromosomes, the small bacterial size and the optical resolution limit of ~ 200-300 nm impair unveiling the underlying mechanisms. With the emergence of super-resolution fluorescence microscopy techniques and advanced labeling methods, a new toolbox became available enabling scientists to visualize biomolecules and cellular processes in unprecedented detail. Single-molecule localization microscopy (SMLM) represents a set of super-resolution microscopy techniques which relies on the temporal separation of the fluorescence signal and detection of single fluorophores. Separation can be achieved using photoactivatable or -convertible fluorescent proteins (FPs) in photoactivated localization microscopy (PALM), photoswitchable organic dyes in direct stochastic optical reconstruction microscopy (dSTORM) or dynamically binding fluorescent probes in point accumulation for imaging in nanoscale topography (PAINT). In all these techniques, the fluorescence emission pattern of single fluorophores is spatially localized with nanometer-precision. An artificial image is finally reconstructed from the coordinates of all single fluorophores detected. This provides a spatial resolution of ~ 20 nm, which is perfectly suited to investigate cellular processes in bacteria. In this thesis, different SMLM techniques were applied to study fundamental processes in E. coli. This includes determination of protein copy numbers and distributions as well as the nanoscale organization of nucleic acids and lipids.
A novel labeling approach was applied and used for super-resolution imaging of the E. coli nucleoid. It is based on the incorporation of the modified thymidine analogue 5-ethynyl-2’- deoxyuridine (EdU) into the replicating chromosome. Azide-functionalized organic fluorophores can be covalently attached to the ethynyl group of incorporated EdU bases using a copper-catalyzed "click chemistry" reaction. Under the investigated growth condition, E. coli cells exhibited overlapping replication cycles, which is commonly referred to as multi-fork replication and enables cells to divide faster than they can replicate the entire chromosome. dSTORM imaging of such labeled nucleoids revealed chromosome features with diameters of 50 - 200 nm, representing highly condensed DNA filaments. Sorting single E. coli cells by length allowed visualizing structural changes of the nucleoid throughout the cell cycle. Replicating nucleoids segregated and expanded along the bacterial long axis, while constantly covering the entire width of the cell. Measuring cell and nucleoid length revealed a relative nucleoid expansion rate of 78 ± 6 %. At the same time, nucleoids populated 63 ± 8 % of the cell length, almost exclusively being localized to the cylindrical part of the cell. This value was hence normalized to the cylindrical fraction of the cell, yielding a value of 79 ± 10 % (nucleoid-populated fraction of the cell cylinder), which is in good agreement with the observed relative nucleoid expansion rate. These results therefore support a growth-mediated segregation model, in which the chromosome is anchored to the inner membrane and passively segregated into the prospective daughter cells upon cell growth. 3-dimensional dSTORM imaging of labeled nucleoids confirmed that compacted nucleoids helically wrap along the inner membrane. Similar results were obtained by imaging orthogonally aligned E. coli cells using a holographic optical tweezer approach.
In order to visualize particular proteins together with the nucleoid, several correlative imaging workflows were established, facilitating multi-color SMLM imaging in single E. coli cells. These workflows bypass prior limitations of SMLM, including destruction of FPs by reactive oxygen species in copper-catalyzed click reactions or incompatibility of PALM imaging with dSTORM imaging buffers. A sequential SMLM imaging routine was developed which is based on postlabeling and retrieval of previously imaged cells. Optimal imaging conditions can be maintained for each fluorophore, enabling to extract quantitative information from PALM measurements while correlating the protein distribution to the nucleoid ultrastructure within the highly resolved cell envelope. Applying this workflow to an E. coli strain carrying a chromosomal rpoC - photoactivatable mCherry (PAmCh) fusion, transcribing RNA polymerase (RNAP) was found to be localized on the surface of nucleoids, where active genes are exposed towards the cytosol. During growth in nutrient-rich medium, the majority of RNAP molecules was bound to the chromosome, thus ensuring that the RNAP pool is equally distributed to the daughter cells upon cell division. This work represented the first triple-color SMLM study performed in E. coli cells. ...
In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding.
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein–protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that highlights the common mechanistic principles shared by the MHC I editors Tsn and TAPBPR, and the MHC II editor HLA-DM, but also illustrate the distinct quality control strategies employed by these chaperones to sample epitopes. Unraveling the mechanistic underpinnings of catalyzed peptide proofreading will be crucial for a thorough understanding of many aspects of immune recognition, from infection control and tumor immunity to autoimmune diseases and transplant rejection.
The soluble loop BC region guides, but not dictates, the assembly of the transmembrane cytochrome b6
(2017)
Studying folding and assembly of naturally occurring α-helical transmembrane proteins can inspire the design of membrane proteins with defined functions. Thus far, most studies have focused on the role of membrane-integrated protein regions. However, to fully understand folding pathways and stabilization of α–helical membrane proteins, it is vital to also include the role of soluble loops. We have analyzed the impact of interhelical loops on folding, assembly and stability of the heme-containing four-helix bundle transmembrane protein cytochrome b6 that is involved in charge transfer across biomembranes. Cytochrome b6 consists of two transmembrane helical hairpins that sandwich two heme molecules. Our analyses strongly suggest that the loop connecting the helical hairpins is not crucial for positioning the two protein “halves” for proper folding and assembly of the holo-protein. Furthermore, proteolytic removal of any of the remaining two loops, which connect the two transmembrane helices of a hairpin structure, appears to also not crucially effect folding and assembly. Overall, the transmembrane four-helix bundle appears to be mainly stabilized via interhelical interactions in the transmembrane regions, while the soluble loop regions guide assembly and stabilize the holo-protein. The results of this study might steer future strategies aiming at designing heme-binding four-helix bundle structures, involved in transmembrane charge transfer reactions.
Infections with multidrug resistant bacterial strains like Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa or Acinetobacter baumanii that can accumulate resistance mechanisms against different groups of drugs cause increasing problems for the health care system. Multidrug efflux pumps are able to transport different classes of substances, providing a basic resistance to different antibiotics. Especially when they are overexpressed they can keep bacterial cells alive under antibiotic pressure unless other high level resistance mechanisms like expression of β-lactamases are established. One example for a clinically relevant multidrug efflux pump is the AcrAB/TolC tripartite system of E. coli, that transports a variety of different substrates, including besides antibiotics dyes, detergents, bile salts and organic compounds from the periplasm or the inner membrane out of the cell. AcrB is the inner membrane component of the protein complex that determines not only the substrate specificity of the tripartite system but energises the transport through the whole system process via proton transduction as well. TolC is the outer membrane spanning protein that forms a pore in the outer membrane enabling the system to transport drugs over the latter out of the cell. The periplasmic membrane fusion protein AcrA connects AcrB and TolC in the periplasm completing the channel from the periplasm, respective the inner membrane to the extracellular space. AcrB assembles as trimers, in asymmetric crystal structures each of the protomers adapts a different conformation designated L(oose), T(ight) and O(pen). In the protomers tunnels open up and collaps in different conformations. In the L protomer a periplasmic cleft opens up that can initially bind substrates to the periplasmic part of AcrB. In the T conformation the deep binding pocket opens that is assumed to bind substrates tightly that were bound to the access pocket before. As well in the T conformation a second pathway leading to the deep binding pocket opens that can guide substrates from a groove between transmembrane helices TM7, TM8 and TM9, the TM8 groove, that is connected with socalled tunnel 1 that ends in the deep binding pocket. In the O conformation a new tunnel opens that connects the collapsing deep binding pocket with the periplasmic space, respective the channel through the periplasmic space formed from AcrA and TolC. Substrates were cocrystallised in access and deep binding pocket verifying their role in substrate transport. In the TM8 groove in high resolution crystal structures DDM molecules were cocrystallised in L and T conformation, indicating that the AcrB substrate DDM may utilise this entrance to the deep binding pocket. The asymmetry observed in the AcrB trimers trongly suggests a peristaltic pump mechanism. The functional rotation cycle demands communication between the subunits and tight control of substrate load of protomers during the transport to optimise the ration between protons that are transduced and substrates transported. Indeed it was shown that AcrB transport mechanism is positively cooperative for some β-lactam substrates. For the communication between the subunits it was assumed that ionic interaction between ion pairs established between charged amino acids at the interfaces of protomers in different conformations are of special importance. Thus the amino acids engaged in ionic interactions, respective ion pairs D73-K131, E130-K110, D174-K110, R168, R259-E734 were substituted with non-charged amino acids pairwise and phenotypes were determined in plate dilution assays and MIC experiments. No evidence for a general, substrate independent, reduction of AcrB activity, that would be expected when the ionic residues are of special importance for AcrB function, could be found with the methods applied. Substitutions were not only combined pairwise according to the putative ion pairs but as well in combinations of R168A with D174N, E130Q and K131M. AcrB activity is reduced for the variant R168A_D174N significantly, activity decreases further for quadruple variant E130Q_K131M_ R168A_D174N. Because the reduced activity is only observed in this combination of substitutions the phenotype must result from accumulation of small effects of the single substitutions. R168A may destabilise the protomer interfaces, as its side chain is oriented in direction to the neighbouring protomer at all interfaces, enhancing substratespecific effects of substitutions E130Q, K131M, D174N that are not in all conformations oriented towards the neighbouring protomer but as well along the substrate transport pathway. Further investigations to figure out the details of the effects observed were not conducted because fluctuating expression of the variants hindered experimental procedures.
In another approach TM8 was in focus of the interest. As mentioned above it is a possible substrate entrance in the inner membrane. The linker between TM8 and the periplasmic PC2 subdomain undergoes a coil-to-helix transition when AcrB cycles through L, T and O conformations. Linking the transmembrane part of AcrB that provides the energy for the transport process via proton transduction with the periplasmic part harbouring the major part of the substrate pathway assignes TM8 and the periplasmic linker (859-876) an important role in the function of AcrB. Thus it was investigated with an alanine-scan of residues 859 to 884 and G/P respective P/G exchange followed by phenotype characterisation in growth curve and plate dilution assays of selected variants. In the phenotype determinations none of the variants, except G861P that seems to cause massive sterical restriction in an α-helical region, displayed a general, substrate independent decrease of AcrB activity. Thus it is concluded that the individual properties of amino acids in TM8 and the periplasmic linker are not of general importance for the mechanism of AcrB. The substitution of individual amino acids had impact on uptake of different substrates in plate dilution assays in a substrate dependent manner. The uptake of some substrates, like erythromycin or chloramphenicol is more affected than that of others with rhodamine 6G resistance being only reduced for the G861P variant. A relation between the PSA of substrates and reduced activity of AcrB was observed. in Substrates with higher PSA values are more affected by substitutions in TM8 or periplasmic linker, resulting in the conclusion that substrates with higher PSA are more likely to be taken up via the TM8 groove/tunnel 1 pathway than those with lower PSA values.
According to general doctrine canceroselectivity of Cyclophosphamide is based on different activities of the 4-hydroxycyclophosphamide (OHCP) detoxifying cellular enzyme aldehyde dehydrogenase in tumor and normal cells. Aldehyde dehydrogenase converts the OHCP tautomere aldophosphamide (ALDO) to the non-cytotoxic carboxyphosphamide. Due to different activities of the detoxifying enzyme more cytotoxic phosporamide mustard (PAM) is spontaneously released from OHCP/ALDO in tumor cells. PAM unfolds its cytotoxic activity by forming intrastrand and interstrand DNA crosslinks. This hypothesis is supported by in vitro experiments which show inverse correlations of aldehyde dehydrogenase activity and sensitivity of tumor cells against activated congeners of cyclophosphamide like mafosfamide which hydrolyses within a few minutes to OHCP. In protein free rat serum ultrafiltrate however free OHCP and its coexisting tautomer ALDO are stable compounds. Its half-life in protein free rat serum ultrafiltrate (pH7, 37oC) is more than 20 h. Contrary to protein free ultrafiltrate in whole serum ALDO is enzymatically decomposed to PAM and 3-hydroxypropionaldehyde (HPA) within minutes. The decomposing enzyme was identified as 3´-5´ phosphodiesterase, the Michaelis constant was determined to be 10-3 M in human serum.
The experiments presented clearly demonstrate that ALDO is not only cleaved base catalyzed yielding acrolein and PAM but also cleaved enzymatically by serum phosphodiesterases yielding HPA and PAM. It is discussed that the reason of the high canceroselectivity of cyclophosphamide is not only due to enrichment of OHCP/ALDO in tumor cells due to less detoxification of ALDO in tumor cells than in normal cells. It is discussed that there is a good reason for an additional mechanism namely the amplification of apoptosis of PAM damaged cells by HPA.
A two step mechanism for the mechanism of action of OHCP/ALDO is discussed. During the first step, the DNA is damaged by alkylation by PAM. During the second step the cell containing damaged DNA is eliminated by apoptosis, supported by HPA.
N-Allyltetramethylpiperidine is readily isomerized to the corresponding enamine by treatment with catalytic amounts of B(C6F5)3. It adds HB(C6F5)2 at the nucleophilic enamine carbon atom to form a C/B Lewis adduct. This reacts with two molar equivalents of carbon monoxide by selective head to tail coupling to give a five-membered C2O2B heterocycle. In contrast the enamine/HB(C6F5)2 Lewis pair reacts with two molar equiv. of nitric oxide by head to head coupling. This reaction probably proceeds via equilibrium with the corresponding vicinal N/B Lewis pair. Most products were characterized by X-ray diffraction.
Biophysical studies of the translation-regulating add adenine riboswitch from Vibrio vulnificus
(2017)
Bacterial gene expression can be regulated at mRNA level by cis-acting mRNA elements termed riboswitches. Riboswitches operate by conformational switching between a ligand-free and a ligand-bound state with different structures that either activate or inhibit gene expression. This PhD thesis contributes to the molecular level understanding of full-length purine riboswitches. It presents biophysical investigations on the ligand-dependent folding of the full-length translation-regulating add adenine riboswitch from the gram-negative human pathogenic marine bacterium Vibrio vulnificus (Asw). Asw has the typical bipartite riboswitch architecture with a 5’ ligand-sensing aptamer domain and a 3’ regulatory domain termed expression platform. According to the working hypothesis, Asw employs a unique thermodynamically-controlled 3-state conformational switching mechanism between an apoB, an apoA and a holo conformation to regulate translation initiation in a temperature-compensated manner. The two apo conformations are the putative translation-OFF states and the holo conformation is the putative translation-ON state of Asw. In the main project of this PhD thesis, an integrated nuclear magnetic resonance (NMR) and smFRET spectroscopic study of the full-length 112-nucleotide Asw (112Asw) was performed. The adenine-dependent folding of 112Asw was monitored at the level of base pairing interactions by NMR of the RNA imino protons, and at the level of three long-range intramolecular distances by smFRET of immobilized molecules. The integrated NMR and smFRET spectroscopic study of 112Asw yielded two major findings. First, NMR and smFRET both revealed that adenine binding to 112Asw impedes apoB formation by stabilizing the apoA secondary structure in the holo conformation without modulating tertiary structural interactions between the two riboswitch domains. This highlights the central role of competitive P1 and P4 helix formation at the interface of the aptamer and the expression platform for switching the accessibility of the ribosome binding site of 112Asw. Moreover, it strongly corroborates the hypothesis that purine riboswitches in general operate according to the key principle of a spatially decoupled secondary structural allosteric switch that proceeds without ligand-induced tertiary structural interactions between the aptamer domain and the expression platform. Second, it was uncovered by smFRET that the apoA and the holo conformation of 112Asw do not adopt a single folding state at near-physiological Mg2+ concentration. Instead, apoA and holo exhibit a persistent dynamic equilibrium between substates with an undocked (U), a short-lived docked (D1; ~s) and a Mg2+-bound long-lived docked (D2; ~10 s) aptamer kissing loop motif. In the holo conformation, the fractional population of the long-lived docked substate is ~2-fold increased compared to the apoA conformation, but undocked and docked substates are still comparably stable. The here described multiple folding states of the apoA and the holo conformation might have regulatory properties that are in between the apoB translation-OFF state and the holo-D2 translation-ON state. Additonally, an integrated NMR and smFRET analysis of 127-nucleotide Asw (127Asw) is presented. Compared to 112Asw, 127Asw is 3’-elongated by 15 nucleotides of the adenosine deaminase encoding sequence of the add gene from Vibrio vulnificus. 127Asw was chosen as mRNA template for future investigations of the interaction between Asw and the 30S ribosomal subunit. The NMR spectra of 127Asw demonstrated that 127Asw has the same overall secondary structure as 112Asw. Like for 112Asw, the combined NMR and smFRET analysis of 127Asw showed that adenine binding impedes apoB formation and stabilizes a long-lived docked aptamer kissing loop fold. However, compared to 112Asw, 127Asw has a destabilized aptamer kissing loop motif and a stabilized P4 helix in the expression platform. Finally, ligand-observed studies of the transient encounter complex between Asw and the near-cognate ligand hypoxanthine are described. By competition binding WaterLOGSY NMR experiments with hypoxanthine and the adenine analogue 2,6-diaminopurine, it could be shown that hypoxanthine binds to the same binding site of 112Asw as the cognate ligand adenine. The hypoxanthine binding constant measured with the WaterLOGSY method is in the low mM range (1.8 mM) and substantially exceeds the physiological hypoxanthine concentration in E. coli (~0.3 mM), thus ruling out that hypoxanthine binding can significantly impact the translational regulation of Asw in vivo. Also, preliminary FTIR difference spectra of 13C,15N-labelled and unlabelled hypoxanthine in complex with the pbuE adenine riboswitch aptamer and the xpt guanine riboswitch aptamer are discussed. These spectra showed a pattern of multiple IR bands that appeared to be characteristic for the respective complex.
The full-length translation-regulating add adenine riboswitch (Asw) from Vibrio vulnificus has a more complex conformational space than its isolated aptamer domain. In addition to the predicted apo (apoA) and holo conformation that feature the conserved three-way junctional purine riboswitch aptamer, it adopts a second apo (apoB) conformation with a fundamentally different secondary structure. Here, we characterized the ligand-dependent conformational dynamics of the full-length add Asw by NMR and by single-molecule FRET (smFRET) spectroscopy. Both methods revealed an adenine-induced secondary structure switch from the apoB-form to the apoA-form that involves no tertiary structural interactions between aptamer and expression platform. This strongly suggests that the add Asw triggers translation by capturing the apoA-form secondary structure in the holo state. Intriguingly, NMR indicated a homogenous, docked aptamer kissing loop fold for apoA and holo, while smFRET showed persistent aptamer kissing loop docking dynamics between comparably stable, undocked and docked substates of the apoA and the holo conformation. Unraveling the folding of large junctional riboswitches thus requires the integration of complementary solution structural techniques such as NMR and smFRET.
The transcriptional regulator far upstream binding protein 1 (FUBP1) is essential for fetal and adult hematopoietic stem cell (HSC) self-renewal, and the constitutive absence of FUBP1 activity during early development leads to embryonic lethality in homozygous mutant mice. To investigate the role of FUBP1 in murine embryonic stem cells (ESCs) and in particular during differentiation into hematopoietic lineages, we generated Fubp1 knockout (KO) ESC clones using CRISPR/Cas9 technology. Although FUBP1 is expressed in undifferentiated ESCs and during spontaneous differentiation following aggregation into embryoid bodies (EBs), absence of FUBP1 did not affect ESC maintenance. Interestingly, we observed a delayed differentiation of FUBP1-deficient ESCs into the mesoderm germ layer, as indicated by impaired expression of several mesoderm markers including Brachyury at an early time point of ESC differentiation upon aggregation to EBs. Coculture experiments with OP9 cells in the presence of erythropoietin revealed a diminished differentiation capacity of Fubp1 KO ESCs into the erythroid lineage. Our data showed that FUBP1 is important for the onset of mesoderm differentiation and maturation of hematopoietic progenitor cells into the erythroid lineage, a finding that is supported by the phenotype of FUBP1-deficient mice.
Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination
The synergetic effects of combining structural biology and epr spectroscopy on membrane proteins
(2017)
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.
The mfl-riboswitch is a transcriptional off-switch, which down-regulates expression of subunit ß of ribonucleotide reductase in Mesoplasma florum upon 2´-deoxyguanosine binding. We characterized binding of 2´-deoxyguanosine to the mfl-aptamer domain (WT aptamer) and a sequence-stabilized aptamer (MT aptamer) under in vitro and ‘in-cell-like’ conditions by isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) spectroscopy. ‘In-celllike’ environment was simulated by Bacillus subtilis cell extract, in which both aptamers remained sufficiently stable to detect the resonances of structural elements and ligand binding in 2D NMR experiments. Under ‘in-cell-like’-environment, (i) the WT aptamer bound the endogenous metabolite guanosine and (ii) 2´-deoxyguanosine efficiently displaced guanosine from the WT aptamer. In contrast, MT aptamer exhibited moderate binding to 2´-deoxyguanosine and weak binding to guanosine. NMR experiments indicated that binding of guanosine was not limited to the aptamer domain of the riboswitch but also the full-length mfl-riboswitch bound guanosine, impacting on the regulation efficiency of the riboswitch and hinting that, in addition to 2´-deoxyguanosine, guanosine plays a role in riboswitch function in vivo. Reporter gene assays in B. subtilis demonstrated the regulation capacity of the WT aptamer, whereas the MT aptamer with lower affinity to 2´ -deoxyguanosine was not able to regulate gene expression.