CanA from Pyrodictium abyssi, the main constituent of the extracellular protein network of this archaeon, forms a hollow-fiber network in the presence of divalent ions. The polymerization of CanA induced by divalent ions is characterized by (at least) two processes with rate constants of 0.19 and 0.03 ms-1 at 298 K with a critical monomer concentration of 2.48 µM. A non-polymerizing mutant, K1-CanA, was created, and the NMR solution structure could be determined by multidimensional NMR spectroscopy. It mainly consists of β-pleated sheets and 2 small α-helices, arranged as β1β2β3β4α1β5β6α2β7β8β9β10β11β12β13. Of the 13 β-strands, 8 form a non-canonical jellyroll class I fold. Several interaction sites for divalent ions could be identified by [1H, 15N]-SOFAST-HMQC spectroscopy in two main surface areas called BA1 and BA2, located at both ends of the jellyroll. The binding of divalent ions to the monomer induces significant local structural changes in these areas. In general, the affinities for Mg2+-ions to the sites in BA1 are smaller than those for Ca2+-ions. In contrast, in binding area BA2, Mg2+- and Ca2+-affinities are similar. The data suggest a conformational selection mechanism induced by ion binding as a first step in the polymerization process of CanA.

Accurate predictions of chemical shifts of species in aqueous solution are possible by combining ab initio molecular dynamics simulations for ensembles of locally solvated target and reference compound (DSS) with quantum-mechanical solvation models.

Background Type 2 diabetes mellitus (T2D) and corresponding borderline states, impaired fasting glucose (IFG) and/or glucose tolerance (IGT), are associated with dyslipoproteinemia. It is important to distinguish between factors that cause T2D and that are the direct result of T2D. Methods The lipoprotein subclass patterns of blood donors with IFG, IGT, with IFG combined with IGT, and T2D are analyzed by nuclear magnetic resonance (NMR) spectroscopy. The development of lipoprotein patterns with time is investigated by using samples retained for an average period of 6 years. In total 595 blood donors are classified by oral glucose tolerance test (oGTT) and their glycosylated hemoglobin (HbA1c) concentrations. Concentrations of lipoprotein particles of 15 different subclasses are analyzed in the 10,921 NMR spectra recorded under fasting and non-fasting conditions. The subjects are assumed healthy according to the strict regulations for blood donors before performing the oGTT. Results Under fasting conditions manifest T2D exhibits a significant concentration increase of the smallest HDL particles (HDL A) combined with a decrease in all other HDL subclasses. In contrast to other studies reviewed in this paper, a general concentration decrease of all LDL particles is observed that is most prominent for the smallest LDL particles (LDL A). Under normal nutritional conditions a large, significant increase of the concentrations of VLDL and chylomicrons is observed for all groups with IFG and/or IGT and most prominently for manifest T2D. As we show it is possible to obtain an estimate of the concentrations of the apolipoproteins Apo-A1, Apo-B100, and Apo-B48 from the NMR data. In the actual study cohort, under fasting conditions the concentrations of the lipoproteins are not increased significantly in T2D, under non-fasting conditions only Apo-B48 increases significantly. Conclusion In contrast to other studies, in our cohort of “healthy” blood donors the T2D associated dyslipoproteinemia does not change the total concentrations of the lipoprotein particles produced in the liver under fasting and non-fasting conditions significantly but only their subclass distributions. Compared to the control group, under non-fasting conditions participants with IGT and IFG or T2D show a substantial increase of plasma concentrations of those lipoproteins that are produced in the intestinal tract. The intestinal insulin resistance becomes strongly observable.

Besides inherent fullerene-like hollow spheres, the metallasupramolecular chemistry of pentaphosphaferrocenes and CuBr2 afforded a conceptually new product, a compact 3.2 nm sized supramolecule [{1d}6(CuBr)32(CH3CN)6] formed by six largest pentaphosphaferrocene units [CpBIGFe(η5-P5)] (1d: CpBIG = η5-C5(4-nBuC6H4)5) so far and a framework of 32 copper and 32 bromide ions.

Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations. To obtain volumetric information on the open conformation as well as on the transition state structure we made use of RD measurements at elevated pressures. We found that the open Dcp1:Dcp2 conformation has a lower molecular volume than the closed conformation and that the transition state is close in volume to the closed state. In the presence of ATP the volume change upon opening of the complex increases and the volume of the transition state lies in-between the volumes of the closed and open state. These findings show that ATP has an effect on the volume changes that are associated with the opening-closing pathway of the complex. Our results highlight the strength of pressure dependent NMR methods to obtain insights into structural features of protein conformations that are not directly observable. As our work makes use of methyl groups as NMR probes we conclude that the applied methodology is also applicable to high molecular weight complexes.

In recent years, bile acids (BA) have received great interest due to their pleiotropic biological activity and the presence of plasma membrane-bound and nuclear receptors. Moreover, BA in blood have been identified by metabolite screening approaches as biomarkers that are associated with various diseases and even with a human longevity phenotype. With the growing interest in the microbiota contribution to the health-disease trajectory, BA that undergo deconjugation and other modifications by bacteria in the large intestine have become a prime target as a microbiome diversity modifier. We here profiled BA by a quantitative and a semiquantitative approach in 15 healthy and phenotypically very similar young individuals for over a 36-h fasting period, an oral glucose tolerance test (OGTT), and an oral lipid tolerance test (OLTT). We demonstrate a remarkable heterogeneity of the responses and describe the different dynamics of the plasma changes that likely originate from different routes by which BA enters the peripheral blood, and that may represent a direct secretion from the liver into the blood and a route that reaches the blood as a spill-over after passing from the gallbladder through the intestine and the portal system. We discuss the finding that an individual transport process involved in the passage of BA could be a critical determinant in the kinetics of plasma appearance and the overall phenotypic variability found.

Whereas the self-assembly of pentaphosphaferrocenes [CpRFe(η5-P5)] (CpR = Cp*, Cp×, and CpBn) with Cu and Ag salts has been well-studied in the past, the coordination chemistry toward Au complexes has been left untouched so far. Herein, the results of the self-assembly processes of [CpRFe(η5-P5)] with Au salts of different anions (GaCl4-, SbF6-, and Al(OC(CF3)3)4 (TEF-)) are reported. Next to a variety of molecular coordination products, the first coordination polymers based on polyphosphorus ligand complexes and Au salts are also obtained. Thereby, a 2D coordination polymer comprising metal vacancies is isolated. In all products, the Au centers are coordinated in a linear or a trigonal planar environment. In solution, highly dynamic processes are observed. Variable-temperature NMR spectroscopy, solid-state NMR spectroscopy, and X-ray powder diffraction were applied to gain further insight into selected coordination compounds.

: Eintopf-Selbstorganisationsreaktionen des Poly-phosphor-Komplexes [Cp*Fe( h 5 -P 5 )] ( A ), des Mgnzmetallsalzes AgSbF 6 und flexibler aliphatischer Dinitrile NC-(CH 2 ) x CN (x = 1–10) geben 1D-, 2D- und 3D-Koordinati-onspolymere. Die siebengliedrige Kette eines Dinitrils wurde experimentell als Grenze fgr das Selbstorganisationssystem zur Erzeugung verschiedenartiger Produkte detektiert. Bei x < 7 werden ausschließlich verschiedene, eher einfache Polymere gebildet, die entweder 0D- oder 1D-Ag/ A -Strukturmotive besitzen, die durch Dinitril-Linker verbunden sind, w-hrend bei x + 7 die Selbstorganisation zu vçllig neuen außergewçhnli-chen, durch Nitrile verbundenen 3D-Netzwerken nano-di-mensionierter Wirt/Gast-Aggregate von (SbF 6 )@[( A ) 9 Ag 11 ] 11 + (x = 7) oder ( A )@[( A ) 12 Ag 12 ] 12 + (x = 8–10) wechselt. Die polykationischen Knoten stellen die ersten auf A und Silber basierenden Supersph-ren dar, die Wirt/Gast-f-hig

The N-terminal cytosolic T1 domain of the mammalian voltage gated potassium channel Kv1.4 is strongly involved in the tetramerization of the Kv1.4 subunit that is required for forming a functional ion channel. The T1 domain forms a stable tetramer of 48 kDa in solution that cannot be dissociated into monomers. In spite of the high molecular mass it was possible to completely assign the backbone and part of the side chain resonances by multidimensional NMR spectroscopy on uniformly (2)H, (13)C, (15)N enriched protein. The secondary structure analysis derived from the chemical shifts is in line with the expectations from X-ray structures of related proteins.

The nacnac Cu(I) compound [LCu(MeCN)] (2) (L = [{N(C6H3Me2-2,6)C(Me)}2CH]-) was reacted with complexes containing aromatic cyclo-E5 ([Cp*Fe(η5-E5)], E = P (1a), As (1b), Cp* = η5-C5Me5), cyclo-P4 ([Cp‴Co(η4-P4)] (3), Cp‴ = η5-C5H2tBu3) and cyclo-E3 ligands ([Cp‴Ni(η3-E3)], E = P (4a), As (4b)) yielding the heterometallic complexes [(Cp*Fe)(μ,η5:2-E5)(LCu)] (E = P (5a), As (5b)), [(Cp*Fe)(μ3,η5:2:1-E5)(LCu)2] (E = P (6a), As (6b)), [(Cp‴Co)(μ,η4:2-P4)(LCu)] (7), [(Cp‴Co)(μ3,η4:2:1-P4)(LCu)2] (8), and [(Cp‴Ni)(μ,η3:2-E3)(LCu)] (E = P (9a), As (9b)). These complexes are rare examples of the coordination of a group 11 metal to aromatic cyclo-En (E = P, As; n = 3-5) ligands. All products were comprehensively characterized by crystallographic and spectroscopic methods. Their dynamic behavior in solution was studied by VT (variable-temperature) NMR spectroscopy, and their electronic structures were elucidated by DFT calculations.

One-pot self-assembly reactions of the polyphosphorus complex [Cp*Fe(η5 -P5 )] (A), a coinage metal salt AgSbF6 , and flexible aliphatic dinitriles NC(CH2 )x CN (x=1-10) yield 1D, 2D, and 3D coordination polymers. The seven-membered backbone of the dinitrile was experimentally found as the borderline for the self-assembly system furnishing products of different kinds. At x<7, various rather simple polymers are exclusively formed possessing either 0D or 1D Ag/A structural motifs connected by dinitrile spacers, while at x≥7, the self-assembly switches to unprecedented extraordinary 3D networks of nano-sized host-guest assemblies (SbF6 )@[(A)9 Ag11 ]11+ (x=7) or (A)@[(A)12 Ag12 ]12+ (x=8-10) linked by dinitriles. The polycationic nodes represent the first superspheres based on A and silver and are host-guest able. All products are characterized by NMR spectroscopy, mass spectrometry, and single-crystal X-ray diffraction. The assemblies [(A)12 Ag12 ]12+ were visualized by transmission electron microscopy.

Abstract In a high‐yield one‐pot synthesis, the reactions of [Cp*M(η5‐P5)] (M=Fe (1), Ru (2)) with I2 resulted in the selective formation of [Cp*MP6I6]+ salts (3, 4). The products comprise unprecedented all‐cis tripodal triphosphino‐cyclotriphosphine ligands. The iodination of [Cp*Fe(η5‐As5)] (6) gave, in addition to [Fe(CH3CN)6]2+ salts of the rare [As6I8]2− (in 7) and [As4I14]2− (in 8) anions, the first di‐cationic Fe‐As triple decker complex [(Cp*Fe)2(μ,η5:5‐As5)][As6I8] (9). In contrast, the iodination of [Cp*Ru(η5‐As5)] (10) did not result in the full cleavage of the M−As bonds. Instead, a number of dinuclear complexes were obtained: [(Cp*Ru)2(μ,η5:5‐As5)][As6I8]0.5 (11) represents the first Ru‐As5 triple decker complex, thus completing the series of monocationic complexes [(CpRM)2(μ,η5:5‐E5)]+ (M=Fe, Ru; E=P, As). [(Cp*Ru)2As8I6] (12) crystallizes as a racemic mixture of both enantiomers, while [(Cp*Ru)2As4I4] (13) crystallizes as a symmetric and an asymmetric isomer and features a unique tetramer of {AsI} arsinidene units as a middle deck.

The study of the pressure response by NMR spectroscopy provides information on the thermodynamics of conformational equilibria in proteins and nucleic acids. For obtaining a database for expected pressure effects on free nucleotides and nucleotides bound in macromolecular complexes, the pressure response of 1H chemical shifts and J-coupling constants of the purine 5'-ribonucleotides AMP, ADP, ATP, GMP, GDP, and GTP were studied in the absence and presence of Mg2+-ions. Experiments are supported by quantum-chemical calculations of populations and chemical shift differences in order to corroborate structural interpretations and to estimate missing data for AMP. The preference of the ribose S puckering obtained from the analysis of the experimental J-couplings is also confirmed by the calculations. In addition, the pressure response of the non-hydrolysable GTP analogues GppNHp, GppCH2p, and GTPγS was examined within a pressure range up to 200 MPa. As observed earlier for 31P NMR chemical shifts of these nucleotides the pressure dependence of chemical shifts is clearly non-linear in most cases. In di- and tri-phospho nucleosides, the resonances of the two protons bound to the ribose 5' carbon are non-equivalent and can be observed separately. The gg-rotamer at C4'- C5' bond is strongly preferred and the downfield shifted resonance can be assigned to the H5″ proton in the nucleotides. In contrast, in adenosine itself the frequencies of the two resonances are interchanged.

AbstractIn Eintopfsynthesen mit hohen Ausbeuten führten die Reaktionen von [Cp*M(η5‐P5)] (M=Fe (1), Ru (2)) mit I2 zur selektiven Bildung von [Cp*MP6I6]+‐Salzen (3, 4). Die Produkte enthalten beispiellose all‐cis tripodale Triphosphinocyclotriphosphan‐Liganden. Die Iodierung von [Cp*Fe(η5‐As5)] (6) ergab, zusätzlich zu [Fe(CH3CN)6]2+‐Salzen der seltenen [As6I8]2−‐(in 7) und [As4I14]2−‐(in 8) Anionen, den ersten dikationischen Fe‐As Tripeldecker‐Komplex [(Cp*Fe)2(μ,η5:5‐As5)][As6I8] (9). Demgegenüber führte die Iodierung von [Cp*Ru(η5‐As5)] (10) nicht zur vollständigen Spaltung der M‐As‐Bindungen. Stattdessen wurde eine Anzahl zweikerniger Komplexe erhalten; [(Cp*Ru)2(μ,η5:5‐As5)][As6I8]0.5 (11): repräsentiert den ersten Ru‐As5‐Tripeldecker‐Komplex, womit die Reihe monokationischer Komplexe [(CpRM)2(μ,η5:5‐E5)]+ (M=Fe, Ru; E=P, As) vervollständigt wurde; [(Cp*Ru)2As8I6] (12): kristallisiert als ein razemisches Gemisch beider Enantiomere; während [(Cp*Ru)2As4I4] (13): als ein symmetrisches und ein asymmetrisches Isomer kristallisiert und ein einzigartiges Tetramer aus {AsI}‐Arseniden‐Einheiten als Mitteldeck aufweist.

Prokaryotic cold shock proteins (CSPs) are considered to play an important role in the transcriptional and translational regulation of gene expression, possibly by acting as transcription anti-terminators and “RNA chaperones”. They bind with high affinity to single-stranded nucleic acids. Here we report the binding epitope of TmCsp from Thermotoga maritima for both single-stranded DNA and RNA, using heteronuclear 2D NMR spectroscopy. At “physiological” growth temperatures of TmCsp (≥ 343 K), all oligonucleotides studied have dissociation constants between 1.6 ((dT)7) and 25.2 ((dA)7) μM as determined by tryptophan fluorescence quenching. Reduction of the temperature to 303 K leads to a pronounced increase of affinity for thymidylate (dT)7 and uridylate (rU)7 heptamers with dissociation constants of 4.0 and 10.8 nM, respectively, whereas the weak binding of TmCsp to cytidylate, adenylate, and guanylate heptamers (dC)7, (dA)7, and (dT)7 is almost unaffected by temperature. The change of affinities of TmCsp for (dT)7 and (rU)7 by approximately 3 orders of magnitude shows that it represents a cold chock sensor that switches on the cold shock reaction of the cell. A temperature dependent conformational switch of the protein is required for this action. The binding epitope on TmCsp for the ssDNA and RNA heptamers is very similar and comprises β-strands 1 and 2, the loop β1–β2 as well as the loops connecting β3 with β4 and β4 with β5. Besides the loop regions, surprisingly, mainly the RNA-binding motif RNP1 is involved in ssDNA and RNA binding, while only two amino acids, H28 and W29, of the postulated RNA-binding motif RNP2 interact with the uridylate and thymidylate homonucleotides, although a high affinity in the nanomolar range is achieved. This is in contrast to the binding properties of other CSPs or cold shock domains, where RNP1 as well as RNP2 are involved in binding. TmCsp takes up a unique position since it is the only one which possesses a tryptophan residue instead of a usually highly conserved phenylalanine or tyrosine residue at the end of RNP2. NMR titrations suggest that neither (dT)7 nor (rU)7 represent the full binding motif and that non-optimal intercalation of W29 into these oligonucleotides blocks the access of the RNP2 site to the DNA or RNA. NMR-experiments with (dA)7 suggest an interaction of W29 with the adenine ring. Full binding seems to require at least one single purine base well-positioned within a thymine- or uracil-rich stretch of nucleic acids.

CanA from Pyrodictium abyssi forms a heat-resistant organic hollow-fiber network together with CanB and CanC. An N-terminally truncated construct of CanA (K1-CanA) gave NMR spectra of good quality that could be assigned by three-dimensional NMR methods on 15N and 13C–15N enriched protein. We assigned the chemical shifts of 96% of all backbone 1HN atoms, 98% of all backbone 15N atoms, 100% of all 13Cα atoms, 100% of all 1Hα atoms, 90% of all 13C′ atoms, and 100% of the 13Cβ atoms. Two short helices and 10 β-strands are estimated from an analysis of the chemical shifts leading to a secondary structure content of K1-CanA of 6% helices, 44% β-pleated sheets, and 50% coils.

Proteins and nucleic acids are highly dynamic bio-molecules that can populate a variety of conformational states. NMR relaxation dispersion (RD) methods are uniquely suited to quantify the associated kinetic and thermodynamic parameters. Here, we present a consistent suite of 19F-based CPMG, on-resonance R1ρ and off-resonance R1ρ RD experiments. We validate these experiments by studying the unfolding transition of a 7.5 kDa cold shock protein. Furthermore we show that the 19F RD experiments are applicable to very large molecular machines by quantifying dynamics in the 360 kDa half-proteasome. Our approach significantly extends the timescale of chemical exchange that can be studied with 19F RD, adds robustness to the extraction of exchange parameters and can determine the absolute chemical shifts of excited states. Importantly, due to the simplicity of 19F NMR spectra, it is possible to record complete datasets within hours on samples that are of very low costs. This makes the presented experiments ideally suited to complement static structural information from cryo-EM and X-ray crystallography with insights into functionally relevant motions.

For interpreting the pressure induced shifts of resonance lines of folded as well as unfolded proteins the availability of data from well-defined model systems is indispensable. Here, we report the pressure dependence of 1H and 15N chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx is one of the 20 canonical amino acids) measured at 800 MHz proton frequency. As observed earlier for other nuclei the chemical shifts of the side chain nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The pressure response is described by a second degree polynomial with the pressure coefficients B1 and B2 that are dependent on the atom type and type of amino acid studied. A number of resonances could be assigned stereospecifically including the 1H and 15N resonances of the guanidine group of arginine. In addition, stereoselectively isotope labeled SAIL amino acids were used to support the stereochemical assignments. The random-coil pressure coefficients are also dependent on the neighbor in the sequence as an analysis of the data shows. For Hα and HN correction factors for different amino acids were derived. In addition, a simple correction of compression effects in thermodynamic analysis of structural transitions in proteins was derived on the basis of random-coil pressure coefficients.