Heiko M. Möller

Mechanistic Features of Isomerizing Alkoxycarbonylation of Methyl Oleate

The weakly coordinated triflate complex [(P^P)Pd(OTf)](+)(OTf)(-) (1) (P^P = 1,3-bis(di-tert-butylphosphino)propane) is a suitable reactive precursor for mechanistic studies of the isomerizing alkoxcarbonylation of methyl oleate. Addition of CH(3)OH or CD(3)OD to 1 forms the hydride species [(P^P)PdH(CH(3)OH)](+)(OTf)(-) (2-CH(3)OH) or the deuteride [(P^P)PdD(CD(3)OD)](+)(OTf)(-) (2(D)-CD(3)OD), respectively. Further reaction with pyridine cleanly affords the stable and isolable hydride [(P^P)PdH(pyridine)](+)(OTf)(-) (2-pyr). This complex yields the hydride fragment free of methanol by abstraction of pyridine with BF(3)·OEt(2), and thus provides an entry to mechanistic observations including intermediates reactive toward methanol. Exposure of methyl oleate (100 equiv) to 2(D)-CD(3)OD resulted in rapid isomerization to the thermodynamic isomer distribution, 94.3% of internal olefins, 5.5% of α,β-unsaturated ester and <0.2% of terminal olefin. Reaction of 2-pyr/BF(3)·OEt(2) with a stoichiometric amount of 1-(13)C-labeled 1-octene at -80 °C yields a 50:50 mixture of the linear alkyls [(P^P)Pd(13)CH(2)(CH(2))(6)CH(3)](+) and [(P^P)PdCH(2)(CH(2))(6)(13)CH(3)](+) (4a and 4b). Further reaction with (13)CO yields the linear acyls [(P^P)Pd(13)C(═O)(12/13)CH(2)(CH(2))(6)(12/13)CH(3)(L)](+) (5-L; L = solvent or (13)CO). Reaction of 2-pyr/BF(3)·OEt(2) with a stoichiometric amount of methyl oleate at -80 °C also resulted in fast isomerization to form a linear alkyl species [(P^P)PdCH(2)(CH(2))(16)C(═O)OCH(3)](+) (6) and a branched alkyl stabilized by coordination of the ester carbonyl group as a four membered chelate [(P^P)PdCH{(CH(2))(15)CH(3)}C(═O)OCH(3)](+) (7). Addition of carbon monoxide (2.5 equiv) at -80 °C resulted in insertion to form the linear acyl carbonyl [(P^P)PdC(═O)(CH(2))(17)C(═O)OCH(3)(CO)](+) (8-CO) and the five-membered chelate [(P^P)PdC(═O)CH{(CH(2))(15)CH(3)}C(═O)OCH(3)](+) (9). Exposure of 8-CO and 9 to (13)CO at -50 °C results in gradual incorporation of the (13)C label. Reversibility of 7 + CO ⇄ 9 is also evidenced by ΔG = -2.9 kcal mol(-1) and ΔG(‡) = 12.5 kcal mol(-1) from DFT studies. Addition of methanol at -80 °C results in methanolysis of 8-L (L = solvent) to form the linear diester, 1,19-dimethylnonadecandioate, whereas 9 does not react and no branched diester is observed. DFT yields a barrier for methanolysis of ΔG(‡) = 29.7 kcal mol(-1) for the linear (8) vs ΔG(‡) = 37.7 kcal mol(-1) for the branched species (9).

Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins : 2. Level of Theory, Basis Set, and Solvents Model Dependence

It has been demonstrated that the fragmentation scheme of our adjustable density matrix assembler (ADMA) approach for the quantum chemical calculations of very large systems is well-suited to calculate NMR chemical shifts of proteins [ Frank et al. Proteins2011, 79, 2189-2202 ]. The systematic investigation performed here on the influences of the level of theory, basis set size, inclusion or exclusion of an implicit solvent model, and the use of partial charges to describe additional parts of the macromolecule on the accuracy of NMR chemical shifts demonstrates that using a valence triple-ζ basis set leads to large improvement compared to the results given in the previous publication. Additionally, moving from the B3LYP to the mPW1PW91 density functional and including partial charges and implicit solvents gave the best results with mean absolute errors of 0.44 ppm for hydrogen atoms excluding H(N) atoms and between 1.53 and 3.44 ppm for carbon atoms depending on the size and also on the accuracy of the protein structure. Polar hydrogen and nitrogen atoms are more difficult to predict. For the first, explicit hydrogen bonds to the solvents need to be included and, for the latter, going beyond DFT to post-Hartree-Fock methods like MP2 is probably required. Even if empirical methods like SHIFTX+ show similar performance, our calculations give for the first time very reliable chemical shifts that can also be used for complexes of proteins with small-molecule ligands or DNA/RNA. Therefore, taking advantage of its ab initio nature, our approach opens new fields of application that would otherwise be largely inaccessible due to insufficient availability of data for empirical parametrization.

Molecular analysis of Carbohydrate−Antibody interactions : case study using a Bacillus anthracis Tetrasaccharide

The process for selecting potent and effective carbohydrate antigens is not well-established. A combination of synthetic glycan microarray screening, surface plasmon resonance analysis, and saturation transfer difference NMR spectroscopy was used to dissect the antibody-binding surface of a carbohydrate antigen, revealing crucial binding elements with atomic-level detail. This analysis takes the first step toward uncovering the rules for structure-based design of carbohydrate antigens.

Evolution of prokaryotic SPFH proteins

BackgroundThe SPFH protein superfamily is a diverse family of proteins whose eukaryotic members are involved in the scaffolding of detergent-resistant microdomains. Recently the origin of the SPFH proteins has been questioned. Instead, convergent evolution has been proposed. However, an independent, convergent evolution of three large prokaryotic and three eukaryotic families is highly unlikely, especially when other mechanisms such as lateral gene transfer which could also explain their distribution pattern have not yet been considered.To gain better insight into this very diverse protein family, we have analyzed the genomes of 497 microorganisms and investigated the pattern of occurrence as well as the genomic vicinity of the prokaryotic SPFH members.ResultsAccording to sequence and operon structure, a clear division into 12 subfamilies was evident. Three subfamilies (SPFH1, SPFH2 and SPFH5) show a conserved operon structure and two additional subfamilies are linked to those three through functional aspects (SPFH1, SPFH3, SPFH4: interaction with FtsH protease). Therefore these subgroups most likely share common ancestry. The complex pattern of occurrence among the different phyla is indicative of lateral gene transfer. Organisms that do not possess a single SPFH protein are almost exclusively endosymbionts or endoparasites.ConclusionThe conserved operon structure and functional similarities suggest that at least 5 subfamilies that encompass almost 75% of all prokaryotic SPFH members share a common origin. Their similarity to the different eukaryotic SPFH families, as well as functional similarities, suggests that the eukaryotic SPFH families originated from different prokaryotic SPFH families rather than one. This explains the difficulties in obtaining a consistent phylogenetic tree of the eukaryotic SPFH members. Phylogenetic evidence points towards lateral gene transfer as one source of the very diverse patterns of occurrence in bacterial species.The SPFH protein superfamily is a diverse family of proteins whose eukaryotic members are involved in the scaffolding of detergent-resistant microdomains. Recently the origin of the SPFH proteins has been questioned. Instead, convergent evolution has been proposed. However, an independent, convergent evolution of three large prokaryotic and three eukaryotic families is highly unlikely, especially when other mechanisms such as lateral gene transfer which could also explain their distribution pattern have not yet been considered. To gain better insight into this very diverse protein family, we have analyzed the genomes of 497 microorganisms and investigated the pattern of occurrence as well as the genomic vicinity of the prokaryotic SPFH members. According to sequence and operon structure, a clear division into 12 subfamilies was evident. Three subfamilies (SPFH1, SPFH2 and SPFH5) show a conserved operon structure and two additional subfamilies are linked to those three through functional aspects (SPFH1, SPFH3, SPFH4: interaction with FtsH protease). Therefore these subgroups most likely share common ancestry. The complex pattern of occurrence among the different phyla is indicative of lateral gene transfer. Organisms that do not possess a single SPFH protein are almost exclusively endosymbionts or endoparasites. The conserved operon structure and functional similarities suggest that at least 5 subfamilies that encompass almost 75% of all prokaryotic SPFH members share a common origin. Their similarity to the different eukaryotic SPFH families, as well as functional similarities, suggests that the eukaryotic SPFH families originated from different prokaryotic SPFH families rather than one. This explains the difficulties in obtaining a consistent phylogenetic tree of the eukaryotic SPFH members. Phylogenetic evidence points towards lateral gene transfer as one source of the very diverse patterns of occurrence in bacterial species.

Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins

Despite the many protein structures solved successfully by nuclear magnetic resonance (NMR) spectroscopy, quality control of NMR structures is still by far not as well established and standardized as in crystallography. Therefore, there is still the need for new, independent, and unbiased evaluation tools to identify problematic parts and in the best case also to give guidelines that how to fix them. We present here, quantum chemical calculations of NMR chemical shifts for many proteins based on our fragment‐based quantum chemical method: the adjustable density matrix assembler (ADMA). These results show that 13C chemical shifts of reasonable accuracy can be obtained that can already provide a powerful measure for the structure validation. 1H and even more 15N chemical shifts deviate more strongly from experiment due to the insufficient treatment of solvent effects and conformational averaging. Proteins 2011;

Discovery of Two Classes of Potent Glycomimetic Inhibitors of Pseudomonas aeruginosa LecB with Distinct Binding Modes

The treatment of infections due to the opportunistic pathogen Pseudomonas aeruginosa is often difficult, as a consequence of bacterial biofilm formation. Such a protective environment shields the bacterium from host defense and antibiotic treatment and secures its survival. One crucial factor for maintenance of the biofilm architecture is the carbohydrate-binding lectin LecB. Here, we report the identification of potent mannose-based LecB inhibitors from a screening of four series of mannosides in a novel competitive binding assay for LecB. Cinnamide and sulfonamide derivatives are inhibitors of bacterial adhesion with up to a 20-fold increase in affinity to LecB compared to the natural ligand methyl mannoside. Because many lectins of the host require terminal saccharides (e.g., fucosides), such capped structures as reported here may offer a beneficial selectivity profile for the pathogenic lectin. Both classes of compounds show distinct binding modes at the protein, offering the advantage of a simultaneous development of two new lead structures as anti-pseudomonadal drugs with an anti-virulence mode of action.

A Highly Active DNA Polymerase with a Fluorous Core

DNA polymerases catalyze all DNA synthesis in the cell and are key tools in important molecular biological core technologies. Apart from naturally available DNA poly merases, several modified DNA polymerases with new characteristics have been developed. To date, directed evolution using the 20 natural amino acids is a promising method for the creation of nucleic acid polymerases with modified properties. Yet, the incorporation of non natural amino acids may lead to enhanced chemical and biological diversity of protein structures and properties by introduction of functional groups that are not represented by the natural amino acids. The use of auxotrophic strains, which lack the ability to biosynthesize one specific natural amino acid, offers the possibility to replace one amino acid by a non natural analogue. After depletion of the natural amino acid in a defined medium, inducing the expression of the target protein with concomitant addition of the non natural analogue leads to the incorporation of the non natural amino acid by selective pressure incorporation. Fluorinated protein synthesis has been extensively stud ied in the past. It has also been shown that trifluorinated amino acid analogues such as trifluoromethionine (TFM) with drastically enhanced hydrophobicity may lead to proteins with novel characteristics. However, efforts to engineer new enzyme functions and properties by use of TFM instead of methionine are hampered, as the replacement of natural amino acids by trifluorinated analogues can lead to unfavorable interactions. Thus, the global substitution of natural amino acids by trifluorinated analogues may cause the naturally evolved protein scaffold to lose correct folding, sufficient stability, or enzymatic activity. Hence, only a few examples of proteins are known in which methionine was globally replaced by TFM, including one single example of an enzyme (phage lysozyme) that is 18 kDa in size, in which about 70 % of the three methionine residues are replaced by TFM. Herein, we present the generation of a multifluorinated DNA polymerase. The N terminally truncated version of DNA polymerase I from Thermus aquaticus (KlenTaq) is a thermophilic DNA polymerase composed of 540 amino acids (63 kDa), including 13 methionine (Met) residues that were globally replaced by TFM with a substitution level of approximately 82% (Scheme 1). The multifluorinated Klen

Presentation of lipoteichoic acid potentiates its inflammatory activity

Lipoteichoic acid (LTA) is a major immunostimulatory molecule in the cell wall of Gram-positive bacteria. Adhesion of LTA to a polystyrene surface drastically increased its immunostimulatory potency in human whole blood in comparison to soluble LTA, although only 1% of the LTA had bound, as determined using rhodamine-labelled LTA. The release of the proinflammatory cytokines IL-1beta, TNF and IL-6 and the chemokines IL-8 and G-CSF was increased 2- to 10-fold, but IL-10 release was unaltered. This presentation effect was not shared by lipopolysaccharide (LPS) or other toll-like receptor 2 agonists and was less pronounced in polypropylene vessels. LTA did not induce cytokine release in silicone-coated borosilicate vessels, but covalent coupling of LTA to polystyrene beads restored cytokine induction in these vessels, indicating that presentation of LTA on a surface is in fact essential for its immunostimulatory potency. This novel aspect of presentation as a factor in the recognition of LTA may reflect the physiological situation in the bacterial cell wall, where LTA is anchored in the bacterial membrane and projects through the peptidoglycan. In practical terms, contamination of medical devices with components of Gram-positive bacteria may pose an underestimated inflammatory risk.

Synthetic Motility and Cell Shape Defects Associated with Deletions of Flotillin/Reggie Paralogs in Bacillus subtilis and Interplay of These Proteins with NfeD Proteins

Flotillin/reggie proteins are membrane-associated proteins present in all kinds of cells and belong to the family of proteins carrying the SPFH (stomatin, prohibitin, flotillin, and HflK/HflC) domain. In addition to this domain of unknown function, flotillin proteins are characterized by the flotillin domain, which is rich in heptad repeats. Bacterial flotillin orthologs have recently been shown to be part of lipid rafts, like their eukaryotic counterparts, and to be involved in signaling events. Double deletions of floT and the gene encoding the second flotillin-like protein in Bacillus subtilis, floA, show strong synthetic defects in cell morphology, motility, and transformation efficiency. The lack of FloT resulted in a marked defect in motility. Using total internal reflection fluorescence (TIRF) microscopy, we show that both proteins localize in characteristic focal structures within the cell membrane, which move in a highly dynamic and random manner but localize independently of each other. Thus, flotillin paralogs act in a spatially distinct manner. Flotillin domains in both FloA and FloT are essential for focal assemblies and for the proper function of flotillins. Both flotillin genes are situated next to genes encoding NfeD proteins. FloT dramatically affects the localization of NfeD2: FloT apparently recruits NfeD2 into the focal assemblies, documenting a close interaction between flotillins and NfeDs in bacteria. In contrast, the localization of NfeD1b is not affected by FloA, FloT, or NfeD2. FloA does not show a spatial connection with the upstream-encoded NfeD1b (YqeZ). Our work establishes that bacterial flotillin-like proteins have overlapping functions in a variety of membrane-associated processes and that flotillin domain-mediated assembly and NfeD proteins play important roles in setting up the flotillin raft-like structures in vivo.

Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 3. Conformational Sampling and Explicit Solvents Model

Fragment-based quantum chemical calculations are able to accurately calculate NMR chemical shifts even for very large molecules like proteins. But even with systematic optimization of the level of theory and basis sets as well as the use of implicit solvents models, some nuclei like polar protons and nitrogens suffer from poor predictions. Two properties of the real system, strongly influencing the experimental chemical shifts but almost always neglected in the calculations, will be discussed here in great detail: (1) conformational averaging and (2) interactions with first-shell solvent molecules. Classical molecular dynamics simulations in explicit water were carried out for obtaining a representative ensemble including the arrangement of neighboring solvent molecules, which was then subjected to quantum chemical calculations. We could demonstrate with the small test system N-methyl acetamide (NMA) that the calculated chemical shifts show immense variations of up to 6 ppm and 50 ppm for protons and nitrogens, respectively, depending on the snapshot taken from a classical molecular dynamics simulation. Applying the same approach to the HA2 domain of the influenza virus glycoprotein hemagglutinin, a 32-amino-acid-long polypeptide, and comparing averaged values to the experiment, chemical shifts of nonpolar protons and carbon atoms in proteins were calculated with unprecedented accuracy. Additionally, the mean absolute error could be reduced by a factor of 2.43 for polar protons, and reasonable correlations were obtained for nitrogen and carbonyl carbon in contrast to all other studies published so far.