Synthesis of biotin-containing phosphoramidite linker with polyether spacer arm

A phosphoramidite linker unit, based on glycerol backbone and containing a biotin residue attached through a tetraethylene glycol spacer arm, was synthesized. DMTr-Glycidol and tetraethylene glycol were used as starting materials. After conversion of one of hydroxy groups in tetraethylene glycol into an amino group, the epoxy cycle in DMTr-glycidol was opened by this amino alcohol, resulting in the corresponding ether and some quantity of secondary amine. After attaching of biotin residue to the ether followed by phosphitylation, the desirable linker was obtained. The structure of the linker was confirmed by (1)H-(1)H COSY, (1)H-(13)C HSQC, (1)H-(13)C HMBC, (1)H-(15)N HSQC, and (1)H-(15)N HMBC spectra. The resulted phosphoramidite linker unit is suitable for use in common DNA synthesizers. This approach can be used for preparation of various modifiers containing reporter groups attached to the primary amino function using conventional procedures.     

Structure of the O-polysaccharide from the lipopolysaccharide of Providencia alcalifaciens O12

The O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O12. Its structure was studied by sugar analysis using GLC of the alditol acetates and (S)-2-octyl glycosides, methylation analysis, Smith degradation, and ¹H and ¹³C NMR spectroscopy, including 2D ¹H-¹H COSY, TOCSY, ROESY, ¹H-¹³C HSQC, and HMBC experiments. It was found that the polymer is a neutral heteropolysaccharide and has a branched heptasaccharide repeating unit with the following structure:     

A1H-15N NM R study of human c-Ha-ras protein: Biosynthetic incorporation of15N-labeled amino acids

Summary A¹H-¹⁵N NMR study was performed on the GDP-bound form of a truncated human c-Ha-ras oncogene product (171 amino acid residues). Resonance cross peaks of the backbone amide¹H-¹⁵N nuclei of a uniformly¹⁵N-labeled protein were observed with heteronuclear-single-quantum coherence spectroscopy (HSQC). In order to resolve overlapping cross peaks, selective¹⁵N-labeling of one or two types of amino acid residues (Ala, Arg, Asx, Glx, Gly, His, lie, Leu, Lys, Met, Phe, Ser; Thr, Tyr and/or Val) was carried out using appropriateE. coli mutant strains. By this procedure, all the backbone¹H-¹⁵N cross peaks were classified into amino acid types.This work was supported in part by a Grant-in-Aid for Cancer Research from the Ministry of Education, Science and Culture, Japan     

Seven new vernocuminosides from the stem bark of Vernonia cumingiana Benth

Seven new stigmastane-type steroidal glycosides, vernocuminosides H-N, have been isolated from the stem bark of Vernonia cumingiana Benth. The structures of these compounds were determined by NMR spectrometric methods including HSQC, HMBC, ¹H-¹H COSY, and NOE, as well as circular dichroism experiments. Anti-inflammatory activities of vernocuminosides I and K-N were determined.     

Calmodulin tagging provides a general method of using lanthanide induced magnetic field orientation to observe residual dipolar couplings in proteins in solution

A general method is presented for magnetic field alignment of proteins in solution. By tagging a target protein with calmodulin saturated with paramagnetic lanthanide ions it is possible to measure substantial residual dipolar couplings (RDC) whilst minimising the effects of pseudocontact shifts on the target protein. A construct was made consisting of a calmodulin-binding peptide (M13 from sk-MLCK) attached to a target protein, dihydrofolate reductase in this case. The engineered protein binds tightly to calmodulin saturated with terbium, a paramagnetic lanthanide ion. By using only a short linker region between the M13 and the target protein, some of the magnetic field alignment induced in the CaM(Tb^{3 +})₄ is effectively transmitted to the target protein (DHFR). ¹H-¹⁵N HSQC IPAP experiments on the tagged complex containing ¹⁵N-labelled DHFR-M13 protein and unlabelled CaM(Tb^{3 +})₄ allow one to measure RDC contributions in the aligned complex. RDC values in the range +4.0 to –7.4 Hz were measured at 600 MHz. Comparisons of ¹H-¹⁵N HSQC spectra of ¹⁵N-DHFR-M13 alone and its complexes with CaM(Ca^{2 +})₄ and CaM(Tb³⁺)₄ indicated that (i) the structure of the target protein is not affected by the complex formation and (ii) the spectra of the target protein are not seriously perturbed by pseudocontact shifts. The use of a relatively large tagging group (CaM) allows us to use a lanthanide ion with a very high magnetic susceptibility anisotropy (such as Tb³⁺) to give large alignments while maintaining relatively long distances from the target protein nuclei (and hence giving only small pseudocontact shift contributions).     

A solution NMR investigation into the murine amelogenin splice-variant LRAP (Leucine-Rich Amelogenin Protein)

Amelogenins are the dominant proteins present in ameloblasts during the early stages of enamel biomineralization, making up > 90% of the matrix protein. Along with the full-length protein there are several splice-variant isoforms of amelogenin present including LRAP (Leucine-Rich Amelogenin Protein), a protein that consists of the first 33 and the last 26 residues of full-length amelogenin. Using solution-state NMR spectroscopy we have assigned the ¹H-¹⁵N HSQC spectrum of murine LRAP (rp(H)LRAP) in 2% acetic acid at pH 3.0 by making extensive use of previous chemical shift assignments for full-length murine amelogenin (rp(H)M180). This correlation was possible because LRAP, like the full-length protein, is intrinsically disordered under these solution conditions. The major difference between the ¹H-¹⁵N HSQC spectra of rp(H)M180 and rp(H)LRAP was an additional set of amide resonances for each of the seven non-proline residues between S12* and Y12 near the N-terminus of rp(H)LRAP indicating that the N-terminal region of LRAP exists in two different conformations. Analysis of the proline carbon chemical shifts suggests that the molecular basis for the two states is not a cis-trans isomerization of one or more of the proline residues in the N-terminal region. Starting from 2% acetic acid, where rp(H)LRAP was monomeric in solution, NaCl addition effected residue specific changes in molecular dynamics manifested by the reduction in intensity and disappearance of ¹H-¹⁵N HSQC cross peaks. As observed for the full-length protein, these perturbations may signal early events governing supramolecular self-assembly of rp(H)LRAP into nanospheres. However, the different patterns of ¹H-¹⁵N HSQC cross peak perturbation between rp(H)LRAP and rp(H)M180 in high salt suggest that the termini may behave differently in their respective nanospheres, and perhaps, these differences contribute to the cell signaling properties attributable to LRAP but not to the full-length protein.     

Gradient and sensitivity enhanced multiple-quantum coherence in heteronuclear multidimensional NMR experiments

Recent studies have indicated that the relaxation rate of the ¹H-¹³C multiple-quantum coherence is much slower than that of the ¹H-¹³C single-quantum coherence for non-aromatic methine sites in ¹³ C labeled proteins and in nucleic acids at the slow tumbling limit. Several heteronuclear experiments have been designed to use a multiple-quantum coherence transfer scheme instead of the single-quantum transfer method, thereby increasing the sensitivity and resolution of the spectra. Here, we report a constant time, gradient and sensitivity enhanced HMQC experiment (CT-g/s-HMQC) and demonstrate that it has a significant sensitivity enhancement over constant time HMQC and constant time gradient and sensitivity enhanced HSQC experiments (CT-g/s-HSQC) when applied to a ¹³C and ¹⁵ N labeled calmodulin sample in D₂O. We also apply this approach to 3D NOESY-HMQC and doubly sensitivity enhanced TOCSY-HMQC experiments, and demonstrate that they are more sensitive than their HSQC counterparts.     

Multiplet component separation for measurement of methyl 13C-1H dipolar couplings in weakly aligned proteins

A simple spectral editing procedure is described that generates separate subspectra for the methyl ¹³C-¹H₃ multiplet components of ¹H-¹³C HSQC spectra. The editing procedure relies on co-addition of in-phase and antiphase spectra and yields ¹H-coupled constant-time HSQC subspectra for the methyl region that have the simplicity of the regular decoupled CT-HSQC spectrum. Resulting spectra permit rapid and reliable measurement of ¹H-¹³C J and dipolar couplings. The editing procedure is illustrated for a Ca²⁺-calmodulin sample in isotropic and liquid crystalline phases.     

Evidence of glucuronidation of the glycation product LW-1: tentative structure and implications for the long-term complications of diabetes

LW-1 is a collagen-linked blue fluorophore whose skin levels increase with age, diabetes and end-stage renal disease (ESRD), and correlate with the long-term progression of microvascular disease and indices of subclinical cardiovascular disease in type 1 diabetes. The chemical structure of LW-1 is still elusive, but earlier NMR analyses showed it has a lysine residue in an aromatic ring coupled to a sugar molecule reminiscent of advanced glycation end-products (AGEs). We hypothesized and demonstrate here that the unknown sugar is a N-linked glucuronic acid. LW-1 was extracted and highly purified from ~99 g insoluble skin collagen obtained at autopsy from patients with diabetes/ESRD using multiple rounds of proteolytic digestion and purification by liquid chromatography (LC). Advanced NMR techniques (¹H–NMR, ¹³C–NMR, ¹H-¹³C HSQC, ¹H-¹H TOCSY, ¹H-¹³C HMBC) together with LC-mass spectrometry (MS) revealed a loss of 176 amu (atomic mass unit) unequivocally point to the presence of a glucuronic acid moiety in LW-1. To confirm this data, LW-1 was incubated with β-glycosidases (glucosidase, galactosidase, glucuronidase) and products were analyzed by LC-MS. Only glucuronidase could cleave the sugar from the parent molecule. These results establish LW-1 as a glucuronide, now named glucuronidine, and for the first time raise the possible existence of a “glucuronidation pathway of diabetic complications”. Future research is needed to rigorously probe this concept and elucidate the molecular origin and biological source of a circulating glucuronidine aglycone.     

Optimizing <Superscript>19</Superscript>F NMR protein spectroscopy by fractional biosynthetic labeling

In protein NMR experiments which employ nonnative labeling, incomplete enrichment is often associated with inhomogeneous line broadening due to the presence of multiple labeled species. We investigate the merits of fractional enrichment strategies using a monofluorinated phenylalanine species, where resolution is dramatically improved over that achieved by complete enrichment. In NMR studies of calmodulin, a 148 residue calcium binding protein, ¹⁹F and ¹H-¹⁵N HSQC spectra reveal a significant extent of line broadening and the appearance of minor conformers in the presence of complete (>95%) 3-fluorophenylalanine labeling. The effects of varying levels of enrichment of 3-fluorophenylalanine (i.e. between 3 and >95%) were further studied by ¹⁹F and ¹H-¹⁵N HSQC spectra,¹⁵N T₁ and T₂ relaxation measurements, ¹⁹F T₂ relaxation, translational diffusion and heat denaturation experiments via circular dichroism. Our results show that while several properties, including translational diffusion and thermal stability show little variation between non-fluorinated and >95% ¹⁹F labeled samples, ¹⁹F and ¹H-¹⁵N HSQC spectra show significant improvements in line widths and resolution at or below 76% enrichment. Moreover, high levels of fluorination (>80%) appear to increase protein disorder as evidenced by backbone ¹⁵N dynamics. In this study, reasonable signal to noise can be achieved between 60–76% ¹⁹F enrichment, without any detectable perturbations from labeling.     

Three new terpenoids from the Eupatorium chinense

Three new terpenoids compounds (1–3) were obtained from ethyl acetate fraction, which was yielded from Eupatorium chinense’s ethanol extract. Their structures were determined on the basis of 1D and 2D NMR spectroscopy, including ¹H-¹H COSY, HMBC, HSQC and NOESY experiments. All of the isolated compounds were tested in vitro for their cytotoxic activities against the HepG₂, HGC-27 and MDA-MB-231 cancer cell lines.     

Toxic polyketides produced by Fusarium sp., an endophytic fungus isolated from Melia azedarach

A new isocoumarin derivative named fusariumin (1), together with two known related resorcylic acid lactones aigialomycin D (2) and pochonin N (3), has been isolated from the cultures of Fusarium sp. LN-10, an endophytic fungus originated from the leaves of Melia azedarach. Their structures were established on the basis of extensive spectroscopic analyzes including 1D- and 2D- NMR (¹H-¹H COSY, HSQC, HMBC, and NOESY) experiments. Compounds 1-3 displayed significant growth inhibitory activity against the brine shrimp (Artemia salina).     

Structure, dynamics and mapping of membrane-binding residues of micelle-bound antimicrobial peptides by natural abundance C NMR spectroscopy

Worldwide bacterial resistance to traditional antibiotics has drawn much research attention to naturally occurring antimicrobial peptides (AMPs) owing to their potential as alternative antimicrobials. Structural studies of AMPs are essential for an in-depth understanding of their activity, mechanism of action, and in guiding peptide design. Two-dimensional solution proton NMR spectroscopy has been the major tool. In this article, we describe the applications of natural abundance ¹³C NMR spectroscopy that provides complementary information to 2D ¹H NMR. The correlation of ¹³Cα secondary shifts with both 3D structure and heteronuclear ¹⁵N NOE values indicates that natural abundance carbon chemical shifts are useful probes for backbone structure and dynamics of membrane peptides. Using human LL-37-derived peptides (GF-17, KR-12, and RI-10), as well as amphibian antimicrobial and anticancer peptide aurein 1.2 and its analog LLAA, as models, we show that the cross peak intensity plots of 2D ¹H-¹³Cα HSQC spectra versus residue number present a wave-like pattern (HSQC wave) where key hydrophobic residues of micelle-bound peptides are located in the troughs with weaker intensities, probably due to fast exchange between the free and bound forms. In all the cases, the identification of aromatic phenylalanines as a key membrane-binding residue is consistent with previous intermolecular Phe-lipid NOE observations. Furthermore, mutation of one of the key hydrophobic residues of KR-12 to Ala significantly reduced the antibacterial activity of the peptide mutants. These results illustrate that natural abundance heteronuclear-correlated NMR spectroscopy can be utilized to probe backbone structure and dynamics, and perhaps to map key membrane-binding residues of peptides in complex with micelles. ¹H-¹³Cα HSQC wave, along with other NMR waves such as dipolar wave and chemical shift wave, offers novel insights into peptide-membrane interactions from different angles.     

A novel thymidine phosphoramidite synthon for incorporation of internucleoside phosphate linkers during automated oligodeoxynucleotide synthesis

A novel thymidine phosphoramidite synthon was synthesized and successfully used for incorporation of primary amino groups, attached through a triethylene glycol linker to the internucleoside phosphates, at desired locations during automated oligodeoxynucleotide synthesis. The synthesized amino-linker bearing oligonucleotides are stable under deprotection conditions and exhibit Watson-Crick base-pairing properties. Covalent labeling of oligonucleotides with carbocyanine near-infrared fluorochromes resulted in 2.5 times higher labeling yields when compared with oligonucleotides containing base-attached aminolinkers. We anticipate that the developed synthetic approach will be useful for nucleotide sequence-specific attachment of single or multiple ligands or reporter molecules.     

Three new compounds from the bark of Antiaris toxicaria

Three new compounds, namely (+)-pranferol (1), antiarone M (2), and anticerol A (3), together with 9 known compounds, were obtained from the bark of Antiaris toxicaria. Their chemical structures were elucidated on the basis of spectroscopic methods including UV, IR, (HR) ESI–MS, ¹H, ¹³C NMR, HSQC, ¹H-¹H COSY, HMBC and X-ray crystallographic technique. The absolute configurations of compounds 1 and 2 were determined by modified mosher method and CD spectrum.     

Soluble Variants of Human Recombinant Glutaminyl Cyclase

Recombinant human Glutaminyl Cyclase expressed in E. coli is produced as inclusion bodies. Lack of glycosylation is the main origin of its accumulation in insoluble aggregates. Mutation of single isolated hydrophobic amino acids into negative amino acids was not able to circumvent inclusion bodies formation. On the contrary, substitution with carboxyl-terminal residues of two or three aromatic residues belonging to extended hydrophobic patches on the protein surface provided soluble but still active forms of the protein. These mutants could be expressed in isotopically enriched forms for NMR studies and the maximal attainable concentration was sufficient for the acquisition of ¹H-¹⁵N HSQC spectra that represent the starting point for future drug development projects targeting Alzheimer’s disease.     

15N标记蛋白GAL4(62)的2D NMR实验

利用自编的脉冲程序,采用预饱和和自旋锁定对水峰进行双重抑制的方法,得到了 ¹⁵N标记蛋白GAL4(62)的2D ¹H-¹⁵N HSQC、HSQC-NOESY、HSQC-TOCSY谱,并对这几个谱在蛋白质 ¹H谱的归属中所起的作用进行了讨论.     

NMR Structural Studies of Antimicrobial Peptides: LPcin Analogs

Lactophoricin (LPcin), a component of proteose peptone (113–135) isolated from bovine milk, is a cationic amphipathic antimicrobial peptide consisting of 23 amino acids. We designed a series of N- or C-terminal truncated variants, mutated analogs, and truncated mutated analogs using peptide-engineering techniques. Then, we selected three LPcin analogs of LPcin-C8 (LPcin-YK1), LPcin-T2WT6W (LPcin-YK2), and LPcin-T2WT6W-C8 (LPcin-YK3), which may have better antimicrobial activities than LPcin, and successfully expressed them in E. coli with high yield. We elucidated the 3D structures and topologies of the three LPcin analogs in membrane environments by conducting NMR structural studies. We investigated the purity of the LPcin analogs and the α-helical secondary structures by performing ¹H-¹⁵N 2D HSQC and HMQC-NOESY liquid-state NMR spectroscopy using protein-containing micelle samples. We measured the 3D structures and tilt angles in membranes by conducting ¹⁵N 1D and 2D ¹H-¹⁵N SAMMY type solid-state NMR spectroscopy with an 800 MHz in-house-built ¹H-¹⁵N double-resonance solid-state NMR probe with a strip-shield coil, using protein-containing large bicelle samples aligned and confirmed by molecular-dynamics simulations. The three LPcin analogs were found to be curved α-helical structures, with tilt angles of 55–75° for normal membrane bilayers, and their enhanced activities may be correlated with these topologies.     

Sannastatin, a novel toxic macrolactam polyketide glycoside produced by actinomycete Streptomyces sannanensis

A new rare 20-membered macrocyclic lactam incorporating a diene conjugated olefin, designated sannastatin (1), together with the known structurally related vicenistatin (2), has been isolated from the cultures of Streptomyces sannanensis, a bacteria found in the feces of Ailuropoda melanoleuca. The structure of the new compound was established on the basis of extensive spectroscopic analyses including 1D- and 2D-NMR (¹H-¹H COSY, TOCSY, HSQC, HMBC, and NOESY) experiments. Compounds 1 and 2 displayed significant growth inhibitory activity against the brine shrimp (Artemia salina) larvae.     

Amino acid-selective isotope labeling of proteins for nuclear magnetic resonance study: Proteins secreted by Brevibacillus choshinensis

Here we report the first application of amino acid-type selective (AATS) isotope labeling of a recombinant protein secreted by Brevibacillus choshinensis for a nuclear magnetic resonance (NMR) study. To prepare the ¹⁵N-AATS-labeled protein, the transformed B. choshinensis was cultured in ¹⁵N-labeled amino acid-containing C.H.L. medium, which is commonly used in the Escherichia coli expression system. The analyses of the ¹H-¹⁵N heteronuclear single quantum coherence (HSQC) spectra of the secreted proteins with a ¹⁵N-labeled amino acid demonstrated that alanine, arginine, asparagine, cysteine, glutamine, histidine, lysine, methionine, and valine are suitable for selective labeling, although acidic and aromatic amino acids are not suitable. The ¹⁵N labeling for glycine, isoleucine, leucine, serine, and threonine resulted in scrambling to specific amino acids. These results indicate that the B. choshinensis expression system is an alternative tool for AATS labeling of recombinant proteins, especially secretory proteins, for NMR analyses.