Root‐mean‐square‐deviation‐based rapid backbone resonance assignments in proteins

We have shown that the methodology based on the estimation of root‐mean‐square deviation (RMSD) between two sets of chemical shifts is very useful to rapidly assign the spectral signatures of ¹H^N, ¹³C^α, ¹³C^β, ¹³C′, ¹H^α and ¹⁵N spins of a given protein in one state from the knowledge of its resonance assignments in a different state, without resorting to routine established procedures (manual and automated). We demonstrate the utility of this methodology to rapidly assign the 3D spectra of a metal‐binding protein in its holo‐state from the knowledge of its assignments in apo‐state, the spectra of a protein in its paramagnetic state from the knowledge of its assignments in diamagnetic state and, finally, the spectra of a mutant protein from the knowledge of the chemical shifts of the corresponding wild‐type protein. The underlying assumption of this methodology is that, it is impossible for any two amino acid residues in a given protein to have all the six chemical shifts degenerate and that the protein under consideration does not undergo large conformational changes in going from one conformational state to another. The methodology has been tested using experimental data on three proteins, M‐crystallin (8.5 kDa, predominantly β‐sheet, for apo‐ to holo‐state), Calbindin (7.5 kDa, predominantly α‐helical, for diamagnetic to paramagnetic state and apo to holo) and EhCaBP1 (14.3 kDa, α‐helical, the wild‐type protein with one of its mutant). In all the cases, the extent of assignment is found to be greater than 85%. Copyright © 2010 John Wiley & Sons, Ltd.     

In situ proton NMR study of acetyl and formyl group migration in mono‐O‐acyl D‐glucose

Acetyl and formyl group migration, mutarotation, and hydrolysis of mono‐O‐acylated glucose are studied by in situ 1D and 2D ¹H NMR spectroscopy. α‐D ‐Glucosyl‐1‐acetate and α‐D ‐glucosyl‐1‐formate serve as sole starting materials. They are generated in situ by configuration retaining glucosyltransfer from α‐D ‐glucosyl‐1‐phosphate to formate and acetate, which is catalyzed by the Glu‐237 → Gln mutant of Leuconostoc mesenteroides sucrose phosphorylase. Temporary accumulated regio‐isomeric mono‐O‐acyl D ‐glucoses are identified, characterized, and quantified directly from the reaction mixture. Time courses of the transformations give insight into pH dependence of acyl group migration and mutarotation as well as into the stability of various regioisomers. Copyright © 2009 John Wiley & Sons, Ltd.     

Purification and Characterization of Bowman‐Birk Protease Inhibitor from Rice Coleoptiles

A 15 kDa rice Bowman‐Birk inhibitor from fast elongating coleoptiles has been purified and identified using partial N‐terminal sequence, LC‐MS, and MALDI‐TOF MS as a 133 amino acid polypeptide (BBIrc 1). The kinetic study shows this protease inhibitor displays competitive inhibition toward trypsin with Ki of 4.0 × 10^?7 M and non‐competitive inhibition toward α‐chymotrypsin with Ki of 9.3 × 10^?6 M. The Western blotting results of the anti‐sera raised against this 15 kDa protein showed that this anti‐serum recognized two BBI proteins with molecular size around 15 kDa (BBIrc 1) and 25 kDa (BBIrc2) and the quantity of the expression of 15 kDa was nearly constant under both aerobic and hypoxia conditions; however, the 25 kDa expression was greatly up‐regulated when the fast elongating coleoptiles were transferred from hypoxia conditions to the aerobic conditions. The results indicate that the expression pattern of BBIs proteins correlated to the developmental stage in terms of morphological changes. The partial N‐terminal sequence of the first 9 amino acids of 25 kDa was AEAPPRPPK, which is the same as the amino acid sequence of 37th to 45th of RBBI3‐1 and LC‐MS study shows that several mass fragments fit to RBBI3‐1. The 25 kDa protein also shows specific binding to bovine trypsin. This expression pattern demonstrates for the first time that environmental factor, oxygen, can select and enhance specific BBI gene expression. The results of this study suggest BBI proteins might play multiple biological functions inside rice coleoptiles.     

Photoinduced and thermal reactions of α‐cyano‐β‐bromomethylcinnamide with 1‐benzyl‐1,4‐dihydronicotinamide

The photoinduced reaction of a mixture of (Z)‐α‐cyano‐β‐bromomethylcinnamide (1) and (E)‐α‐cyano‐β‐bromomethylcinnamide (2) with 1‐benzyl‐1, 4‐dihydronicotinamide produces a mixture of the (E)‐ and (Z)‐ isomers of α‐cyano‐β‐methylcinnamide (3 and 4). Using spin‐trapping technique for monitoring reactive intermediate, it is shown that the reaction proceeds via electron transfer‐debromination‐H abstraction mechanism. The thermal reaction of the same substrate with BNAH at 60°C in the dark gives three products: the (E)‐ and (Z)‐isomers of α‐cyano‐β‐methylcinnamide and a dehydrodimeric product; 2, 7‐dicyano‐3, 6‐diphenylocta‐2, 4, 6‐trien‐1, 8‐dioic amide (7). Based on product analysis, scavenger experiment and cyclic voltammetry, an electron transfer‐debromination‐disproportionation mechanism is proposed.     

Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α‐Ketoacid‐Hydroxylamine (KAHA) Ligation

The chemical synthesis of the 184‐residue ferric heme‐binding protein nitrophorin 4 was accomplished by sequential couplings of five unprotected peptide segments using α‐ketoacid‐hydroxylamine (KAHA) ligation reactions. The fully assembled protein was folded to its native structure and coordinated to the ferric heme b cofactor. The synthetic holoprotein, despite four homoserine residues at the ligation sites, showed identical properties to the wild‐type protein in nitric oxide binding and nitrite dismutase reactivity. This work establishes the KAHA ligation as a valuable and viable approach for the chemical synthesis of proteins up to 20 kDa and demonstrates that it is well‐suited for the preparation of hydrophobic protein targets.     

A comparative analysis of human plasma and serum proteins by combining native PAGE,whole‐gel slicing and quantitative LC‐MS/MS: Utilizing native MS‐electropherograms in proteomic analysis for discovering structure and interaction‐correlated differences

MS identification has long been used for PAGE‐separated protein bands, but global and systematic quantitation utilizing MS after PAGE has remained rare and not been reported for native PAGE. Here we reported on a new method combining native PAGE, whole‐gel slicing and quantitative LC‐MS/MS, aiming at comparative analysis on not only abundance, but also structures and interactions of proteins. A pair of human plasma and serum samples were used as test samples and separated on a native PAGE gel. Six lanes of each sample were cut, each lane was further sliced into thirty‐five 1.1 mm × 1.1 mm squares and all the squares were subjected to standardized procedures of in‐gel digestion and quantitative LC‐MS/MS. The results comprised 958 data rows that each contained abundance values of a protein detected in one square in eleven gel lanes (one plasma lane excluded). The data were evaluated to have satisfactory reproducibility of assignment and quantitation. Totally 315 proteins were assigned, with each protein assigned in 1–28 squares. The abundance distributions in the plasma and serum gel lanes were reconstructed for each protein, named as “native MS‐electropherograms”. Comparison of the electropherograms revealed significant plasma‐versus‐serum differences on 33 proteins in 87 squares (fold difference > 2 or < 0.5, p < 0.05). Many of the differences matched with accumulated knowledge on protein interactions and proteolysis involved in blood coagulation, complement and wound healing processes. We expect this method would be useful to provide more comprehensive information in comparative proteomic analysis, on both quantities and structures/interactions.     

Three‐phase hollow‐fiber microextraction combined with ion‐pair high‐performance liquid chromatography for the simultaneous determination of five components of compound α‐ketoacid tablets in human urine

The determination of α‐ketoacid concentration is demanded to evaluate the absorption and metabolic behavior of compound α‐ketoacid tablets taken by chronic kidney disease patients. To eliminate the interference of endogenous substance of urine and enrich the analytes, a three‐phase hollow‐fiber liquid‐phase microextraction combined with ion‐pair high‐performance liquid chromatography method was established for the determination of d ,l ‐α‐hydroxymethionine calcium, d ,l ‐α‐ketoisoleucine calcium, α‐ketovaline calcium, α‐ketoleucine calcium, and α‐ketophenylalanine calcium of compound α‐ketoacid tablets in human urine samples. The extraction parameters, such as organic solvent, pH of donor phase and acceptor phase, stirring rate, and extraction time were optimized. Under the optimal conditions, the obtained enrichment factors were up to 11‐, 110‐, 198‐, 202‐, and 50‐fold, respectively. The calibration curves for these analytes were linear over the range of 0.1–10 mg/L for α‐ketovaline calcium, d ,l ‐α‐ketoisoleucine calcium, and α‐ketoleucine calcium, 0.5–10 mg/L for d ,l ‐α‐hydroxymethionine calcium, and α‐ketophenylalanine calcium with r > 0.99. The relative standard deviations (n = 5) were less than 6.27% and the LODs were 100.7, 10.0, 5.8, 7.8, and 8.6 μg/L (based on S/N = 3), respectively. Good recoveries from spiked urine samples (92–118%) were obtained. The proposed method demonstrated excellent sample clean‐up and analytes enrichment to determine the five components in human urine.     

Amperometric Immunosensor for the Determination of α‐1‐Fetoprotein Based on Core‐Shell‐Shell Prussian Blue‐BSA‐Nanogold Functionalized Interface

In the present work, a newly functional nanoparticle has been prepared to immobilize the protein for the detection of α‐1‐fetoprotein (AFP). Prussian blue (PB) nanoparticle was initially synthesized under ultrasonic condition, then bovine serum albumin (BSA) was used to coat the PB nanoparticle to improve the stability of the PB nanoparticle as well as functionalize the surface of PB nanoparticle, and then gold colloids were loaded on the BSA‐coated PB nanoparticle to construct a core‐shell‐shell nanostructure via the conjunction of thiolate linkages or alkylamines of the BSA. Finally, a convenient, effective and sensitivity amperometric immunosensor for the detection of α‐1‐fetoprotein (AFP) was constructed by the employment of these functional core‐shell‐shell microspheres. The preparation of the nanoparticle (Au‐BSA‐PB NPs) was characterized by transmission electron microscopy (TEM), and the assembly of the biosensor was characterized with cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The dynamic range of the resulted immunosensor for the detection of AFP is from 0.02 ng/mL to 200.0 ng/mL with a detection limit of 0.006 ng/mL (S/N=3). Moreover, this biosensor displays good selectivity, stability and reproducibility.     

Analysis of low‐density lipoprotein‐associated proteins using the method of digitized native protein mapping

The method of digitized native protein mapping, combining nondenaturing micro 2DE, grid gel‐cutting, and quantitative LC‐MS/MS (in data‐independent acquisition mode, or MS^E), was improved by using a new MS/MS mode, ion mobility separation enhanced‐MS^E (HDMS^E), and applied to analyze the area of human plasma low‐density lipoprotein (LDL). An 18 mm × 4.8 mm rectangular area which included LDL on a nondenaturing micro 2D gel of human plasma was grid‐cut into 72 square gel pieces and subjected to quantitative LC‐MS/MS. Compared with MS^E, HDMS^E showed significantly higher performance, by assigning 50% more proteins and detecting each protein in more squares. A total of 253 proteins were assigned with LC‐HDMS^E and the quantity distribution of each was reconstructed as a native protein map. The maps showed that Apo B‐100 was the most abundant protein in the grid‐cut area, concentrated at pI ca. 5.4–6.1 and apparent mass ca. 1000 kDa, which corresponded to four gel pieces, squares 39–42. An Excel macro was prepared to search protein maps which showed protein quantity peaks localized within this concentrated region of Apo B‐100. Twenty‐two proteins out of the 252 matched this criterion, in which 19 proteins have been reported to be associated with LDL. This method only requires several microliters of a plasma sample and the principle of the protein separation is totally different from the commonly used ultracentrifugation. The results obtained by this method would provide new insights on the structure and function of LDL.     

Two New 4‐Hydroxyisoflavanes from the Root of Codonopsis cordifolioidea and Their Anti‐virus Activities

Two new 4‐hydroxyisoflavanes, cordifoliflavanes A and B (1 and 2), were isolated from the roots of Codonopsis cordifolioidea. Their structures were elucidated by spectroscopic methods, including extensive 1D‐ and 2D‐NMR techniques. Compounds 1 and 2 were tested for their anti‐HIV‐1 activities and anti‐tobacco mosaic virus activities. The results showed that compounds 1 and 2 have modest anti‐HIV‐1 activities and anti‐tobacco mosaic virus activities, respectively.     

Detection of recombinant growth hormone in human plasma by a 2‐D PAGE method

Human growth hormone (GH) has several central metabolic functions including bone growth in childhood, and its anabolic and lipolytic effects in particular are assumed reasons for the abuse of GH by athletes. Human endogenous GH consists of a main 22 kDa variant and several isoforms. In contrast, recombinant GH consists of only one variant being identical to the main endogenous isoform. The method presented here separates different isoforms by 2‐D PAGE after isolation of GH from plasma using an immunoaffinity purification system. While samples containing endogenous GH yield up to four isoforms, samples with recombinant GH contain the main 22 kDa spot only. Normalized spot volumes (NSV) are calculated after addition of an internal standard and a discrimination limit was determined at 0.52 for the NSV of the main 22 kDa spot. Above this value, samples containing endogenous GH show at least the main 22 kDa isoform and the 20 kDa splice variant. In contrast, samples with a NSV >0.52 and only one spot are suspicious to contain recombinant GH. This method detects discrete isoforms of GH from plasma and discriminates endogenous GH from its recombinant analog, which makes it useful for doping control purposes.     

Flavonoids Isolated from Heat‐Processed Epimedium koreanum and Their Anti‐HIV‐1 Activities

Systematic phytochemical investigation on heat‐processed Epimedium koreanum led to the isolation of 13 flavonoids, including five new prenyl‐flavonol glycosides, koreanosides A–E ( 1 – 5 , resp.). Their structures were elucidated on the basis of detailed analysis of the 1D‐ and 2D‐NMR spectroscopic data and chemical reactions. Apigenin ( 11 ) exhibited moderate anti‐HIV‐1 activity with an EC₅₀ value of 12.8±3.27 μg/ml.     

Alkylamines‐intercalated α‐zirconium phosphate as latent thermal anionic initiators

The reaction of glycidyl phenyl ether (GPE) with 1‐aminoalkanes‐intercalated α‐zirconium phosphate (α‐ZrP·1‐aminoalkane): 1‐aminoalkanes 1‐aminopropane (α‐ZrP·Pr), 1‐aminobutane (α‐ZrP·Bu), 1‐aminooctane (α‐ZrP·Oct), and 1‐aminohexadecane (α‐ZrP·Hed) was carried out at varying temperatures for 1 h periods. Reaction progress was not observed until the reactants were heated to 80 °C or above. On increasing the temperature, the conversion factors increased such that, at 140 °C, conversions of 62% (α‐ZrP·Pr), 60% (α‐ZrP·Bu), 67% (α‐ZrP·Oct), and 64% (α‐ZrP·Hed) were obtained. The thermal stabilities as latent initiators were tested: GPEs reacted with α‐ZrP·Pr, α‐ZrP·Bu, and α‐ZrP·Oct at 40 °C for 360 h achieved conversions of 83, 55, and 59%, respectively. In contrast, the reaction in the presence of α‐ZrP·Hed did not proceed at 40 °C. The order of the thermal stability of GPE in the presence of α‐ZrP·1‐aminoalkane intercalation compounds was: α‐ZrP·Hed > α‐ZrP·Bu ≈ α‐ZrP·Oct > α‐ZrP·Pr. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 1854–1861     

The achiral tetrapeptide Z‐Aib‐Aib‐Aib‐Gly‐OtBu

The title achiral peptide N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐α‐aminoisobutyrylglycine tert‐butyl ester or Z‐Aib‐Aib‐Aib‐Gly‐OtBu (Aib is α‐aminoisobutyric acid, Z is benzyloxycarbonyl, Gly is glycine and OtBu indicates the tert‐butyl ester), C₂₆H₄₀N₄O₇, is partly hydrated (0.075H₂O) and has two different conformations which together constitute the asymmetric unit. Both molecules form incipient 3₁₀‐helices. They differ in the relative orientation of the N‐terminal protection group and at the C‐terminus. There are two 4→1 intramolecular hydrogen bonds.     

Effect of sialic acid content on glycoprotein pI analyzed by two‐dimensional electrophoresis

2‐DE is broadly used for quantitative analysis of differential protein expression in complex mixtures such as serum samples or cell lysates. PTMs directly influence the 2‐DE pattern, and knowledge of the rules of protein separation is required in order to understand the protein distribution in a 2‐DE gel. Glycosylation is the most common PTM and can modify both the molecular weight and the pI of a protein. In particular, the effect of charged monosaccharides (mainly sialic acids, SAs) on the 2‐DE pattern of a protein is of major interest since changes in sialylation are regularly observed in comparative studies. Little is known about the pI shift of a glycoprotein induced by the presence of SAs, or whether this shift is the same for all glycoproteins. To address this issue, this study examined the influence of SA on the 2‐DE pattern of three serum glycoproteins (haptoglobin, α1‐antitrypsin and ribonuclease 1), which N‐glycan chains had been previously characterised, and reviewed existing bibliographic data. The SA content of the different glycoforms of a glycoprotein showed a negative linear correlation with the pI, although the slope varied among the studied glycoproteins. We also described a positive correlation between the protein pI and the pI decrease per SA molecule.     

Highly Enantioselective Synthesis of 1,2,3‐Substituted Cyclopropanes by Using α‐Iodo‐ and α‐Chloromethylzinc Carbenoids

Herein, we report the enantio‐ and diastereoselective formation of trans‐iodo‐ and trans‐chlorocyclopropanes from α‐iodo‐ and α‐chlorozinc carbenoids by using a dioxaborolane‐derived chiral ligand. The synthetically useful iodocyclopropane building blocks were derivatized by an electrophilic trapping of the corresponding cyclopropyl lithium species or a Negishi coupling to give access to a variety of enantioenriched 1,2,3‐substituted cyclopropanes. The synthetic utility of this method was demonstrated by the formal synthesis of an HIV‐1 protease inhibitor. In addition, the related stereoselective bromocyclopropanation was also investigated. New insights about the relative electrophilicity of haloiodomethylzinc carbenoids are also presented.     

Conformational analysis of the disaccharide methyl α‐d‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d‐mannopyranoside monohydrate

The crystal structure of methyl α‐d ‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₆O₁₂·H₂O, ( II ), has been determined and the structural parameters for its constituent α‐d ‐mannopyranosyl residue compared with those for methyl α‐d ‐mannopyranoside. Mono‐O‐acetylation appears to promote the crystallization of ( II ), inferred from the difficulty in crystallizing methyl α‐d ‐mannopyranosyl‐(1→3)‐β‐d ‐mannopyranoside despite repeated attempts. The conformational properties of the O‐acetyl side chain in ( II ) are similar to those observed in recent studies of peracetylated mannose‐containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in ( II ) elongates by ～0.02 Å upon O‐acetylation. The phi (?) and psi (ψ) torsion angles that dictate the conformation of the internal O‐glycosidic linkage in ( II ) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated ( II ) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ～16°) than for ? (Δ = ～6°).     

The Syntheses of 4‐Arylamino‐1,2,3‐Triazoles and Stable 6‐Sydnonyl Verdazyls from Sydnone Derivatives and Their Fragments

α‐Chloroformylarylhydrazones 1 and α‐chloroformylarylhydrazones of sydnonecarbaldehydes 3 have been prepared by a new synthetic route: α‐chloroformylarylhydrazines hydrochlorides 2 reacted with corresponding carbonyl compounds. Reactions of compounds 3 with various hydrazines to give 6‐sydnonyl‐1,2,4,5‐tetrazinan‐3‐ones 7 and/or carbazones 8 were also investigated. By oxidization with lead dioxide, compounds 7 were trans formed to stable 6‐sydnonyl‐3,4‐dihydro‐3‐oxo‐1,2,4,5‐tetrazin‐1(2H)‐yl radical derivatives 9 (sydnonyl verdazyls). Furthermore, sydnonecarbaldehydes arylhydrazones 5 through acidic conditions could be transferred to 4‐arylamino‐1,2,3‐triazoles 6 which were also obtained by means of acidic decompositions of 4‐formylsydnones 10 .