Immobilization of proteins as a tool for studying primary structure around their cysteinyl residues

The primary structure around the single cysteinyl residue of chicken pepsin was investigated by binding the protein via this residue to an insoluble carrier. Carriers stable towards reagents used for the fragmentation of proteins and sequence analysis were prepared by coupling a spacer arm to polyN-hydroxymethyl acrylamide using a thioether bond that is potentially cleavable by mercuric ions (1). Phenacyl bromide group, attached to the free end of the spacer, reacted rapidly and specifically with the cysteinyl residue of chicken pepsin. Up to 300 mg of the enzyme were bound to 1 g of carrier. The polymer-bound protein was cleaved by trypsin or by cyanogen bromide or by a sequence of both. Fragments of 40–120 amino acid residues, depending on the method of cleavage, remained attached to the polymer through the cysteinyl residue. The compositions and partial sequences of these fragments revealed that the cysteinyl residue is located within or in the vicinity of a loop in the molecule formed by a disulfide bond.     

PHOTOLYSIS OF THE SINGLE TRYPTOPHAN RESIDUE OF EEL TROPONIN C

Abstract— The tryptophan (TRP) residue of eel troponin C was selectively degraded by direct UV irradiation, at 302 nm, in Ar-saturated solution. Depending on the absence or presence of calcium ions, this TRP residue is exposed to aqueous medium or buried in a hydrophobic environment. Tryptophan loss was determined by both absorption and fluorescence spectroscopy and by amino acid analysis. The photodegradation yield was significantly higher for the exposed TRP residue than for the buried ones. These results give more detail on previous observations on several other proteins and corroborate the predominant influence of the polarity on the photosensitivity of a TRP residue in polypeptidic structures.     

Tryptic hydrolysis of inorcanic pyrophosphate modified by phosphate and O-phosphoethanolamine

By the peptide map method, a phosphorylated peptide has been isolated from a tryptic hydrolysate of phosphorylated yeast inorganic pyrophosphatase (I), and this is a direct proof of the formation of a covalent bond between (I) and phosphate in the course of this reaction. The isolation and analysis of the peptide from the tryptic hydrolysate shows that the phosphate acceptor is probably the aspartic acid residue 240 or 248. Analysis of a tryptic hydrolysate of (I) modified with O-phosphoethanolamine has shown that O-phosphoethanolamine forms an amide bond with the carboxy group of the same aspartic acid residue. In an alkaline medium, the phosphate residue migrates to the imidazole ring of a histidine residue, apparently that present in position 222.     

Quantum theory of the structure and bonding in proteins: Part 11. A simplified method and its application to the α-amino-isobutyric acid residue

Information about the preferred conformation of the α-amino-isobutyric acid residue (α-AIB) is obtained without explicit computation of its wave function. The conformation of lowest energy of this residue is close to the usual helical conformation and so the residue may occur at the 2 position of a type I or I' bend or in either position of a type Ill or Ill' bend. The available experimental information refers to a β bend formed from α-AIB-PRO and then the theory and experiment agree that the only possibility is a type III bend.It is predicted that a β sheet structure may be formed at rather higher energy and in the planar and not the pleated form. There is no apparent reason why this residue should not form an α helix.The simplified method used here is closely related to the partitioned potential energy methods which are widely used in this subject.     

Structural investigation of "cis" and "trans" vinylogous peptides: cis-vinylog turn in folded cis-vinylogous peptides, an excellent mimic of the natural beta-turn

[structure: see text] Various sequences of modified peptides including those containing a cis- or trans-vinylogous residue have been studied using X-ray diffraction in the solid state and 1H NMR and IR spectroscopy in solution. A cis-vinylogous residue promotes an NH to CO intramolecular H-bond, closing a nine-membered pseudocycle that stabilizes a folded moiety that we proposed to name the cis-vinylogous turn. A trans-vinylogous residue involves an extended conformation. Two consecutive vinylogous residues retain their own structural propensity: "Xaa(tr)"-"Xaa(cis)" or "Xaa(cis)"-"Xaa(tr)" sequence is singly folded, whereas "Xaa(cis)"-"Xaa(cis)" sequence is doubly folded. Oligo vinylogs with all-trans or all-cis or alternating cis-trans motifs could constitute new classes of foldamers.     

Solid-phase synthesis of 5-arylhistidines via a microwave-assisted Suzuki-Miyaura cross-coupling

Microwave irradiation efficiently promoted the solid-phase Suzuki-Miyaura reaction of a 5-bromohistidine with various arylboronic acids in the presence of a palladium catalyst. This methodology allowed the synthesis of peptides bearing a histidine residue substituted at position 5 of the imidazole ring with a phenyl, a substituted phenyl, a pyridyl, or a thienyl ring, as well as with the benzene ring of a tyrosine residue.     

Chemometric classification of gunshot residues based on energy dispersive X-ray microanalysis and inductively coupled plasma analysis with mass-spectrometric detection

A gunshot residue sample that was collected from an object or a suspected person is automatically searched for gunshot residue relevant particles. Particle data (such as size, morphology, position on the sample for manual relocation, etc.) as well as the corresponding X-ray spectra and images are stored. According to these data, particles are classified by the analysis-software into different groups: ‘gunshot residue characteristic’, ‘consistent with gunshot residue’ and environmental particles, respectively. Potential gunshot residue particles are manually checked and – if necessary – confirmed by the operating forensic scientist.     

The statistical significance of selected sense–antisense peptide interactions

Sense and antisense peptides, encoded by sense and corresponding antisense DNA strands, are capable of specific interactions that could be a driving force to mediate protein–protein or protein–peptide binding associations. The complementary residue hypothesis suggests that these interactions are founded upon the sum of pairwise interactions between amino acids encoded by corresponding sense and antisense codons. Despite many successful experimental results obtained with the hypothesis, however, the physicochemical basis for these interactions is poorly understood. We examined the potential of the hypothesis for general identification of protein–protein interaction sites, and the possible role of the hypothesis in determining folding in a broad set of protein structures. In addition, we performed a structural study to investigate the binding of a complementary peptide to IL‐1F2. Our results suggest that complementary residue pairs are no more frequent or conserved than average in protein–protein interfaces, and are statistically under‐represented amongst contacting residue pairs in folded protein structures. Although our structural results matched experimental observations of binding between the peptide and IL‐1F2, complementary residue interactions do not appear to be dominant in the bound structure. Overall, our data do not allow us to conclude that the complementary residue hypothesis accounts for specific sense–antisense peptide interactions. © 2012 Wiley Periodicals, Inc.     

Contribution of sampling to the variability of pesticide residue data

The uneven distribution of pesticide residues among the treated objects leads to an inevitable variability of pesticide residue levels measured in the samples, which may significantly contribute to the combined uncertainty of the analytical results. A total of 8844 unit-crop residue data derived from 57 lots and 19 field trials were evaluated to determine the characteristic features of residue distribution in unit crops and composite samples. The average residue levels and the corresponding coefficient of variation (CV) values obtained for individual units taken from a given lot showed wide variation from lot to lot. There was no significant difference between the CVs of residue levels in sample sets of various unit crops or composite sample populations of different sizes taken from various crops. The CV values for levels of residues taken from individual lots followed normal distribution. Very good correlation was found between the CVs of the parent and sample populations. The experimentally obtained values were very close to those expected on the basis of the central limit theorem. The estimated typical relative standard uncertainties of sampling medium-size crops for pesticide residue analysis in the cases of sample sizes of 5, 10, and 25 were 37, 25, and 16%, respectively.     

典型塑料载体与助燃剂燃烧残留物的闪蒸气相色谱-质谱分析

通过对火场常见塑料载体与助燃剂混合燃烧残留物的分析,发展一种适用此类燃烧残留物的火灾物证鉴定方法,对火场中是否存在助燃剂进行判断,避免漏检情况的发生。应用热分析技术确定合适的闪蒸温度,在此温度下对塑料载体与助燃剂混合燃烧残留物进行闪蒸分析,并从实验条件选择、可行性分析、定性分析三方面对闪蒸技术进行评价。结果表明,闪蒸气相色谱-质谱（Flash GC-MS）技术可以检测到热塑性聚合物塑料载体与助燃剂混合燃烧残留物中残留的助燃剂特征组分,可对火场中是否存在过助燃剂进行辨别。闪蒸气相色谱-质谱技术丰富了现代火灾物证鉴定技术,能进一步辅助火灾物证鉴定工作,使鉴定结论更准确、可靠。     

A comparison of the fragmentation pathways of [Cu(II)(Ma)(Mb)]•2+ complexes where Ma and Mb are peptides containing either a tryptophan or a tyrosine residue

[Cu^II(M_a)(M_b)]^?2+ complexes, where M_a and M_b are dipeptides or tripeptides each containing either a tryptophan (W) or tyrosine (Y) residue, have been examined by means of electrospray tandem mass spectrometry. Collision‐induced dissociations (CIDs) of complexes containing identical peptides having a tryptophan residue generated abundant radical cations of the peptides; by contrast, for complexes containing peptides having a tyrosine residue, the main fragmentation channel is dissociative proton transfer to give [M_a + H]⁺ and [Cu^II(M_b – H)]^?+. When there are two different peptides in the complex, each containing a tryptophan residue, radical cations are again the major products, with their relative abundances depending on the locations of the tryptophan residue in the peptides. In the CIDs of mixed complexes, where one peptide contains a tryptophan residue and the other a tyrosine residue, the main fragmentation channel is formation of the radical cation of the tryptophan‐containing peptide and not proton transfer from the tyrosine‐containing peptide to give a protonated peptide. Copyright © 2010 John Wiley & Sons, Ltd.     

Effect of charge at an amino acid of basic fibroblast growth factor on its mitogenic activity

<正>The amino acid at the 119th position of human basic fibroblast growth factor(hbFGF),lysine(K119),is a critical component for its mitogenic activity.However,little is known about the effects of the characteristics of this residue including charge on the mitogenic activity of hbFGF.Herein,this basic residue was replaced with neutral glutamine residue and acidic glutamic acid residue to construct mutants hbFGF~(K119Q) and hbFGF~(K119E),respectively.The mutants were produced by BL21(DE3)/pET3c expression system and purified to homogeneity by ionic exchange and heparin affinity chromatography from the supernatant of bacteria lysate. The mitogenic activity analysis showed that neutralization of charge at the 119th residue diminished the mitogenic activity of hbFGF,whereas change of positive charge to negative charge at this residue had no significant effect on its mitogenic activity. Further MAP kinase activation assay revealed that the influence of different charge at the 119th position on the mitogenic activity of hbFGF was related to the signal molecular activation in MAPK pathway.It was deduced that the charge,either positive or negative, at the 119th position of hbFGF is crucial for its full mitogenic activity.     

C-terminal amino acid residue loss for deprotonated peptide ions containing glutamic acid, aspartic acid, or serine residues at the C-terminus

Deprotonated peptides containing C-terminal glutamic acid, aspartic acid, or serine residues were studied by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer with ion production by electrospray ionization (ESI). Additional studies were performed by post source decay (PSD) in a matrix-assisted laser desorption ionization/time-of-flight (MALDI/TOF) mass spectrometer. This work included both model peptides synthesized in our laboratory and bioactive peptides with more complex sequences. During SORI-CID and PSD, [M - H]- and [M - 2H]2- underwent an unusual cleavage corresponding to the elimination of the C-terminal residue. Two mechanisms are proposed to occur. They involve nucleophilic attack on the carbonyl carbon of the adjacent residue by either the carboxylate group of the C-terminus or the side chain carboxylate group of C-terminal glutamic acid and aspartic acid residues. To confirm the proposed mechanisms, AAAAAD was labelled by 18O specifically on the side chain of the aspartic acid residue. For peptides that contain multiple C-terminal glutamic acid residues, each of these residues can be sequentially eliminated from the deprotonated ions; a driving force may be the formation of a very stable pyroglutamatic acid neutral. For peptides with multiple aspartic acid residues at the C-terminus, aspartic acid residue loss is not sequential. For peptides with multiple serine residues at the C-terminus, C-terminal residue loss is sequential; however, abundant loss of other neutral molecules also occurs. In addition, the presence of basic residues (arginine or lysine) in the sequence has no effect on C-terminal residue elimination in the negative ion mode.     

Quantitation of the nearest-neighbour effects of amino acid side-chains that restrict conformational freedom of the polypeptide chain using reversed-phase liquid chromatography of synthetic model peptides with L- and D-amino acid substitutions

Side-chain backbone interactions (or "effects") between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects (i to i+1) in peptides through reversed-phase liquid chromatography (RP-HPLC) of model synthetic peptides, where L- and D-amino acids were substituted at the N-terminal end of the peptide sequence, adjacent to a L-Leu residue. These nearest-neighbour effects (expressed as the difference in retention times of L- and D-peptide diastereomers at pHs 2 and 7) were frequently dramatic, depending on the type of side-chain adjacent to the L-Leu residue, albeit such effects were independent of mobile phase conditions. No nearest-neighbour effects were observed when residue i is adjacent to a Gly residue. Calculation of minimum energy conformations of selected peptides supported the view that, whether a L- or D-amino acid is substituted adjacent to L-Leu, its orientation relative to this bulky Leu side-chain represents the most energetically favourable configuration. We believe that such energetically favourable, and different, configurations of L- and D-peptide diastereomers affect their respective interactions with a hydrophobic stationary phase, which are thus quantified by different RP-HPLC retention times. Side-chain hydrophilicity/hydrophobicity coefficients were generated in the presence of these nearest-neighbour effects and, despite the relative difference in such coefficients generated from peptides substituted with L- or D-amino acids, the relative difference in hydrophilicity/hydrophobicity between different amino acids in the L- or D-series is maintained. Overall, our results demonstrate that such nearest-neighbour effects can clearly restrict conformational space of an amino acid side-chain in a polypeptide chain.     

INFLUENCE OF THE LOCATION OF TRYPTOPHANYL RESIDUES IN PROTEINS ON THEIR PHOTOSENSITIVITY

The environmental effect on Trp residues photolysis was investigated on four proteins containing a single Trp residue in environments of various polarities: glucagon (exposed residue), nuclease (partially buried residue), RNase T₁ (fully buried residue) and melittin (exposed or partially buried residue depending on the salt concentration). Direct photolysis was performed in neutral N₂-saturated phosphate solution at 20°C using 302 nm monochromatic light. Tryptophan loss was monitored by both absorption and fluorescence spectroscopy and by amino acid analysis. The results suggest that tryptophan photodegradation depends on the location of the residue in the protein, with regard to the exposure to the aqueous medium and to the neighbouring amino acids in the primary amino acid sequence and in the three dimensional structure. Photochemical products were not analysed but fluorescence spectra indicate that they vary with protein.     

Identification of α- and β-hydroxy acid containing cyclodepsipeptides in natural peptide mixtures using negative ion mass spectrometry

Natural peptide libraries often contain cyclodepsipeptides containing α- or β-hydroxy residues. Extracts of fungal hyphae of Isaria yield a microheterogenous cyclodepsipeptide mixture in which two classes of molecules can be identified by mass spectral fragmentation of negative ions. In the case of isaridins, which contain an α-hydroxy residue and a β-amino acid residue, a characteristic product ion corresponding to a neutral loss of 72 Da is obtained. In addition, neutral loss of water followed by a 72 Da loss is also observed. Two distinct modes of fragmentation rationalize the observed product ion distribution. The neutral loss of 72 Da has also been obtained for a roseotoxin component, which is also an α-hydroxy residue containing cyclodepsipeptide. In the case of isariins, which contain a β-hydroxy acid residue, ring opening and subsequent loss of the terminal residue as an unsaturated ketene fragment, rationalizes the observed product ion formation. Fragmentation of negative ions provide characteristic neutral losses, which are diagnostic of the presence of α-hydroxy or β-hydroxy residues.     

Characteristics of photodissociation at 193 nm of singly protonated peptides generated by matrix-assisted laser desorption ionization (MALDI)

Photodissociation (PD) at 193 nm of various singly protonated peptides was investigated. These include peptides with an arginine residue at the C-terminus, N-terminus, at both termini, inside the chain, and those without an arginine residue. Monoisotopomeric selection was made for the precursor ions. Interference from the post-source decay (PSD) product signals was reduced as much as possible by using the deflection system (reported previously) and subtracting the remaining signals from the laser-on signals. The presence of an arginine residue and its position inside the peptide were found to significantly affect the PD spectra, as reported previously. Presence of a proline, aspartic acid, or glutamic acid residue hardly affected the PD spectral patterns. By comparing the PD spectra obtained at a few different wavelengths, it is concluded that the dissociation of the photoexcited ions occurs in their ground electronic states. Tentative explanations for the observed spectral correlations based on the statistical picture for the reactions are also presented.     

Selective mono-O-sulfonylation of A,B-di-altro- β-cyclodextrin by utilizing restricted orientation of a guest-type sulfonylating reactant in the elliptically distorted cavity: the 2-O- and 3-O-2-naphthalenesulfonates as a versatile scaffold to prepare artificial enzymes with controlling substrate orientation

A,B-di-altro-β-cyclodextrin, which has 21 different hydroxyl groups, was selectively sulfonylated by 2-naphthalenesulfonyl chloride at the 2^A-OH of the altrose residue and the 3^G-OH of the glucoside residue adjacent to the altroside residue. The latter sulfonate provides for the first time a possibility for the synthesis of functional cyclodextrins that have two altrose residues adjacent to the functionalized one (either of glucose type or of altrose type) to control the orientation of substrate.     

Co-pyrolysis of waste polymers with coal

Co-pyrolysis of coal with waste polymers in a stationary quartz reactor was performed. Mass balance of the process was evaluated and properties of products were characterized. The main product (solid carbonaceous residue) exhibits low ash and sulfur contents and, from the point of view of application, satisfactory surface properties. Therefore, the solid residue is suitable as a smokeless fuel or as an industrial sorbent. The by-products were tar and gas. The tar may be used as a source of chemicals or a low-sulfur heating oil, the gas was highly calorific, therefore it may serve as a heating gas for energetical purposes.     

Chromophore effect in photodissociation at 266 nm of protonated peptides generated by matrix-assisted laser desorption ionization (MALDI)

Chromophore effect in the photodissociation of protonated peptides at 266 nm was investigated using synthetic peptides with the sequence RGGXGGGGGR where X was a phenylalanyl(F), tyrosyl(Y), cysteinyl(C), glycyl(G), seryl(S), or histidyl(H) residue. The peptides with an F or Y residue dissociated efficiently. Fragment ions due to cleavages at either end of the chromophore were especially prominent just as for the peptide with a tryptophanyl residue reported previously.1Photodissociation was observed even for the peptides without any noticeable chromophore at 266 nm. Here, dissociation at all the peptide bonds was almost equally prominent. Photodissociation of the protonated angiotensin I was investigated using the spectral correlation rules observed in the model systems. Role of the chromophores and the plausible mechanisms involved are discussed.