Spectra amino acids

Fifty-three peptide samples were submitted by 48 laboratories. Previous studies by this committee have demonstrated the need for multiple analytical methods for the assessment of purity. Therefore the peptides in this study were analyzed by AAA, HPLC, ESI-MS and MALDI-MS to determine purity (Table I). Only two peptide samples had less than 50% of the desired product, and three other samples had less than 70% of the desired product, as judged by their mass spectra, amino acid composition and HPLC retention time. Overall, the peptides were of excellent quality. 

Hepatotoxins were isolated as new hepatotoxic compounds from the cyanobacterium Nostoc sp. strain 152 and assigned structures based on their high resolution FAB (fast atom bombardment) MS/MS, H and C NMR spectra, amino acid analysis and gas chromatography on a chiral capillary column by Namikoshi et al ... 

Four distinct exo-cellobiohydrolases (1,4-p-o-glucan cellobiohydrolases) have been isolated from cultures of TYichoderma viride They have similar u.v. spectra, amino-acid and amino-sugar compositions, thermal stabilities, molecular weights, specific activities, and COjH-terminal residues, but have different contents and compositions of hexoses. 

First, it is possible to excite a chromophore corresponding to the active site, and detennine which modes interact with it. Second, by using UV excitation, the amino acids with phenyl rings (tryptophan and tyrosine, and a small contribution from phenylalanine) can be selectively excited [4], The frequency shifts in the resonance Raman spectrum associated with them provide infomiation on their enviromnent. 

Fig. 3. Some representative pair potentials Uy(r), sealed to move their interesting range to [0,5]. The numbers above each potential denote the class label 7 and the iiinnber of data points available for the fit. (For example, elass 63 gives distanee 3 potentials for the amino acid pairs Lys-Asp, Arg-Lys and Glu-Tyr.) The spectrum below each potential consists of 50 lines pieked uniformly from the data.

Neural networks have been applied to IR spectrum interpreting systems in many variations and applications. Anand [108] introduced a neural network approach to analyze the presence of amino acids in protein molecules with a reliability of nearly 90%. Robb and Munk [109] used a linear neural network model for interpreting IR spectra for routine analysis purposes, with a similar performance. Ehrentreich et al. [110] used a counterpropagation network based on a strategy of Novic and Zupan [111] to model the correlation of structures and IR spectra. Penchev and co-workers [112] compared three types of spectral features derived from IR peak tables for their ability to be used in automatic classification of IR spectra. 

The amino add analysis of all peptide chains on the resins indicated a ratio of Pro Val 6.6 6.0 (calcd. 6 6). The peptides were then cleaved from the resin with 30% HBr in acetic acid and chromatogra phed on sephadex LH-20 in 0.001 M HCl. 335 mg dodecapeptide was isolated. Hydrolysis followed by quantitative amino acid analysis gave a ratio of Pro Val - 6.0 5.6 (calcd. 6 6). Cycll2ation in DMF with Woodward s reagent K (see scheme below) yielded after purification 138 mg of needles of the desired cyc-lododecapeptide with one equiv of acetic add. The compound yielded a yellow adduct with potassium picrate, and here an analytically more acceptable ratio Pro Val of 1.03 1.00 (calcd. 1 1) was found. The mass spectrum contained a molecular ion peak. No other spectral measurements (lack of ORD, NMR) have been reported. For a thirty-six step synthesis in which each step may cause side-reaaions the characterization of the final product should, of course, be more elaborate. 

An alternative approach to peptide sequencing uses a dry method in which the whole sequence is obtained from a mass spectrum, thereby obviating the need for multiple reactions. Mass spec-trometrically, a chain of amino acids breaks down predominantly through cleavage of the amide bonds, similar to the result of chemical hydrolysis. From the mass spectrum, identification of the molecular ion, which gives the total molecular mass, followed by examination of the spectrum for characteristic fragment ions representing successive amino acid residues allows the sequence to be read off in the most favorable cases. 

Figure 18.16 One-dlmenslonal NMR spectra, (a) H-NMR spectrum of ethanol. The NMR signals (chemical shifts) for all the hydrogen atoms In this small molecule are clearly separated from each other. In this spectrum the signal from the CH3 protons Is split Into three peaks and that from the CH2 protons Into four peaks close to each other, due to the experimental conditions, (b) H-NMR spectrum of a small protein, the C-terminal domain of a cellulase, comprising 36 amino acid residues. The NMR signals from many individual hydrogen atoms overlap and peaks are obtained that comprise signals from many hydrogen atoms. (Courtesy of Per Kraulis, Uppsala, from data published in Kraulis et al.. Biochemistry 28 7241-7257, 1989.)...

These signals in the NOE spectra therefore in principle make it possible to determine which fingerprint in the COSY spectrum comes from a residue adjacent to the one previously identified. For example, in the case of the lac-repressor fragment the specific Ser residue that was identified from the COSY spectrum was shown in the NOE spectrum to interact with a His residue, which in turn interacted with a Val residue. Comparison with the known amino acid sequence revealed that the tripeptide Ser-His-Val occurred only once, for residues 28-30. 

At the other extreme of the stereoselectivity spectrum of the Bucherer-Bergs reaction, the steric bias is sometimes not powerful enough to exert any selectivity at all, as exemplified by the conversion of 37 — 38. " Amino acid 38 was produced as a 1 1 mixture of two diastereomers. 

The enolic form of 2 was confirmed by a ferric chloride color reaction and by its acidity and ultraviolet spectrum, A-Aroyl derivatives of amino acids other than glycine fail to form such azlactones, probably because the stabilization afforded by enolization cannot occur. 

According to Charbonneau et al. (1985), aequorin is a single chain peptide consisting of 189 amino acid residues, with an unblocked amino terminal. The molecule contains three cysteine residues and three EF-hand Ca2+-binding domains. The absorption spectra of aequorin and BFP are shown in Fig. 4.1.3, together with the luminescence spectrum of aequorin and the fluorescence spectrum of BFP. 

E. Sample Mass Spectrum TBDMS Derivatized Amino Acids... 

FIGURE 3 The infrared spectrum of an amino acid, with the groups contributing to some ol the peaks identified. Notice that the spectrum displays the intensity of absorption. 

How do Phytoplankton Cope with Enhanced UV Several investigators have reported the existence in Antarctic algae of UV-absorbing mycosporine amino acids identical to those of tropical and temperate marine species (37). These compounds absorb in the UV-B region of the spectrum and may act as sunscreens which may provide some measure of protection from damaging UV-B. 

Figure 5.20 shows an MS-MS spectrum produced from a peptide of molecular weight 1782.96 Da. The mass losses observed and corresponding amino acid assignments are shown in Table 5.11. 

The checkers obtained 12.8-13.0 g. (52-53%), m.p. 84-86°, in the first crop and 2.7-3.4 g. (11-14%), m.p. 52-62°, in the second crop. Recrystallization of the former from methanol gave 11.5 g. of crystals, m.p. 84-86°, suggesting that the first crop is a pure single isomer. A proton magnetic resonance spectrum in chloroform-d of the second crop shows two singlets at 8 1.62 and 1.64 for the terf-butyl groups. Thus this material is a mixture of syn and anti isomers. Both the first and second crops proved equally useful for tcrf-butoxycarbonylation of an amino acid. 

In the presence of air, the roots, coleoptile, mesocotyl, endosperm, scutellum, and anther wall of maize synthesise a tissue-specific spectrum of polypeptides. The scutellum and endosperm of the immature kernel synthesise many or all of the ANPs constitutively, along with many other proteins under aerobic conditions. Under anaerobic conditions all of the above organs selectively synthesise only the ANPs. Moreover, except for a few characteristic qualitative and quantitative differences, the patterns of anaerobic protein synthesis in these diverse organs are remarkably similar (Okimoto et al., 1980). On the other hand, maize leaves, which have emerged from the coleoptile, do not incorporate labelled amino acids under anaerobic conditions and do not survive even a brief exposure to anaerobiosis (Okimoto et al., 1980). 

The finding that substantial 2.5-helicity may be retained in water upon the introduction of a limited number of acyclic or y9 -amino acid residues at chosen positions in the sequence, further expand the side-chain array available for functionalization of the 2.5-helical scaffold. In water, y9-heptapeptides 107 and 108 which contain two -amino acid residues [184a] and two y9 -amino acids [184b], respectively, still display a CD spectrum and NOE coimectivities characteristic of the 2.5-helix. However, the addition of a third acycHc amino acid is detrimental to the formation of the 2.5-helix in water. 

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