Standard amino acids, described

To demonstrate the use of binary substructure descriptors and Tanimoto indices for cluster analysis of chemical structures we consider the 20 standard amino acids (Figure 6.3) and characterize each molecular structure by eight binary variables describing presence/absence of eight substructures (Figure 6.4). Note that in most practical applications—for instance, evaluation of results from searches in structure databases—more diverse molecular structures have to be handled and usually several hundred different substructures are considered. Table 6.1 contains the binary substructure descriptors (variables) with value 0 if the substructure is absent and 1 if the substructure is present in the amino acid these numbers form the A-matrix. Binary substructure descriptors have been calculated by the software SubMat (Scsibrany and Varmuza 2004), which requires as input the molecular structures in one file and the substructures in another file, all structures are in Molfile format (Gasteiger and Engel 2003) output is an ASCII file with the binary descriptors. 

Prepare a table of R values for the standard amino acids. You should also describe the color of the original ninhydrin spot. Since the colors vary slightly with the amino acids, this aids in the identification of an unknown amino acid. Calculate the R values for the constituent amino acids of the unknown peptide. From these data you should be able to identify the amino acids present in your unknown. 

Figure 1 An aliquot of one picomole of diluted Hewlett Packard PTH standard amino acids was delivered to the conversion flask, dried and subjected to conversion with the modified R4 and reconstitution in the modified S4 as described in the text. Two thirds of the converted aliquot was injected onto the microbore HPLC for this analysis.

Recall Describe citrulline and ornithine based on their similarity to one of the 20 standard amino acids. 

The hydrocarbon skeleton of the target is that of the amino acid phenylalanine. The configuration is (S), the same as the natural amino acid, so we can use the standard amino acid to hydroxy acid conversion via diazotization, described on p. 1105 of the textbook, which goes with retention of configuration. The aromatic ring needs hydrogenating too. 

Use of DNP-amino acids, formed by condensation of l-fluoro-2,4-dinitrobenzene (FDNB) with the free amino group of an amino acid, was first described by Sanger in 1945 (83). Sanger identified DNP-amino acids by paper chromatography. Since then many modifications in the methods of obtaining derivatives of amino acids for sequence analysis and in identification of such derivatives have been reported, and the use of DNP-amino acids for sequencing purposes is rapidly going out of date. Nevertheless, the importance of DNP-amino acids is not yet lost. In view of the limited applications of DNP-amino acids at present, the methods of preparation of these derivatives from standard amino acids or peptides are not described here. However, the details of those procedures can be obtained from Rosmus and Deyl (88) and Bailey (146). 

Figure C2.5.10. The figure gives tire foldability index ct of 27-mer lattice chains witli sets containing different number of amino acids. The sets are generated according to scheme described in [27], The set of 20 amino acids is taken as a standard sample. Each sequence witli 20 amino acids is optimized to fulfil tire stability gap [5]. The residues in tire standard samples are substituted witli four different sets containing a smaller number of amino acids [27]. The foldability of tliese substitutions is indicated by tire full circles. The open diamonds correspond to tire sequences witli same composition. However, tire amino acids are chosen from tire reduced representation and tire resultant sequence is optimized using tire stability gap [5].

Weber, P. L. Buck, D. R. Capillary Electrophoresis A Past and Simple Method for the Determination of the Amino Acid Composition of Proteins, /. Chem. Educ. 1994, 71, 609-612. This experiment describes a method for determining the amino acid composition of cyctochrome c and lysozyme. The proteins are hydrolyzed in acid, and an internal standard of a-aminoadipic acid is added. Derivatization with naphthalene-2,3-dicarboxaldehyde gives derivatives that absorb at 420 nm. Separation is by MEKC using a buffer solution of 50 mM SDS in 20 mM sodium borate. 

The metabolism of amino acids is complex and is described in standard text books. These are usually converted by aminotransferases to the corresponding 2-oxoacids which are partly oxidized in the matrix of muscle mitochondria and partly exported to the liver. Glutamate and aspartate yield 2-oxoglutarate and oxaloacetate, respectively, which enter the citrate cycle directly, and other 2-... 

Table 4.1 Effect of selected thiols, disulphides, amino acids and antioxidants on the time to the onset and the time to reach maximal ischaemic contracture in isolated perfused rat hearts. Hearts were perfused for a control period of 10 min at the end of which global low-flow (10% of control) ischaemia was initiated. The interventions described above were included in the perfusion fluid 5 min prior to the onset and throughout the ischaemic period. The data are shown as means standard errors of the means (n = 6)...

A method for the preparation of 1,3,2-diazaphospholidine heterocydes has been described by Deng and Chen (Scheme 6.225) [402], The authors found that treating hindered 1,2-diamino substrates such as a-amino acid amides with tris(diethylami-no)phosphine as reagent/solvent under open-vessel microwave conditions at 250 °C for 1 min furnished a trivalent phosphorus intermediate. Subsequent thiation of this intermediate with elemental sulfur in refluxing benzene provided the target l,3,2-diazaphospholidin-4-ones in good overall yields. The yields were much improved compared to those achieved by standard thermal methods. 

However, this multistep procedure is experimentally complex. A simpler variation described in 199127 consists of the reaction of an aldehyde and a nitro compound in the presence of triethylamine, TBAF and tert-butyl-dimethylsilyl chloride. Under these conditions, nitro sugars are obtained in good yieds and higher diastereoselectivities than those afforded by the standard conditions. This procedure was used in several synthesis of 2-nitro-2-deoxyaldoses, as for the condensation of l,l-diethoxy-2-nitroethane and l,2 3,4-di-0-isopropylidene-a-D-galacto-hexodialdo-l,5-piranose.28 More recently, it was applied to the addition of ethyl nitroacetate to the D-glucose derived aldehyde 18, to give nitro sugar derivatives 26, key precursors of polysubstituted cyclohexane a-amino acids (Scheme 10).29... 

When chromatographic resolution of species based on modifications located at the protein surface is desired, it may be advisable to use conditions that favor retention of native conformation.17 Here, the standard acidic conditions described in the preceding text may be inappropriate, and mobile phases buffered near neutrality may be required. Buffers based on ammonium acetate, ammonium bicarbonate, and triethylammonium phosphate may prove more useful in resolving polypeptide variants with differing posttranslational modifications, amino acid substitutions, or oxidation and deamidation products. The addition of more hydro-phobic ion-pairing agents may be needed to obtain polypeptide retention, and a variety of alkyl sulfonates and alkyl amines have been described for specific applications.17... 

The cosmopolitan cyanobacterium Microcystis aeruginosa is frequently the major component of freshwater cyanobacterial blooms. These blooms can cause serious water management problems and are occasionally associated with animal poisoning. The aeruginosa toxins are potent lethal peptides which contain three invariant D-amino acids (Ala, erythro-3-methyl Asp, and Glu), two variant L-amino acids, N-methyl dehydroalanine, and a 3 amino acid (1-3). Multiple toxins have been purified from clonal isolates (1,4). The toxic peptide described in this chapter is denoted toxin-LR using the standard one-letter abbreviations for its two variant amino acids, leucine and arginine. 

Cho et al. describes an alternative synthesis (Scheme 20) of the 2,5 DKP scaffold 92 = 123 via a bifunctional dipeptide 120, an aldehyde 121, and an isocyanide 122 [42]. These commercially available starting materials were added in equimolar amounts to trifluoroethanol at 40°C under nitrogen. The reaction was brought to room temperature and allowed to complete. The standard Ugi workup was used followed by column chromatography. Yields were shown in the range of 21-87%. When this reaction was done in a microwave, time taken for the reaction to complete was decreased significantly and yields increased by a factor of 4. The substitution pattern of this and the previously described (in Scheme 15) are identical however, the reactions use different types of starting materials, for example, dipeptide vs. N- and C-protected amino acids. Thus different stereochemical outcomes can be expected for the two syntheses. 

The left hand fragment of epoxymycin 3 was assembled from the previously-described amino acid derivatives 4, S, and 7, using standard coupling techniques. 

Additional or different labeled and unlabeled standards can be used. However, note that the incubation as described here includes isotopically labeled L-valine and L-isoleucine and that the metabolites of these branched chain amino acids can interfere with isotopically labeled internal standards for butyrylcarnitine or propi-onylcarnitine. 

Viability of Starch Derivatives as Flavoring Encapsulants. The capillary GC vapor phase flux term (defined by a percent external standard or ZEStD flux) previously described (34) was used to screen starch derivatives (oxidized, dextrinized and/or covalent amino acid linkage) as to their flavor encapsulation potential. The samples were prepared as previously described (34) with the exception of an added reduced pressure deaeration step, thus allowing the use of the headspace diffusivity versus retention standard curves to predict volatile lemon oil retention following spray drying. 

Sometimes the subscript s or g is added to a d or l prefix to indicate whether the chirality of a compound is being related to that of serine, the traditional configurational standard for amino acids, or to that of gly-ceraldehyde. In the latter case the sugar convention (Chapter 4) is followed. In this convention the configurations of the chiral centers furthest from Cl are compared. Ordinary threonine is ls- or d -threonine. The configuration of dextrorotatory (+)-tartaric acid can be described as 2R, 3R, or as ds, or as l. ... 

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