Common peptides

The ability to resolve and characterize complicated protein mixtures by the combination of 2DLC and online mass spectrometry permits the combination of sample fractionation/simplification, top-down protein mass information, and bottom-up peptide level studies. In our lab, the simplified fractions generated by 2D(IEX-RP)LC are digested and analyzed using common peptide-level analysis approaches, including peptide mass fingerprinting (Henzel et al., 1993 Mann et al., 1993), matrix-assisted laser desorption/ionization (MALDI) QTOF MS/MS (Millea et al., 2006), and various capillary LC/MS/MS methodologies (e.g., Ducret et al., 1998). 

Table 6.2. Some Less-Common Peptide Constituentsa) ... 

In 1991, Newkome and Lin 121 reported a series of acid terminated poly(ether amido) dendrimers (e.g., 3, 4), generated from the tetraacid core (1) and sequential use of the amino acid building block 2 (Scheme 7.1). These acid-terminated dendrimers were readily transformed 131 into the related polytryptophane analogues (5-7) by treatment with tryptophane methylester hydrochloride employing a common peptide coupling procedure (DCC 1-HBT in DMF). 141 The resultant chiral cascade series was examined via ORD/CD and the preliminary data indicate a linear relationship between optical rotation and the number of surface tryptophane moieties. 

It is possible that in the future we may recognize Kossel s idea of the anlage, a basic protein determiner found in all cells, to be the modern-day equivalent of the coat or masking protein which actually determines the particular areas of the DNA (deoxyribonucleic acid) molecule which are to function in RNA (ribonucleic acid) formation in a given cell—that is, Kossel s anlage may be the intellectual antecedent of the principle of cellular differentiation as viewed by many today. On the other hand, if such kindness to our predecessors is to be extended to the ideas of Richard Block, who transformed KossePs anlage first to the basic amino acids (7) and then to common peptides, it can easily be said that the concept of the common active site sequence of many enzymes (20) is what Block meant when he inferred that a peptide anlage determined the function of many proteins. 

In modern terminology the messenger RNA would collect the amino acid of peptides represented by A + B + C, etc., and deposit them on a ribosome where they would be assembled to give rise to A + C, or albumin AC, )3-globulin and various proportions of B + C in addition to A to give rise to a continuous system. A, B, and C are model peptides, but the system is not necessarily limited to these three, in that these three are not discrete peptides but rather areas on the template by this mechanism common peptides should appear in high incidence among the serum proteins. 

Naturally the implication arose that there should be a high incidence of common peptides in the partial hydrolyzates of each of the serum proteins. This, of course, is the same implication that arose in Block s mind (3). Since 1956 this laboratory has been busy trying to isolate common peptides from each of the serum proteins as obtained from electrophoresis on starch slabs. In order to be able to prepare each of the protein hydrolyzates simultaneously we examined nonenzy-matic procedures and devised the dilute acid partial hydrolyzate method which has recently been described in detail (33, 34). In this method aspartic acid is preferentially eliminated from the peptide chain, the re-... 

The remarkable similarity in the molar ratios of the amino acids offers encouragement to the proposition that common peptides will be found in the electrophoretic components of the serum proteins. The peptide of spot 7 probably differs from spot 8 in leucine content, which would account for the higher Rf of spot 8. More encouraging are the recent reports of Edelman (2, 13) who found that gamma-globulin, the Bence-Jones proteins, and the myeloma proteins have a peptide unit of common amino acid composition. 

Values in parentheses represent moles of tryptophan per mole of protein, assuming a common peptide-chain molecular weight of 18,000. 

The deconvolution of orthogonal libraries is based on the fact that each peptide of the library is present in one sublibrary of A and one sublibrary of B, and that particular peptide is the only one these two sublibraries have in common (see Section 4.3.V.3.2.3). Consequently, after having determined the most-active sublibraries in both libraries A and B in a given bioassay, individual active peptides are identified by deciphering the peptide that the active sublibraries of A and B have in common. If more than one sublibrary is active in each library, many individual peptides representing the common peptides of the different sublibrary pairs from both libraries have to be synthesized and tested in order to identify the... 

Perhaps the colleague was referring to ordinary peptides composed of proteinogenic amino acids, and not to substances as complex and sensitive as luzopeptins. Even so, our experience with the preparation of a number of "common" peptides, not to mention the deceptively simple tripeptide 47, led us to a thorough appreciation of a statement that is found in the introduction to M. Bodanszky s landmark book, " Peptide Chemistry," and that goes as follows ... 

Peptide antibiotics include a wide range of compounds such as cycloserine (an amino acid), bacitracin (a cyclic peptide), thiostrepton (a Unear peptide), neocarzinostatin (a polypeptide) and bleomycin (a glycoprotein). These compounds possess either antibacterial and/or antitumor activity and should be regarded as conventional peptides for the purposes of HPLC. For a detailed overview of the HPLC retention times of the more common peptide antibiotics in various buffer systems the reader is referred to a recent review (Aszalos and Aquilar, 1984). The recommended stationary phase is a Vydac RP-18 column because it produced the least amount of peak taiUng. Mobile... 

Lamaty et al. used another common peptide-coupling reagent N,N -carbonyldiimidazole (CDI) in the mechanosynthesis of amides. They succeeded in the development of complete solvent-free process for amide bond formation... 

Fig. 5.6 Theoretical proteome similarities between E. colt K-12 and other DB alpha-, beta-, gamma-, delta-, and epsilon-proteobacterial strains, expressed by tryptic peptide FSPs calculated as Dice indices that take into account the proportion of shared (common) peptides to the averaged number of unique peptides found in both proteomes. Note that only bacterial strains from the same family (Enterobacteriaceae) share more than 2% of tryptic peptides...

Tripeptide glutathione, Y-L-glutamyl-L-cysteinylglycine (2-85), is a common peptide, which is found in animal and plant tissues and microorganisms. It occurs in two forms, a reduced form (denoted G-SH) and an oxidised form (G-S-S-G), which are part of an important redox system, similar to cysteine and cystine ... 

Each subunit of a haemoglobin tetramer has a haem prosthetic group with Fe +, which is identical to that described for myoglobin. The common peptide subunits are designated a, p, y and 8. Both the a and (S subunits have structural characteristics similar to that of myoglobin. 

After chromatographic separation of the diastereomers (1 1) of the condensation product 121, facile deprotection of the amine with TFA liberates the secondary amide 122 in moderate yield (58%). The following amidation reaction was performed without prior activation of the ester by employing l,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD). The resulting extensive racemization, however, indicated that the chiral center was rather acidic. Therefore, common peptide coupling methods were explored, which resulted in good yield and poor enantiomeric excess or vice versa. 

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