Peptide fragments amino acid sequences

Fragmentation of Protonated Peptides. The amino acid sequence-specific fragmentation of peptides is directed by the site of protonation. For peptides containing arginine and lysine, protonation occurs primarily on these basic residues. However, in order to anticipate the entire set of possible protonated fragments that may be... 

At the time of the discovery of Met-enkephalin, its sequence was observed to be identical to that of residues 61—65 contained in the C-fragment of the pituitary hormone p-Hpotropin [12584-99-5] (p-LPH) (see Hormones), first isolated in 1964 (11). In 1976, the isolation of a larger peptide fragment, P-endorphin [60617-12-1] that also displayed opiate-like activity was reported (12). This peptide s 31-amino-acid sequence comprised residues 61—91 of P-LPH. Subsequentiy, another potent opioid peptide, dynorphin [72957-38-17, was isolated from pituitary (13). The first five amino acids (qv) of this 17-amino-acid peptide are identical to the Leu-enkephalin sequence (see Table 1). 

The primary structure of a peptide is given by its amino acid sequence plus any disulfide bonds between two cysteine residues. The primary structure is detemnined by a systematic approach in which the protein is cleaved to smaller fragments, even individual amino acids. The smaller fragments are sequenced and the main sequence deduced by finding regions of overlap among the smaller peptides. 

With the use of oligonucleotide probes based on the amino acid sequences of these protease V8-obtained peptides and of cyanogen bromide fragments of the porcine H,K-ATPase P subunit, cDNA clones for the rat [12,25] and rabbit [74] H,K-ATPase P subunit were then isolated. 

Figure 2.3. A. Mass spectrometer consisting of an ionization source, a mass analyzer and an ion detector. The mass analyzer shown is a time-of -flight (TOF) mass spectrometer. Mass-to-charge (m/z) ratios are determined hy measuring the amount of time it takes an ion to reach the detector. B. Tandem mass spectrometer consisting of an ion source, a first mass analyzer, a collision cell, a second mass analyzer and a detector. The first mass analyzer is used to choose a particular peptide ion to send to the collision cell where the peptide is fragmented. The mass of the spectrum of fragments is determined in the second mass analyzer and is diagnostic of the amino acid sequence of the peptide. Figure adapted from Yates III (2000).

El, Ed electrophilic peptide fragments consisting of 17 D- and L-amino acid residues T condensation product formed from E and N TlL, Tdd peptide containing only L- or D-amino acid sequences Tdl peptide containing both amino acid species... 

In moths, it was discovered in Helicoverpa zea that a peptide produced in the subesophageal ganglion portion of the brain complex regulates pheromone production in female moths (19). This factor has been purified and characterized in three species, Helicoverpa zea (20), Bombyx mori (21, 22), and Lymantria dispar (23). They are all a 33- or 34-amino acid peptide (named pheromone biosynthesis activating neuropeptide, PBAN) and have in common an amidated C-terminal 5-amino acid sequence (FXPRL-amide), which is the minimum peptide fragment required for pheromon-tropic activity. In the redbanded leafroller moth, it was shown that PBAN from the brain stimulates the release of a different peptide from the bursae copulatrix that is used to stimulate pheromone production in the pheromone gland found at the posterior tip of the abdomen (24). 

The primary goal of peptide mapping is the verification of the amino acid sequence deduced from the genetic code of the recombinant protein. The protein backbone gets cleaved by typically two or three different endoproteinases like Lys-C, trypsin, and Glu-C to achieve maps with sequence-overlapping peptide fragments. These peptide mixtures can then be separated by LC or CE and analyzed on-line by MS to obtain sequence information. Often simple mass analysis matches the predicted primary sequence of the protein. However, sometimes mutations can lead to isobaric masses of peptides that can be overseen, if no further sequence analysis like N-terminal Edman sequencing and MS/MS is carried out. 

Figure 10.6 Peptide mapping of PIXY321. (A) Cleavage of the primary sequence with Lys-C endoprotease results in 14 theoretical fragments. (B) As detailed in the text, LC-MS analysis of the Lys-C digest shows that a few peptides, notably LI, L7, and L14, elute at several retention times due to heterogeneity of both their glycan structures and amino acid sequence. The insets illustrate the complexity of the mass spectra of glycopeptide LI eluting under peaks 17 (inset C) and 18 (inset D).

A further application of direct injection APl-electrospray to the structural elucidation of peptides is to partially fragment the peptide. In this way, one can often determine the partial or complete amino acid sequence of the peptide of interest (Ramstrom et al., 2003). This is particularly useful in rapidly estabhshing amino acid sequences of synthetic peptides in which the confirmation of a sequence can be done in a few moments rather than going through a complex amino acid analysis derived from a sequential hydrolysis process. 

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