Nomenclature of peptides

Figure 3.3. Nomenclature of peptide ions chemical structure of b, c, z, and y product io...

Figure 6.5. Nomenclature of peptide ions resulting from backbone fragmentation.

Fig. 5. Fragmentation nomenclature of peptides. Bond breakages of all bonds of the peptide backbone have a systematic name (I). When fragmenting multiply charged peptide ions the peptide bond breaks preferentially since it is among the most labile bonds and only relatively low collision energies are involved (II).

AMINO ACIDS, PEPTIDES PROTEINS Recommended nomenclature and symbolism for amino acids and peptides J. Biol Chem. (1985) 260, 14-42 Biochemistry (1975) 14, 449-462 Abbreviations and symbols for the description of the conformation of polypeptide chains /. Biol Chem. (1970) 245, 6489-6497 Nomenclature of iron-sulfur proteins Eur. J. Biochem. (1979) 93, 427-430 Corrections Eur. J. Biochem. (1979) 102, 315 Nomenclature of peptide hormones J. Biol Chem. (1975) 250, 3215-3216 Nomenclature of human immunoglobulins Eur. J. Biochem. (1974) 45, 5-6 Recommended nomenclature of glycoproteins, glyco-peptides, and peptidoglycans /. Biol Chem. (1987) 262, 13-18 Recommended nomenclature of electron-transfer proteins... 

Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences http //www.chem.qmul.ac.uk/iubmb/misc/naseq.html Nomenclature of Peptide Hormones http //www.cliem.qimil.ac.uk/iubmb/misc/ phorm.html... 

Summary Reactions of Amino Acids 1172 24-8 Structure and Nomenclature of Peptides and Proteins 1173... 

Amino acid residues in peptides will be those recommended by lUPAC-IUB for the nomenclature of peptides. 

Figure 2 Nomenclature of peptide fragmentation. The possible product ion series that arise by cleavages along the peptide backbone are a-, b-, and c-series (N-terminal) and x-, y-, and z-series (C-terminal). (The designation +2H denotes addition of two hydrogens that are transferred onto the structures depicted in the figure to form the corresponding singly charged y- or c- product ions (21)). Under low-energy CID, y- and b-ions usually predominate. The mass differences between adjacent ions of the same series can be used to deduce portions of the peptide sequence.

Michel MC, Beck-Sickinger AG, H Cox et al (1998) XVI. International Union of Pharmacology recommendations for the nomenclature of neuropeptide Y, peptide YY and pancreatic polypeptide receptors. Pharmacol Rev 50 143-150... 

Peptidases are enzymes that catalyse the hydrolysis of peptide bonds - the bonds between amino acids that are found in peptides and proteins. The terms protease , proteinase and proteolytic enzyme are synonymous, but strictly speaking can only be applied to peptidases that hydrolase bonds in proteins. Because there are many peptidases that act only on peptides, the term peptidase is recommended. Peptidases are included in subclass 3.4 of enzyme nomenclature [1,5]. 

Table 5.5 Nomenclature of the ions formed in the mass spectral fragmentation of polypeptides. From Chapman, J. R. (Ed.), Protein and Peptide Analysis by Mass Spectrometry, Methods in Molecular Biology, Vol. 61, 1996. Reproduced by permission of Humana Press, Inc. 

Another potentially paralytic conotoxin was recently described this was a peptide purified from Conus geographus venom, which like / -conotoxin appeared to target to voltage-sensitive Na channels. However, the structure of "conotoxin GS" [nomenclature of Yanagawa et al. (J7)] was less homologous to / -conotoxins than to the w-conotoxins, which are Ca channel blockers. The same peptide was purified and characterized using a different assay, the induction of highly aberrant behavior upon ic injection of mice (L. J. Cruz, unpublished data). 

These are a family of peptides which include substance P, isolated in 1931 but only sequenced in 1971. This peptide has been extensively studied since it was the first major peptide to be extracted from brain but only now are useful antagonists becoming available. Two closely related peptides were then isolated from mammalian tissues and can be added to a number of other tachykinins, many of which are found in amphibians. The name tachykinins originated from the vasoactive effects of substance P but the nomenclature has been resolved into calling the three major mammalian peptides substance P, neurokinin A (NKA) and neurokinin B (NKB) with the corresponding receptors being numbered 1 to 3. The order of potencies at the three receptors as follows ... 

Fig. 7.14 Nomenclature for characteristic regions of peptide c >,t /-space taken from Karplus (1996). The frequencies of observed peptide conformations in protein crystal structures decrease from areas enclosed by a heavy solid line to regions enclosed by a plain solid line, to dashed outlines. Areas outside the dashed lines are disallowed in peptide conformational space. The lines are an approximate rendering of the exact contours given by Karplus (1996).

No tandem MS experiment can be successful if the precursor ions fail to fragment (at the right time and place). The ion activation step is crucial to the experiment and ultimately defines what types of products result. Hence, the ion activation method that is appropriate for a specific application depends on the MS instrument configuration as well as on the analyzed compounds and the structural information that is wanted. Various, more or less complementary, ion activation methods have been developed during the history of tandem MS. Below we give brief descriptions of several of these approaches. A more detailed description of peptide fragmentation mles and nomenclature is provided in Chapter 2. An excellent review of ion activation methods for tandem mass spectrometry is written by Sleno and Volmer, see Reference 12, and for a more detailed review on slow heating methods in tandem MS, see Reference 13. 

Figure 6.10. Nomenclature of product ions of cyclic peptides.

P. Roepstorff and J. Fohlman, Proposal for a Common Nomenclature for Sequence Ions in Mass Spectra of Peptides. Biomed. Mass Spectrom., 11(1984) 601. 

Roepstorff P. and Fohlman J. (1984), Proposal for a common nomenclature of sequence ions in mass spectra of peptides, Biomed. Mass Spectrom. 11, 601. 

Scheme 1 The Expected Fragmentation Pattern of Protonated Peptide Ions and the Nomenclature of the Amino Acid Sequence Fragment Ions for Determining Amino Acid Sequences...

Substrate specificity. Like most other enzymes, proteases display distinct preferences for certain substrates. These are often discussed using the nomenclature of Fig. 12-14. The substrate residue contributing the carbonyl of the amide group to be cleaved is designated Pj and residues toward the N terminus as P2, P3, etc., as is shown in Fig. 12-14. Residues toward the C terminus from the peptide linkage to be cleaved are designated P P etc. Chymotrypsin acts... 

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