Peptides structure, nomenclature

Cooper, G.J.S. (1994) Amylin compared with calcitonin gene-related peptide Structure, biology, and relevance to metabolic disease. Endocr. Rev.. 1. 163 201. Wimalawansa, S.J. (1997) Amylin. calcitonin gene-related peptide, calcitonin, and adrenomedullin a peptide superfamlly. Cr/r. Rev. Neurobiol., 11.167-239. Alexander. S.P.H. et al. (1998) Receptors and ion channel nomenclature supplement. Ninth Edition. Trends Pharmacol. Sc/.. Suppl.. 19.1-98. 

Nomenclature for conformational features of peptide structure is covered in Chapter 2. 

This chapter will present the most fundamental concepts for structure, nomenclature, and chemical reactions of amines. Biological applications will focus on the characteristics, formation, and reactions of amino acids. The use of amino acids in proteins and relatively simple reactions that form peptides will be discussed. In addition, several chemical reactions that lead to controlled degradation of peptides and proteins will be introduced. 

Figure 5.12 Structures and nomenclature of the ions formed in the mass spectral fragmentation of peptides which involve scission of the polypeptide backbone. 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characterized using a different assay, the induction of highly aberrant behavior upon ic injection of mice (L. J. Cruz, unpublished data). 

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

The three-dimensional structural architecture of plant defensins is exemplified by the structure of Rs-AFP, ° which comprises an N-terminal /3-strand followed by an ct-helix and two /3-strands (/3a/3/3 configuration). The /3-strands form a triple-stranded antiparallel /3-sheet. The three-dimensional structure is stabilized by three disulfide bonds. In general, in plant defensins two disulfide bonds form between the ct-helix and the central /3-strand. A third disulfide bond stabilizes the structure by linking the /3-strand after the helix to the coiled part after the ct-helix. This motif is called the cysteine-stabilized a/3-motif (CSa/3)" and also occurs in toxins isolated from insects, spiders, and scorpions.The fourth disulfide bond links the C-terminal end of the peptide with the N-terminal /3-strand. Two plant defensins, PhDl and PhD2, feature a fifth disulfide bond and have been proposed to be the prototypes of a new subclass within plant defensins." As a result of these structural features the global structure of plant defensins is notably different from o //3-thionins, which is one of the reasons for the different nomenclature. The structures of plant defensins Rs-AFP ° and NaDf are shown in Figure 6, where they are compared to the thionin /3-purothionin and the structurally more related drosomycin and charybdotoxin. ... 

Peptides extracted from casein with N, N-dimethyl formamide have complex electrophoretic patterns identical to those of the fraction first prepared by Long and co-workers and called X-casein (El-Negoumy 1973). These peptides are identical electrophoretically to those released by the action of plasmin, which is present in fresh raw milk, upon asr casein (Aimutis and Eigel 1982). Two of these peptides have tryptic peptide maps and molecular weights identical to those of a pair of the peptides produced by plasmin degradation of asl-casein. These peptides appear to be fragments of a8l-casein which are present in milk as the result of plasmin proteolysis. More definitive information on their primary structure is needed before nomenclature for these fragments can be established. 

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

Such structural homology is shown by the AKH/red pigment concentrating hormone (RPCH) family (S) and the myotropic neuropeptide family (S). As separation and characterization occur, e factors are assigned chemical and/or structural identity and, in the case of peptides, become identified by amino acid sequences. It is not suprising that a nomenclature standard has been proposed (M) to catalog the burgeoning number of reported sequences. 

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.

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