Peptide definition

Because it is desirable to break a peptide this way, some flexibility is required in the rigorous definition of sp -sp single bond. In particular, the dative Cqj-N bond in the backbone of a peptide is considered to be such a bond since the definition is based on the number of neighbors — four for carbon, three for nitrogen, two for Oxygen, etc. If this were not the case, you couldn t break a protein into classical and quantum regions at all. 

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

Litde is known about metaboHc inactivation of ( -endorphin and the dynorphins. NEP, and to a lesser extent APN, are only weaMy active against P-endorphin (183). Enzymes are known which degrade P-endorphin in vitro under nonphysiological conditions (202) or which inactivate P-endorphin by N-acetjlation (203). Alack of specific degradative enzymes for these peptides may account for their relatively long half-life in vivo though this has not been definitively estabUshed. 

By far the majority of carbohydrate material in nature occurs in the form of polysaccharides. By our definition, polysaccharides include not only those substances composed only of glycosidically linked sugar residues but also molecules that contain polymeric saccharide structures linked via covalent bonds to amino acids, peptides, proteins, lipids, and other structures. 

Sweetness is a quality that defies definition, but whose complexity can be appreciated merely by examining the molecular structures of those compounds that elicit the sensation. They come in all molecular shapes and sizes, and they belong to such seemingly unrelated classes of compounds as aliphatic and aromatic organic compounds, amino acids, peptides and proteins, carbohydrates, complex glycosides, and even certain inorganic salts. 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

From the definitions given above it follows that the configurational space (continuous) of a peptide is infinite, even if its conformational space... 

These results strongly suggest that unstructured peptides have definite backbone conformations and that the concept of a denatured protein as a structureless random chain breaks down when backbone conformations of individual residues are described, although the random chain concept may still be useful when describing the overall chain conformation. 

Similarly opioid peptides are important in nicotine addiction and may have a role in causing nicotine withdrawal symptoms in some smokers [35]. Opioid antagonists such as naltrexone are licensed treatments for dependence syndromes arising from other addictive drugs and could also be of use in some smokers to aid nicotine withdrawal [59] although there is no definitive evidence overall that they are beneficial [60]. 

The use of PIR compounds to study protein interactions is a significant advance over the use of standard homobifunctional crosslinkers. The unique design of the PIR reagent facilitates deconvolution of putative protein interaction complexes through a simplified mass spec analysis. The software can ignore all irrelevant peak data and just focus analysis on the two labeled peptide peaks, which accompany the reporter signal of appropriate mass. This greatly simplifies the bioinformatics of data analysis and provides definitive conformation of protein-protein crosslinks. 

The Novartis group used the X-ray structure of a Grb2-peptide complex [68] as the structural basis for a design attempt that yielded entirely new non-peptide SH2 domain ligands [164]. As mentioned several times throughout this contribution, the interaction of the pTyr sidechain and the Asn sidechain in pTyr+2 position of the peptide ligand have been identified as key elements for molecular recognition (see Fig. 10). The obvious relevance of these two sidechain functionalities allowed the definition of a minimal pharmacophore pattern that... 

Tandem MS has emerged as a definitive approach for identifying proteins from multiple sources including complex mixtures. In comparison to PMF, MS/MS permits more definitive identification of proteins. Matching of multiple MS/MS spectra to peptide sequences within the same protein... 

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