Peptides bonds, definition

Proteinases (Prt), again by definition, are responsible for the cleavage of peptide bonds, usually with a preference for particular types of side chain on the amino acid residues on one or the other or both sides of the scissile bond (Equation (7)). 

Figure 1.10 Definitions of the torsional angles fa ip, and w. These are all equal to 180° for a fully extended polypeptide chain (top left). to, defines rotation about the C,—Nl+1 bond. The normal tram planar peptide bond has = i/r = 180°, bottom) left, fa viewed along N —C bond (N >C) right, fa viewed along the C —C(C , — C j).

For determination of peptide sequences as well as protein modifications, MS/MS has become the definitive approach. However, for database searches MS/MS spectra have to be perfect. This is not always given because there are differences in tendencies of peptide bonds to fragment and certain amino acids show unique fragmentation characteristics. 

The system of intraglobular residue-residue contacts of a protein of N residues may be represented as an N x N matrix of the carbon-alphas, whose elements are ones (contact) or zeros (lack of contact). Any reasonable definition of contact provides ones in the positions (i, i + l)that correspond to a peptide bond between two adjacent residues in the sequence. The same is true for the residues corresponding to the pair of cysteines forming a disulfide bond (these data may not be available as input and may be used as a test of correct prediction). This set of contacts describes the sequential covalent topology and is a constant part of the contact matrix which does not depend on the spatial structure of the polypeptide chain however, any additional information on existing intraglobular contacts (e.g., from NMR data or disulfide linkage) can easily be introduced in the constant part of the contact matrix A ... 

The optimal pH of the system was approximately 7 (Fig. 4) however, a definite shoulder was found at pH 8-9. Oshima suggests that at least two different catalytically active molecular species, with different ionic properties, are present. Michaelis-Menten kinetics were demonstrated (Fig. 5). Kra was 1.4 x 10 M, which is about 10 times greater than literature values for natural phosphatases. Digestion by pronase cleaved 10% of the peptide bonds and caused 30% loss of activity. 3-0-Methyl-fluorescein phosphate was hydrolyzed by the thermal polymers about one-sixth as fast as was NPA. 

This result is in stark contrast to a study of Moyna et alf who applied nearly the same formalism for calculating the proton chemical shifts [Eq. (40)]. For the tripeptide under investigation only a limited set of intra-residue proton distances was available. The definition of structure was therefore greatly improved when the proton chemical shift constraints were switched on. The chemical shift refinement reduced the rmsd for the backbone atoms from 1.2 A to 0.2 A, and it revealed a single set of conformers with both peptide bonds in trans conformation. The shift constraints drove the molecule energetically uphill by 3.9 kcal/mol but produced a well-defined minimum within the energy hyper-surface. Obviously, chemical shift constraints will produce well-defined structures when other constraints are not available from experiment. 

Mass balance considerations on the definition of DH, i.e. the percentage of peptide bonds cleaved, immediately lead to the result that an instantaneous change in S leads to an inversely proportional change in DH. 

Surface-active materials consist of molecules containing both polar and nonpolar portions, i.e., amphiphilic molecules. The proteins are typically amphiphilic, polymeric substances made of amino acid residues combined in definite sequences by peptide bonds (primary structure). In many cases polypeptide chains are present in helical or /3-sheet configuration (secondary structure) which are stabilized by intramolecular (S-S and hydrogen) bonding. The next structural level, the tertiary structure, is determined by the folding of the polypeptide chains to more or less compact globules, maintained by hy-... 

As an initial working hypothesis it will be assumed that the peptide theory is valid, in other words, that a protein molecule is built up only of chains of a-amino (and a-imino) acids bound together by peptide bonds between their a-amino and a-carboxyl groups. While this peptide theory is almost certainly valid (see Vickery and Osborne, 1928 Pauling and Niemann, 1939 Synge, 1943), it should be remembered that it is still a hypothesis and has not been definitely proved. Probably the best evidence in support of it is that since its enunciation in 1902 no facts have been found to contradict it. It is to be expected that investigations of the types described in the present article will throw further light on the accuracy of the peptide theory and on the possible existence of nonpeptide bonds in proteins. 

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