N- or C-terminus

Figure 2.5. Tandem mass spectrometry. A. A peptide mixture is electrosprayed into the mass spectrometer. Individual peptides from the mixture are isolated (circled peptide) and fragmented. B. The fragments from the peptide are mass analyzed to obtain sequence information. The fragments obtained are derived from the N or C terminus of the peptide and are designated "b" or "y" ions, respectively. The spectrum shown indicates peptides that differ in size by the amino acids shown.

Peptide hydrolases (peptidases or proteases, i.e., enzymes hydrolyzing peptide bonds in peptides and proteins, see Chapt. 2) have received particular attention among hydrolases. As already described in Chapt. 2, peptidases are divided into exopeptidases (EC 3.4.11 -19), which cleave one or a few amino acids from the N- or C-terminus, and endopeptidas-es (proteinases, EC 3.4.21-99), which act internally in polypeptide chains [2], The presentation of enzymatic mechanisms of hydrolysis in the following sections will begin with peptidases and continue with other hydrolases such as esterases. 

Six of the CSN subunits contain PCI (proteasome, COP9 signalosome, initiation factor 3) domains and two contain MPN (Mpr-Padl-JV-terminal) domains [58]. These two characteristic domains have been found in three protein complexes the CSN, the 26S proteasome lid complex (lid) and the eIF3 complex. The two domains are composed of about 150 to 200 amino acids at the N- or C-terminus of the CSN subunits. Apparently, the PCI domain has been shown to be important for interactions between CSN subunits. Thus, it might have a scaffolding function [22, 59). 

The two examples from our work we are going to describe below are the design and study of liposomal diepitope constructs combining either (i) B and T-helper (Th) peptide epitopes, which induced particularly powerful humoral responses (21) (Fig. 3) or (ii) CTL and Th epitopes, which provided a powerful antitumor vaccine (74) (Fig. 4). For the production of these constructs we have conjugated peptides that contain a cysteine residue either at the N- or C-terminus, to the surface of preformed liposomes by reaction with thiol reactive functionalized phospholipids and/or PamaCys lipopeptide anchors (Fig. 2). To that end, we have developed strategies that give, in aqueous media, high... 

Most of the other posttranslational modifications involving the N- or C-terminus (Table 1) as well as the side-chain functionalities (Table 2) of the polypeptide chains occur under the control of enzymes that also dictate the regioselectivity of such chemical transformations. This regioselectivity is difficult to attain by synthetic procedures. Sophisticated protection schemes are required when additional chemistry must be performed on preassembled peptides, unless enzymatic methods can be used to supplement the synthetic strategies. As a consequence, the use of suitably modified amino acids as synthons is generally the preferred approach as will be discussed in the following sections. 

Backbone cleavages may involve removal of the N-terminal formyl moiety from the methionine, the removal of one or more amino acids at either the N- or C-terminus of the chain, and cuts in the backbone at one or more sites, possibly with the removal of internal peptide sequences. 

The positional preferences of amino acids, for either the N- or C-terminus of peptides, have varied when reported on by different groups. The differences in rankings may be due to differences in methods used to determine the ranking. Statistical methods apply different definitions and assumptions, while mutation studies suffer from inherent differences in environments, as well as short- and long-range interactions. Despite the differences, however, certain general observations have been made. 

Peptidases are often classified as either exopeptidases or endopeptidases, depending on the positional specificity of the bonds they hydrolyze. Exopeptidases act at peptide bonds located at either the N or C terminus of the protein. Those acting at the C terminus are referred to as carboxypeptidases, those acting at the N terminus as aminopeptidases. Endopeptidases, on the other hand, act at peptide bonds internal to the polypeptide chain. 

To avoid self-association the overall shape of larger structures has been chosen to be slightly curved, or ionic groups have been incorporated for recognition of the N-or C-terminus. 

Most biocatalytic conversions are performed with the enzyme immobilized in the microreactor. Miyazaki et al. [426] developed a simple noncovalent immobilization method for His-tagged enzymes on a microchannel surface. These enzymes contain a polyhistidine-tag motif that consists of at least six histidine residues, often located at the N- or C-terminus. The H is-tag has a strong affinity for nickel and can be reversibly immobilized by a nickel-nitrilotriacetic acid (Ni-NTA) complex (Scheme 4.103), a strategy commonly used in affinity chromatography. 

Question At what end of a growing polypeptide chain, N or C terminus, is the initiating amino acid found ... 

Here and later whether PNA is attached to N- or C-terminus of peptide depends on structural requirements for active peptide. Wrongly attached PNA can abolish peptide interactions with membrane or receptor. 

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