Cationic peptides, basic residues

Small ACTH fragments related to ACTH-(4-10) have also been investigated for the presence of ordered structure. CD of ACTH--(5-10) in TFE showed a random structure (50) as was found with H-NMR for fragment 4-10 (51). The addition of anionic or cationic surfactants to an aqueous solution of ACTH-(4-11) dit not promote any a-helix or 3-form in this peptide (CD experiments S2). When ACTH-(1-14) and 1-10 were measured by CD and NMR respectively, indications for a helical or ordered structure were found (90, ). Thus it seems that the addition of the non-helix "prone" fragment 1-3 or 1-4 can promote the formation of a helical structure in the adjacent sequence. Arguments in favour of this come from the theoretical work of Argos and Palau (53) on amino acid distribution in protein secondary structures. They found that Ser and Thr frequently occur at the N-terminal helical position (cf. Ser in ACTH) to provide stability the position adjacent to the helical C-terminus is often occupied by Gly or Pro (adjacent toTrp in ACTH we have Gly ) acidic amino acid residues are frequently found at the helix N-terminus (cf. Glu in ACTH) and/or basic residues at the C-terminus (cf. Arg ). 

The cationic peptides possess two predominant themes either a hydrophobic core (often helical) with an adjacent cluster of Lys and Arg residues (e.g., melittin and cecropins) or an amphipathic helix with basic side chains aligned along one helical face (e.g., magainins and the S4 segment of the sodium channel). The basic residues promote association with the acidic... 

An alternative is to use a metalloendopeptidase with Lys-N cleavage specificity combined with strong cation exchange enrichment. MALDl MS/MS analysis of such peptide ions containing a single lysine residue (and no other basic residue) has been found to result in spectra containing almost exclusively b-ions [37]. 

In many cases broad, asymmetric peaks are observed that can be indicative of solute interactions with the capillary wall. If cationic analytes are involved, this behavior is to be expected, since at pH 4.0, silanols are deprotonated and will attract cationic species (e.g., basic residues of peptide side chains). 

Piscidins are a family of AMPs found in a fish species and show broad-spectrum activity against bacteria, fungi and viruses (Cole et al, 1997 Yin et /., 2006 Fernandes et al, 2010). These molecules have a marked amphipa-thic character, due to well-defined hydrophobic and hydrophilic regions, and most are linear peptides with less than 26 residues and a high proportion of basic amino acids (phenylalanine and isoleucine). They are unstructured in water but have a high a-helix content in dodecylphosphocholine (DPC) micelles, a structure similar to those determined for other cationic peptides involved in permeabilization of bacterial membranes (Campagna et al., 2007). 

In an attempt to rationalize the large variety of buffers used to date in protein HPLC separations, it is necessary to briefly return to the separation mechanism based on the hydrophobic effect. This mechanism related the retention of a sample on a reversed-phase column to the nonpolar surface area of a sample molecule. A possible explanation of the dramatic effect of ion-pairing reagents on the retention of proteins on reversed-phase columns can then be based on the modification of surface polarity of the protein molecule on association with suitable counterions. In the absence of salts dissolved in the mobile phase, the peptide or protein sample probably has some counterions associated with the sample. Alternatively, the basic side chains of the protein may be neutralized by a salt bridge with an acidic residue which is adjacent in the three-dimensional structure. In either case, the contribution of the ammonium group to the surface polarity is relatively small. Figure 13 shows the result of association of the amine cation with a highly polar anion such as phosphate, which has a substantial sphere of hydration. In this case, the nonpolar area of the... 

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