Amidation peptide motifs

Figure 7.17. Molecular structure of a peptide fragment characterized by a retro-inverso amide bond motif.

GnIH-related peptides, peptides present in the brains of vertebrates, such as mammals, amphibians, and fish, characterized by a C-terminal LPXRFa (X = L or Q) sequence motif. They belong to the - LPXRFa peptides, which are member of the RF-amide peptide family [K. Ukena, K. Tsutsui, Mass Spectrom. Rev. 2005, 24,469]. 

QRFP, a 43-peptide amide bearing an N-terminal pyroglutamyl residue and the C-terminal RFamide consensus motif. This novel RFamide peptide is implicated in food intake and aldosterone release from the adrenal cortex in the rat. QRFP is conserved in humans, cattle, rat, and mouse. The term QRFP is derived from pyroglutamylated arginine-phenylalanine-amide peptide [S. Fukusami et al., J. Biol. Chem. 2003, 278, 46387 C. Kutzleb et al., Curr. Prot. Pept. Sci. 2005, 6, 265]. 

As such, the magainins provide a useful initial target for peptoid-based peptido-mimetic efforts. Since the helical structure and sequence patterning of these peptides seem primarily responsible for their antibacterial activity and specificity, it is conceivable that an appropriately designed, non-peptide helix should be capable of these same activities. As previously described (Section 1.6.2), peptoids have been shown to form remarkably stable hehces, with physical characterishcs similar to those of peptide polyprohne type-I hehces (e.g. cis-amide bonds, three residues per helical turn, and 6A pitch). A faciaUy amphipathic peptoid helix design, based on the magainin structural motif, would therefore incorporate cationic residues, hydrophobic aromatic residues, and hydrophobic aliphathic residues with threefold sequence periodicity. 

It was determined that the minimal peptide sequence required to stimulate pheromone biosynthesis was the C-terminal 5 amino acids, FXPRLamide, and that the carboxy terminus needs to be amidated [148,149]. This sequence was also established as the minimal sequence required for myotropic activity in cockroaches [ 150] and induction of embryonic diapause in B. mori [ 151 ]. Crossreactivity of peptides containing the FXPRLamide motif was also established for myotropic, diapause induction, and pheromone biosynthesis [152-154]. Therefore, the common C-terminal FXPRLamide defines this family of peptides. A partial listing of peptides identified to date is shown in Table 1. 

Based on the CAAX motif, peptide analogues were designed in which peptide amide bonds are replaced by amine and ether groups [18]. In particular /I-turn mimetic 1 (Fig. 1) inhibits the FTase in vitro with an IC50 value of 1.8 nmol/1 and shows highly specific activity in comparison to inhibition of GGTase I. 

The new crystal structure of the ribosome—RFl complex sheds more light into the interactions between the GGQ motif and the peptidyltransferase center. This complex represents the product state of peptide release since a deacylated tRNA is bound to the P site. Importantly, the main chain amide of the conserved glutamine hydrogen bonds to the 3 OH of A76 in the P site, which is the leaving group of the hydrolysis... 

Many NRPs such as cyclosporin, complestatin, actinomycin, and chondramide contain N-methyl amides. M-Methyl transferase (N-MT) domains utilize S-adenosylmethionine (SAM) as a cofactor to catalyze the transfer of the methyl group from SAM to the a-amine of an aminoacyl-S-PCP substrate. The presence of M-methylamides in NRPs is believed to protect the peptide from proteolysis. Interestingly, N-MT domains are incorporated into the A domains of C-A-MT-PCP modules, between two of the core motifs (A8 and A9). MT domains contain three sequence motifs important for catalysis. ° 0-Methyl transferase domains are also found in NRPSs and likewise use the SAM cofactor. For instance, cryptophycin and anabaenopeptilide synthetases contain 0-MT domains for the methylation of tyrosine side chains. These 0-MT domains lack one of the three core motifs described for N-MT domains. ... 

Flg.1. In the amino acid sequence of KO-42 is encoded its fold and its function as it controls the formation of a hairpin helix-loop-helix motif that dimerizes to form a four-helix bundle. On the surface of the folded motif a reactive site is formed that catalyzes hydrolysis, transesterification and amidation reactions of reactive esters, whereas unfolded peptides are incapable of cooperative catalysis. In addition the values, and thus the reactivities, of the histidine residues are controlled by the fold. The pK of each His residue of KO-42 is shown in the figure and deviate by as much as 1.2 units from that of random coil peptides which is 6.4... 

Vibrational spectroscopy has been used in the past as an indicator of protein structural motifs. Most of the work utilized IR spectroscopy (see, for example, Refs. 118-128), but Raman spectroscopy has also been demonstrated to be extremely useful (129,130). Amide modes are vibrational eigenmodes localized on the peptide backbone, whose frequencies and intensities are related to the structure of the protein. The protein secondary structures must be the main factors determining the force fields and hence the spectra of the amide bands. In particular the amide I band (1600-1700 cm-1), which mainly involves the C=0-stretching motion of the peptide backbone, is ideal for infrared spectroscopy since it has an large transition dipole moment and is spectrally isolated... 

Coherent transport of vibrational energy is further limited by vibrational energy relaxation. Experiments on the amide I band of different peptides (NMA, apamin, scyllatoxin BPTI, and the cyclic pentapeptide) revealed a vibrational relaxation rate of approximately Ti = 1.2 ps, which is essentially independent of the particular peptide (30,53). A similar value has recently been reported for myoglobin at room temperature, with only a weak dependence of the relaxation rate on temperature down to cryogenic temperatures (140). In other words, vibrational relaxation of the amide I mode reflects an intrinsic property of the peptide group itself rather than a specific characteristic of the primary or secondary structural motifs of the... 

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