Hydrophobicity peptides

Host defense peptide hydrophobicity and polar angle 183... 

Host defense peptide hydrophobicity (H) is defined as the proportion of hydrophobic amino acids within a peptide. Typically, these peptides are comprised of >30% hydrophobic residues and this governs the ability of a host defense peptide to partition into the lipid bilayer, an essential requirement for antimicrobial peptide-membrane interactions. Typically, the hydrophobic and hydrophilic amino acids of natural peptides are segregated to create specific regions or domains that allow for optimal interaction with microbial membranes. This likely represents evolutionary optimization to maximize the selectivity of these defense molecules. It has been established that increasing antimicrobial peptide hydrophobicity above a specific threshold correlates... 

Fig. 12. Correlation between peptide hydrophobicity and both the free energy of ligation and equilibrium reduction potential in Fe(III)-coproporphyrin I-peptide complexes. Reprinted with permission from Ref. (.125). Copyright 1998 American Chemical Society.

The energetics of peptide-porphyrin interactions and peptide ligand-metal binding have also been observed in another self-assembly system constructed by Huffman et al. (125). Using monomeric helices binding to iron(III) coproporphyrin I, a fourfold symmetric tetracarboxylate porphyrin, these authors demonstrate a correlation between the hydropho-bicity of the peptide and the affinity for heme as well as the reduction potential of the encapsulated ferric ion, as shown in Fig. 12. These data clearly demonstrate that heme macrocycle-peptide hydrophobic interactions are important for both the stability of ferric heme proteins and the resultant electrochemistry. 

Recently an extremely simple 2D-LC separation system with integrated sample clean-up has been developed for profiling of endogenous peptides in sputum as a biofluid. After loading the RAM-SCX column of 30 x 15 mm I. D., washing was accomplished and the trapped peptides were eluted from RAM-SCX column by five salt steps with increasing salt concentrations. Each of the five fractions were transferred and desalted directly on a monoHfhic 4.6 mm I. D. RP column, and further separated into 20 fractions according to peptide hydrophobicity [70]. 

IPC proved valnable for estimating peptide hydrophobicity [13]. Pharmaceutical science utilized IPC to monitor rat serum esterase activities [14] and also to analyze relationship between plasma concentrations at the end of infusion and toxicity profiles of fixed-dose-rate gemcitabine plus carboplatin [15]. An IPC trap was also used in an online desalting-mass spectrometry system. This system allows ionic compounds in a nonvolatile buffer to be introduced into a MS for strutural elucidation. The trap column was equilibrated with a volatile IPR, the target analyte and the nonvolatile buffer ions (phosphate and sodium ions) were transferred into the trap column, but only the target analyte that interacts with the volative IPR can be retained phospahte buffer ion were eluted from the trap column and the target analyte was eluted by oragnic solvent in a backflush mode and introduced into the MS. 

Hydrolysis of proteins without taste by proteases often produces bitter peptides. Hydrophobic amino acid residues located in the interior of protein molecules in aqueous solution are exposed by fragmentation of the protein molecules treated with proteases, and the peptides containing a number of hydrophobic amino acid residues occur in the solution (13). Many bitter peptides as shovm in Table 4-have been isolated from protein digests with proteinases (14-22). 

Fig. 7. Plots of k versus summated peptide hydrophobicity Sx calculated according to [36] at two different gradient times 120 min for /8-endorphin-related analogues 1-29. See Table 2 for...

Zanen, G. et al (2005) Signal peptide hydrophobicity is critical for early stages in protein export by Bacillus subtUis. FEBS /., 272 (18), 4617-4630. 

Figure 4 shows the separation of the cytochrome c digest employing an alternative separation mechanism (MECC) illustrating the quite different selectivity that can be obtained. The different separation mechanism can often provide additional structural clues as to the physical properties of the peptides (hydrophobicity). 

De Planque MRR, Greathous DV, Koeppe 11 RE, Schafer H, Marsh D, Killian JA (1998) Influence of lipid-peptide hydrophobic mismatch on the thickness of diacylphosphatidylcho-line bilayers. A 2H NMR and ESR study using designed transmembrane a-helical peptides and gramicidin A. Biochemistry 37(26) 9333-9345... 

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