Peptides hydrophobic interaction

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. 

Figure 17.15 Schematic diagrams of the main-chain conformations of the second zinc finger domain of Zif 268 (red) and the designed peptide FSD-1 (blue). The zinc finger domain is stabilized by a zinc atom whereas FSD-1 is stabilized by hydrophobic interactions between the p strands and the a helix. (Adapted from B.I. Dahiyat and S.L. Mayo, Science 278 82-87, 1997.)...

Ionic interactions between solutes and Superose are negligible at ionic strengths above 50 mM. However, some hydrophobic interactions have been observed with small hydrophobic peptides, membrane proteins, and lipopro-... 

Small peptides may be difficult to chromatograph by aqueous GFC due to complex nonsize effects such as ionic and hydrophobic interactions. Elution... 

In a first step towards the design of / -peptides tyligomers (oligomers that fold into predictable tertiary structures [8]), carefully controlled interhelical hydrophobic interactions have been utilized to stabilize a / -peptide two-helix bundle (92) [179] (Fig. 2.17). 

Fig. 20 Vertical model of complementary assembly of peptide mixtures. Hydrophobic interactions are represented by the interlocking of raised sections and holes. The axis is indicated by dots. Reproduced from Takahashi et al. [57] with permission. Copyright Wiley-VCH. Numbers refer to the peptide entries in Fig. 18. Positively charged residues are dark shaded in contrast with the negatively charged residues which are light shaded...

The characteristic coiled-coil motifs found in proteins share an (abcdefg) heptad repeat of polar and nonpolar amino acid residues (Fig. 1). In this motif, positions a, d, e, and g are responsible for directing the dimer interface, whereas positions b, c, and f are exposed on the surfaces of coiled-coil assemblies. Positions a and d are usually occupied by hydrophobic residues responsible for interhelical hydrophobic interactions. Tailoring positions a, d, e, and g facilitates responsiveness to environmental conditions. Two or more a-helix peptides can self-assemble with one another and exclude hydrophobic regions from the aqueous environment [74]. Seven-helix coiled-coil geometries have also been demonstrated [75]. 

Folding of a peptide probably occurs coincident with its biosynthesis (see Chapter 38). The physiologically active conformation reflects the amino acid sequence, steric hindrance, and noncovalent interactions (eg, hydrogen bonding, hydrophobic interactions) between residues. Common conformations include a-helices and P pleated sheets (see Chapter 5). 

Amphipathic peptides contain amino acid sequences that allow them to adopt membrane active conformations [219]. Usually amphipathic peptides contain a sequence with both hydrophobic amino acids (e.g., isoleucine, valine) and hydrophilic amino acids (e.g., glutamic acid, aspartic acid). These sequences allow the peptide to interact with lipid bilayer. Depending on the peptide sequence these peptides may form a-helix or j6-sheet conformation [219]. They may also interact with different parts of the bilayer. Importantly, these interactions result in a leaky lipid bilayer and, therefore, these features are quite interesting for drug delivery application. Obviously, many of these peptides are toxic due to their strong membrane interactions. 

Seebach, D., Abele, S., Gademann, K., Guichard, G., Hintermann, T., Jaun, B., Matthews, J. L., and Schreiber, J. V. (1998). /32- and /3 -peptides with proteinaceous side chains Synthesis and solution structures of constitutional isomers, a novel helical secondary structure and the influence of solvation and hydrophobic interactions on folding. Helv. Chim. Acta 81, 932-982. 

Burke, T.W., Mant, C.T., Black, J.A., Hodges, R.S. (1989). Strong cation-exchange high-performance liquid chromatography of peptides. Effect of non-specific hydrophobic interactions and linearization of peptide retention behaviour. J. Chromatogr. 476, 377-389. 

One inherent property of peptides that interact with membranes is that self-association or even aggregation will interfere with solubilization by organic solvents or micelles. The preparation, purification and sample preparation of extremely hydrophobic (often transmembrane) peptides is nontrivial and has been addressed by only a few papers [74—79]. 

Peptides larger than 10 to 20 residues adopt conformations in solution through the interplay of hydrogen bonding, electrostatic and hydrophobic interactions, positioning of polar residues on the solvated surface of the polypeptide, and sequestering of hydrophobic residues in the nonpolar interior. Protein shape is dynamic, changing continuously in response to the solvent environment. The retention process in RPLC is initiated as the protein approaches the stationary-phase surface. Structured water associated at the phase surface and adjacent to hydrophobic contact surfaces on the polypeptide is released into the bulk mobile... 

M.T.W. Hearn, Reversed-phase and hydrophobic interaction chromatography of proteins and peptides, in HPLC of Biological Macromolecules, 2nd ed., K.M. Gooding and F. Regnier (Eds.), Marcel Dekker, New York, 2002, pp. 172-173. 

Module 3, Column and Mobile Phase Design (CMP). This is the core module for ECAT. It can currently specify i) analytical column and mobile phase constituents for reverse phase chromatography of common classes of organic molecules ii) reverse phase, ion exchange phase and hydrophobic interaction chromatography of proteins and peptides iii) a limited set of specialty classes of molecules best treated by straight phase chromatography (e.g., mono- and disaccharides). The rules for selection of the HPLC detector are under development within Module 3. Some of the rules for detector mobile phase compatibility are already encoded. A set of rules for detector selection is ready but not yet encoded. 

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