Peptide aggregation

At a molar ratio of peptide to lipid of 0.002 (0.2 mol%) and 0.005 (0.5 mol%) at process start, all of the peptide was incorporated into the liposomal membrane bilayer. At a 5 mol% value of the peptide in relation to the lipid amount at the start of the experiments, only 33% of the total peptide was recovered in the final liposomal formulation after extrusion a concomitant loss in lipid content was also observed. This led us to the conclusion that at higher TRP-2 peptide ratios lipid-peptide aggregates may be formed, which cannot be extruded. 

Although MC is an underutilized tool in the field of computational molecular biophysics, there are beneficial features that can be exploited, especially in conjunction with implicit solvent models. Specifically, MC has the potential of accessing length scales that are inaccessible to MD in complex phenomena like peptide aggregation or conformational sampling of intrinsically disordered proteins. 

Meli, M., Morra, G., Colombo, G. Investigating the mechanism of peptide aggregation insights from mixed Monte Carlo-molecular dynamics simulations. Biophys. J. 2008, 94, 4414-26. 

The insolubility of peptides is not limited to the solution phase and can occur during peptide synthesis on the solid phase where it manifests itself as the difficult sequence problem. On-resin peptide aggregation and poor peptide segment solubility are due to the formation of (3-sheet-like structures. Difficult sequences contain predominantly hydrophobic residues that consistently show incomplete acylation and a characteristic shrinkage of the peptide-resin during synthesis.111 Reversible backbone protection was introduced into Fmoc/ tBu SPPS after the study of synthesis failure during the assembly of difficult sequences1121 and is now routinely used to circumvent synthesis failure in SPPS. 

Fluorescence quantum yield and emission maximum determinations as a function of peptide concentration may also permit the detection of peptide self-aggregation at concentrations below 10-4 M, because the peptide fluorophore is likely to be located in a different environment in the peptide aggregate. For example, the concentration-dependent changes in the tryptophan fluorescence emission maximum of mellitin were monitored to determine the equilibrium dissociation constant and thermodynamic parameters of the monomer-tetramer self-association reaction of this peptide. 25 Similarly, measurement of the changes in the tryptophan fluorescence intensity of gramicidin A as a function of its concentration permitted the determination of an average monomer-dimer equilibrium con-stant. 26 ... 

D. It is associated with the deposition of neurotoxic amyloid peptide aggregates. 

Due to the preference for a cis-amide bond[93] with the preceding residue of C2-substituted pseudoprolines, their incorporation results in a kink conformation of the peptide backbone, thus preventing peptide aggregation, self-association, or (3-structure formation. 

ID NMR experiments are often used for quality-control purposes and can readily be used to confirm the purity of peptides. Simple ID spectra are also often used to determine whether a peptide is structured or unstructured or whether aggregation is present. Dispersion of the amide chemical shifts is an indicator of the former, whereas a narrow distribution, in the range of 7.5-8.5 ppm, is characteristic of unstructured peptides. Aggregation leads to broad peaks and spectra of poor quality. Adjustment of conditions by varying pH, buffer, cosolvent (e.g., acetonitrile for hydrophobic peptides), or peptide concentration and monitoring the effects on ID spectra is often used to find optimum conditions. 

Fig. 5.6 Chloride transport by peptide aggregation in an artificial system [14]...

Oradd, G., and G. Lindblom (2004) NMR Studies of lipid lateral diffusion in the DMPC/gramicidin D/water system peptide aggregation and obstruction effects. 

By introducing a crown ether unit at the C-terminal region of hydrophobic helical peptides, Otoda et al.19 were able to demonstrate increased stabilization of the peptide aggregate in the membrane by the formation of sandwich-type complexes with large cations. Ion channel activity was also increased due to the ability of the crown peptide to bind ions to the terminal portion of the hydrophobic helix bundle at the water-lipid interface. Ueda et al.20 considered the problem of insolubility of hydrophobic peptides which restricts the distribution of peptides in water to a phospholipid bilayer membrane. In consequence they constructed a hydrophobic helix bundle shielded by hydrophilic peptides that acts rather like an umbrella. 

Pike CJ, Walencewicz AJ, Glabe CG, Cotman CW (1991) In vitro aging of beta-amyloid protein causes peptide aggregation and neurotoxicity. Brain Res 563 311—314 Prasad AS, Miale A Jr., Farid Z, Sandstead HH, Schulert AR (1963) Zinc metabolism in patients with the syndrome of iron deficiency anemia, hepatosplenomegaly, dwaifism, and hypognadism. J Lab Qin Med 61 537-549... 

Wadhwani, P., Biirck, J., Strandberg, E., et al. (2008) Using a sterically restrictive amino acid as a 19F NMR label to monitor and to control peptide aggregation in membranes. Journal of the American Chemical Society, 130, 16515-16517. 

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