Peptides partitioning

Fig. 17. Fluorous patches direct the pairing of protein segments in lipid micelles. The hydrophobic peptides partition into lipid micelles, forming a-helices. Then, the superhydrophobic hexafluoroleucine residues seek each other, causing self-association into dimers and higher order aggregates. Fluorine is light, while the backbone of the a-helices is dark. From Ref. [81], with permission.

The effect of amino acid sequence on peptide partitioning was discussed... 

The most frequendy used technique to shift the equiUbrium toward peptide synthesis is based on differences in solubiUty of starting materials and products. Introduction of suitable apolar protective groups or increase of ionic strength decreases the product solubiUty to an extent that often allows neady quantitative conversions. Another solubiUty-controUed technique is based on introduction of a water-immiscible solvent to give a two-phase system. Products preferentially partition away from the reaction medium thereby shifting the equiUbrium toward peptide synthesis. 

Many proteins are targeted to their destinations by signal sequences. A major sorting decision is made when proteins are partitioned between cytosohc and membrane-bound polyribosomes by virtue of the absence or presence of a signal peptide. 

The importance of lipophilicity to bitterness has been well established, both directly and indirectly. The importance of partitioning effects in bitterness perception has been stressed by Rubin and coworkers, and Gardner demonstrated that the threshold concentration of bitter amino acids and peptides correlates very well with molecular connectivity (which is generally regarded as a steric parameter, but is correlated with the octanol-water partition coefficient ). Studies on the surface pressure in monolayers of lipids from bovine, circumvallate papillae also indicated that there is a very good correlation between the concentration of a bitter compound that is necessary in order to give an increase in the surface pressure with the taste threshold in humans. These results and the observations of others suggested that the ability of bitter compounds to penetrate cell membranes is an important factor in bitterness perception. 

Buchwald, P., Bodor, N. Octanol-water partition of nonzwitterionic peptides predictive power of a molecular size-based model. Proteins 1998, 30, 86-99. 

When the log /J/pH measurement of a peptide is performed by the shake-flask or the partition chromatography method (using hydrophilic buffers to control pH), usually the shape of the curve is that of a parabola (see Ref. 371 and Fig. 1 in Ref. 282), where the maximum log I) value corresponds to the pH at the isoelectric point (near pH 5-6). Surprisingly, when the potentiometric method is used to characterize the same peptide [275], the curve produced is a step function, as indicated by the thick line in Fig. 4.5 for dipeptide Trp-Phe. 

Using liposomes made from phospholipids as models of membrane barriers, Chakrabarti and Deamer [417] characterized the permeabilities of several amino acids and simple ions. Phosphate, sodium and potassium ions displayed effective permeabilities 0.1-1.0 x 10 12 cm/s. Hydrophilic amino acids permeated membranes with coefficients 5.1-5.7 x 10 12 cm/s. More lipophilic amino acids indicated values of 250 -10 x 10-12 cm/s. The investigators proposed that the extremely low permeability rates observed for the polar molecules must be controlled by bilayer fluctuations and transient defects, rather than normal partitioning behavior and Born energy barriers. More recently, similar magnitude values of permeabilities were measured for a series of enkephalin peptides [418]. 

To illustrate the potential of the three-layer ONIOM method, we show results from a systematic comparison of three- and two-layer ONIOM methods with full QM benchmark calculations [11], The system studied is a zwitterionic peptide, NH3+—CHnBu—CO—NH—CH2—CO—NH—CH Bu—COO-, and the partition scheme illustrated in Figure 2-2 is used. In this partition, both model and mid... 

In this model, one can argue that a peptide must have both an affinity for the interface (favorable n-octanol partition coefficient) and small desolvation energy (favorable A log PC) in order to efficiently cross a cell membrane. On the other hand, this model also predicts that a peptide with a large n-octanol/water partition coefficient and large desolvation energy, due to a significant number of polar groups, should adsorb and remain at the membrane interface. Both of these predicted events have been observed in the laboratory. 

Instead of using the oral bioavailability of a drug, one can attempt to correlate PM values with permeability coefficients generated from in situ perfused intestinal preparations. Here, one eliminates the complexities of liver metabolism, clearance, and formulation variables. Recently, this type of in vitro-in situ correlation has been conducted using the model peptides (described previously in Section V.B.2). The permeabilities of these model peptides were determined using a perfused rat intestinal preparation which involved cannulation of the mesenteric vein (Kim et al., 1993). With this preparation, it was possible to measure both the disappearance of the peptides from the intestinal perfusate and the appearance of the peptides in the mesenteric vein. Thus, clearance values (CLapp) could be calculated for each peptide. Knowing the effective surface area of the perfused rat ileum, the CLapp values could be converted to permeability coefficients (P). When the permeability coefficients of the model peptides were plotted as a function of the lipophilicity of the peptides, as measured by partition coefficients in octanol-water, a poor correlation (r2 = 0.02) was observed. A better correlation was observed between the permeabilities of these peptides and the number of potential hydrogen bonds the peptide can make with water (r2 = 0.56,... 

Fig. 37), suggesting that desolvation of the polar bonds in the molecule is a major determinant of permeability. Consistent with this, good correlations were found between the permeabilities of these peptides and their partition coefficients between heptane-ethylene glycol (r2 = 0.87) or the differences in partition coefficients between n-octanol-buffer and isooctane-buffer (r2 = 0.82) both these buffer systems provide experimental estimates of hydrogen-bonding potential. These results are qualitatively identical with those described earlier for the permeability of these peptides across Caco-2 cell monolayers. 

Figure 37 Correlations of log monolayer permeability coefficients for a series of related peptides and various physicochemical indices (see Table 14). In plot (C) the log PC values refer to the immiscible n-heptane/ethylene glycol partitioning system. [Redrawn from Kim et al. (1993) with permission from the publisher.]...

A careful comparative pharmacokinetic study of the tripeptoid 6.108 and the tetrapeptide N-phenylacetyl-Leu-Asp-Phe-D-Pro-amide (6.109) in rats has provided insights on absorption and disposition [233]. The two compounds have comparable backbone structures but differ in the presence or absence of peptide bonds. They also have similar octanol/water partition coefficients, although the H-bonding capacity of the tetrapeptide is greater. In an in vitro model, the two compounds had comparable, and low, absorption clearances (6.7 x 10 4 vs. 4.8 x 10 4 ml min-1 cnT1 for the peptoid and the... 

The order of elution of peptides (charged compounds) is governed by a combination of electrophoresis and partitioning, with hydrophobic as well as electrostatic contributions. In this study it was demonstrated that sulfonic acid functionalities in the methacrylate monolith provide high stability and maintain a constant EOF over a wide range of pH (2—12). It was also demonstrated that a better separation of a mixture of therapeutic peptides was obtained at high pH values (Figure 16) due to the suppression of electrostatic attraction. 

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... 

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