Hydrophobicity, scale

Hydrophobicity scales measure the degree of hydrophobicity of different amino acid side chains... 

Y Ishihama, Y Oda, N Asakawa. A hydrophobicity scale based on the migration index from microemulsion electrokinetic chromatography of anionic solutes. Anal. Chem. 68 1028-1032 (1996). 

L-phenyl-jJanine and various other amino acids Aliquat-336 KCland KOH Coimter-trans- ELM port of CL Concentration as anion carrier specificity for various aminoacids depends on hydrophobicity scale [45,95 ... 

Di- and tripeptides D2EHPA HCl Counter-trans- ELM port of H - Concentration and permeation depends on hydrophobicity scale [97]... 

In a more recent paper [160], Urry et al. reported that x20-poly (GGAP) was nonadhesive to both bovine ligamentum nuchae fibroblast and human umbilical vein endothelial cells (HUVECs), even in the presence of serum. Urry et al. interpreted this behavior in terms of their hydrophobicity scale. They suggested that x20-poly[50(GGAP), (GRGDSP)], for example, could provide the inner lamina for a vascular prosthesis. 

Wilce, M.C J., Aguilar, M.-L, and Heam, T.W. 1995. Physicochemical basis of amino acid hydrophobicity scales Evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides. Anal. Chem. 67 1210-1219. 

Figure 11.5. ProtScale (ExPASy Proteomic Tools) output of hydrophobicity parameter. The hydrophobicity profile of cod alcohol dehydrogenase is generated with ProtScale using Eisenberg hydrophobic scale. The individual values for the 20 amino acids used in the profile are also listed in the report.

Thien et al. (18) also showed that the degree of solubilisation depends on the relative hydrophobicities of the amino acid residues. A measure of this effect is the slope of the solubilisation curve when replotted as a function of the net solute charge, as shown in Figure 10 for arginine. It was found that this slope correlated well with the hydrophobicity scale proposed by Bull and Breese (1j)), as is evident from Figure 11. It is intriguing to note that the more hydrophobic the residue the greater the solubilisation of the amino acid. This could be due to one of three effects, as discussed below. 

Table 2.11. Hydrophobicity scale for amino acids based on partition of residues between protein surface and interior. Data in kcal mol-1 give transfer free energies surface/interior, s/i [138]...

The hydrophobicity profile is a simple way to quantify the concentration of hydrophobic residues along the linear polypeptide chain (Rose Dworkin, 1989). The construction of the profiles depends on the choice of the hydrophobicity scale and the window size. The profile is computed by averaging the hydrophobicity scales of amino acid residues within... 

The amino acid and protein features can be represented in different ways to maximize information extraction. They may be represented as real-numbered measurements in a continuous scale (such as mass or hydrophobicity scales in Table 6.1), or as vectors of distances or frequencies (such as PAM matrix and sequence profile in Figures 6.2 and 6.3). But they can also be conveniently categorized into classes based on these properties. This effectively reduces the original 20-letter amino acid alphabet set to an alternative alphabet set of smaller sizes and emphasizes the various properties of the molecular residues and maximizes feature extraction. 

Using the hydrophobicity scale as an example, the amino acid residues can be represented by the real-numbered scalar value. They can also be classified with respect to their side chains as polar, nonpolar, or amphipathic, depending on the range of the hydrophobicity in the scale, such as in... 

In addition to the use of binary numbers to represent the identity of individual sequence residues, real numbers that characterize the residues can be used in the direct sequence encoding method. Each residue can be represented by a single feature, such as the hydrophobicity scale (Xin et al., 1993), or by multiple properties that may or may not be orthogonal (Lohmann et al., 1994). Each sequence position can also be represented by the residue flequency derived from multiple sequence alignments (Le., sequence profile of a family) (Rost Sander, 1993) or the substitution vector. The values of the vectors are usually normalized to a scale of 0 to 1, or -1 to 1 (Xin, 1993 Lohmann et al., 1994). 

Wimley, W. C., and White, S. H. (1996). Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3, 842-848. 

The residues have been listed in the tables in the following order the acidic amino acids (Asp and Glu) and their amides (Asn and Gin) are listed first, followed by His and then the basic amino acids (Lys and Arg). They are followed by the remaining amino acids in, broadly, their order of increasing hydrophobicity. This order is a crude consensus order based on the several hydrophobicity scales discussed by Edsall and McKenzie (1983). 

Two of the hydrophihcity scales in Table 2 were derived from experimental measures of the behavior of amino acids in various solvents, namely partitioning coefficients [K-D index of Kyte and Doolittle (30)] or mobility in paper chromatography [Rf index of Zimmerman et al. (31)]. By contrast, the Hp index was obtained from quantum mechanics (QM) calculations of electron densities of side chain atoms in comparison with water (32). The Hp index is correlated highly with these two established hydrophobicity scales (Table 4). Therefore, like the polarizability index, it is possible to represent fundamental chemical properties of amino acids (hydrophUicity, Hp) with parameters derived from ab initio calculations of electronic properties. However, in contrast to polarizabihty (steric effects), hydrophihcity shows significant correlation with preference for secondary structure. Thus, hydrophobic amino acids prefer fi-strands (and fi-sheet conformations) and typically are buried in protein structures, whereas hydrophilic residues are found commonly in turns (coil structure) at the protein surface. 

From Both Ends of the Hydrophobicity Scale" Trend in Thermophilic Adaptation... 

The limitations of standard reversed-phase materials have been partially overcome by introducing modem, specially deactivated hydrocarbon-silica pha.ses ]126]. the hydrocarbonaceous phases immobilized on alumina or zirconia support ]127] and the polymeric materials ]128]. Using the latter two types of stationary phase materials one can determine the HPLC capacity factors at acidic, neutral and alkaline conditions. This way a universal, continuous chromatographic hydrophobicity scale can be constructed like the standard log P scale ] 129]. 

---