Amino acid residues hydrophobicity scale based

Figure 3 (a) Comparison of the turbidimetric profiles for a series of chemosynthetic elastin polypeptides based on random copolymers of the repeat sequence [(Val-Pro-Gly-Val-Gly)i x(Val-Pro-Gly-Xaa-Gly)J, where fx refers to the mole fraction of variant pentapeptides within the polymer sequence. " (b) Hydrophobicity scale based on ft values for the copolymers described above as a function of guest residue identity and mole fraction, f. Note that hydrophobic amino acids shift the position of 7 toward lower temperature and that more polar guest residues shift the position of 7i toward higher temperatures in a manner commensurate with the level of substitution within the polypeptide sequence. Reprinted from Uriy, D. W. Gowda, D. C. Parker, T. M. etal. Biopolymers 99Z, 32(9), 1243 20(b) Copyright 1992, with permission from Wiley. 

The T,-based Hydrophobicity Scale for Amino Acid Residues... 

Figure 5.9. Experimental data for development of the T,-based hydrophobicity scale. The general composition for the protein-based polymer is poly [f,(GXGVP),fv(GVGVP)], where X is the guest amino acid residue to be evaluated and fx and E are mole fractions wherein fj -i- E = 1. Part A contains the raw data for a number of guest residues substituted at a mole fraction of 0.2, which means 4 substituted residues per 100 residues of poly(GVGVP). The experimental conditions were 40mg/ml of polymer of a molecular weight of about 100,000 Da in 0.15 N NaCl and 0.01 M phosphate at pH 7.4. Experimental T,-values were obtained as shown in part A for fx = 0.2, and additional polymers were characterized with different fx values such that a plot of fx versus T, could be constructed as in part B. Extrapolation of the linear plots in part B to fx = 1 gave the T,-values that became the basis for the T,-based hydrophobicity scale given in Table 5.1. (Adapted with permission from Urry. )...

The relative oil-like character of each amino acid residue is given in terms of the Tt-based hydrophobicity scale in Table 5.1. T, is measured by plotting as indicated in Figure 5.9 and the technical term for oil-like, hydrophobic (meaning water fearing), is used. The more commonly used technical term, hydrophobicity, replaces the equivalent statement of oil-like character. 

B, Plots of Tj versus fx, the mole fraction of pentamers containing guest residues, are essentially linear to fx = 0.5. Extrapolation to the value of Tj at fx = 1 is used to provide an index of the relative hydrophobicities of the amino acid residues. This provides for a hydrophobicity scale which is based on the hydrophobic folding and assembly of interest. Adapted with permission from Urry, 1993a. 

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]...

Volume = Volume enclosed by van der Waals radii Mass = molecular weight of nonionized amino acid minus that of water both adopted from Creighton (1993) HP scale = degree of hydrophobicity of amino acid side chains, based on Kyte Doolittle (1982) Surface Area = mean fraction buried, based on Rose et al. (1985) and Secondary structure propensity = the normalized frequencies for each conformation, adopted from Creighton (1993), is the fraction of residues of each amino acid that occurred in that conformation, divided by this fraction for all residues. 

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. 

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). 

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