Hydrophobicity values

Figure 14. Hydrophobicity analysis of five P-type ATPases according to the Kyte-Doolittle method. A hydrophobicity value between -4.5 and +4.5 is assigned to each type of amino acid residue and mean values are successively calculated along the peptide sequence using a window of 18 residues. Segments corresponding to the transmembrane helices M1-M10 in the structural model in Figure 15 are shaded. Modified from Verma et al., 1988.

Hydrophobicity was quantified by the logarithm of the 1-octanol-water partition coefficient (log KoW) values. The hydrophobicity values were measured or estimated by the ClogP (ver 3.55) software (BIOBYTE Corp., Claremont, CA, USA). The acceptor superdelocalizabilities were determined as a sum of the ratios between the squared eigenvectors (coefficients) of the i-th atomic... 

Table 3-6 Hydrophobicity Values of Some Food Proteins...

Bitterness occurs as a defect in dairy products as a result of casein proteolysis by enzymes that produce bitter peptides. Bitter peptides are produced in cheese because of an undesirable pattern of hydrolysis of milk casein (Habibi-Najafi and Lee 1996). According to Ney (1979), bitterness in amino acids and peptides is related to hydrophobic-ity. Each amino acid has a hydrophobicity value (Af), which is defined as the free energy of transfer of the side chains and is based on solubility properties (Table 7-6). The average hydrophobicity of a peptide, Q, is obtained as the sum of the Af of component amino acids divided by the number of amino acid residues. Ney (1979) reported that bitterness is found only in peptides with molecular weights... 

Table 7-6 Hydrophobicity Values (Af) of the Side Chains of Amino Acids...

Aznar et al. (2004) used static headspace-APCI-MS to study the release of volatiles from water and hydroalcoholic systems (12 vol.%). They found a decrease in the headspace concentration of volatile compounds with an increase in the log P values (hydrophobicity values) until log P = 3. Nevertheless, for very non-polar compounds (log P > 3), they did not find this trend this could be due to changes in hydrophobic interactions in the solution. 

Almost all peptides of hydrophobic L-amino acids elicit a bitter taste, which indicates that the bitterness of peptides is caused by the hydrophobic property of the amino acid side chain. Ney (12) has reported that whether a peptide has a bitter taste or not depends on its hydrophobic value Q. The value Q is obtained by adding the Af-values (Table 3) of each constituent amino acid residue of a peptide and dividing the sum by the number of amino acid residues (n). 

Fig. 5.38. Logarithmic plot of the capacity factors (k ) versus the hydrophobicity values (log Pow) of the different triazines measured on (A) a reference column and (B) a PRO imprinted column, using mobile phases with different aqueous contents. From Dauwe and Sellergren [32].

Local hydrophobicityplays an important role in molecular recognition processes. It is generally accepted that the hydrophobic interaction between two molecules is related to both energetic and entropic contributions, but there is still no simple physical model available for hydrophobicity and hydrophobic interactions. However, there have been several attempts to define relative hydrophobicity values on the basis of empirical findings. 

There are now a wide range of methods available to detect domains with amphipathic helicial characteristics at the residue level. However, new methods for describing the amphipathic nature of protein segments at the atomic level are still under development. Attempts to incorporate atomic hydrophobicity values (Cornette et ai, 1987 Tanford, 1978) in describing the amphipathic nature of peptides or other molecules have been described (Eisenberg and McLachlan, 1986). In the future, however, side-chain flexibility, effective solvent-accessible surfaces, electrostatics, and molecular dynamics will have to be included to obtain an accurate description of the amphipathic nature of these protein fragments at an atomic level. 

It should be emphasized that all these methods give only relative hydrophobicity values. In contrast, for the hydrophobically modified proteins, it is possible to determine the exact number of hydrophobic groups attached to each protein molecule. Such methods are based on the determination of the amount of attached groups by radioac-tively labeled groups [31], elementary analysis [63], or even sophisticated mass spectrometry methods [33]. The degree of modification can also be determined by measuring the number of unreacted modification sites on the protein, before and after modification. 

The hydropathy index is a measure of the hydrophobicity of the amino aoid (the higher the number, the more hydrophobic). Values based on Kyte J, Doolittle RF. J Mol Biol 1982 157 105B132. 

There are a plethora of very critical and most vital pharmacokinetic characteristic properties so as to obtain a highly specific and effective therapeutic drug substance. Lipinski et. al. (1997) postulated that the three major physical variables viz., potency, solubility and permeability may be carefully adapted to increase the overall activity of potential oral drug substances predominantly. They also observed that relatively poor permeation i.e., absorption) is commonly attributed by the following characteristic features either inducted alone or more than one right into the proposed drug molecule a Plus five H-bond donors, a Plus ten H-bond acceptors, a More than 500 molecular weight, and a More than five computed Tog P (hydrophobicity) values. 

As shown in Table 9-2, Trp is less hydrophobic than aNal. Nevertheless, the corresponding 1-47 analogs Tyr3Trp and Tyr3aNal display very similar inhibitory activity. Conversely, although aNal and pNal have the same hydrophobicity value,... 

The calculated T, value for Pro comes from poly(GVGVP) when the experimental values of Val and Gly are used. This hydrophobicity value of —8°C is unique to the /1-spiral structure where there is hydrophobic contact between the Val 7CH3 and the adjacent Prof 5CH2 and the intertum Prof+3 /KIH2 moieties. 

Hie hydrophobicity scale in Table 5.3 lists the contribution of each amino add residue to the Gibbs free energy of hydrophobic association, AGha- Table 5.3 also provides the information required to calculate numbers for the relative hydrophobidties of the faces of the y-rotor. The resulting numbers are tabulated and summed in Table 8.2, where the LAGHA(P-empty face) = -20 kcal/mole. This is indeed a very hydrophobic value. 

Percent weight fractions of amino acids with different chain type and average molecular weight of amino acids are also reported. Theoretical hydrophobicity values are calculated by the authors following values given in Ref. 65 (see Section III.A.4). 

The hydrophobic character of proteins and peptides depends primarily on their amino acid composition, i.e., the relative amount and lipophilicity of nonpolar residues in the molecule. A measurement of protein hydrophobicity (average hydrophobicity HOave) can be derived theoretically as the average of the individual A/t values based on the molar amino acid composition, where A/, is the change in free energy for the transfer of one mole of amino acid from ethanol to water (63-65). The average hydrophobicity values of the principal source proteins of cosmetic interest are listed in Table 3. A different way to express protein hydrophobicity is the so-called surface hydrophobicity, an entity measured experimentally on proteins by the adsorption of a chemical compound (cis-... 

Table 2. Hydrophobicity values of some food proteins measured by two fluorescence probes. (Adapted from Li-Chan, 1991) ...

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