5 α-Amino Acids In Water: A Review of VCD and ROA Spectra
91
after the introduction of a non-polar compound which cannot form hydrogen bonds
and thus replaces the disrupted ones.
Apart from the qualitative description of amino acids as hydrophobic or hydrophilic, there have been numerous attempts at quantitatively characterising the hydrophobicity of amino acids by means of both experimental and theoretical methods. An exhaustive review on different scales is provided by Biswas et al. [41]. the
derived hydrophobicity scales were divided by the authors according to the type of
studied solutes (simple amino acids, side chain analogues, their derivatives, or peptides) and the method used (partitioning experiments, chromatography, site-directed
mutagenesis, accessible surface area calculations, and the measurement of physical
properties).
depending on the method used, hydrophobicity is expressed as a different experimental observable. In partitioning approaches, one uses the free energy of transfer
between phases, while in chromatographic studies, hydrophobicity is related to retention factors. there have also been attempts to quantify this property as a function
of some physical property, e.g. surface tension, transition temperature, solvation
energy, and partial molar heat capacity [41].
table 5.2 presents amino acids ranked according to different hydrophobicity
scales. Levitt’s scale is based on the solubility of single amino acids in water and
ethanol and the derived free energy of transfer between the two phases [42]. Parker
et al. used for his hydrophobicity scale the hPLC parameters of some synthetic oligopeptides where two residues were sequentially substituted with different amino
acids [43]. Radzicka and Wolfenden determined the distribution coefficients of solutes related to amino acid side chains (e.g. toluene for phenylalanine, methanol for
serine, isobutene for leucine, etc.) in water and wet cyclohexane [44]. Kyte and
doolittle combined various experimental observations in the literature [45]; their
hydropathy scale was based on water vapour transfer free energies and the interiorexterior distribution of amino acid side chains determined by Chothia [46]. Janin
[47] and Rose et al. [48] examine the tendency of amino acid side chains to be found
inside (hydrophobicity) or outside (hydrophilicity) some proteins with known 3-d
structures. one of the newest and most interesting scales is the one proposed by
moret and Zebende [49]. they used variations in the accessible surface area determined for amino acids in short protein fragments randomly extracted from PdB
proteins as a measure of hydrophobicity.
the scales based on different assumptions differ, as shown in table 5.2. Particular compounds are not ranked in the same order according to different scales.
In many cases, there is no correlation between scales, whether theoretical or experimental, although there are some regularities. For example, charged amino
acids are generally more polar [49]. It is very important to stress that most measurements have been performed on peptides, and only rarely on single amino
acids (or their derivatives). this is why the length, structure, and kind of peptide
used, the neighbourhood of the studied amino acid, etc. substantially influence the
obtained values. Another non-trivial issue is the selection of proper experimental
91
after the introduction of a non-polar compound which cannot form hydrogen bonds
and thus replaces the disrupted ones.
Apart from the qualitative description of amino acids as hydrophobic or hydrophilic, there have been numerous attempts at quantitatively characterising the hydrophobicity of amino acids by means of both experimental and theoretical methods. An exhaustive review on different scales is provided by Biswas et al. [41]. the
derived hydrophobicity scales were divided by the authors according to the type of
studied solutes (simple amino acids, side chain analogues, their derivatives, or peptides) and the method used (partitioning experiments, chromatography, site-directed
mutagenesis, accessible surface area calculations, and the measurement of physical
properties).
depending on the method used, hydrophobicity is expressed as a different experimental observable. In partitioning approaches, one uses the free energy of transfer
between phases, while in chromatographic studies, hydrophobicity is related to retention factors. there have also been attempts to quantify this property as a function
of some physical property, e.g. surface tension, transition temperature, solvation
energy, and partial molar heat capacity [41].
table 5.2 presents amino acids ranked according to different hydrophobicity
scales. Levitt’s scale is based on the solubility of single amino acids in water and
ethanol and the derived free energy of transfer between the two phases [42]. Parker
et al. used for his hydrophobicity scale the hPLC parameters of some synthetic oligopeptides where two residues were sequentially substituted with different amino
acids [43]. Radzicka and Wolfenden determined the distribution coefficients of solutes related to amino acid side chains (e.g. toluene for phenylalanine, methanol for
serine, isobutene for leucine, etc.) in water and wet cyclohexane [44]. Kyte and
doolittle combined various experimental observations in the literature [45]; their
hydropathy scale was based on water vapour transfer free energies and the interiorexterior distribution of amino acid side chains determined by Chothia [46]. Janin
[47] and Rose et al. [48] examine the tendency of amino acid side chains to be found
inside (hydrophobicity) or outside (hydrophilicity) some proteins with known 3-d
structures. one of the newest and most interesting scales is the one proposed by
moret and Zebende [49]. they used variations in the accessible surface area determined for amino acids in short protein fragments randomly extracted from PdB
proteins as a measure of hydrophobicity.
the scales based on different assumptions differ, as shown in table 5.2. Particular compounds are not ranked in the same order according to different scales.
In many cases, there is no correlation between scales, whether theoretical or experimental, although there are some regularities. For example, charged amino
acids are generally more polar [49]. It is very important to stress that most measurements have been performed on peptides, and only rarely on single amino
acids (or their derivatives). this is why the length, structure, and kind of peptide
used, the neighbourhood of the studied amino acid, etc. substantially influence the
obtained values. Another non-trivial issue is the selection of proper experimental