Which proteins are water soluble
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A simple example: predictions about hydrophilic and hydrophobic areas
Water-soluble, globular proteins have a hydrophobic interior, which usually consists of only a few domains, while hydrophilic residues are oriented outwards towards the surrounding water. Most of the α-helices and β-sheet areas in such proteins are amphipathic, i.e. they have a hydrophobic side that is directed towards the inside of the protein and a hydrophilic side that faces outwards. Since loop areas that connect the secondary structural elements are also usually hydrophilic, areas of more than 10 hydrophobic amino acids in a row are rarely found in these proteins, and the inside of the protein is often not easy to identify.
The situation is different with transmembrane areas of integral membrane proteins. These areas do not consist exclusively of hydrophobic amino acids (charged side chains are often essential for function), but the transmembrane domain must have a minimum length of 19 to 20 amino acids in order to be able to span a membrane. Which amino acids are typical for transmembrane domains? This question is not easy to answer: although hydrophobic amino acids such as Val, Met and Leu can certainly be found in such areas and charged amino acids such as Asp and Arg are not, but what about Ala, Ser or His?
Different tables show the hydrophobicity of each amino acid (e.g. measured by its solubility in different solvents or based on theoretical calculations). From Kyte and Doolittle and Engelmann et al. the tables listed here, which are often used for hydrophobicity calculations, come from:
- Tab. 1
- Hydrophobicity indices
|Kyte & Doolittle||2.8||1.9||4.5||3.8||4.2||2.5||-0.9||1.8||-0.7||-0.4||-0.8||-1.6||-1.3||-3.2||-3.5||-3.5||-3.5||-3.9||-3.5||-4.5|
|Engelmann et al.||3.7||3.4||3.1||2.8||2.6||2.0||1.9||1.6||1.2||1.0||0.6||-0.2||-0.7||-3.0||-4.1||-4.8||-8.2||-8.8||-9.2||-12.3|
|Garnier, J .; Osguthorpe, D. J .; Robson, B. (1978): Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. In: J. Mol. Biol.. 120 , 97-120|
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