50 years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification

BACKGROUND: Physicochemical properties are frequently analyzed to characterize protein-sequences of known and unknown function. Especially the hydrophobicity of amino acids is often used for structural prediction or for the detection of membrane associated or embedded ß-sheets and α-helices. For this purpose many scales classifying amino acids according to their physicochemical properties have been defined over the past decades. In parallel, several hydrophobicity parameters have been defined for calculation of peptide properties. We analyzed the performance of separating sequence pools using 98 hydrophobicity scales and five different hydrophobicity parameters, namely the overall hydrophobicity, the hydrophobic moment for detection of the α-helical and ß-sheet membrane segments, the alternating hydrophobicity and the exact ß-strand score. RESULTS: Most of the scales are capable of discriminating between transmembrane α-helices and transmembrane ß-sheets, but assignment of peptides to pools of soluble peptides of different secondary structures is not achieved at the same quality. The separation capacity as measure of the discrimination between different structural elements is best by using the five different hydrophobicity parameters, but addition of the alternating hydrophobicity does not provide a large benefit. An in silico evolutionary approach shows that scales have limitation in separation capacity with a maximal threshold of 0.6 in general. We observed that scales derived from the evolutionary approach performed best in separating the different peptide pools when values for arginine and tyrosine were largely distinct from the value of glutamate. Finally, the separation of secondary structure pools via hydrophobicity can be supported by specific detectable patterns of four amino acids. CONCLUSION: It could be assumed that the quality of separation capacity of a certain scale depends on the spacing of the hydrophobicity value of certain amino acids. Irrespective of the wealth of hydrophobicity scales a scale separating all different kinds of secondary structures or between soluble and transmembrane peptides does not exist reflecting that properties other than hydrophobicity affect secondary structure formation as well. Nevertheless, application of hydrophobicity scales allows distinguishing between peptides with transmembrane α-helices and ß-sheets. Furthermore, the overall separation capacity score of 0.6 using different hydrophobicity parameters could be assisted by pattern search on the protein sequence level for specific peptides with a length of four amino acids.

Amino acid pattern in polytrauma patients: Non-sepsis patients.

Some studies of the protein metabolism in severely injured patients with sepsis are reported. Knowledge of changes in blood amino acid levels will improve patient management. A prospective study was performed in severely injured patients (ISS 20-40) admitted to ICU as trauma cases, at Siriraj Hospital between January 1993 and December 1994. Ten patients were involved : five non-sepsis patients and five sepsis patients. Blood samples were drawn for determining amino acids levels on the first day of injury, then 7 and day 14. Blood samples were also obtained from three normal non-trauma volunteers as the control group. After injury, amino acids levels increased, in most of the patients, especially serine and lysine which significantly increased, both in non-sepsis groups. Only the especially serine and lysine which significantly decreased in the non-sepsis group at day 14. The branched chain amino acids (valine, leucine, isoleucine) increases more than the aromatic amino acids (phenylalanine, tyrosine, tryptophan). Glutamic acid, for the functional maintenance of mucosal cells of the intestine, and arginine, the immune supporter, were found to have increased in the sepsis group.