Modelling Analysis of Amino Acids Hydrophobicity

The aim of the research was to perform a structural modelling analysis on amino acids hydrophobicity in order to identify, characterize and quantify the relationship between the structure and the property. A sample of twenty essential amino acids (alanine, arginine, asparagine, aspartate, cysteine, glutamine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine) was investigated by using the Molecular Descriptors Family on the Structure-Activity/Property Relationship approach. The property of interest was the hydrophobic or hydrophilic character measured on twenty-four different scales. The information extracted from the amino acids structure was used in order to generate and to calculate the Molecular Descriptors Family. For each hydrophobicity scale the best performing monovariate model in terms of goodness-of-fit were collected and analyzed. The resulted models have been used in order to predict the hydrophobicity of a sample of eleven non standard amino acids (seleno-L-cysteine, pyrrolysine, lanthionine, 2aminoisobutyric acid, dehydroalanine, gamma-aminobutyric acid, ornithine, citrulline, homocysteine, hydroxyproline, and dopamine). All identified models were statistically significant (p < 0.0001). An internal validation approach was applied for analyzing the validity of the obtained models. The correlation coefficient calculated between the measured and estimated hydrophobicity varied from 0.6649 (hydrophobicity reported by Welling et al. 1985) to 0.9504 (hydrophobicity reported by Monera et al., 1995). The obtained results showed that the amino acids hydrophobicity is a property linear related with compounds structure. The amino acids hydrophobicity is strong related with atomic charge through geometry interaction.