Amino physico-chemical features

Schneider and others (Schneider et al., 1993) applied the perception approach to identifying cleavage sites in protein sequences. Again, a matrix approach was used, with 12 rows representing a sequence of 12 amino acid residues (one row per residue) and four columns representing physico-chemical features of each residue hydrophobicity, hydrophilicity, polarity and volume. The trained perceptron predicted cleavage sites correctly in 100% of test cases. 

Amino acids side chains differ in their physico-chemical features. For example, some like to be exposed to water, i.e., they are hydrophilic, while the hydrophobic amino acids tend to avoid exposure to water. Charge, size, or flexibility in the backbone are only some of the other examples of amino acid parameters. These parameters are usually measured on a numerical scale such that for every parameter there exists a table assigning a number to each amino acid. For the case of hydrophobicity two such scales have become famous. The first is due to Hopp and Woods [1] while the other is due to Kyte and Doolittle [2]. A large collection of amino acid parameters... 

In order to evaluate the influence of side-chains on the ability and on the specificity of binding to DNA of 9-Aminoacridines, some physico-chemical features of complexes derived from the interaction of DNA of different sources with 9-Aminoacridine and with N-9 alkyl (A), N-9-o)-hydroxyalkyl (B) and N-9-(jo-diethylaminoalkyl - 9 amino-acridines (C) have been examined. 

By means of the macromolecular graph, the peptide description is simplified, considering that (a) the physico-chemical properties of the amino acids are responsible for the 3D structure and the functionality of the peptide and (b) all amino acids share common structural features, including an a-carbon to which an amino group, a carboxyl group, and a variable side chain are... 

This Chapter focuses on analyses that can be performed based solely on the primary sequence of a protein. Several rationales can be applied. Physico-chemical characteristics of individual amino acids are one basis for predictions of gross structural features. For example, particular repetitive patterns may suggest a coiled-coil structure while in general secondary structure can be predicted based on an a statistical analysis of the primary sequence. The definition of signals recognized by the cellular transport machinery allow the prediction of subcellular location. Although somewhat unsystematic such observations can provide valuable hints as to the structure and/or function of a protein. 

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