Co-inertia analysis of amino-acid physico-chemical properties and protein composition with the ADE package

• Published in: Bioinformatics Vol. 11; no. 3; pp. 321 - 329
• Main Authors: Thioulouse, J., Lobry, J.R.
• Format: Journal Article
• Language: English
• Published: Washington, DC Oxford University Press 01.06.1995; Oxford Oxford University Press (OUP)
• Subjects: Amino Acids - chemistry; Bacterial Proteins - chemistry; Biological and medical sciences; Chemical Phenomena; Chemistry, Physical; Data Interpretation, Statistical; Escherichia coli - chemistry; Evaluation Studies as Topic; Fundamental and applied biological sciences. Psychology; General aspects; Life Sciences; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Multivariate Analysis; Other; Proteins - chemistry; Software; Proteins; Data analysis; Molecular structure; Computerized processing; Chemical composition; Software; Algorithm; Implementation; Physicochemical properties; Aminoacid sequence; Microcomputer
• ISSN: 1367-4803; 0266-7061; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/11.3.321

A multivariate analysis method called co-inertia analysis was used to determine the main relationships between two data tables having identical rows. This method is available in the ADE multivariate analysis package for Macintosh micro-computers. It was applied to two data sets, one containing the amino-acid composition of 999 E. coli proteins, and the other the values of 402 physico-chemical properties for the 20 natural amino-acids. There were strong relationships between amino-acid physico-chemical properties and the composition of proteins. The first common factor was hydrophobicity; it is linked to the biological environment of proteins, either in the cytoplasm (or outside the cell), or in the nonpolar environment of the phospholipid bilayer of biological membranes. The second factor linked the expressivity of protein genes and the propensity of amino-acids to form alpha helix/beta sheets. The third factor showed that heavy, aromatic amino-acids tend to be avoided, except when they are needed for structural or functional reasons. These results are discussed in terms of selective pressure acting on amino-acid composition of proteins.