Characterization of the amino acid contribution to the folding degree of proteins.
The folding degree index (Estrada, Bioinformatics 2002;18:697-704) is extended to account for the contribution of amino acids to folding. First, the mathematical formalism for extending the folding degree index is presented. Then, the amino acid contributions to folding degree of several proteins are used to analyze its relation to secondary structure. The possibilities of using these contributions in helping or checking the assignation of secondary structure to amino acids are also introduced. The influence of external factors to the amino acids contribution to folding degree is studied through the temperature effect on ribonuclease A. Finally, the analysis of 3D protein similarity through the use of amino acid contributions to folding degree is studied by selecting a series of lysozymes. These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach.
Estrada
Ernesto
E
Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Beds, and RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Spain. estrada66@yahoo.com
D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism*; D000818:Animals; D030562:Databases, Protein; D008956:Models, Chemical; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012259:Ribonuclease, Pancreatic / Q000737:chemistry / Q000378:metabolism; D013045:Species Specificity; D013696:Temperature
D000596:Amino Acids; D011506:Proteins; D012259:Ribonuclease, Pancreatic; D009113:Muramidase