Analysis of Protein Three-Dimension Structure Using Amino Acids Depths |
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Authors: | Shiyi Shen Gang Hu Jack A Tuszynski |
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Institution: | (1) School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China;(2) Cross Cancer Institute, 11560 University Avenue, T6G 1Z2 Edmonton, AB, Canada |
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Abstract: | The issue of amino acid depth in proteins gives important insights to our understanding of protein’s three-dimensional structure.
There has already been much research done in mathematical and statistical sciences regarding the general definitions, properties
and algorithms describing the particle depth of spatially extended systems. We constructed a method of calculating the amino
acids depths and applied it to a set of 527 protein structures. We propose the introduction of amino acid depth tendency factors
for three-dimensional structures of proteins. The depth tendency factors relate not only to the hydrophobicity indices but
also to the electrostatic charge. We found a relationship between the protein size and the number of residues using the distance
between the deepest residue and surface residues. We made a prediction regarding the number of residues on the surface of
a protein, the deepest amino acid, and the average depth, all of which are fitted well to a linear functional relationship
with the length of the protein. Finally, we have predicted the depths of multiple peptides in protein’s three-dimension structure.
Electronic supplementary material The online version of this article () contains supplementary material, which is available to authorized users. |
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Keywords: | Statistics depth depth tendency factor protein depth indexes protein size |
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