Biomedical Engineering Reference
In-Depth Information
Chapter 3
Secondary Structure Classification of Isoform
Protein Markers in Oncology
Gregorio Patrizi, Claudio Cifarelli, Valentina Losacco, and Giacomo Patrizi
Abstract
The determination of the secondary structure of proteins can be consid-
ered a relevant procedure to characterise isoform protein markers for cancer and
other pathologies. Their recognition is modeled as a classification problem and
solved using a nonlinear complementarity problem restricted to binary variables.
The procedure will be tested on an available data sets of proteins to determine the
differences in the isoforms which affect the pathologies. Recognition accuracy is
attributable to the implementation of a nonlinear binary optimization problem and a
strict statistical methodology that does not require extraneous assumptions.
3.1
Introduction
Proteins assume a well-defined three-dimensional structure, which is determined
principally by their amino acid sequence. Per contra the structure of a protein deter-
mines its function and the sequence of amino acids which compose a given protein
determines its spatial relationship. Also in general, isoforms are different forms of
a protein that may be produced from small differences between alleles of a gene or
from the same gene by alternating splicing which differs in structure, but may also
be due to differences in their spatial characteristics, arising from small differences in
the amino acid chain, or other mechanisms not well defined [
6
,
20
,
28
]. There are 20
different amino acids which form proteins, and their combinations may be presented
in four levels of structures: the primary structure characterized by the sequence of
amino acids, a secondary structure in which their structure is distinguished by the
folding characteristics of the protein, classified by segments of the amino acids in-
dicated by ˛-helix, a helical type structure, ˇ-strand, a sheet-like structure, and a
residual class indicated as coil. Often the classification of segments is extended to
eight to ten classes, depending on requirements. The tertiary structure consists of
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