Biomedical Engineering Reference
In-Depth Information
Chapter 1
Complete and Exact Peptide Sequence Analysis
Based on Propositional Logic
Renato Bruni
Abstract
Peptides are the short polymeric molecules constituting all the proteins.
They are formed by the linking of amino acids, and the determination of the amino
acid sequence of a peptide is a fundamental issue in many areas of chemistry,
medicine and biology. Nowadays, the prevalent approach to this problem consists
in using a mass spectrometry analysis. This gives information about the molecular
weight of the full peptidic molecule and of its fragments. Such information should
be used in order to find the sequence, but this constitutes, in the general case, a dif-
ficult mathematical problem. After a brief overview of the approaches proposed in
literature, and of their features and limits, the chapter describes in detail a promising
one based on propositional logic. Differently from the others, this approach can be
proved to be complete and exact.
1.1
Introduction
Peptides are short polymeric molecules formed by the linking of components called
amino acids
by means of covalent bonds called
peptide bonds
, in order to form a
chain
. Proteins are polypeptide chains; they are formed by a similar linking of amino
acids, but the chain is generally longer. There are several different conventions to
determine this distinction, see e.g. [
4
,
32
].
The determination of the
sequence
of amino acids forming a peptide or a pro-
tein is one of the most important and frequent issues in many areas of chemistry,
medicine and biology, as well as in several other applicative fields. In the case
of peptides, this is often called de novo sequencing, whereas in the case of pro-
tein, this is often called determination of the primary structure. However, proteins
are generally too extended for performing an accurate sequence analysis on the
whole chain in a single step. Therefore, a protein molecule is usually divided into
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