Proteins: Structure, Amino Acids, and Machine Learning

Proteins
Proteins are polymers of amino acids [1]. In nature, 20 amino acids exist that arrange in
different linear combinations through condensation by formation of a peptide bond to give
rise to short sequences known as peptides. These peptides through polymerization and
formation of covalent bonds ultimately form proteins. In a cell, proteins form structural
components, participate in signalling cascades, perform cell recognition and adhesion and
also function as biocatalysts in biochemical reactions [2].
Amino Acids
Amino acids are monomers of proteins [3]. In nature, so far, 20 amino acids are known to
exist that participate in various cellular reactions and in the formation of proteins. All amino
acids contain a central carbon atom (C) which has a valency of four [4]. It is linked to an
amino group (NH2) on one side and to a carboxyl group (COOH) on the other. The central
carbon, also known as the alpha (α) carbon is linked to a hydrogen atom (H) and to a side
chain (R). Among the different amino acids, the R group differs while the other three groups
remain conserved [5]. The general structure of an amino acid is shown below:
Figure 1: General structure of an amino acid
Since the amino group and the carboxyl group are linked to the central alpha carbon atom,
these amino acids are referred to as the α-amino acids. The 20 α -amino acids possess
different physical and chemical properties that are imparted to them by the virtue of the R
group. The twenty α-amino acids are classified into different groups, such as- polar, non-
polar, acidic, basic amino acids, on the basis of the differences in the R group [6]. Some
prominent examples from different subs-classes of amino acids are:

Amino Acid Structure
Non-polar amino acids
Glycine
Alanine
Valine
Methionine
Isoleucine
Leucine
Proline
Phenylalanine
Tryptophan

Polar amino acids
Cysteine
Asparagine
Glutamine
Tyrosine
Serine
Threonine
Acidic amino acids
Glutamic acid
Aspartic acid