Electrical Seminar Abstract And Report 7

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Introduction to Bioinformatics

Secondary structure prediction
• History and Context
• Chou and Fasman
• Garnier-Osguthorpe-Robson
• Comparison of Methods
• Newer Approaches


Protein Sequence Analysis

Secondary Structure Prediction
The primary structure of proteins is the sequance of amino acids from which it is
constructed.
There are 20 naturally occuring amino acids. All amino acids have a common chemical
structure: a tetrahedral (sp3) carbon atom (C_alpha) to which four asymmetric groups are
connected: an amino group (NH2), a carboxy group (COOH), a H atom and another chemical
group (denoted by R) which varies from one amino acid to another. Two amino acids connect
via a peptide bond to form a poly-peptide structure - the protein. The peptide bond is
formed by a condensation reaction between the amino and carboxy group, which releases a
water molecule and forms a covalent bond between them. Due to a partial double-bond
character, the peptide unit NH-CO is planar and is always in a trans configuration. The
peptide unit together with the C_alpha are termed back-bone and the residue R is termed
side-chain , and is different from one amino acid to another. As the central C_alpha atom
has four different groups connected to it, it is chiral; all naturally occuring amino
acids are L amino acids.

Protein Sequence Analysis

Secondary Structure Prediction
Each amino acid contains an "amine" group
(NH3) and a "carboxy" group (COOH) (shown
in black in the diagram).
The amino acids vary in their side chains
(indicated in blue in the diagram).
The eight amino acids in the orange area
are nonpolar and hydrophobic.
The other amino acids are polar and
hydrophilic ("water loving").
The two amino acids in the magenta box are
acidic ("carboxy" group in the side chain).
The three amino acids in the light blue box
are basic ("amine" group in the side
chain).

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