Structure and Function of Proteins 2010
Exercise 5: Prediction of Secondary Structure

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Introduction: Prediction of protein structure step by step

We have learned from the analysis of the globin family (Exercise 4) that the structure of globins is conserved throughout evolution, even though the sequence can show some variance.
The multiple alignment has shown us that the secondary structure elements (i.e. helices) are conserved, while the loops contain gaps.
This has led us to conclude that conservation of the secondary structure is required to maintain the globin structure.

This may suggest that the prediction of protein structure could be significantly simplified by dividing the prediction into distinct, subsequent steps:

According to this simplified model:

• In a first step, the secondary structure is predicted based on the primary structure, i.e. the sequence.
• The secondary structure elements are then arranged to produce the tertiary structure, i.e. the structure of a protein chain.
• For molecules which are composed of different subunits, the protein chains are arranged to form the quaternary structure, i.e. the oligomer.

Is this simplified approach justified ?

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