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From conformational analysis to secondary structure prediction
While the energetically favorable conformations of a dipeptide can still be calculated relatively easily, the number of possibilities increases exponentially with each newly added amino acid. Such a method is therefore completely unsuitable for peptides and proteins, since the computational effort would be far too high. Nevertheless, certain predictions about the conformation of proteins can be made on the basis of relatively simple principles.
Many proteins contain a significant proportion of secondary structural elements. One possible way to elucidate the 3D structure is therefore to first determine which structural elements a protein contains and then to put them together. Three types of structural elements are relevant:
- and more or less disordered areas (randomcoil)
In some approaches the β-loop (β-turn) considered. Which amino acids occur preferentially in one of these secondary structures can be calculated with the Chou-Fasman algorithm. By analyzing 15 proteins whose X-ray structures were known, these scientists derived a probability for each amino acid that this amino acid would occur in a helix or a leaflet. There are many other methods of predicting secondary structure elements (see on the EXPASY server under Topography Prediction), but all of them are more or less precise and do not achieve a hit rate of more than 60-65% (33% would be random if all three structural elements occur equally often). This low success rate results from the fact that interactions of amino acids that are far apart in the primary structure but are in close proximity in the 3-D arrangement of a molecule are not taken into account.