Intrinsically disordered proteins (IDPs) are proteins that lack a well-defined 3D structure. Their spatial arrangement is constantly changing, and we can only describe them (at a given temperature) as a set of distinct conformational shapes with very similar conformational energies. Apart from IDPs, intrinsically disordered regions (IDRs) are also very common. Because of their functional properties, IDPs are involved in many cellular processes such as signalization and regulation. The most common structural element that is found in IDPs is the α-helix.
In this work, we focus on AGADIR, which is an algorithm for predicting α-helical content in monomeric peptides based on amino acid sequence. We gathered experimental data obtained with CD spectroscopy of peptides from IDPs with a significant helix propensity and compared the values with the ones determined by AGADIR. In addition, we also ran an analysis of amino acid sequences of the peptides used and the possible interactions between functional groups. As a reference set of data, we used seven alanine-based peptides.
From the obtained data, we can see that AGADIR underestimates the α-helical content of peptides from IDPs, but on the other hand predicts the helical content of alanine-based peptides with a much higher degree of accuracy. The results of the sequence analysis suggest that AGADIR underscores the positive interactions between amino acid functional groups, responsible for stabilizing the α-helix.
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