Beta turns are common found motifs in proteins. In general, they assume a coil-like conformation. Preliminary analysis using Profunc revealed that the extreme c-terminal region (of a protein we are studying) containing beta turns. Also other studies indicate that this region is very likely to undergo coil-helix transformation during protein-protein interactions. Is such kind of conformational change involving beta turn (or any other kind of turns) possible or is this observation due to inaccuracy of the tool Profunc?
By about ten years the world of proteins is profoundly changed. Before we had only the globular proteins, now there are also intrinsically disordered proteins (IDP). They are more than 50% of the human genome and play the most important pathophysiological roles, so it is not possible to disregard it. The programs of the existing structural prediction, usually do not take into account in their predictions of their presence, so very often these predictions leave the time they find.
Turns, sheets and helices are structure fixed in time, while IDPs can have different organizations also as compact globule or coil, but very flexible and fluctuating (see Pappu’s paper in the literature). Beta sheets have turns called beta turns, these consist of three amino acids in a hairpin turn with H-bonding; alpha helices have often proline residues at turns. Beta sheets are usually twisted into what are called barrel structures because they look like staves in barrel. Therefore, the turns cannot spontaneously change their organization.
Coils are not characteristic structures of globular proteins. In a globular protein with structural organization fixed in time we can find also segment intrinsically disordered. How long are you coils? If they are more than 8 – 10 residues you must analyze them, also in terms of IDPs. You can visually inspect this segment. If there are many small, charged, polar residues e few hydrophobics, you can reasonably suspect the presence of IDP. Another check is the net charge of your protein, or of your segment or coil or loop, at pH 7. If the net charge at pH 7 is not around zero or non-more than ± 1, characteristic of week polyampholytes (globular proteins are week polyampholytes), you have a polyelectrolyte, i.e., an IDP or IDP segment.
Without these preventive controls it is difficult to give reasonable answers to your question because globular and intrinsically disordered proteins behave in different way.
This is a very helpful explanation. The coil is is disordered in nature, and is assumed to attain a helical conformation during PPIs. There was a confusion based on the Profunc results.
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