The alpha-alpha corner


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Short loop regions connecting helices which are roughly perpendicular to one another are refered to as alpha-alpha-corners. Efimov has shown that the shortest alpha-alpha-corner has its first residue in the left-handed alpha-helical conformation and the next two residues in beta-strand conformations. This conformation can only be adopted when the two helices form a right-handed corner. Indeed, if the helices were linked to form a left-handed corner there would be steric hindrance. This may explain the scarcity of left-handed alpha-alpha corners in protein X-ray structures. Here is a coordinate file for RasMol.

The C-terminal residue of the first helix, which is in the left-handed alpha-helical conformation, must have a short side chain to avoid steric hindrance and is observed commonly to be glycine. The first residue of the second helix, which is in the beta-conformation, frequently has a small polar side chain such as Ser or Asp which can form hydrogen bonds with the free NH groups at the amino-terminal end of the second helix. The central residue of the alpha-alpha-corner is almost always hydrophobic as it is buried and interacts with other non-polar side chains buried where the ends of the two helices contact each other.


The loop regions connecting alpha-helical segments can have important functions. For example, in parvalbumin there is helix-turn-helix motif which appears three times in the structure. Two of these motifs are involved in binding calcium by virtue of carboxyl side chains and main chain carbonyl groups. This motif has been called the EF hand as one is located between the E and F helices of parvalbumin. It now appears to be a ubiquitous calcium binding motif present in several other calcium-sensing proteins such as calmodulin and troponin C.

EF hands are made up from a loop of around 12 residues which has polar and hydrophobic amino acids at conserved positions. These are crucial for ligating the metal ion and forming a stable hydrophobic core. Glycine is invariant at the sixth position in the loop for structural reasons. The calcium ion is octahedrally coordinated by carboxyl side chains, main chain groups and bound solvent. Here is another coordinate file file for RasMol.

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j.cooper 26/1/95