Alpha/Beta Structures. Beta strands. 3 type of Alpha/Beta structure exists Barrels Open sheets Horseshoe (I don’t believe we covered this)
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They are all built up from beta-alpha-beta motif and are all virtually right handed (this is an empirical rule that almost always applies, although no convincing explanation has been found)
In alpha/beta barrels the side chains of the alpha helices are packed against the h-phobic side chains of the B-sheet and this packing interaction between the alpha and beta are dominated by branched h-phobic residues (V, I, L)
The alpha helices are anti-parallel to the adjacent B-strands
A/B Barrels Cont…
In a given sequence of beta strand, it is known that h-phobic residues and h-philic residues alternate, thus the h-phobic residues face inward of the barrel forming the h-phobic core
Also, the formation of the interior of the barrel is not limited to h-phobic residues, because the top and bottom surface can comprise of polar/charged group as the polar end will be in contact with the solvent whereas the h-phobic parts of the side chain will interact with the core of the protein
Alpha/Beta Barrel Cont…
In these barrels the active site is commonly found in very similar positions, usually situated at the bottom of the funnel-shaped pocket created by eight loops that connect the carboxy end of the beta-strand to the amino end of the alpha helices.
Alpha/Beta twisted Open-Sheet
Open twisted parallel or mixed B-sheet with alpha helices on both sides of the B-sheet.
For an active site in the alpha/beta open-sheet, the active site is present at the carboxy edge of the B-sheet
Functional residues are provided by the loop regions that connect the carboxy end of the B-strands with the amino end of the alpha helices
These active sites are a result of the formation of crevices which occur when there are two adjacent connections that are on opposite sides of the Beta-Sheet