Alpha/Beta Structures

1. Alpha/Beta Structures

2. Beta strands • 3 type of Alpha/Beta structure exists • Barrels • Open sheets • Horseshoe (I don’t believe we covered this) • 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)

3. Alpha/Beta Barrels • 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

4. 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

5. 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.

6. 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

7. Crevices • 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