ALL questions must be answered Problem Set Questions: 1) Provide two reasons why

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ALL questions must be answered
Problem Set Questions: 1) Provide two reasons why anti-parallel -sheets are more common than parallel -sheets. Fill in the blanks. The distance between Ca's on neighbouring strands in a - sheet is about 2) Å. 3) Fill in the blanks. In a type II -turn, residue"i" hydrogen bonds with residue 1 + 4) why are type II -turns often found on the surface of proteins? 5) why are proline residues disfavoured in both a-helices and -sheets? Why do secondary structure prediction algorithms tend to have problems correctly predicting secondary structure in regions where the secondary structure changes (ie, boundaries between a-helices and -sheets)? 6)

Explanation / Answer

1)

The major reason that antiparallel -stranded protein structures are more common than parallel -stranded structures is due to:

i) have weaker hydrogen bonds laterally between adjacent strands.

ii) The side chains of the amino acids alternate above and below the sheet.

iii) hydrogen bonds are formed between the amine and carbonyl groups across strands.

iv) The amino acids are more extended than in helices, with 3.5 Å between adjacent residues.

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