Biochemistry The alpha helix is a regular coiled configurati

Biochemistry: The alpha helix is a regular coiled configuration of a polypeptide chain with 3.6 amino acid residues per helical turn, spanning an axial distance of 0.56 nm. Each peptide nitrogen H-bonds to a peptide carbonyl oxygen four residues down the chain. The H-bonds are maximally stable because the helix allows for linear alignment of the H-bonding components. The side chains of the amino acids are located on the outside, pointing away from the helix. The alpha helix is flexible and elastic, but remarkably stable.

The following amino acid residues/arrangements are rare in alpha helices:

proline

two or more consecutive residues with side chains that branch at the beta-carbon

two or more consecutive residues with ionized side chains of like charge

Beta sheets are favored when there are repeating sequences composed of amino acid residues with compact side chains. The side chains are perpendicular to the plane of the sheet, with H-bonds between the peptide units of neighboring (parallel or antiparallel) chains. The beta sheet is flexible but inelastic.

Given the following sequence, write down partial sequences where you might find

alpha helices:

beta sheets:

random coil:

disulfide bond pairs:

Every fifth residue is bold, there are 67 residues. Each amino acid residue is denoted by its number – eg Tyr 7, Pro 66, etc,

ile-cys-pro-val-gln-his-tyr-thr-ala-phe-cys-trp-leu-met-pro-gly-gly-pro-phe-gly-ala-gly- ala-gly-ser-gly-ala-gly-ile-glu-asn-glu-gln-asn-met-ala-his-phe-trp-tyr-lys-gly-lys-lys-arg-arg-cys-glu-ile-gly-ser-gly-ser-gly-ala-gly-ser-gly-arg-arg-lys-gly-arg-gly-arg-pro-pro

Solution

Answer:

Alpha Helices:

1) glu 32 - gln 33 - asn 34 - met 35 - ala 36 - his 37

Beta sheets:

1) thr 8 - ala 9 - phe 10 - cys 11 - trp 12 - leu 13

2) phe 38 - trp 39 - tyr 40

3) arg 45 - arg 46 - cys 47 - glu 48 - ile 49

Random Coil:

1) pro 3 - val 4 - gln 5 - his 6 - tyr 7

2) met 14 - pro 15 - gly 16 - gly 17 - pro 18 - phe 19 - gly 20 - ala 21 - gly 22 - ala 23 - gly 24 - ser 25 - gly 26 - ala 27 -gly 28 - ile 29 - glu 30 - asn 31

3) lys 41 - gly 42 - lys 43 - lys 44

4) gly 50 - ser 51 - gly 52 - ser 53 - gly 54 - ala 55 - gly 56 - ser 57 - gly 58 - arg 59 - arg 60 - lys 61 - gly 62 - arg 63 -gly 64 - arg 65 - pro 66 - pro 67

Disylfide bridges:

1) cys 2 - cys 11

2) cys 2 - cys 47

3) cys 11 - cys 47