Question

[1] What secondary structure would you predict the following peptides to adopt? Where would you expect to find each of these polypeptides?

GlyAlaGlySer GlyAlaGlyAlaGlyAlaGlyVal GlyAlaGlySer

GlyPrpHypGlyProHypGlyProHypGlyProHyp

DDRIKSWVAELKSE

please explain! thanks.

Answer 1

There are two secondary structure's in proteins

Alpha helices

1. All are right-handed

2. Each amino acid contributes to rise (pitch (p)– distance traveled to make 1 turn (.54nm)  rise (r) – distance between amino acid residues = .15nm/residue  n = residues per turn = 3.6  3.6 residues x .15nm/residue = .54nm pitch)

3. COOH of one residue H bonds to NH2 of aa 4 residues ahead (i + 4)

4. Side chains project to outside

5. Amino acid residues that interrupt alpha helical structure:  Branched (ie Val, Ile, Phe) amino acids in succession (because of space)  bulky (Trp, Tyr) amino acids in succession  Charged aa in succession PROTEINS – STRUCTURE AND FUNCTION (DR. TRAISH)  Prolyl residues (cyclic)

6. Ala, Cys, Met, Glu, Gln, His, Lys favor alpha helix

Beta sheets

1. Polypeptide strands of at least 5-10 amino acids lay adjacent and interact to form sheet

2. Can be parallel (N and N terminus together) or antiparallel (a bit more stable – H bond is at a 90° angle)

3. Sheet is perpendicular to axis

4. In alpha helix, peptides can still stretch; in beta sheet, they are already stretched (ex: silk)

5. In alpha helix, hydrogen bonds within same polypeptide; in beta, bonding between different polypeptides

6. Beta sheets can lie on top of each other – bound together by hydrophobic interactions

7. Val, Ile, Phe, Tyr, Trp, and Thr favor beta sheet structure iii. Gly, Ser, Asp, Asn, Pro, and Arg favor turns (don’t have to know about)

a) GlyPrpHypGlyProHypGlyProHypGlyProHyp

   Secondary structure: Collagen helix or type-2 helix (left handed). It consists of a triple helix made of the repetitious amino acid sequence glycine - X - Y, where X and Y are frequently proline or hydroxyproline.

Hence, you can find this type of peptide in collagen

b) GlyAlaGlySer GlyAlaGlyAlaGlyAlaGlyVal GlyAlaGlySer

Secondary structure: Due to presence opf Glycine repeat the peptide will not undergo alpha helix conformation; however such motifs can form beta pleated sheeta with antiparallel strands or form flexible coiled structures

The peptide represents a classic glycine rich repeat i.e. (Gly-X)_n; found in structural proteins in cell wall, RNA-binding proteins and Cytokeratin like proteins.

c) DDRIKSWVAELKSE

Structure: alpha helix (right handed) and beta pleated sheet

Not sure but may be present in proteins controlling cell signalling or gene expression due to the nature of amino acids present and looks mostly part of transmembrane protein (but not sure)

ACIDIC POLAR NEGATIVE       2 amino acids

BASIC POLAR POSITIVE           2 amino acids

NONPOLAR    NEUTRAL 6 amino acids