Question

briefly describe how the secondary structures called a alpha-helical and beta-sheet are different in their folding

Answer 1

Ans. α- Helix: The presence of L-amino acids in proteins favors thermodynamically stable right-handed helix in living organisms. The amino acid residues appear to turn around and upward along an imaginary cylinder. Comparing to a curled right hand with thumb upward, the direction of curling of fingers indicate the direction of turning the peptide chain and the projection of thumb represent the direction of rise of the helix. It has a pitch (the vertical distance taken to complete a turn i.e. 360⁰) of 0.54 nm (5.4 Å). Each complete turn consists of 3.6 residues. The peptide backbone takes the shape of helical strand. The side chains project downward minimizing stearic hindrance and maximizing the feasibility of H-bond formation. The O-atom of carbonyl (-C=O) group of a peptide bond forms H-bond with H-atom of imine group (–NH) group of the fourth peptide bond towards C terminal. H-bonds stabilize helix. Van der Waal’s forces and hydrophobic interactions also aid in its stability. Proline is generally present at the first position in turns.

Presence of P and G residues helps the peptide chain take bends and greater extent of rotations (dihedral angles) around the peptide bonds. These kinks destabilize the a-helix. However, these conditions favor the formation of b-chain (two or more b-chains associated together are called b-sheet).

β- Sheet: When viewed from edge, the peptide chain appears to be in zig-zag or pleated (folded) form. The side chains of adjacent amino acid residues are in trans- form to minimize stearic hindrance. The carbonyl (-C=O) of a peptide bond in one peptide chain form H-bond with imine (-NH) group of adjacent peptide bond of the other peptide chain. These inter chain H-bonds stabilize beta sheets/ beta pleated sheets. In a parallel beta sheet, the amino terminal (or carboxyl terminal) of the peptide chain lie at the same side. In antiparallel b-sheet, the amino terminal (or carboxyl terminal) of two peptide chains lie in opposite direction. These sheets can be stretched lengthwise, so predominantly present in proteins involved in movement, for example- actin, myosin, and fibroin protein of silk and spider web.

In a protein two or more secondary structures may be linked together by 3-4 residues long peptide chain. These short peptide chains are called bend (turn). A turn joining two β sheets is called β turn. Proline, glycine, serine and threonine are most frequently present in bends.