Question

H-bonding in secondary structures – what is the geometry

·      Β-turns – what causes these

·      Approx dimensions for an α helix and β-sheet? o   Locations of H Bonds in the 2D structures

·      CD spectra of α helix, β-sheet and random coil – How can specific rotation show something about protein structure?

Answer 1

The accepted (and most frequently observed) geometry for a hydrogen bond is a distance of less than 2.5 Å (1.9 Å) between hydrogen and the acceptor and a donor‐hydrogen‐acceptor angle of between 90° and 180° (160°).

Beta turns, also known as beta bends or tight turns, are a type of secondary structure. In a beta turn, a tight loop is formed  when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain. This hydrogen bond stabilizes the beta bend structure.Beta turns often promote the formation of antiparallel beta sheets.

The most stable conformations of polypeptide chains that maximize intrachain hydrogen‐bonding potential are α helices and β sheets.There are 3.6 residues/turn in an α-helix, which means that there is one residue every 100 degrees of rotation (360/3.6). Each residue is translated 1.5 Å along the helix axis, which gives a vertical distance of 5.4 Å between structurally equivalent atoms in a turn (pitch of a turn). The second major type of secondary structure in proteins is the β-sheet. β-sheets consist of several β-strands, stretched segments of the polypeptide chain kept together by a network of hydrogen bonds.