Secondary Protein Structure. What to Know. You will only be tested on what is discussed in class Pay particular attention to topics that are stressed or mentioned several times Most important are the general principles, not details that require memorization
You will only be tested on what is discussed in class
Pay particular attention to topics that are stressed or mentioned several times
Most important are the general principles, not details that require memorization
All these are local structures that are stabilized by hydrogen bonds
Many of the possible conformations about an α-carbon between two peptide planes are forbidden because of steric crowding. Several noteworthy examples are shown here.
Ramachandran diagram showing the sterically reasonable values of the angles φ & ψ.
Shaded regions indicate particularly favorable values of these angles.
Dots in purple indicate actual angles measured for 1000 residues (excluding glycine, for which a wider range of angles is permitted) in eight proteins.
A hydrogen bond between a a backbone C=O and a backbone N-H in an acetylcholine binding protein of a snail, Lymnaea stagnalis.
Schematic drawing of a hydrogen bond between a backbone C=O and a backbone N-H.
Four different representations of the α-helix
First proposed by Linus Pauling and Robert Corey in 1951
A ubiquitous component of proteins, stabilized by H bonds
frequently occurs as a single turn transition between the end of an a-helix and the next portion of the polypeptide chain
comparatively wide and flat conformation results in axial hole too small to admit H2O yet too wide to allow van der Waals associations across the helix axis
Four N-H groups at the N-terminal end of an α-helix and four C=O groups at the C-terminal end lack partners for H-bond formation.
An amphiphilic helixin flavodoxin:
A nonpolar helix incitrate synthase:
A polar helixin calmodulin:
3.3Ao for parallel strands
An antiparallel β-pleated sheet. R groups project alternately above and below the plane of the sheet. Sheet structure is derived from the tetrahedral placement of substituents on the α carbon atoms. This is the more stable form of a β-sheet.
Arrangement of hydrogen bonds in (a) parallel and (b) antiparallel -pleated sheets.
Parallel sheets: Large; hydrophobic on both sides of sheet; interior of globular proteins.
Antiparallel sheets: 2-3 strands; amphipathic allowing good boundaries with aqueous surroundings.
The structures of two kinds of -turns (also called tight turns or -bends). Proline and glycine are frequently situated in positions 2 and 3, respectively.
Silk fibroin consists of a unique stacked array of b-sheets. The primary structure of fibroin molecules consists of long stretches of alternating glycine and alanine or serine residues.
When the sheets stack, the more bulky alanine and serine residues on one side of a sheet interdigitate with similar residues on an adjoining sheet. Glycinehydrogens on the alternating faces interdigitate in a similar manner, but with a smaller intersheet spacing.