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The linear sequence of amino acids (primary structure) is able to coil and fold upon itself, resulting in 3D formations such as α-helices and β-sheets. These are held together by hydrogen bonding between amino acids. The term for these 3D formations is the secondary structure of the protein. Secondary structural features are held together by hydrogen bonds between an oxygen lone pair of one amino acid and the hydrogen attached to the nitrogen of another. In proteins, the hydrogen bonds are always between C=O and N-H groups. H-bond What makes the structural features different is the pattern of hydrogen bonds and how the amino acid chain is folded. Give a definition for a hydrogen bond. Nitrogen The alpha helix is a rod-like structure. The peptide main chain forms the inner part of the rod as shown in the figure on the left (amino acid R-groups are not shown for simplicity). H-bond Oxygen The coil is held together by hydrogen bonds between a carbonyl oxygen and the hydrogen attached to nitrogen four residues ahead. If you look down the helix from the top, you can see it is like a tube. The amino acid side chains extend out from the rod, as shown here. In a β-sheet, the polypeptide chain is almost fully extended to form a β-strand. β-strands are folded so that sections of the chain lie alongside each other. β-sheets are stabilised by hydrogen bonding between strands, in the same way as shown previously for the αhelix. Strands can run in the same direction (parallel sheet) or the opposite direction (anti-parallel sheet). H-bond In 3D images of proteins, β-sheets are often represented by long flat arrows, pointing in the direction the strand is running. This makes it easy to pick out parallel or antiparallel sheets. β-turns are regular structures which allow the βstrands to reverse direction. Each β-turn is made up of 4 amino acid residues. The C=O of residue 1 hydrogen bonds with the N-H of residue 3. H-bond β-turn These 3D images show how the βturn allows two βsheets to run in opposite directions. Notice the shape of the turn, which is common in many protein structures. Produced by Lucy Jakubecz at Newcastle University as part of an MChem project.