In: Biology
(a) Describe how secondary structural elements fold to produce
(i) The Rossmann fold
(ii) The four-helix-bundle motif
(b) Explain why proline is more often found at the ends of α-helices but not in the middle.
(a) the rossmann fold is one of the most common and widely distributed super secondary structure. Rossmann fold as a twisted linear beta-alpha repeats. Beta strands are hydrogen bonded forming a beta sheets. Rossman fold is proposed to be twice rearranged twisted sheet. The initial ,rearrangement to form a rossman fold is to place beta 4 next to beta 1 rather than next to beta 3. The second rearrangement to form rossman fold is to pair both beta7 and beta8 with an elongated beta 6. Rearrangements in the rossmann fold is necessary to prevent curvature into a horseshoe and barrel shapes. The more linear rossman sheet is maintained by changing the curvature and orientation of beta 1- beta3 relative to beta 4- beta 8.
(b) the four_ helix bundle motif occur in many structural content and in protein that are functionally diverse. The four helices may slay apart to generate a binding pockets for cofactor and metal ions or they may coil around each other to form a supercoil. The motif can be classified into individual folds on the basis of topological and geometrical properties. Many mutants of 4 helix bundle have been generated and the motif also been target denovo design studies. In 4 helix bundles protein the interfaces between the helices consist mostly of hydrophobic residue while polar side chains on exposed surface interact with the aqueous environment.
(b) proline is the only amino acid where the side chain is connected to the protein backbone twice, forming a five membered nitrogen containing ring. The highest preference of the proline at the beginning of alpha helices is due to the favored electrostatic and nonbonded energies between 2 residues preceding proline and the intrinsic stability of alpha helical conformation of the proline residue as well as no disturbances in the hydrogen bonds of alpha helices by proline.