(a) Use Pymol software (http://www.pymol.org) and draw RAD-16-IV and DAR-16-IV in a beta-sheet form and measure the fully stretched distance of the molecules (5).
(b) Indicate possible hydrogen bonds, electrostatic interactions, and hydrophobic-hydrophobic interactions at pH 7 when they form self-assembled structures (5).
(c) Explain possible effects on the resulting self-assembled structures when the pH changes to pH 2 and pH 12 (5).
The CD spectra below were taken from DAR-16-IV. Depending on the pH, DAR-16-IV exhibits the switching behavior between alpha helix and beta sheet structure.
Calculate the ratio of the protonated/deprotonated species ([HA]/[[A–]) for N-terminal amine, C-terminal acid, and acidic/basic side chain from Asp (D) and Arg (R) at physiological pH (pH 7.4) condition (5).
Explain why RAD-16-IV does not exhibit this switching behavior (5).
As discussed in class, RAD16-I is known to have a specific interaction with cells due to structural similarity of its backbone structure with the peptide RGD. Discuss the possibility that DAR-16-IV also has similar cell interaction properties (5).
Suppose that you synthesize the following peptide to design a novel peptide-based nanostructure.
Molecule 1: AAAAAAK
Use Pymol software (http://www.pymol.org) to draw an alpha helix and a beta sheet conformation of Molecule 1. Estimate the surfactant number (surfactant packing parameter) and predict the self-assembled structure Molecule 1 might adopt in each conformation (5).
Draw a schematic diagram of the self-assembled structures both in alpha helix form and beta-sheet form and indicate all possible weak interactions in the resulting structures (5).
At pH, 2, 7 and 12, indicate the possible charge states in the beta-sheet conformation of Molecule 1 and discuss how they affect the self-assembled structures. Explain the effect of ionic strength on the self-assembly of these structures (10).
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