| The three-dimensional shape of proteins is determined by a complex network of forces specific to the amino acid sequence. In order to study these forces separately, excised portions of the protein can sometimes be designed to fold independently. These small peptide models are amino acid specificity to local protein structure. Herein, the study of alpha helices is presented using the Trp-cage. This 20-residue peptide is characterized by an N-terminal alpha helix and a hydrophobic collapse centered on a tryptophan indole ring. Several key interactions of the Trp-cage were explored, including the essential long-rage interaction between Tyr3 and Pro19. The importance of this interaction prompted the design of the cyclic Trp-cage, which was found to have a very high melting temperature (Tm ∼ 98°C). The Trp-cage was then applied to studying alpha helices. The N-terminal helix was extended beyond possible interactions with the C-terminal part, and systematic mutations are made to quantitatively determine the propensity of amino acids within the helix. Using this methodology, the Lifson-Roig propagation value of alanine was determined (WAla = 1.54) as well as for lysine (WLys = 0.79). This definitively proves that alanine is unique in its propensity to form helices. Other studies using the extended Trp-cage were able to quantitate for the first time the YxxxL interaction in a helices as well as the cation-pi interaction of KxxxY and the hydrophobic interaction of YxxxQ. The Trp-cage helix can also be used to study carbon-13 chemical shift differences between exposed and sequestered carbonyls in a helix. Characterizing the effect of temperature on these chemical shifts could be applied to similar situations in proteins, which would allow for the use of isotopically labeled carbonyls in protein contexts. |
