VCD spectroscopic and molecular dynamics analysis of the Trp-cage miniprotein TC5b

TC5b is a 20 residue polypeptide notable for its compact tertiary structure, a rarity for a short peptide. This structure is due to the "Trp-cage" motif, an association of aromatic, Pro, and Gly residues. The structure of TC5b has been fully characterized by NMR and electronic circular dichroism (ECD) studies, but has never been studied with vibrational circular dichroism (VCD) spectroscopy, which may reveal finer structure. In this study, we examine the VCD spectra of TC5b to characterize the spectroscopic signature of the peptide and its comprising structural elements. TC5b exhibited a negative-positive-negative triplet which is associated with alpha-helical structure in deuterated solvents but also signs of a polyproline II (PPII) helix in the amide I' region. Detection of this element was complicated by the aforementioned triplet form, as well as by an upfrequency shift in PPII helical elements due to the use of the deuterated organic solvents DMSO-d(6) and TFE-d(1). Nevertheless, while ECD spectra showed only alpha-helical structure for TC5b, VCD spectroscopy revealed a more complex structure which was in agreement with NMR results. VCD spectroscopy also showed a rapid conformational change of the peptide at temperatures above 35 degrees C in D(2)O and in aqueous solvent with greater than 75% DMSO-d(6) content. Molecular dynamics (MD) simulations to investigate this latter effect of DMSO-d(6) on TC5b were conducted in DMSO and 50% (v/v) DMSO in H(2)O. In DMSO unfolding of the peptide was rapid while in 50% (v/v) DMSO in H(2)O the unfolding was more gradual.