Solution structure, dimerization, and dynamics of a lipophylic alpha/3-10-helical, C-alpha-methylated peptide. Implications for folding of membrane proteins

The solution structure and the dimerization behavior of the lipophilic, highly C-alpha-methylated model peptide, mBrBz-Iva-Val-Iva-(alphaMe)Val-(alphaMe)Phe-(alphaMe)Val-Iva-NHMe, was studied by NMR spectroscopy and molecular dynamics simulations. The conformational analysis resulted in a right-handed 3(10)/alpha-helical equilibrium fast on the NMR time scale with a slight preference for the alpha-helical conformation. The NOESY spectrum showed intermolecular NOEs due to an aggregation of the heptapeptide. In addition, temperature-dependent diffusion measurements were performed to calculate the hydrodynamic radius. All these findings are consistent with an antiparallel side-by-side dimerization. The structure of the dimeric peptide was calculated with a simulated annealing strategy. The lipophilic dimer is held together by favorable van der Waals interactions in the sense of a bulge fitting into a groove. The flexibility of the helical conformations concerning an alpha/3(10)-helical equilibrium is shown in a 3 ns molecular dynamics simulation of the resulting dimeric structure. Both overall helical structures of each monomer and the antiparallel mode of dimerization are stable. However, transitions were seen of several residues from a 3(10)-helical into an alpha-helical conformation and vice versa. Hence, this peptide represents a good model in which two often-discussed aspects of hierarchical transmembrane protein folding are present: i - i+3 and i - i+4 local H-bonding interactions cause a specific molecular shape which is then recognized as attractive by other surrounding structures.