Femtosecond two-dimensional infrared spectroscopy in combination with isotope labeling and molecular dynamics simulation has been used to investigate the structures and dynamics of nonfolding peptides and collagen peptides.
Homopolymeric peptides are simple yet important, serve as model systems for investigating the intrinsic propensity of protein folding, especially for those disordered or unfolded peptides in aqueous solution. Here the full structure of (Ala)5 has been studied. Two different isotope-labeled peptides, Ala-(13C)Ala-(13C,18O)Ala-Ala-Ala, and Ala-Ala-(13C,18O)Ala-(13C)Ala-Ala were strategically designed to simplify the four-oscillator system into three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, coupling constant β and angle θ between transition dipoles has been extracted through spectral fitting. The coupling constant is around 4 cm-1 and angle around 100. These parameters were related to the dihedral angles characterizing the peptide backbone structure through DFT calculated maps. The derived dihedrals are all located in the polyproline-II region.
These results were compared to the conformations sampled by hamiltonian replica-exchange MD simulation with 3 different CHARMM force fields: C22, C36 and Drude. The C22 force field predicted too high α-helix population, whereas C36 predicted that polyproline-II is the dominate conformation, consistent with experimental findings. The Drude model predicted dominating beta-sheet. Since the 2D-IR derived results were obtained from fitting to a single set of structural parameters, the effect of structural fluctuation within one conformation and structural transition between different conformations was also discussed. The C36 MD trajectories were used to simulate 2D IR spectra using the sum-over-state method and the time-averaging approximation (TAA) method. Reasonable agreement with the experimental data was achieved.
Collagen is the most abundant protein in mammal. Its structural properties are important for biological functions. Here, the structure and thermal melting of a model collagen peptide, (PPG)10, has been investigated. The temperature dependent linear IR spectra of the unlabeled peptide and two isotopomers (either 13C-16O or 13C-18O labeled on the 4th glycine residue) showed that the triple helix unravels with increasing temperature and leads to greater solvent exposure. With some adjustments of calculation parameters according to linear IR spectra, 2D IR spectral simulation based on MD trajectories and TAA reasonably reproduced experimental spectra taken at the parallel and perpendicular polarization conditions. Further refinement of models and parameters are needed to improve the simulation. Our results for model nonfolding peptides and collagen peptides contribute to the fundamental understanding of peptide structure and dynamics, and to the further development of theoretical models for simulating 2D IR spectra.