Structure and Dynamics of Helical Protein Fragments Investigated by Theory and Experiment

This work addresses the conformation and dynamics of model peptides using spectroscopy and molecular dynamics simulations. Experimentally, we investigate the structure and dynamics of peptide fragments taken from coiled coil and three helical bundle motifs of bacterial coat proteins. Theoretically, we use molecular dynamics simulations of isolated helices with explicit water molecules to derive trajectories which reveal features about picosecond dynamics and local unfolding events. The assignment of the ^1H, ^{15}N, and ^ {13}C resonances, secondary structure, backbone dynamics, hydration and other biophysical parameters of a 30 residue recombinant peptide corresponding to an immunogenic site on the coiled coil region of Streptococcus pyogenes 24M protein are reported. Our results suggest that this peptide is a symmetric parallel dimeric alpha-helical coiled coil with local defects within the helix and fraying at the termini. The ^1H and ^ {15}N assignments, the hydration, the overall fold, and other biophysical parameters of a recombinant B domain of Staphylococcal protein A (FB) are reported. Our results indicate FB is a highly stable monomeric three helical bundle. A symmetric two domain construct was used to probe the modular assembly of two B domains. Here, spectroscopic results suggest weak interactions between the two domains. The folding pathway of FB was investigated using amide exchange data of the native protein and peptide models. We propose that the helical hairpin consisting of helices II and III is an on-pathway intermediate in the folding of FB. Two 1 ns molecular dynamics simulations (MD) on two mainly helical peptides--an 18 residue peptide corresponding to a portion of the H helix of myoglobin (MBH) and a 14 residue analogue of the C-peptide of ribonuclease A (CRNA) --were carried out in water using the united atom AMBER/OPLS force-field. In the case of MBH, the initial helical conformation progressively frays to a more disordered structure. A common motif in the unfolding mechanism involves the formation of transient turn structures involving several water molecules. In contrast to the MBH simulation, the CRNA trajectory was characterized by the presence of fairly stable i ... i+4 (alpha-helical) hydrogen bonds throughout the simulation, except at the N-terminus where some fraying was observed.