Journal of Physical Chemistry B, Vol.102, No.32, 6260-6272, 1998
Use of multiple molecular dynamics trajectories to study biomolecules in solution : The YTGP peptide
NMR studies of the YTGP tetrapeptide in aqueous solution show a large structural shift on the glycine peptide proton, indicating that the peptide adopts structures in which the aromatic ring lies close to this proton in an aromatic-(i+2) amine interaction (Kemmink and Creighton, J. Mel. Biol. 1993, 234, 861). Here, molecular dynamics simulations are used to obtain details at the atomic level of the structural properties of this system. To maximize the volume of conformational space searched, 13 separate trajectories of 300 ps were calculated at 300 K, with starting structures chosen from a conformational search, protein crystal structures, and modeling. Analysis shows that together the trajectories sample all the important regions of conformational space. Structures from the trajectories were clustered into conformational states, defined as regions in coordinate space around maxima in the probability distribution. Nine conformational states with significant populations were identified in which the glycine peptide proton has a large structural NMR shift. The relative importance of the trajectories for the system were assigned using energetic weighting factors, and the four most important trajectories were then extended to 1 ns. The structural shift spectra calculated from the significantly populated conformational states with an aromatic-(i+2) amine interaction are in good agreement with the experimental spectrum. The analysis shows that the potential energy surface of the system is complicated and divided into two separate regions at this temperature.
Keywords:PANCREATIC TRYPSIN-INHIBITOR;PARTIALLY FOLDED CONFORMATION;AMINO-AROMATIC INTERACTIONS;DISULFIDE FOLDING PATHWAY;FREE-ENERGY CALCULATIONS;MAGNETIC-RESONANCE;PROTEIN STRUCTURES;CHEMICAL-SHIFTS;SIDE-CHAINS;BORN MODEL