Dynamic Structure And Vibrational Spectra Of Polypeptides Under Solvation Environment

In this paper, structural dynamics of model peptides were investigated, the correlation between molecular dynamic structure and vibrational spectra was constructed, and the influence on the molecular structure and vibrational spectra induced by solvent effect was examined. An amide-? vibrational frequency map was constructed, based on a model ?-peptide for the fast and accurate prediction of vibrational spectra. Thus, method built on the model molecule was applied to A? and graphene system, in order to explore the mechanism of protein folding by using vibrational probes.We explored the solvent effect on the three dimensional structure and the vibrational spectra of ALAD. The results show that the most probable species of ALAD obtained from MD simulations are PP?, ?L, ?R and C5 in water, PP? and C5 in DMSO, and C5 in CHCI3. Then, Ab initio caculations were performed on ALAD-clusters which were selected from MD trajectories, and PCM model was introduced to simulate the solvent effect from the bulk, thus expanding the scope of the solvation structure and frequency red shift of amide ? band. A general applicable amide-? vibrational frequency map for ?-peptides in a number of common solvents was constructed to predict the vibrational features quickly and accurately, based on N-ethylpropionamide (NEPA). The results indicate that the GH map works well. Then, molecular dynamics simulations were carried out for AP(37-42) on graphene, the structural feature and spectra were revealed at atomic level.The method based on ab initio calculation has the advantage of being accurate in computing vibrational frequencies, and also in describing short-distance intermolecular interactions, but limited by computational power and since one can neither have unlimited sample size for solute-solvent clusters nor use sufficiently high-level theory and basis sets for electronic structure and vibrational frequency calculations. The method based on molecular mechanics force field has the advantage of being simple in scheme and efficient in construction, but lacks accuracy in assessing short distance intermolecular interactions. These considerations inspire the construction of a map that can take the advantages of the merits of both. We combined the ab initio calculation and molecular mechanics force field to build a general map, followed by linear IR spectral simulations. This approach laid the foundation of the study of vibrational spectra of protein, and also provided a theoretical basis for further research of protein configuration of beta-amyloid.