Structural Dynamics Of Polypeptide In Solution Phase

The structural dynamics of model dipeptides (glycine dipeptide, alanine dipeptide, valine dipeptide) in solution phase were systematically investigated, the conformational distributions of model dipeptides with different sidechain and performance of the amide vibrational band were examined. Azido group was inserted into the sidechain of alanine dipeptide to minitor its dynamical structure in a clear region of the vibrational spectrum and its impact on the secondary structure was also revealed. Vibrational frequency map was constructed for azido group based on ?-azidoalanine dipeptide to achieve fast prediction of vibrational spectrum of azide group in solution phase. Azido group was inserted into A?37-42 to explore the influence of azido group to the conformational distributions of A?37-42. The results provided a basis for revealing the factors which affect the protein folding and detecting the dynamical structure of polypeptide.The conformational distributions of the model dipeptides in D2O were systematically investigated by using molecular dynamics simulations, The results show that, dipeptides tend to form more extended conformers due to strong intermolecular hydrogen-bonding interactions between amide units and D2O, the conformational preferences of alanine dipeptide did not changed after azido group inserted. The sensitivity of amide-? bands to the structure was investigated by using the ab initio calculation for representative conformers of model dipeptides, azido group was inserted into dipeptide, and its vibrational motion was used to detect the dynamical structure of dipeptides. Vibrational frequency map for azido group in ?-azidoalanine dipeptide was constructed using electric potential, electric field and electric field gradient methods to achieve fast prediction of its vibrational frequency in solution phase. The conformational feature of A?37-42-N3 was explored, the results show that, the azido group increases the hydrophobicity and intramolecular hydrogen-bonding interactions between A?37-42 and D2O, therefore A?37-42 was easy to form a large circle ring. Replica exchange molecular dynamics was performed for enhancing sampling of possible peptide conformers.Molecular dynamics simulations were performed for dipeptides to obtain the conformational distributions in solution phase, ab initio calculation were used to build vibrational frequency map of azido group. Thus, the molecular structure was identified by simulating infrared spectrum. The results provided a basis for further research of the aggregation mechanism of A? and monitor dynamical structure in solution phase.