Studies Amino Acid Tetrapeptides In Aqueous Solution By Using ABEEMσπ/MM Model

Many chemical reactions and life processes are carried out in a solvent, especially inaqueous solution, proper description of the solvent environment is crucial in simulations ofbiological molecules.ABEEMσπ fluctuating charge force field was used to investigate thestructures and properties of the five conformations of Ala tetrapeptide and the αLconformation of other five amino acids tetrapeptides in this thesis. The detailed contents areas follows:(1) The conformational energies are calculated by means of Atom-Bond ElectronegativityEqualization Method Fused into Molecular Mechanics i.e., ABEEMσπ fluctuating chargemodel, and the results are consistent with the MP2/aug-cc-pVTZ results.(2) The dynamic behavior of the five conformations of Ala tetrapeptide has beeninvestigated at298K and NVT ensemble. The dynamics properties of these tetrapeptides areinvestigated, including the root-mean-square deviations (RMSD) of several kinds ofnon-hydrogen atoms [Cαatoms, backbone atoms(C, Cα, N, O) and heavy atoms] and initialstructure. The hydrophobic surface, hydrophilic surface and the solvent-accessible surfacearea, the non-polar solvent free energies are calculated the ABEEMσπ fluctuating chargemodel. Generalized Born (GB) model was employed to calculate polar part of salvation freeenergies (SFE), and then SFEs of the five conformations of Ala tetrapeptide were obtained.SFEs of Rand β conformations are greater than those of the other conformations. Draw aconclusion that αRand β-sheet conformations of Ala tetrapeptide are in aqueous solution.(3) The dynamic simulations of the αLconformation of Gly, Leu, Val, Asn and Asptetrapeptides have been investigated in the similar way. The RMSD of backbone atoms,solvent-accessible surface area, non-polar SFE, polar SFE and total SFE were calculated,respectively. Their solubility in aqueous solution is analyzed and discussed. All the resultsobtained by fluctuating charge model combination with GB/SA demonstrate that thehydrophilicity of Asp and Asn tetrapeptides are stronger, the hydrophobic of Leu, Val and Alatetrapeptides are stronger, and Gly tetrapeptide is placed in the middle.In summary, the ABEEMσπ/MM force field can be used to study the structures andproperties of amino acid tetrapeptides. It lays a good foundation to make ABEEM fluctuating charge model expand the application of other macromolecule systems.