Theoretical Study On Histidine Dipeptide-water Clusters And Histidine Dipeptide In Aqueous Solution

The imidazole ring of histidine(His) side chain has a number of unique role that candicatate function in proteins. Many chemical reactions and life processes are carried out in asolvent, especially in aqueous solution, so proper description of the solvent environment iscrucial in simulations of biological molecules. The histidine dipeptide has three kinds ofprotonation states, including two neutral histidine dipetidine (His[NδH] and His[NεH]) andpositively charged histidine dipetidine His+. The detailed contents are as follows:(1) The properties of the interaction of two neutral histidine dipeptide and water clustersstudied by ab initio method and the atom-bond electronegativity equalization fluctuatingcharge model (ABEEMσπ model). The geometries, energies, the vibration frequency of stableconformations were calculated by MP2/aug-cc-pVDZ//B3LYP/6-311++G (d, p) methodwith BSSE and Zero-point correction. The structures and properties of two neutral histidinedipeptide and water clusters studied by using ABEEMσπ model, can be divided into two parts:The first part is the properties of histidine dipeptide, namely optimized geometry, backbonetorsion angles, charge distribution and dipole moment. The second part is the properties ofHis(H2O)n(n=1~6), including hydrogen bond, hydrogen angle, binding energy, interactionenergies and so on. These properties and structure were compared with MP2/aug-cc-pVDZ,OPLS-AA, AMBER force field and ABEEMσπ model.(2) In the positively charged, doubly protonated state, structure switches two neutraltautomers. So the property of His+is meaningful by ABEEMσπ model, such as optimizedgeometries, backbone torsion angles, charge distribution and so on. The properties of the Sixstable conformation were optimized by MP2/aug-cc-pVDZ//B3LYP/6-311++G (d, p) levels.(3) The dynamic behavior of histidine dipeptide(His[NδH] and His[NεH]) has beeninvestigated at298K and NVT ensemble. The dynamics properties of these dipeptides 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 are calculated the ABEEMσπ fluctuating charge model. Generalized Born (GB) modelwas employed to calculate salvation free energies (SFE), and then SFEs of histidine dipeptidewere obtained. Draw a conclusion that the conformations of His[NδH] are much more stablethan His[NεH] in aqueous solution.