Search Of The Stable Conformations Of Oligopeptides By ABEEM??/MM

As an excellent medical functions,biopeptides(such as antibodies)are benefit for many diseases diagnosis and therapeusis,which are compounds linked by two or more different kinds of amino acids in the form of peptide bonds and play a helpful physiological role in various organs of the human body.Active peptides have more research value.The study of the stable conformations of peptides is of great significance in real life.In order to better explore the stable conformations of polypeptide molecules,this thesis primarily focuses on the stable conformations of glycine(Gly)and threonine(Thr)dipeptides,Gly-Thr and Gly-Thr tripeptides and biological macromolecules to establish an accurate method to test and verify the essentiality of the stable conformations in biological macromolecules.Firstly,this thesis applies B3LYP/6-311+G(d,p)method to optimize Gly-Thr tripeptide and Thr-Gly tripeptide,which are in the Gaussian09 and GaussView5.0.The stable conformations and relative energies of the above tripeptides were investigated by the Atom-Bond Electronegativity Equalization Fluctuating Charge Force Field(ABEEM??/MM),OPLS/AA,AMBER 99 sb,CHARMM 27 and AMOEBA bio09 force field.On the basis of ab initio calculation results of B3LYP/6-311,it is found that using ABEEM??/MM can obtain the same number of stable conformation as B3 LYP,the coincidence degree is the best and the results are more accurate.Secondly,the stable conformations of methionine-enkephalin obtained by the same method was used as the model molecule to calculate their backbone dihedral angles and relative energies.This thesis applies the Atom-Bond Electronegativity Equalization Fluctuating Charge Force Field(ABEEM??/MM),OPLS/AA,AMBER 99 sb,CHARMM 27 and AMOEBA bio09 to explore the stable conformations of methionine-enkephalin.Based on ab initio B3LYP/6-311+G(d,p)to calculate the stable conformations.In the ABEEM??/MM force field,we can obtain the same numbers of the stable conformations as B3LYP(methionine-enkephalin could find more stable conformations by the ABEEM??/MM force field),which have an outstanding coincidence degree,while using OPLS/AA,AMBER 99 sb,CHARMM 27 fixed charge force field and AMOEBA bio09 fluctuating charge force field can just partially get some results as ab initio.The polarizable force fields have more favorable edges.For the polarized force field,the AMOEBA09 force field takes about five times as long as the ABEEM??/MM floating charge polarization force field.So the ABEEM??/MM floating charge polarization force field has higher calculation efficiency.The conformation and property results of Gly-Thr tripeptide,Thr-Gly tripeptide and methionine-enkephalin were obtained by the ABEEM??/MM,which were compared with the backbone dihedral angles of the stable conformations by ab initio nextly,show that the method not only takes very short time to scan and optimize the stable conformations,but also can find all the stable conformations found by the ab initio accurately with little deviation.