Search Of The Stable Conformations Of Gly-dipeptide、Gly-tripeptide、Thr-dipeptide As Well As Thr-tripeptide By ABEEMσπ/MM Method

The polypeptide is a kind of important biological molecule.Many peptides form protein by processing and deforming.Research on the stable conformation of the polypeptide is very important in the actual life.In order to explore the properties of stable conformation of polypeptide,we have studied the stable conformations of dipeptides and tripeptides of glycine and threonine,which is a good foundation for studying the conformation of biological macromolecule.The scan of the potential energy surface and the optimization of molecular structure of gly-dipeptide and thr-dipeptide were performed in the gas phase and the aqueous phase with Gaussian09 software at the level of B3LYP/6-311++G(d,p).The results are discussed in detail.The five torsion types of gly-dipeptide and ten torsion types of thr-dipeptide were combined respectively to obtain initial tripeptides conformation,i.e.twenty-five and one hundred types.The optimization and the frequency calculation were performed at the same level,and then 25 types of stable conformations of gly-tripeptide and 40 types of stable conformations of thr-tripeptide were obtained.The ABEEMσπ、OPLS/AA、AMBER 99 sb and CHARMM27 force fields were applied to explore the stable conformations of gly-dipeptide、gly-tripeptide、thr-dipeptide and thr-tripeptide.Compared with the stable conformations obtained from ab initio at the B3LYP/6-311+++G(d,p)level,only ABEEMσπ polarizable force field can obtain the same stable conformations corresponding to dipeptides and tripeptides.The mean absolute deviation(MAD)of backbone dihedral angles of gly-dipeptide and thr-dipeptide are 2.0 ° and4.6 °,respectively;and the root mean square deviation(RMSD)are 2.3 ° and 6.2 °,respectively.The MAD of backbone dihedral angles of gly-tripeptide and thr-tripeptide are11.8 ° and 5.2 °,respectively;and the RMSD are 13.4 ° and 7.7 °,respectively.However,the number of stable conformations obtained from OPLS/AA、AMBER99sb and CHARMM27 force field are less than that of high level ab initio calculation,and the MAD of backbone dihedral angles obtained from above methods are larger than ABEEMσπ.From the results above,the minima points of gly-dipeptide and thr-dipeptide obtained from ABEEMσπ were set to be the initial structures.We further minimize the structures by using ABEEMσπ,the obtained stable structures are close to these obtained from ab initio.In searching the stable conformation of glycine and threonine,ABEEMσπ is a good choice because of its accuracy and high efficiency.