The Researching Of The Cys-dipeptide And Cys-tripeptide Stable Conformations In ABEEMσπ/MM

Natural amino acids tend to exist in stable conformation in natural conditions,and have an important role in physiology.Thus,the study of the conformation of natural amino acids peptide is significant.In this paper,the fluctuating charge force field ABEEMσπ/MM method was used to study the stable conformation of cys-dipeptide and cys-tripeptide model molecule in natural amino acids.First,the potential energy surface of cys-dipeptide was obtained by ab initio B3LYP/6-311++G（d,p）method.From the 2D and 3D energy image,all of the local minima were obtained.After been optimized,16 types of stable conformations of cys-dipeptide were obtained.The whole 16 types conformations are minimized by ABEEMσπ/MM.Compared with the result of ab initio method,while the other three fixed charge force field OPLS/AA,AMBER99sb and CHARMM27 can only obtain 12,12 and 8categories of cys-dipeptide molecule stable conformations,and the backbone dihedral angle（φ,ψ）of the cys-dipeptide molecular,the MAD in four force fields are 7.7°,32.7°,21.5°and24.2°,respectively.Considering the function of dihedral angle in total energy,the parameters V₁,V₂ and V₃ofφandψin side chain of cys-dipeptide model molecule were adjusted.Next,the same parameters V₁,V₂ and V₃ are used in studying cys-tripeptide.The initial cys-tripeptide structural main chain torsions are built by combining the torsions of cys-dipeptid stable structures with each other.After optimized by ab initio B3LYP/6-311++G（d,p）method,27types of cys-tripeptide stable conformations were obtained.The 27 conformations were also obtained by ABEEMσπ/MM force field.But the other three force fields OPLS/AA,AMBER99sb and CHARMM27 methods can only find 12,16 and 10 categories stable conformations.The backbone dihedral angle（φ₁,ψ₁）（φ₂,ψ₂）MAD of cys-tripeptide model molecular in the four force fields are 4.8°,14.2°,21.1°and 18.7°,respectively.Thus,ABEEMσπ/MM method can abtain all stable structures,which is as same as ab initio method,with smaller MAD compared with other force fields.This makes it possible to study larger systems and providing a foundation for exploring the stable conformation of natural amino acids in biological macromolecules.