Establishment And Application Of Coarse-grained Force Field For The Probe

Coarse-grained molecular dynamics is one of the important methods to study the dynamic characteristics of the microstructure of biological macromolecules.Coarsegrained molecular dynamics calculates multiple atoms as one coarse-grained particle.At present,the Martini force field suitable for biological macromolecules is based on the method of reproducing the free energy of the system to determine the coarse-grained force field parameters.It is a force field designed and developed for the entire biological system.The Martini force field is only suitable for qualitative analysis of biology The structural characteristics of the molecular structure cannot be specific enough to accurately express the change process of the molecular structure with data.In this paper,the iterative Boltzmann inversion(IBI)method is used to explore the calculation method for establishing the coarse-grained force field of the probe molecular structure suitable for the peptide chain of a specific sequence.The IBI method is a method for determining the parameters of the potential function based on the molecular structure.Based on the Henderson uniqueness principle,it is determined by reproducing the distribution function of the all-atom molecular dynamics trajectory under the premise that the distribution function and the potential function are known to be uniquely corresponding.Potential field parameters.Through iterative calculation,the error between the coarse-grained molecular dynamics calculation results and the allatom results is gradually reduced,and the coarse-grained force field is finally obtained.The coarse-grained force field calculated by the IBI method can calculate the structural characteristics of the molecule more accurately,and the calculation efficiency is greatly improved.The molecular structure of the peptide chain probe with a specific sequence composed of amino acids studied in this paper is more complicated due to the variety of amino acids themselves and the secondary structure of the peptide chain.Therefore,before inverting and fitting the distribution function in this paper,the distribution function is further subdivided according to the structural characteristics of the peptide chain and fitted separately.Through the IBI method,the coarse-grained force field of the peptide chain probe molecular structure of the specific sequence is obtained for the first time.Finally,through the comparison of the distribution function,the calculation result is far closer to the all-atom force field than the Martini force field.The result shows that the distribution function obtained by this scheme is in good agreement with the all-atom result.Specific sequence peptide chain probe molecules are used in experiments to measure the force of the tested structure.By adding a fluorescent group to the probe,the deformation of the probe leads to a change in the relative position of the fluorescent group,resulting in a change in the brightness of the fluorescent group,so that the deformation of the probe can be reversed by the brightness,and then the force of the probe itself can be used Characteristic,the force is pushed by the deformation,and the force of the structure under test can be measured.In this paper,using the obtained coarse-grained force field,GROMACS is used to control the molecular dynamics simulation of the probe molecule to obtain the partial force characteristics of the probe molecule.Due to the special structure in the specific sequence peptide chain probe molecule,the quantitative relationship between the complete deformation and displacement needs to be further studied.