Research Of Backbone Torsional Pair Correlations In Proteins

With the development of the X-ray diffraction and NMR,more and more protein structures are resolved at high resolution.As of there are about 120000 protein structures in protein data bank.But the protein structure usually doesn't provide enough information for us to explain the function of protein.The development of computer technology and molecular dynamics simulation provides a feasible way for us to explore the microscopic movement of protein molecules.As computer speeds improve,long-time scale molecular dynamics simulations of large molecules are possible.But molecular dynamics simulations still require a large amount of computational resources.For the protein structures in the PDB data bank our simulation ability is limited.In order to better use of existing protein structure,it is necessary to study the law of protein structure movement,correlation analysis is the main method we study the movement.In this paper,we analysis the main chain dihedral angle correlation of protein simulations.(1)long range correlation analysis:In biochemistry,allosteric regulation(or allosteric control)is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site.Most biologically relevant are long ranged.Therefore,understanding of structural correlations,especially long range ones,are essential for elucidation and manipulation of protein allosteric.We analysis ten protein simulation trajectories and found that most of the protein have long-range correlation.Most of the long-range correlation exit in loop region with aharmonic torsional state transition and have a long-time scale.Long time scales and long range nonlinear correlations make them strong candidates for mediation of allosteric in proteins.This can help us to understand protein and regulate the function of proteins.(2)short range correlation analysis:In protein,short range correlations are common.The neighbor dihedral angles in protein have large correlations.With twenty protein simulation,we analysis the short-range correlations of protein dihedral angles.We find that most of the short-range correlations are linear correlation and the nonlinear correlation mainly exist in loop regions.We evaluate the contribution of the 2,3,4 order correlation.And find that the second order correlation is the most important.Finally,we learned the characteristics of correlation in different second structures and construct protein local structure with these correlation features.