Poly Electrolyte And The Phase Transition Of Biological Macromolecules And Molecular Interactions

Regulation of gene expression is one of centers in molecular biology research,in the process of which is full of protein-protein and protein-DNA interactions.This is involved in the study on most basic principles of lives.As a result,the study of biological macromolecules,specially protein-DNA interaction system is very impotant in the life sciences,which require a high precise energy function in computer simulations.Here,we modify a statistical potential based on the distance-scaled,finite ideal-gas reference state(DFIRE) so that it is optimized for protein-DNA interactions.The changes include a volume-fraction correction to account for unmixable atom types in proteins and DNA in addition to the usage of a low-count correction based on bayesian statistics, residue/base-specific atom types,and a shorter cutoff distance for protein-DNA interactions.The new statistical energy functions are tested in threading and docking decoy discriminations and prediction of protein-DNA binding affinities and transcriptionfactor binding profiles.Results indicate that new proposed energy functions are among the best in existing energy functions for protein-DNA interactions.We also employed small-world network theory into the study of three-dimensional protein structure model.The new explorer shows some pattern of these models which can be used to build a new method of studying proteins in the future.The thermodynamic properties of 6-mer polyampholyte chains were simulated with the multicanonical Monte Carlo method in a three-dimensional off-lattice model.The results demonstrate that the number of the charged monomers on the chain and the sequence significantly affect the transition behaviors of polyampholyte chains.In the case of the random distribution of the charged monomers,two oppositely charged monomers act as two stickers during a collapse process,due to which the movement of monomers is suppressed and the chains can more directly reach their solid state.Interestingly,in a proper arrangement of the charged monomers,the chains may have a proteinlike nondegenerate state,i.e.,the chain is designable.The transition of such polyampholyte chains appears to be of a two-state,all-or-none type.