Influence Of Parameters Such As Major Groove Width And Bonded Interaction Energy In The Tertiary Structure Of MRNA On Protein Folding Rate

Proteins are an important component of organism.Proteins can only have biological activity and execute its specific biological function when folded into a distinct spatial configuration.Recent studies have discovered that the secondary structures of mRNA are an essential element impacting the protein folding rate during the co-translation folding process,and we believe that the tertiary structures of mRNA must also have important influence on the folding rate of protein.In this paper,proteins with experimental data on folding rates were collected,and the tertiary structures of the corresponding mRNA of the selected protein were predicted and studied using 3dRNA and 3DNA.The parameters such as major groove width were selected.Two values of major groove width,local base pair parameters,simple base pair parameters and bonded interaction energy are calculated.Based on this,the correlation between different parameters and protein folding rate were analyzed.Considering that the different effects of various parameters on the folding rates of different proteins,the selected proteins were divided into different groups according to different folding types and secondary structures,and the correlation between major groove width,local base pair parameters et al.and folding rates of different protein groups were analyzed.The specific research contents are as follows:1.The parameters of major groove width in the tertiary structures of mRNA were calculated,and the correlation between the major groove width of each base pair steps and protein folding rate were analyzed.The results show that the major groove width significantly and negatively correlated with the folding rate of each kind of proteins.It is indicated that the increase of major groove width will hider protein folding process.2.The local base pair parameters in the tertiary structures of mRNA were calculated,and the effects of local base pair parameters on the protein folding rate were analyzed.The results show that the local base pair parameters of Stretch,Stagger,Buckle and Propeller are related to the protein folding rate,indicating that the local base pair parameters of the tertiary structure of mRNA are effective factors affecting the protein folding rate.3.The related data of simple base pair parameters in the tertiary structure of mRNA were calculated,and the correlation between simple base pair parameters and protein folding rate was analyzed.The results show that the simple base pair parameters of Shear,Stretch,Propeller and Opening are related to the protein folding rate,which means that the simple base pair parameters of the tertiary structure of mRNA have an important effect in the protein folding rate.4.The bonded interaction energy of mRNA were calculated using the3 dRNA program,and the correlation between bonded interaction energy and protein folding rate were analyzed.The results show that except for two-state proteins,the bonded interaction energy of the tertiary structure of mRNA are related to the protein folding rate,and they all restrain the protein folding.It shows that the bonded interaction energy of mRNA are an important factor affecting the protein.