Influences Of The Parameters Such As Base-pair Step And Stacking Energy Of MRNA On Protein Folding Rate

Protein folding refers to the process in which proteins transform from one-dimensional linear amino acid sequences to natural spatial structures with biological functions under specific PH and certain temperature conditions.Protein folding has always been a hot topic in the field of biophysics,and exploring the mechanism of protein folding is helpful to understand the central law of molecular biology,decipher the riddle of genetic information,and uncovering the pathogenesis of protein misfolding diseases.In addition,protein folding rate is regarded as an important parameter to measure protein folding speed,and the previous studies are mainly based on the environment,protein structure and amino acid sequence.In recent years,under the influence of protein co-translation theory,it is speculated that the translocation rate of mRNA on ribosome may affect protein folding rate.And in light of the influences of GC content in mRNA,the palindrome density and secondary structure of mRNA on protein folding rates reported in related research,so does mRNA tertiary structure also have an important effect on protein folding rate? Based on the above ideas,we analyzed the effects of parameters such as base pair steps of mRNA on protein folding rate.The main contributions are summarized as follows:1.The existing protein folding databases and related literature data were reviewed,redundant data was removed,a large experimental protein folding rates data were constructed.According to the cross-reference among PDB,EMBL and NCBI databases,the corresponding mRNA information of the selected protein in the database is found.The tertiary structure of mRNA is analyzed by using the software 3d RNA and X3 DNA,and the local base-pair step information and the simple base-pair step information based on consecutive C1'-C1' vectors of the corresponding mRNA tertiary structure of each protein were extracted and classified according to different base-pair steps,the average values of the local base pair step parameters of the mRNA tertiary structure and the simple base-pair step parameters based on consecutive C1'-C1' vectors were calculated,and the effects of various parameters on the protein folding rate were analyzed.1)The relationship analyses reveal that the effects of the local base-pair step parameters of mRNA tertiary structure on protein folding rate are in different degrees.The effective factors influencing on protein folding rates are the parameter of shift,slide,rise and tilt.These results indicate that the local base-pair step parameters of mRNA tertiary structure play an important role in protein folding rates.2)Simple base-pair step parameters based on consecutive C1'-C1' vectors of mRNA tertiary structure of shift,slide,rise and twist are related to the protein folding rate.These results indicate that the simple base-pair step parameters based on consecutive C1'-C1' vectors of mRNA tertiary structure play an important role in protein folding rates.In addition,the effects of the step parameters of the local base pairs of the tertiary structure of mRNA and the simple base pairs based on the consecutive C1'-C1' vectors on the protein folding rate are compared.The correlation results show that under the same base-pair step,the local base-pair step parameters have the same effect on the protein folding rate as the simple base-pair parameters based on the consecutive C1'-C1' vectors,but the magnitude of the influence is different.2.The groove width parameters of mRNA tertiary structure are extracted from the analysis results of mRNA structure by software 3d RNA and X3 DNA,and the selected proteins were classed into different folding types and different secondary structural types.Then each group of proteins are classified according to base-pair step types to explore the effect of the groove width parameters of mRNA tertiary structure on protein folding rate.The results show that the groove width parameter of the tertiary structure of mRNA has an important effect on the protein folding rate.Direct P-P distances and refined P-P distances of mRNA tertiary structure on the protein folding rate is different.3.The information of the corresponding mRNA of the protein was obtained from the database established earlier,and predicted by the software 3d RNA,and the relevant information of the non-bonding energy of mRNA was obtained.The average values of the non-bonding energy of mRNA: the base pairing energy and the base stacking energy were calculated,and the correlation between the non-bonding energy and the protein folding rate was analyzed.And related studies have shown that mRNA base pairing energy is positively correlated with protein folding rate,while mRNA base stacking energy shows no correlation with protein folding rate,so the effective factors influencing on protein folding rates are the base pairing energy of mRNA.