Background:
It is currently believed that protein folding rates are influenced by protein
structure, environment and temperature, amino acid sequence and so on. We have been working for
long to determine whether and in what ways mRNA affects the protein folding rate. A large number
of palindromes aroused our attention in our previous research. Whether these palindromes do have
important influences on protein folding rates and what’s the mechanism? Very few related studies
are focused on these problems.
Objective:
In this article, our motivation is to find out if palindromes have important influences on
protein folding rates and what’s the mechanism.
Method:
In this article, the parameters of the palindromes were defined and calculated, the linear
regression analysis between the values of each parameter and the experimental protein folding rates
were done. Furthermore, to compare the results of different kinds of proteins, proteins were
classified into the two-state proteins and the multi-state proteins. For the two kinds of proteins, the
above linear regression analysis were performed respectively.
Results :
Protein folding rates were negatively correlated to the palindrome frequencies for all
proteins. An extremely significant negative linear correlation appeared in the relationship between
palindrome densities and protein folding rates. And the repeatedly used bases by different
palindromes simultaneously have an important effect on the relationship between palindrome
density and protein folding rate.
Conclusion:
The palindromes have important influences on protein folding rates, and the
repeatedly used bases in different palindromes simultaneously play a key role in influencing the
protein folding rates.
Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences
