Distribution of edited residues in protein 3D

Residues coded by codons under the influence of RNA editing tend to be located in protein structural core (Yura and Go, 2008). The graph above is automatically generated from the data in this database to test the previous statement on the current dataset.

The biased distribution of edited residues toward protein structural core can still be observed, even when the statistics is performed only on Leucine and Phenylalanine (Here is the result). RNA editing tends to change a hydrophilic to a hydrophobic residue and hydrophobic residues tend to be in protein structural core. Therefore, the biased distribution may derived just from the combination of these tendencies. To deny this warrant, the test is performed only on two types of hydrophobic residues.

In detail;

In a general protein, 14% of residues reside in protein structural core. A structural core is defined based on solvent accessibility of residues. A cluster of virtually solvent-inaccessible residues are defined as a structural core.

In this database, residues exchanged by RNA editing are mapped onto protein 3D structures (See List of Proteins), and accumulation of these data enables us to test the biased distribution of edited residues to a type of protein structure. The procedure of the significance test is the following;

  1. divide residues in structure known proteins into core and non-core types,
  2. count the number of residues in each type (N_c and N_n, respectively)
  3. count the number of edited residues in each type (Ne_c and Ne_n, respectively),
  4. expected number of finding edited residues in core is
    Ee_c = (Ne_c + Ne_n) x N_c/(N_c + N_n)
  5. expected number of finding edited residues in non-core is
    Ee_n = (Ne_c + Ne_n) x N_n/(N_c + N_n)
  6. χ2 = (Ne_c - Ee_c)2/Ee_c + (Ne_n - Ee_n)2/Ee_n, and
  7. calculate the probability of obtaining the current distribution, if the location of edited residues was determined randomly by converting χ2 using incomplete Γ function.
In this procedure, the number of edited sites are counted residues-wise, and hence RNA editing on the first letter and the second letter, for instance, are treated as one event. In addition, RNA editing events on the same site in homologous proteins are counted as one event, because the editing may be introduced in the common ancestor of the two genes.

Go back to the top

Disclaimer
Liability: For documents available from this server, we do not warrant or assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information.

External Links: Some of the web-based database may provide links to other Internet sites for the convenience of users. We are not responsible for the availability or content of these external sites, nor do we endorse, warrant, or guarantee the products, services, or information described or offered at these other Internet sites. It is the responsibility of the user to examine the copyright and licensing restrictions of linked pages and to secure all necessary permissions.