Protein Structure prediction and human variation

This blog is much about the protein and allelic variant analysis that I have done using DNA STAR.

Online Mendelian Inheritance in Man (OMIM)provides the allelic variants that are  required for the analysis. My gene has 3 allelic variants. These changes corresponds to  change in the amino acids by substitution, deletion etc.,

TOLBUTAMIDE POOR METABOLIZER - ILU359LEU
WARFARIN SENSITIVITY - ARG144CYS
WARFARIN SENSITIVITY - LEU208VAL

 I considered the first allelic variant and performed analysis for my protein.

The ile359-to-leu (I359L) substitution results from a 1075A-C transversion in the CYP2C9 gene and is also known as rs1057910 and CYP2C9*3. The variant leads to reduced warfarin metabolism and increased risk of bleeding. This variation is done using Edit seq module from DNA STAR where we can edit the protein sequence and convert it into allelic variant protein sequence. A quick screenshot showing the change in the protein sequence at position 359. Note: If you want to recheck that the aminoacid substitution is correct try reverse translating the protein which is edited see that you have a corresponding change in gene sequence. Aminoacid changed has been performed which is converted to Leucine to Isoleucine. After the replacement of the amino acid then we need to analyze the changes that we notice in the protein structure, hydrophobicity and other physical properties. For this we have an application called Protean and Protean 3D ( next version of protean where it is better in visualization but little difficult to navigate through the window) I have selected a window of 355-365 amino acid to know the changes either in the secondary structures or the hydrophobicity. The reason we do this is because the values for either hydrophobicity vary with different algorithms. We can use the DNA stat protean tool to view the changes in the physical properties.                                                                         CYP2C9 actual protein                                                                       Allelic variant (ILE359LEU) We notice that there is no significant change in the allelic region to that of the original protein features. We can see the Kyte-Doolittle Hydrophobicity plot was showing no significant difference even after the amino acid change. We have the threshold values for the aminoacid's hydrophobicity obtained by different algorithms. Table 1: Representing threshold values for hydrophobicity in amino acids Secondary structure prediction: I used Protean 3D for analyzing the secondary structure of natural and variant proteins. This prediction is done by Chou-Fasman algorithm which is an empirical technique developed for prediction of secondary structures in proteins.                                                                       Natural protein                                                                          Allelic Variant First we need to select the 10 aminoacid window in which we need to see that 359th position of amino acid would be median value. With the present procedure for finding out any difference between these two proteins we see that there is not much of a change but Beta sheets show little difference. I could see that rather than flexibility there is not much of a change observed. I suppose with some vivid analysis of the protein in the future we could know the reason why isn't there a change when an amino acid corresponding to the functionality of protein is changed. My gene is not associated with the membrane so there is not much of a difference in the trans membrane region which we can visualize in Protean-3D.  Key points: A codon change in the CDS region of gene should generally correspond to functional or structural change. This aminoacid or codon change is resulting in a functional change but not a structural or any kind of physical change.