we have a question in class and it goes like this.
I have a protein sequence of 1-100AA and another one identical but just amino acid shift (2-101AA) .
If I measure RMSD of C-alpha only what will be the maximum? my answer is Ca-Ca bond (3.6A).
But now in the case of alpha-helix structure why it will be lower?
In my opinion it can be 0 because if it's an alpha-helix and we are only comparing the backbone (carbon-alpha) then it can put the 3d structure perfectly top on each other. My teacher told me something that it can be 0 only if it's perfect alpha helix...
any suggestions what will be the RMSD in that case? (for sure it will be lower than 3.6A, but why and how much?)
Thanks
My guess would have agreed with yours, as long as the comparison is made from residue 2 to 100 only and the structures are aligned. This assumes that residues 1 and 101 do not have any effect on the structure of residues 2 to 100.
1 - You first need to understand that Ca and backbone are different references, and that they will probably give you different information or sometimes very close ones.
2 - The RMSD calculation formula itself states that 2 coordinates are needed to do the calculation, ie if any AA is left it will not be calculated.
3 - I do not know what you're doing, but your RMSD will hardly be 0
For real experimental data, an RMSD of 0 is probably impossible because there is always going to be some experimental variation between 2 structures, even of the same protein, but I was thinking about it from a theoretical perspective.
- Badges
- Science topic
- Similar topics
- Chemistry
- Biochemistry