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How can I mutate cytosine to 5-methylcytosine
(1/1)
xiangjun:
Methylation of cytosines in DNA is a crucial epigenetic modification that regulate expression of many genes. Chemically, it is the addition of a methyl group to the 5 position of cytosine (C).
The mutate_bases program in 3DNA v2.x performs in silico base mutations given a nucleic acid structure in PDB format. It is not a problem to mutate any C to a 5-methylcytosine (5CM) provided that users set a 5CM in its standard base reference frame. Given the importance of 5CM in epigenetics and the increasing simulation studies to understand its effects, I have included Atomic_5CM.pdb in the 3DNA v2.1 distribution as of 2012oct26.
According to PDB, the three-letter nucleotide name for 5-methylcytosine is 5CM instead of 5MC -- see for example PDB entries 4mht and 2uz4. The methyl carbon is named " C5A" instead of " C5M" or " C7 ". Thus, the content of the Atomic_5CM.pdb file is:
--- Code: ---REMARK 3DNA by Dr. Xiang-Jun Lu [2012-10-26] (xiangjun@x3dna.org)
ATOM 1 C1' 5CM A 1 -2.477 5.402 0.000 1.00 0.00 C
ATOM 2 N1 5CM A 1 -1.285 4.542 0.000 1.00 0.00 N
ATOM 3 C2 5CM A 1 -1.472 3.158 0.000 1.00 0.00 C
ATOM 4 O2 5CM A 1 -2.628 2.709 0.001 1.00 0.00 O
ATOM 5 N3 5CM A 1 -0.391 2.344 0.000 1.00 0.00 N
ATOM 6 C4 5CM A 1 0.837 2.868 0.000 1.00 0.00 C
ATOM 7 N4 5CM A 1 1.875 2.027 0.001 1.00 0.00 N
ATOM 8 C5 5CM A 1 1.056 4.275 0.000 1.00 0.00 C
ATOM 9 C5A 5CM A 1 2.466 4.961 0.001 1.00 0.00 C
ATOM 10 C6 5CM A 1 -0.023 5.068 0.000 1.00 0.00 C
END
--- End code ---
With this new addition, it is now very straightforward to mutate Cs to 5CMs with mutate_bases, as illustrated by the following two examples:
* Mutate C1 on chain A and C23 on chain B of the Dickerson B-DNA dodecamer (PDB entry 355d) to 5CMs:
mutate_bases 'chain=A snum=1 m=5CM; chain=B snum=23 m=5CM' 355d.pdb 355d_AC1BC23_5CM.pdb
* Mutate C2 on chain A of the yeast phenylalanine tRNA (PDB entry 6tna) to 5CM:
mutate_bases 'chain=A snum=2 name=C m=5CM' 6tna.pdb 6tna_C2_5CM.pdb
The mutated files 355d_AC1BC23_5CM.pdb and 6tna_C2_5CM.pdb are attached for your verification. For comparison, shown below are the original atomic coordinates of the above tRNA 6tna cytosine and coordinates of its 5CM mutant in red. Note that the coordinates of the backbone atoms are the same, and coordinates of common base atoms are very close.
* The original atomic coordinates of a cytosine from PDB entry 6tna:
--------------------------------------------------------------------------------
ATOM 25 P C A 2 31.659 20.469 70.978 1.00 10.00 P
ATOM 26 OP1 C A 2 32.973 21.044 71.364 1.00 10.00 O
ATOM 27 OP2 C A 2 30.973 21.143 69.849 1.00 10.00 O
ATOM 28 O5' C A 2 31.815 18.912 70.652 1.00 10.00 O
ATOM 29 C5' C A 2 30.629 18.184 70.293 1.00 10.00 C
ATOM 30 C4' C A 2 30.507 16.914 71.139 1.00 10.00 C
ATOM 31 O4' C A 2 29.293 17.051 71.947 1.00 10.00 O
ATOM 32 C3' C A 2 30.455 15.607 70.367 1.00 10.00 C
ATOM 33 O3' C A 2 31.724 14.971 70.316 1.00 10.00 O
ATOM 34 C2' C A 2 29.411 14.815 71.146 1.00 10.00 C
ATOM 35 O2' C A 2 29.987 14.227 72.301 1.00 10.00 O
ATOM 36 C1' C A 2 28.473 15.927 71.630 1.00 10.00 C
ATOM 37 N1 C A 2 27.474 16.346 70.621 1.00 10.00 N
ATOM 38 C2 C A 2 26.658 15.368 70.068 1.00 10.00 C
ATOM 39 O2 C A 2 26.802 14.198 70.441 1.00 10.00 O
ATOM 40 N3 C A 2 25.726 15.730 69.143 1.00 10.00 N
ATOM 41 C4 C A 2 25.601 17.008 68.767 1.00 10.00 C
ATOM 42 N4 C A 2 24.682 17.314 67.872 1.00 10.00 N
ATOM 43 C5 C A 2 26.436 18.041 69.324 1.00 10.00 C
ATOM 44 C6 C A 2 27.351 17.658 70.243 1.00 10.00 C
--------------------------------------------------------------------------------
The coordinates of the mutant 5-methylcytosine generated by 'mutate_bases'
REMARK Mutation#1 A:...2@:[..C] to [5CM]
ATOM 25 P 5CM A 2 31.659 20.469 70.978 1.00 10.00 P
ATOM 26 OP1 5CM A 2 32.973 21.044 71.364 1.00 10.00 O
ATOM 27 OP2 5CM A 2 30.973 21.143 69.849 1.00 10.00 O
ATOM 28 O5' 5CM A 2 31.815 18.912 70.652 1.00 10.00 O
ATOM 29 C5' 5CM A 2 30.629 18.184 70.293 1.00 10.00 C
ATOM 30 C4' 5CM A 2 30.507 16.914 71.139 1.00 10.00 C
ATOM 31 O4' 5CM A 2 29.293 17.051 71.947 1.00 10.00 O
ATOM 32 C3' 5CM A 2 30.455 15.607 70.367 1.00 10.00 C
ATOM 33 O3' 5CM A 2 31.724 14.971 70.316 1.00 10.00 O
ATOM 34 C2' 5CM A 2 29.411 14.815 71.146 1.00 10.00 C
ATOM 35 O2' 5CM A 2 29.987 14.227 72.301 1.00 10.00 O
ATOM 36 C1' 5CM A 2 28.473 15.927 71.630 1.00 10.00 C
ATOM 37 N1 5CM A 2 27.475 16.353 70.620 1.00 1.00 N
ATOM 38 C2 5CM A 2 26.651 15.372 70.062 1.00 1.00 C
ATOM 39 O2 5CM A 2 26.789 14.195 70.427 1.00 1.00 O
ATOM 40 N3 5CM A 2 25.726 15.730 69.141 1.00 1.00 N
ATOM 41 C4 5CM A 2 25.610 17.009 68.776 1.00 1.00 C
ATOM 42 N4 5CM A 2 24.685 17.316 67.863 1.00 1.00 N
ATOM 43 C5 5CM A 2 26.437 18.028 69.328 1.00 1.00 C
ATOM 44 C5A 5CM A 2 26.359 19.547 68.947 1.00 1.00 C
ATOM 45 C6 5CM A 2 27.347 17.660 70.238 1.00 1.00 C
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.