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Offline xiangjun

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mutate_bases
« on: February 11, 2012, 06:47:28 pm »
The utility program mutate_bases can be used to mutate bases in nucleic-acid-containing structures (DNA, RNA, and their complexes with ligands and proteins). It has two key and unique features: (1) the sugar-phosphate backbone conformation is untouched; (2) the base reference frame (position and orientation) is conserved, i.e., the mutated structure shares the same base-pair/step parameters as those of the native structure.

The mutate_bases program was created in response to repeated requests from 3DNA users over the years. Written as a standalone ANSI C program, it is on a par with other major 3DNA components (e.g., find_pair, analyze, rebuild and fiber). The program was first released as a supplement to 3DNA v2.0, and then became an essential part of the v2.1 release.

Overall, mutate_bases has been designed to solve the in silico base mutation problem in a practical sense: robust and efficient, getting its job done and then out of the way. The program can have many possible applications: in addition to perform base-pair mutations in DNA-protein complexes, it should also prove handy in RNA modeling and in providing initial structures for QM/MM/MD energy calculations, and in DNA/RNA modeling studies.

The standard command line help (mutate_bases -h) is as below:
NAME
        mutate_bases -- mutate bases, with backbone conformation unchanged
SYNOPSIS
        mutate_bases [OPTIONS] mutinfo pdbfile outfile
DESCRIPTION
        perform in silico base mutations of 3-dimensional nucleic acid
        structures, with two key and unique features: (1) the sugar-
        phosphate backbone conformation is untouched; (2) the base
        reference frame (position and orientation) is reserved, i.e.,
        the mutated structure shares the same base-pair/step
        parameters as the original one.
        -e    enumeration of all bases in the structure
        -l    name of file, containing list of mutations
        'mutinfo' can contain upto 5 fields for each mutation
                  [name=residue_name] [icode=insertion_code]
                  chain=chain_id seqnum=residue_number
                  mutation=residue_name
            The five fields per mutation can be in any order or CaSe.
            Each field can be abbreviated to its first character.
            Multiple mutations specified per line are separated by ';'.
            Fields in [] (i.e., name and icode) are optional.
            Mutation info should be QUOTED to be taken as one entry.
INPUT
        Nucleic-acid-containing structure file in PDB format
EXAMPLES
            # mutate G2 in chain A of B-DNA 355d to Adenine
        mutate_bases 'c=a s=2 m=DA' 355d.pdb 355d_G2A.pdb
            # mutate the second base-pair G-C to A-T in 355d
        mutate_bases 'c=a s=2 m=DA; c=B s=23 m=DT' 355d.pdb 355d_GC2AT.pdb
            # the above also generates file 'mutations.dat'
            # and the following command gives the same results
        mutate_bases -l mutations.dat 355d.pdb 355d_GC2AT_v2.pdb
            # mutate C74 in chain A of tRNA 1evv to U       
        mutate_bases 'c=A s=74 m=U' 1evv.pdb 1evv_C74U.pdb
            # list all bases to be tailored for mutation
        mutate_bases -e 355d.pdb stdout
OUTPUT
        mutated structure in PDB format, sharing the same backbone
        conformation and base pair parameters as the original one.
SEE ALSO
        analyze, find_pair, rebuild
AUTHOR
        3DNA v2.1 (c) 2012 Dr. Xiang-Jun Lu (http://x3dna.org)

Now let's take advantage of the web to illustrate the key features of mutate_bases using a set of worked examples. The scripts and corresponding data files & images are attached, so you can repeat the procedures in order to have a better understanding of how the program works.

In our GpU dinucleotide platform paper, we reported a previously unnoticed intra-dinucleotide sugar-phosphate H-bond that is unique to the GpU platform. This O2′(G)···O2P(U) H-bond readily rationalizes the over 60% occurrence of GpU over other platforms (e.g., ApA and UpC). Moreover, this H-bond has recently been validated by state-of-the-art quantum-chemical techniques.

In this section, we will use mutate_bases to answer the questions of (1) why GpU, not GpT? i.e., why the GpU platform is RNA-specific? (2) why no UpG platforms observed? i.e., why the GpU platform is directional? The GpU platform (1msy_gu.pdb) is derived from PDB entry 1msy. The figure below shows the identity of the two nucleotides (G2655 and U2656 on chain A) and names of the base atoms.

"GpU platform" title="GpU platform"

  • Why no GpT platform?
    mutate_bases 'c=a s=2656 m=t' 1msy_gu.pdb 1msy_gt.pdb
    With the above command, we mutate U (which is residue #2656 on chain A) to T (see figure below). Clearly, the methyl group of T protrudes into the pocket, causing steric clash. Thus GpT is incompatible with the platform conformation.

    "GpT platform?" title="GpT platform?"

  • Why no UpG platform?
    mutate_bases 'c=a s=2655 m=u; c=a s=2656 m=g' 1msy_gu.pdb 1msy_ug.pdb
    Using the above command, we mutate G (which is residue #2655 on chain A) to U, and U to G simultaneously. That's what the plural 's' in mutate_bases stands for. From the figure below, one can see clearly that no intra-base H-bond is now possible, consistent with the fact that no UpG platform has been observed.

    "no UpG platform!" title="no UpG platform!"

    Note that the above command also generates a file named 'mutations.dat', which has the following content:
    c=a s=2655 m=u
    c=a s=2656 m=g
    You can then use the -l option of mutate_bases as such:
    mutate_bases -l mutations.dat 1msy_gu.pdb 1msy_ug2.pdb.
    The two mutated PDB files, 1msy_ug.pdb and 1msy_ug2.pdb, are identical.
You can run find_pair and analyze to the raw and mutated PDB files and verify that they indeed have the same base-pair parameters and backbone conformation.

To summarize, here is the command-script:
Code: [Select]
mutate_bases 'c=a s=2656 m=t' 1msy_gu.pdb 1msy_gt.pdb
mutate_bases 'c=a s=2655 m=u; c=a s=2656 m=g' 1msy_gu.pdb 1msy_ug.pdb
mutate_bases -l mutations.dat 1msy_gu.pdb 1msy_ug2.pdb

The PDB files referred:

Note all the images used in this post were generated using Jmol. As much I like RasMol (v2.6.4), I am now gradually switching to Jmol and PyMOL.
« Last Edit: April 21, 2012, 09:04:21 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.