RE: Modeling of RNA duplex with MD force field

[Yuki Toyama]

Dear Samuel,

I have been using MacroMolecularBuilder to model a duplex structure of self-complementary RNA. My main goal is to calculate a bunch of 1H-1H distances of a typical A-form duplex that was used in my NMR experiments. Several programs, such as Avogadro and PyMOL, have an option to model nucleic acid from scratch. However, I found that these programs cannot easily model double-stranded RNA. In this regard, MMB can model DNA and RNA duplexes of any arbitrary sequence, which is very useful. During the course of my initial attempts, I found some interesting behaviors. I am a novice in this field, so I would like to confirm whether I am doing it right and ask for your expert opinion. I am using MMB 3.4 for Windows.

First, I modeled the structure of the A-form duplex of self-complementary RNA (5-UUAUAUAUAUAUAA-3) using the code below by referring to "commands.DNA-helix.dat" in the example directory. The crystal structure of the A-form duplex of this sequence is available (PDB ID: 1RNA), so I chose this sequence as a benchmark.

===========================
RNA A 1 UUAUAUAUAUAUAA
RNA B 1 UUAUAUAUAUAUAA
reportingInterval 4.0
numReportingIntervals 20
temperature 10
firstStage 1
lastStage 1
baseInteractionScaleFactor 200
nucleicAcidDuplex A 1 14 B 14 1
===========================

The obtained structure (magenta) was in good agreement with the crystal structure (cyan) with an RMSD value of >2 A as shown in the attached Figure 1, which is quite impressive.

Figure 1

magenta_sim_cyan_1RNA.png (67.1 KiB) Viewed 124 times

Then, I wondered whether I can obtain a better structure by incorporating an MD force field into the calculation. To achieve this, I added an additional step and turned on "setDefaultMDParameters" only in the second stage. The reason for this is that the two strands did not interact with each other when I activated the force field from the beginning.

===========================
RNA A 1 UUAUAUAUAUAUAA
RNA B 1 UUAUAUAUAUAUAA
reportingInterval 4.0
numReportingIntervals 10
temperature 10
firstStage 1
lastStage 2
baseInteractionScaleFactor 200
nucleicAcidDuplex A 1 14 B 14 1
readAtStage 2
setDefaultMDParameters
readBlockEnd
===========================

Interestingly, the above script gave a structure that looks more extended than a conventional A-form duplex (see the attached Figure 2. Magenta: MMB model, Cyan: Crystal structure).

Figure 2

magenta_sim_cyan_1RNA_MD.png (51.34 KiB) Viewed 124 times

It seems to me that the application of the force field makes the structure to be too extended, and the structure obtained without adding any force field is actually more in line with the known A-form duplex. This is contrary to my expectation that the application of the force field should yield a more physically reasonable structure.

So my question is why does the application of "setDefaultMDParameters" result in the more extended structure? I also tried adding NtC commands (NtC A 1 14 AA00 1.5, NtC B 1 14 AA00 1.5), but the result was very similar.

I would appreciate it if you could take a look at the script and comment on it whenever you have the chance.

Best regards,

Yuki

[Samuel Flores]

Toyoma san Konbanwa!

MD of nucleic acids is quite complex, you would need to add counterions and water. Even then, MMB is not really an MD code.

You might want to try nucleotide conformers. These will improve the backbone structure. should be available in versions 3 and 4, download that and then look in the docs

sam

[Yuki Toyama]

Dear Samuel,

Thank you so much for the quick reply! I did try the Ntc module to stabilize the A-form geometry, but still the MDparam tends to make my duplex extended. It makes sense that we do not have any solvent molecules and counter ions, so modeling the highly charged molecule is going to be very difficult. It was good to know that MD of nucleic acids is so complicated. Even for a simple duplex, it is not straightforward to calculate the structure!

Cheers,

Yuki