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Topics - lvelve0901

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1
DNA-protein interactions (SNAP) / Implement Json
« on: March 10, 2018, 09:43:32 pm »
Hi Xiangjun,

Do you plan to implement Json output for SNAP?

Best,
Honglue

2
Hi Xiangjun,

My new target structure is 1F1T from RCSB. It is a malachite green aptamer with a ligand called N,N'-TETRAMETHYL-ROSAMINE (ROS).
If you go to the PDB website and search for this PDB, you can see there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

Here, I also attach the PDB file and json file that I generated for your convenience.

Best,
Honglue




3
RNA structures (DSSR) / General questions of H-bond section in DSSR
« on: November 01, 2017, 11:37:03 am »
Hi Xiangjun,

Sorry I gave a long list of questions yesterday. Here, I just post a few questions in terms of the H-bond in DSSR json.

For the H-bond between protein/peptide/ligand to nucleic acid, my target structure is 1PFE, which is a DNA bound to an antibiotic, echinomycin. I downloaded the biological assembly file and used the following command:

x3dna-dssr -i=1PFE.pdb -o=1PFE.json --json --more --symm

In the "hbonds" session of the output json file, I did found the all the DNA-drug interactions. For example,

{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}

However, I have a few questions in terms of the hbonds output.

(1) How do I know which atom is H-bond donor and which is acceptor, like do you always put acceptor in the first place(atom1)?
(2) If the 'donAcc_type' is questionable, what does it mean? Does it mean that DSSR probably doesn't guess the valence properly?
(3) Wha does the 'serNum' mean here?

Here, I attached all my files.

Thank you.

Best,
Honglue

4
RNA structures (DSSR) / Can DSSR detect nucleic acid ligand interaction
« on: October 31, 2017, 03:48:34 pm »
Hi Xiangjun,

I am just curious whether DSSR can detect something like RNA and ligand/metal interaction in a PDB file.
For example, list all the hydrogen bond between RNA and ligand?

Best,
Honglue

5
RNA structures (DSSR) / FRABASE
« on: October 18, 2017, 11:35:30 am »
Hi Xiangjun,

Do you have any idea that how different between DSSR and some online RNA database such as FRABASE in terms of secondary structure identification.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-231

Thanks.

Best,
Honglue

6
RNA structures (DSSR) / Bulge motif
« on: August 21, 2017, 11:27:58 am »
Hi Xiangjun,

Long time no contact. How is everything going?

I am using DSSR to analyze the structure 1FUF to look for bulge motif.

The DSSR tells me there are two bulge motif in this structure. However, some of the bulge residue base have contact with other base and forms a base triple. I am not sure if these count some additional bulge or other motif?

In general, could you tell me how 3DNA detect secondary motif like bulge or internal loop? Is it just based on dot-bracket notation?

Best,
Honglue

7
Hi Xiangjun,

I have a general question about the definition of gamma torsion angles in 3DNA.

I read some paper about gamma torsion angles and it seems the angular space for the angles are from -360 ~ 360 degree.

For example, in paper titled "Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves" The paper defined

Values of γ angle were classified according to
classical three-fold pattern into: gauche + (60° ± 30°),
trans (180° ± 30°), gauche – (300° ± 30°) conformations.


However, in 3DNA, the angular space of gamma is from -180 --> 180. So I am wondering whether there is any degeneracy in the angular space defined in 3DNA?

Best,
Honglue





8
Hi Xiangjun,

I know that when you run x3dna-dssr on a RNA structure. You can output secondary motif like bulge, hairpin, internal loop etc as a pdb file.
But is there any way that we can search and output structures called helix-junction-helix motif. Junction means either internal loop or bulge while helix means helices with 3 bps.

For example, in 1anr.pdb (HIV-1-TAR), when you run DSSR, there are a dssr-iloops.pdb.
That dssr-iloops file only have G21 A22 U23 C24 U25 G26 C39 U40 C41.
My question is is there any way to also output C19 A20 U42 G43 and A27 G28 C37 U38 to make the stem part like 3 bps long? I plan to calculate inter-helical angles for these helix-junction-helix motif across all the pdb structures. If there is no such option in DSSR, I might have to think about it by myself.

Thank you.

Best,
Honglue

9
RNA structures (DSSR) / How to look for abasic site using DSSR
« on: April 26, 2017, 12:50:57 pm »
Hi Xiangjun,

Long time no contact. I hope you had a good time recently.

I have a question about DSSR. Can DSSR detect abasic site?

For example, in 1l2c.pdb and 1l2d.pdb, there is a abasic site HPD18DG7. I thought this could be written in internal loop; however, the internal loop only detect a lower base pair open (DA23DT2).

Best,
Honglue

10
General discussions (Q&As) / nucleic acid sugar structure
« on: February 21, 2017, 01:13:21 pm »
Hi, xiangjun,

Here is the snapshot of a deoxyribose in a idealized B-form generated by 3DNA and some distance and angle measurement.

I am just curious where these bond length and bond angle details come from. How do you build the idealized model? Is it purely from previous crystal structure or literature. Or you build them based on your own criteria.

Best,
Honglue

11
General discussions (Q&As) / Swap the dinucleotide step index
« on: February 09, 2017, 05:39:06 pm »
Hi, xiangjun,

I have a general question about the coordinate frame.

For a given dinucleotide step, you can swap the dinucleotide step (5'-CA-3' ==> (3'-AC-5') 5'-TG-3') by renumber the residue id and the sign of shear, buckle, shift, tilt, y-displacement and tip will also be swapped.

Could you kindly explain to me? Is it because the coordinate frame changes? Does that mean we should be cautious to interpret the sign of those parameters above when we analyze structure?

Best,
Honglue

12
RNA structures (DSSR) / Definition of Helix Form
« on: February 07, 2017, 10:44:31 pm »
Hi, xiangjun,

How is everything going?

In DSSR helices section, there is helix-form part including 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone.

My question is:
How do you identify the the helix form? Which parameter did you use to define the 'A' 'B' 'Z' form?

Best,
Honglue

13
RNA structures (DSSR) / Groove width distance in DSSR
« on: January 25, 2017, 04:58:23 pm »
Hi, xiangjun,

Did DSSR output json files have minor groove width information?

If so, could you kindly tell me where is it stored in the json file?

Best,
Honglue

14
General discussions (Q&As) / pdb files with multiple coordinates
« on: January 06, 2017, 04:56:56 pm »
Hi, xiangjun,

I have some pdb files from crystal structures which have multiple coordinates for certain atoms and when I do 3DNA to analyze it, what is the exact result, is it average result?

Best,
Honglue


15
Hi, xiangjun,

I am confused about the phosphorous label in DNA.

Normally, phosphorous of a given NTP is the one connected to the 5'-end of sugar right?
So when we say phosphorous of a DA or DT etc., we mean 5'-phosphorous of DA and DT, is it correct?

However, epsilon and zeta by definition is at the 3'-end of a sugar (related to BI/BII). So when we say BI/BII of a residue, it is related to the 3'-end of the phosphorous which is the next residue's phosphorous, am I right?

The reason why I ask this question is I find that some papers label the 31P to be 3'-end of the sugar and other label the 31P to be 5'-end of the sugar which are not consistent.

Is there any standard opinion about which phosphorous belongs to which residue?

Thanks.

Best,
Honglue


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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.