Topics

1

RNA structures (DSSR) / How to detect very distorted base pair?

« on: January 20, 2020, 05:09:25 pm »

Dear Xiangjun,

I have a structure of a very distorted G-C base pair (C is modified) see attached. I want to output the base pair parameters like shear, buckle, opening but if I detect the base pair in DSSR it is not in the pair list. Could you please let me know how to analyze such very distorted base pair? Do I need to modify any cutoff?

Thanks.

Best,
Honglue

2

DNA/RNA-protein interactions (SNAP) / About sugar-pi stacking

« on: October 17, 2019, 04:36:41 pm »

Hi Xiangjun,

Is sugar-pi stacking currently implemented in the most updated version of SNAP? I am trying analyze the TBP-DNA interaction by using SNAP (PDB: 1QNE)

In the paper: Wilson, K. A., et al. (2014). "DNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar." Nucleic Acids Res 42(10): 6726-6741. (https://academic.oup.com/nar/article/42/10/6726/2435280).

The author detect four sugar-pi interaction in the supplementary table.

Amino Acid         Nucleotide
Res Chain ResID Res Chain ResID
F   A   74    A   C   209   sugar-π
F   A   165    T   D   225   sugar-π
F   A   148    A   C   204   sugar-π

When I tried to use x3dna-snap to analyze the structure by typing:
x3dna-snap -i=1qne.pdb --t-shape --more

The output seems only report nt-AA pi-pi stacking.
****************************************************************************
List of 2 base/amino-acid stacks
       id   nt-aa   nt           aa      vertical-distance   plane-angle
   1  1qne  A-phe  C.DA204      A.PHE148        3.45             18
   2  1qne  T-phe  D.DT220      A.PHE57         3.57             23

Could you please let me know whether this is what we expected? Do you know if there are other softwares that can be used to analyze the stacking interaction in general between protein and DNA?

Thank you so much.

Best,
Honglue

3

RNA structures (DSSR) / strange exception

« on: June 30, 2019, 08:48:31 pm »

Hi Xiangjun,

I was trying to use DSSR to parse this attached PDB file.

x3dna-dssr -i=S_000300_115.pdb

However, the program complain an error:

Command: x3dna-dssr -i=S_000300_115.pdb
Date and time: Sun Jun 30 20:57:27 2019
File name: S_000300_115.pdb
    no. of DNA/RNA chains: 1 [_=25]
    no. of nucleotides:    25
    no. of atoms:          796
    no. of waters:         0
    no. of metals:         0
    total number of base pairs: 11
    total number of multiplets: 1
    total number of helices: 2
    total number of stems: 1
    total number of isolated WC/wobble pairs: 3
    total number of atom-base capping interactions: 1
    total number of splayed-apart dinucleotides: 3
    total number of hairpin loops: 1
Uncaught exception 'Assertion failed' raised at [fncs_loop.c:1564]
aborting...

Do you know what is going on?

Thanks.

Best,
Honglue

4

DNA/RNA-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

5

RNA structures (DSSR) / Can DSSR detect stacking interaction between ligand and nucleic acid

« on: November 16, 2017, 11:22:19 pm »

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

6

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

7

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

8

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

9

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

10

General discussions (Q&As) / Definition of gauche and trans for gamma torsion angles

« on: May 15, 2017, 02:30:20 pm »

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

11

RNA structures (DSSR) / Can we output helix-junction-helix structure using DSSR

« on: April 28, 2017, 02:54:44 pm »

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

12

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

13

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

14

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

15

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

16

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

17

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

18

General discussions (Q&As) / epsilon and zeta should be 5'-end or 3'-end of sugar

« on: December 23, 2016, 07:41:03 pm »

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

19

General discussions (Q&As) / How to build different sugar pucker model

« on: December 14, 2016, 03:06:14 pm »

Hi, xiangjun,

How is everything going?

I have a question about how to build a model sugar with different sugar pucker? I am assuming there is an easy way to do that but I don't know.

I know that you can calculate v0-v4 based on equation:ν_i = τ_m*cos(P+144(i-2))
Every time when I adjust v0-v4 dihedral angle in pymol or Gaussian, those dihedral angle always change correlated (because they are linked), like if you vary v0, then v1, then v2, then v3, then v4, and after that you go back to v0, the v0 will change again. Besides, the sugar Carbon Carbon bond length will also vary in this procedure.

I guess I am just wandering is there any way to synthesize a sugar model yielding an exact phase angle and amplitude (also better control bond length) as what I want.

The reason why I want to build this model because I want to perform DFT chemical shift calculation on different sugar pucker. The annoying thing is DFT is sensitive to certain bond length or bond angle, that's why I want to do a good control of these detail.

Thank you so much.

Best,
Honglue

20

RNA structures (DSSR) / Hoogsteen base pair coordinate frame

« on: August 29, 2016, 06:18:47 pm »

Hi, xiangjun,

I hope you have a good time.

Recently, I am analyzing a 12-mer DNA (MD trajectory) with N1-methyladenine in ADE16 which adopt a syn conformation and form Hoogsteen base pair with THY9. When I use X3DNA to analyzing it, I find some parameters are kinda wired. I analyze the base pair parameters in 3-22, 4-21, 5-20, 6-19, 7-18, 8-17, 9-16, 10-15 bps and step and helical parameters in 3-4, 4-5, 5-6, 6-7, 7-8, 8-9. 9-10.

First, let's just look at the analysis of first snapshots in this MD simulation (A6me_50ps.pdb).
(1) Base pair parameters: There are clear differences in the 9-16 step (HG base pairs) like shear, stretch and especially opening.
(2) Step and helical parameters: There are some sort of difference in tilt, twist, inclination.

My first question is: Where are these difference come from. I know that you define a coordinate frame for idealized DNA before analyzing, but is this definition also applied to Hoogsteen base pair? Do we need to redefine a coordinate frame for Hoogsteen base pair when we want to analyzing base pair parameters (or just use the idealized coordinate frame)? Are the step and helical parameters also intrinsically influenced by the coordinate frame of Hoogsteen base pair so we should expect to see these difference?

I also attach the full MD trajectory analysis for your reference. Some parameters' error bar is very large like x-displacement, y-displacement, that could be due to some MD issue which I plan to double check that.

Many thanks,

Best,
Honglue

21

RNA structures (DSSR) / A question about base inclination

« on: August 24, 2016, 09:28:49 am »

Hi, xiangjun,

I read a paper about A-tract DNA and it seemed that they reported base inclination for two base in a base pair respectively.

(MacDonald, D., et al. (2001). "Solution structure of an A-tract DNA bend." J Mol Biol 306(5): 1081-1098.)

But in DSSR there is only one inclination value in helical parameters. I am wondering are they the same definition?

Thank you so much for your help.

Best,
Honglue

22

RNA structures (DSSR) / How to calculate groove parameters

« on: August 22, 2016, 02:35:23 pm »

Hi,

Can we calculate groove parameters (like major groove width, minor groove depth etc.) in dssr?

Best,
Honglue

23

RNA structures (DSSR) / How to change the criteria of base pair

« on: July 27, 2016, 06:06:35 pm »

Hi,

I am using DSSR to find base pairs in a DNA duplex MD structure. It is a 12-mer DNA duplex which I expect there should be only 12 canonical base pairs. However, DSSR told me there are 13 base pairs which means it over counted one base pair. Is there any way to change the criteria to define a base pair (like hydrogen bond length) in DSSR?

I would really appreciate your reply.

Best,
Honglue