Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Download/Licensing · {Video Overview of DSSR}

Messages - kogucior

Pages: [1]
1
RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 28, 2021, 11:35:38 am »
Ok, I'll check these structures, but it looks like our discussion goes beyond the canonical G-quadruplex structures (think in Webb da Silva's convention), hence the problems.
I look forward to the update if everything will be clearly explain in the publication. However, I hope that the "new convention" will be consistent with eg interpretations of CD spectra.
Unfortunately I am using the basic version of DSSR,  I have to think about buying the PRO version.

2
RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 27, 2021, 10:56:19 am »
Quote
loop#1 type=propeller strands=[#1,#4] nts=1 C A.DC5
    loop#2 type=propeller strands=[#4,#3] nts=5 CACGA A.DC9,A.DA10,A.DC11,A.DG12,A.DA13
    loop#3 type=propeller strands=[#3,#2] nts=1 A A.DA17

I still have doubts about assigning strand numbers, e.g. loop #1 in my opinion occurs between strand #1 and #2. Until now I thought that the order of the strands is due to their relative arrangement in the space and that the counting starts at the 5'-end and goes counterclockwise.

3
RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 27, 2021, 07:10:42 am »
Quote
As long the first G is in syn conformation, you will observe the same behavior for other G4 structures in DSSR-G4DB. The results should be self-consistent.

I don't understand why the anti/syn conformation is having an effect on this. Theoretically, according to the Webba da Silva formalism [Geometric Formalism for DNA QuadruplexFolding] -P-P-P and +P+P+P topology may have a composition of fully syn or anti G-tetrad.

If the topology determination is based on the syn/anti  composition of 4 guanines in G-tetrad then I would expect +/-(LPP) topology for 2kqg. While the identical structure (2kqh) has a -P-P-P topology.

I expected that the order of the guanines in the planes is based on the order in sequence and the interaction edge (WC or H) with the other adjacent guanines.

4
RNA structures (DSSR) / Re: Incorrect topology assignment
« on: May 27, 2021, 07:01:39 am »
Quote
As another concrete example, what do you think the descriptor for PDB entry 6r9k should be?

I believe it should be as it is currently described as: +L+P+P.

5
RNA structures (DSSR) / Incorrect topology assignment
« on: May 26, 2021, 10:57:27 am »
Dear Dr. Xiang-Jun Lu,

I was browsing prepared by you the G-quadruplex database (DSSR-G4DB) and I
encountered an error.
I think that for "http://g4.x3dna.org/entries/2kqg/index.html" the
"+P+P+P" topology is wrongly assigned, it should be "-P-P-P".
I discovered that maybe this is due to a mis-ordering of G-strands
(#1-#4-#3-#2), where the first plane has a composition:
1 glyco-bond = s --- groove = w - n Major -> WC nts = 4 GGGG A.DG2,
A.DG18, A.DG14, A.DG6

and it should have:

1 glyco-bond = s --- groove = w - n Major -> WC nts = 4 GGGG A.DG2, A.DG6,
A.DG14, A.DG18

It is possible that there are more mistakes. I am curious what they come
from and I am looking forward to the revised version of the database.

Pages: [1]

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.