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Author Topic: Strange bp parameters in 1FFK  (Read 4245 times)

Offline febos

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Strange bp parameters in 1FFK
« on: November 05, 2015, 03:33:58 am »
Good Afternoon, Dr. Lu.

I've noticed some strange numbers in the 1st bp in the 1FFK file (in pdb format):

Code: [Select]
   nt1            nt2           bp  name        Saenger    LW  DSSR
   1 .0.U.12.       .0.G.531.      U-G --          n/a       tHS  tM-m
       [-171.2(anti) ~C3'-endo lambda=8.4] [-159.4(anti) ~C3'-endo lambda=97.9]
       d(C1'-C1')=10.93 d(N1-N9)=9.76 d(C6-C8)=10.33 tor(C1'-N1-N9-C1')=-76.3
       H-bonds[1]: "O4(carbonyl)-N2(amino)[2.99]"
       interBase-angle=12  Simple-bpParams: Shear=-7.49 Stretch=3.77 Buckle=-5.4 Propeller=10.8
       bp-pars: [-7.75   -3.20   0.40    -11.69  2.97    -4.39]

in all other basepairs there is a respectivity (is it a right word?) between "Shear=" and №1 of "bp-pars"; "Stretch=" and №2; "Buckle=" and №4; "Propeller=" and №5.
But in this bp there is no such thing. Do I missing something or it is in fact a bug? And which parameters are actually real?

Best regards,
Eugene

Offline xiangjun

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Re: Strange bp parameters in 1FFK
« Reply #1 on: November 05, 2015, 06:41:20 am »
Hi Eugene,

Thank you for your question regarding the two sets of base-pair (bp) parameters. I am glad that you pay attention to this 'little' detail, because it is quite subtle and take some effort to really make sense of.

Please read the following two blog posts to get the background information why the 'Simple-bpParams' came into being.
By and large, the set of 'simple' bp parameters was inspired by a recent article, titled "A context-sensitive guide to RNA & DNA base-pair & base-stack geometry",  by Dr. Jane Richardson, published in CCN (Computational Crystallography Newsletter, 2015, 5, 42—49). Highlighted in the article are Buckle and Propeller twist, two of the angular parameters to characterize bp non-planarity.

Both set of parameters are 'correct': they represent different perspectives of seeing the same 'real' world. Using U12–G531 in 1ffk as an example, the 'Simple' Propeller is +11.8º which matches more 'intuitively' the image below; the 'rigorous' Propeller is +2.97º, which appears to a bit 'too' small. More strikingly, the signs of Stretch are opposite in this example. You will notice quite different values in different ways for non-canonical pairs.


Technically, the differences come from the reference frames used. The 'simple' set is just for getting a set of parameters for 'description' only, and it makes more 'intuitive' sense (per Jane Richardson) without considering rebuilding. The six rigid-body parameters as in the original 3DNA program are rigorous, and can be used for exact reconstruction of the corresponding bp geometry. These two sets match very well for the most common Watson-Crick bps, but differ to various extent for non-canonical pairs.

HTH,

Xiang-Jun
« Last Edit: November 05, 2015, 06:58:39 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline febos

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Re: Strange bp parameters in 1FFK
« Reply #2 on: November 06, 2015, 11:14:47 am »
Dr. Lu,

Thank you for your explanation.
I will read those blog posts and the article of Richardson.
I think I will be able to understand the difference between two sets of parameters after that.

Best regards,
Eugene

 

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.