Hi Dale and Cecil,
This is quite a circular argument, isn't it? Deficient NOE's for some regions
(e.g. loops) arise from their flexibility, hence they are not as well resolved
as other (e.g. internal ) regions for which the number of NOE is large. So they
are flexible by all accounts and, not surprisingly, align usually with high
B-factor regions in the corresponding crystal structures. In cases where such
flexible regions are held by crystal contacts the situations would likely be
different.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale Tronrud
<de...@daletronrud.com>
Sent: Wednesday, May 26, 2021 10:46 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Analysis of NMR ensembles
I agree with Dr Breyton. The variability in an NMR ensemble does not
reflect "mobility" but simply "uncertainty" in conformation. The spread
in coordinates in some regions simply reflects the lack of experimental
data which could define a single conformation. There are many reasons
why these data are be absent and high mobility is only one.
Dale Tronrud
On 5/26/2021 8:45 AM, Cécile Breyton wrote:
> Hello,
>
> In my understanding of NMR, the loops and terminii that adopt very
> different conformations in the structure ensemble rather reflect the
> fact that for those residues, the number of constraints is lower, thus
> the number of structures that fulfil the constraints is larger.... A
> dynamics study of the protein will be much more informative.
>
> Cécile
>
> Le 26/05/2021 à 17:29, S. Mohanty a écrit :
>> Hi Harry,
>>
>> The superpose/overlay of all the structures in PyMol should inform you
>> the rigid part of the protein as well as the flexible part. The rigid
>> part would have very low backbone RMSD or overlay tightly and the
>> flexible part (loops, N-term and C-term etc.) would not superpose
>> tightly. If you check literature, the dynamics of the protein may have
>> been studied through NMR relaxation.
>>
>> Smita
>>
>>
>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB
>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Hi
>>
>> Given that there are plenty of people on this BB who are structural
>> biologists rather than “just” crystallographers, I thought someone
>> here might be able to help.
>>
>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of
>> structures that fit the NOEs, is there a tool available that will give
>> me some idea about the bits of the structure that do not vary much
>> (“rigid”) and the bits that are all over the place (“flexible”)?
>>
>> Would superpose or gesamt be a good tool for this? Ideally I’d like
>> something that could add a figure to the B columns in a PDB file so I
>> could see something in QTMG (or PyMol if forced…) or do other useful
>> things with the information.
>>
>> Harry
>>
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