URL:
<http://gna.org/support/?3127>
Summary: Opposite S2 values to expected
Project: relax
Submitted by: soumya__joseph
Submitted on: Wed 05 Mar 2014 06:33:41 UTC
Category: None
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Assigned to: None
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: GNU/Linux
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Details:
Hi,
I've conducted model-free analysis on relax using relaxation data (T1, T2 adn
NOE) collected on 600 and 800 MHz instruments. I used the GUI with the default
settings except for estimated rotational correlation time (for me it is 5 ns).
My S2 order parameters are the inverse of what I expect. Disordered regions
appear to have values closer to one and regions I know are structured have
values that are closer to zero (see attached). The errors associated with the
"ordered" NHs are quite large whereas those for dynamic residues are smaller.
Here's what I observed. The calculation ran without any errors. It took about
three days to run with a single processor. Is that normal or is there
something wrong here?
I have conducted consistency tests on these data. I guess I'd like to know
what the threshold might be for something that has a Tc = 5 ns.
My protein behaves as a single domain to the best of my knowledge. It is
actually a tethered complex between two proteins but they bind each other. The
dynamic region near the C-terminus is the glycine-serine loop that connects
the two entities. I don't believe it comes apart very often as one of the
proteins precipitates if left on its own.
There appears to be no concentration-dependent dimerisation. The HSQC spectra
of the protein at 0.04 and 0.6 mM look identical.
The relaxation data for the 600 and 800 MHz exp are attached. The S2 has also
been graphed. Does anyone know why my S2 parameters are the opposite to what
I'm expecting?
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wed 05 Mar 2014 06:33:41 UTC Name: 800 rlx data.png Size: 78kB By:
soumya__joseph
T1, T2 and NOE relaxation data at 600 and 800 MHz and calculated S2 order
parameters.
<http://gna.org/support/download.php?file_id=20264>
-------------------------------------------------------
Date: Wed 05 Mar 2014 06:33:41 UTC Name: relax600800_S2.png Size: 93kB By:
soumya__joseph
T1, T2 and NOE relaxation data at 600 and 800 MHz and calculated S2 order
parameters.
<http://gna.org/support/download.php?file_id=20265>
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<http://gna.org/support/?3127>
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