Hi,
I agree with you, Alex. You're right, this small difference of 2 ppm
for the CSA is quite small compared to the real deviation observed
experimentally...
However, since few people actually measure the 'real' csa, I think that
the best available approximation should be the default and that relax
should promote a consistent use, for better comparison between
published studies...
Also, I think that these default values (for csa and r, for example)
should be the same throughout all the relax program, for more
consistency... Maybe, in the 1.3 line, these default values should be
in a common file so that the jw_mapping and consistency_tests codes
(and others if so) could use the same default values. (Maybe this has
been discussed before...)
Ok.
Cheers !
Séb :)
Alexandar Hansen wrote:
I'm not a protein expert, but unless you're at ~GHz
fields, a 2 ppm
difference in 15N CSA magnitude is going to be negligible. The error
in the site-by-site CSA is going to be ~5-10 ppm, if not more,
anyways. The important thing, I imagine, is that you know what the
value you are using is and what assumptions are involved (ie.
collinearity with NH bond, symmetric CSA tensor).
Alex Hansen
On 7/16/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx>
wrote:
Hi,
It's been a long time since we discussed this (the CSA / bond length
issue in spin relaxation analysis).
I would agree in using a combination of 1.02 A for bond length and -172
ppm for CSA (for 15N-1H vectors).
Should the default values in the relax code be modified, changing the
CSA from -170 (at least in the jw_mapping code) to -172 ppm ?
Cheers
Séb :)
Edward d'Auvergne wrote:
> There has been much work describing the importance of the CSA and
the
> bond length. It would be interesting to see how much of a
difference
> measuring the CSA (and the bond length) would make to the final
> dynamic results. As Sébastien said, the 1.04 Angstrom bond length
> should be used with a lower CSA value. My preference though would
be
> to use -172 ppm together with 1.02 Angstrom.
>
> Edward
>
>
> On 9/30/06, Michael S. Marlow <marlowms@xxxxxxxxxxxxxxxxxx>
wrote:
>> I agree with the value of -170. Here are my favorite
references:
>>
>> Variability of the 15N Chemical Shift Anisotropy in
Escherichia coli
>> Ribonuclease H in Solution
>> Christopher D. Kroenke, Mark Rance, and Arthur G. Palmer, III
>> J. Am. Chem. Soc.; 1999; 121(43) pp 10119 - 10125
>> "For this data set, the values of are approximately Gaussian
>> distributed with a
>> mean of -172 ± 13 ppm."
>>
>> Protein Backbone Dynamics and 15N Chemical Shift Anisotropy
from
>> Quantitative
>> Measurement of Relaxation Interference Effects
>> Nico Tjandra, Attila Szabo, and Ad Bax
>> J. Am. Chem. Soc.; 1996; 118(29) pp 6986 - 6991
>> Essentially the same value, but identified larger outliers
>>
>> Another aspect of this thread which has not received much
attention
>> is the bond
>> length. The refence below suggest 1.04 Angstroms.
>>
>> Determination of Relative N-HN, N-C', C-C', and C-H Effective
Bond
>> Lengths in a
>> Protein by NMR in a Dilute Liquid Crystalline Phase
>> Marcel Ottiger and Ad Bax
>> J. Am. Chem. Soc.; 1998; 120(47) pp 12334 - 12341
>>
>> Mike
>> --
>> Michael S. Marlow, Ph.D.
>> Department of Biochemistry and Biophysics
>> University of Pennsylvania
>>
>>
>> Quoting Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>:
>>
>> > Salut Séb, welcome to the relax users mailing
list. Thank you for
>> > responding Alex. The CSA value is important as the
example shows.
>> > However I would call this a 'fringe' example as it
represents a highly
>> > restricted nanosecond motion. The relaxation data for
this example
>> > was generated by back calculation using the CSA value of
-160 ppm.
>> > Although as Alex pointed out relax is capable of
optimising the CSA
>> > value, I would be wary of these models as they are
essentially
>> > untested. I've played around with the models a little
and I have a
>> > feeling that the R1, R2, and NOE values are not
sufficient to tease
>> > out the CSA. To test these models using just the R1, R2,
and NOE at
>> > multiple field strengths, the CSA would need to be
accurately measured
>> > using one of David Fushman's techniques (I'll talk about
this next)
>> > and the values compared to those fitted using the models
built into
>> > relax.
>> >
>> > I believe that the value of -160 ppm was determined by
solid state NMR
>> > of small peptides (it's been a few years since I read the
litterature
>> > on the CSA value in proteins, so I could be
wrong). However a number
>> > of publications have demonstrated that the average CSA
value in
>> > solution is higher. I would say that the authorative
expert in the
>> > field is David Fushman. The JACS reference you cite is
just one of
>> > many of his publications on measuring the CSA. He has
demonstrated,
>> > using I think three different techniques now, that the
CSA in proteins
>> > is highly variable.
>> >
>> > Idealy for highly accurate model-free analysis, the CSA
value should
>> > be determined either prior to or during model-free
analysis using one
>> > of his techniques. However most people appear happy to
just set the
>> > CSA value to either the 'ancient' value of -160 ppm or
the solution
>> > average of -170 ppm (David's work again). Using the data
you have
>> > currently collected, I would personally use the value of
-170 ppm. Is
>> > the value of -172 ppm from the Hall and Fushman paper you
cited? I
>> > haven't read that paper yet.
>> >
>> > Edward
>> >
>> >
>> > P.S. I might change the sample scripts to -170 ppm. I
had intended
>> > to change the value a while back but forgot about it.
>> >
>> >
>> >
>> > On 9/30/06, Sebastien Morin <sebastien.morin.1@xxxxxxxxx>
wrote:
>> > >
>> > > Hi again
>> > >
>> > > Thanks for your answer !
>> > >
>> > > I think that, for me, the CSA value would have a
significant
>> impact on my
>> > > analysis since my protein has a tumbling time of
about 13 ns and
>> I have
>> > data
>> > > from 500, 600 and 800 MHz...
>> > >
>> > > I don't know if this is relevant, but I performed
simple tests
>> with the
>> > > test data and sample scripts provided with relax
(path :
>> > >
'relax/test_suite/data/model_free/S2_0.970_te_2048_Rex_0.149'
>> > > in version 1.2.7 and the sample script
'mf_multimodel.py')...
>> > >
>> > > TEST 1
>> > > =====
>> > > r = 1.02
>> > > CSA = -160 ppm
>> > > m4
>> > > S2 = 0.97
>> > > te = 2048
>> > > Rex = 0.149
>> > > X2 = 7.3e-28
>> > >
>> > > TEST 2
>> > > =====
>> > > r = 1.02
>> > > CSA = -172 ppm
>> > > m4
>> > > S2 = 0.97
>> > > te = 82
>> > > Rex = 4.34
>> > > X2 = 2.27
>> > >
>> > > As you can see, for this single residue (with data
at 500 and
>> 600 MHz),
>> > > there is no effect for the value of S2, but the
effect is
>> important for te
>> > > and Rex... And still, the best model (the lower X2)
is m4 for both
>> > > situations...
>> > >
>> > > I think that this ambiguity in the value for CSA
leads to important
>> > > variations in the interpretation of relaxation data.
>> > >
>> > > Thanks for getting me to understand more this topic
and also
>> choose the
>> > > best value to use...
>> > >
>> > > Séb
>> > >
>> > >
>> > >
>> > >
>> > > Alexandar Hansen wrote:
>> > > Hi Sebastien,
>> > >
>> > > I'm quite new to relax as well, but I can give you
at least a
>> some answer
>> > > to the questions you pose.
>> > >
>> > > In general, the CSA mechanism is a little
underappreciated. At low
>> > enough
>> > > field strengths for 15N relaxation (400-500MHz), the
15N CSA
>> accounts for
>> > > somewhere between 10-20% of your R1 and R2
rates. Varying the CSA
>> > magnitude
>> > > between 160 and 172 only changes this by 2-3%. So,
if relaxation
>> rates
>> > are
>> > > measured with, let's say, 5% error, there's no
statistical reason
>> to vary
>> > > the CSA. As we go to higher fields (800MHz), the
CSA can account
>> for
>> > 50-60%
>> > > of the R1 and R2 rates and varying the CSA between
160 and 172
>> can affect
>> > > those rates by up to 10%. So, now people are
finding that this
>> thing
>> > called
>> > > CSA is relatively improtant and should be better
understood.
>> > >
>> > > In many analysis techniques, such as relax, you
have the option of
>> > letting
>> > > the CSA vary. For relax, I believe that's models
m10-m19 and
>> tm10-tm19.
>> > > One word of warning though, I wouldn't encourage
fitting the CSA
>> unless
>> > you
>> > > have data at multiple field strengths as you're
adding another
>> variable to
>> > > the analysis, so the standard 3 measurements at a
single field
>> strength
>> > are
>> > > likely not enough to do this. You also run the risk
of
>> overinterpretting
>> > > your data because, in my opinion, varying the CSA
freely in
>> relaxation
>> > > analysis is not unlike simply throwing in a fudge
factor. :-)
>> > >
>> > > As for what is the best value to use, I can't
really help you
>> there.
>> > We'll
>> > > have to wait for some of the protein people to
respond (I know
>> RNA better
>> > > ;-) ). But if you're at low enough fields or tiny
proteins (<2-3
>> ns tau(
>> > m
>> > > )) it shouldn't really matter what you use.
>> > >
>> > > I hope all of this makes sense and I haven't said
anything
>> blatantly
>> > > incorrect. If I have, hopefully someone will follow
up on both
>> of our
>> > > posts. Thanks, and good luck!
>> > >
>> > > Alex Hansen
>> > >
>> > >
>> > >
>> > >
>> > > Hi
>> > >
>> > > I am new to relax and have a quite general question
about the
>> value used
>> > > for the CSA while studying proteins' 15N-1H vectors
with model-free
>> > > approach.
>> > >
>> > > In the litterature, we mainly find two values for
the CSA (-160
>> and -172
>> > >
>> > > ppm).
>> > >
>> > > There is, if I understand well, a link between the
bond length
>> and the
>> > > CSA, but everyone seems to agree about using the
same value of
>> 1.02 A
>> > > which should give rise to a mean S2 of 0.85 for
secondary
>> structure when
>> > >
>> > > combined to a CSA of -172 ppm.
>> > >
>> > > In the relax sample scripts (as well as in the
Model-free manual), a
>> > > value of -160 ppm is used for CSA.
>> > >
>> > > What is the best value to use and, most importantly,
why ?
>> > >
>> > >
>> > > Also, what about the CSA variability from one vector
to another
>> (JACS,
>> > > 128 (24), 7855 -7870, 2006) ?
>> > >
>> > > Thanks !
>> > >
>> > >
>> > > Sébastien
>> > >
>> > > ________________________________
>> > >
>> > > _______________________________________________
>> > > relax (http://nmr-relax.com)
>> > >
>> > > This is the relax-users mailing list
>> > >
relax-users@xxxxxxx
>> > >
>> > > To unsubscribe from this list, get a password
>> > > reminder, or change your subscription options,
>> > > visit the list information page at
>> > > https://mail.gna.org/listinfo/relax-users
>> > >
>> > >
>> > >
>> > > --
>> > >
>> > > ______________________________________
>> > > _______________________________________________
>> > > | |
>> > > || Sebastien Morin ||
>> > > ||| Etudiant au doctorat en biochimie |||
>> > > |||| Laboratoire de resonance magnetique nucleaire
||||
>> > > ||||| Dr Stephane Gagne |||||
>> > > |||| CREFSIP (Universite Laval) ||||
>> > > ||| 1-418-656-2131 poste 4530 |||
>> > > || sebastien.morin.1@xxxxxxxxx
||
>> > > |_______________________________________________|
>> > > ______________________________________
>> > >
>> > >
>> > > _______________________________________________
>> > > relax (http://nmr-relax.com)
>> > >
>> > > This is the relax-users mailing list
>> > > relax-users@xxxxxxx
>> > >
>> > > To unsubscribe from this list, get a password
>> > > reminder, or change your subscription options,
>> > > visit the list information page at
>> > > https://mail.gna.org/listinfo/relax-users
>> > >
>> > >
>> > >
>> >
>> > _______________________________________________
>> > relax (http://nmr-relax.com
)
>> >
>> > This is the relax-users mailing list
>> > relax-users@xxxxxxx
>> >
>> > To unsubscribe from this list, get a password
>> > reminder, or change your subscription options,
>> > visit the list information page at
>> > https://mail.gna.org/listinfo/relax-users
>> >
>> >
>>
>>
>
>
--
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
--
4635 Hunt Club Dr Apt 1C
Ypsilanti, MI - 48197
Cell: (734) 819-0928
Work: (734) 615-7421
--
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
|
Re: CSA & bond length