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)
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>> > >
>> > >
>> > > --
>> > >
>> > > ______________________________________
>> > > _______________________________________________
>> > > | |
>> > > || 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 ||
>> > > |_______________________________________________|
>> > > ______________________________________
>> > >
>> > >
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--
______________________________________
_______________________________________________
| |
|| 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 |||
|| ||
|_______________________________________________|
______________________________________
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Re: CSA & bond length