mailRe: CSA & bond length


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Posted by Alexandar Hansen on September 29, 2006 - 15:35:
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


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