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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>: >> >> > 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 <[EMAIL PROTECTED]> 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 >> > > [email protected] >> > > >> > > 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 ||| >> > > || [EMAIL PROTECTED] || >> > > |_______________________________________________| >> > > ______________________________________ >> > > >> > > >> > > _______________________________________________ >> > > relax (http://nmr-relax.com) >> > > >> > > This is the relax-users mailing list >> > > [email protected] >> > > >> > > 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 >> > [email protected] >> > >> > 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
_______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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
