Salut Edward ! Hi Alexander ! The value of -172 (with r=1.02 A) is from a review by Palmer (Annu.Rev.Biophys.Biomol., 2001, 30:129-155). In the same review, Palmer talks about another combination (-163 ppm and 1.04 A) which should give similar results...
Hall and Fushman, in their last paper (JACS, 128 (24), 7855 -7870, 2006) say that the true mean CSA values (for ubiquitin) range from -173.9 ppm (2R2 - R1) to -177.2 ppm (Rn). I guess one should then use values around -175 ppm instead of -160 and even -170 or -172... I guess I'll take some time to read papers and have a deeper understanding of this quite important issue and then choose if I use a fixed value or if I measure CSAs as well... I hope to read more about this on the mailing list ! Cheers Sébastien Edward d'Auvergne wrote: > 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 >> >> >> > -- ______________________________________ _______________________________________________ | | || 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
