Palmer et al. 1993 JACS 115, 6333-45, measures side chain dynamics in a Zinc finger peptide using natural 13C abundance but I can not really follow all the treatment that they did. Lee et al. 1999 JACS 121, 2891-2902 also measure CH3 dynamics with ubiquitin.
Still, my doubt is that, due to the rotation of the methyl protons you can never describe a J(w) for any of the three protons if the molecule has non isotropic diffusion. Even if you have a CHD2 methyl group, you will never now the orientation of the CH vector relative to the diffusion tensor. What I seem to understand from the literature is that methyl rotation about the symmetry axis is usually fixed to S2=0.111 assuming a perfect tetrahedral geometry of the methyl groups. So it is not the C-H vector itself that is question but rather the vector that is aligned with the methyl rotation symmetry axis. Then, you have the reorientation of the methyl symmetry axis which also contributes for the motion of the methyl group. So if you get an S2 much lower than 0.111 it means that there is additional motion to the CH3 group which can only appear from the reorientation of the symmetry axis. Does this make any sense to you? I will look at the paper of Schurr to see if I can get a better idea. I have already implemented Kay's pulse sequences to minimize the contribution of cross relaxation but now I am a bit stuck with this part of the analysis. Cheers Tiago Pais PS: The dll problem disappeared after I installed Relax in Ubuntu. Windows is definitely not a good solution. Especially with these virtual machines working so well nowadays it really doesn't make sense suffering with windows! -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 16 de Setembro de 2009 16:49 To: Tiago Pais Cc: [email protected]; Vic Vostr Subject: Re: CH3 relaxation Hi, One can always analyse any collected data, but whether the results are meaningful is another kettle of fish. So, yes you can use relax - it won't stop you from doing anything! You just have to be careful and not fall into the pitfalls already documented in the literature. There is pseudo-atom capabilities built into the program now that you might be able to take advantage of. This has not been tested for standard relaxation data yet, due to the theoretical limitations, but you're most welcome to try if a pseudo atom is the route you would like to take. If it fails, just make a bug report (https://gna.org/bugs/?func=additem&group=relax) and then I or one of the relax developers should be able to fix it for you. The issue of orientation is due to the diffusion tensor. If it is purely isotropic, bond vector orientation is not important. If it is not, then a false orientation will cause either artificial ns motions (Schurr, 1994) or artificial Rex (Tjandra et al., 1995) to appear. But maybe a pseudoatom position between the three proton positions (i.e. the symmetry axis) would be good enough, if the tensor isn't too anisotropic? There are also sidechain movements meaning that the methyl rotation is only one part - yet the most important part - of the methyl dynamics. Lipari and Szabo used isotropic tensors (well the looked a little at anisotropy but got that very wrong), so they never looked at this in detail. The Schurr and Tjandra publications are what you want. For the interference issues, this will be found in Kay's papers. The exact reference I don't remember off the top of my head. Do you have a reference of anyone doing R-CH3 a model-free analysis before? Regards, Edward P.S. Did you work out what the DLL issue was in the end? 2009/9/16 Tiago Pais <[email protected]>: > Hi, > > The original papers of Lipari and Szabo on model-free address the > interpretation of relaxation data from methyl groups. I found no reference > to the issue of the three reorienting CH vectors. It seems to me that the > axis of symmetry of methyl rotation is used as a reference. Then, a Woessner > model for the methyl motion is assumed, leading to a theoretical S2 of about > 0.111 for methyl groups with perfect tetrahedral geometry. In this way one > can obtain the S2 of the symmetry axis (eg. Ca-Cb vector in Alanine) by > dividing the experimentally obtained S2 by 0.111. > > In any case, even with deuterium partial labeling you would have the proton > jumping between positions meaning a time dependent vector orientation, no? I > think the advantage of Deuterium is about the purity of the relaxation > mechanism which is dominated by quadrupolar effects. > > Considering that I have acquired all the data in the absence of relaxation > interference, is it feasible to use RELAX to fit the modelfree models? > > Regards > Tiago Pais > > > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 12 de Agosto de 2009 15:07 > To: Tiago Pais > Cc: Vic Vostr; [email protected] > Subject: Re: value.display() > > Hi, > > Please see below for answers to your questions. > > > On Wed, Aug 12, 2009 at 12:53 PM, Tiago Pais<[email protected]> wrote: >> Dear Edward, >> I have some questions relating the functioning of relax 1.3.3: >> 1- When I initiate the relax command a get an error message about a > missing >> DLL (python25.dll). However the program manages to start anf get to the >> command line. Is this DLL related to the "curve fitting" module? Does the >> relax program run properly without this DLL > > This is a strange error. It is related to Python and not relax, and > is the main Python library used by all Python programs. Do you have > Python 2.5 installed? Could you cut and paste the error message? Do > you get the same message if you run python from the command prompt as > well? > > >> 2- The "relax --test-suite" routine seems to stall after a while. I have >> three "F" in the middle of the dotted line. Can this be related to the DLL > > I'm not sure. If you're using Python 2.5 and getting this error, then > relax should not run. This is strange. > > The stalling is likely to be on a system test which takes a while to > run. It should be finished in 1-3 min though, unless you are using a > very old machine. I'm currently fixing all the tests on windows in > the 1.3 repository code, and relax 1.3.4 when released should pass > most tests (note that 2 unit tests of the float module are know to > fail). > > >> 3- The "TAB" button is not working within relax > > This is a windows only problem as there is no special library called > 'readline'. If this is too annoying, maybe running this in GNU/Linux > (in a virtual machine if necessary) would be the easiest way to remove > this lack of TAB key. > > >> And now some question related to my specific case: >> 1- What is the nomenclature to describe the C nucleus in a methyl group? I >> will have to assume an effective CH vector and not three different ones > for >> each proton; how do I tell this to the program? > > This is slightly problematic because of all the cross-correlated > relation rates (interference). There is no theory to handle this, > that I am aware of. People overcome this by specific labelling so > that there is one hydrogen and two deuteriums (e.g. see Lewis Kay's > papers). Not only are the interference effects fatal, but the three > CH vectors experience different spectral density functions J(w). The > J(w) are direction dependent, and here you have three different > directions which constantly change. Again the theory is completely > missing, as far as I know. What you need is a reference where someone > has handled the 1H-13C relaxation rates from a CH3 group before! Or > you'll need to derive the necessary theory. > > >> 2- What is the format for the input R1,R2, and NOE data? Couldn't seem to >> find it written in the manual. > > relax will handle any column formatted file. See the help for the > relax_data.read() user function in the manual for full details, or > type: > > relax> help(relax_data.read) > > >> Sorry for all these questions but I am just starting dealing with this >> program. > > No problems. If you have any other questions, please don't hesitate to ask. > > Regards, > > Edward > > > _______________________________________________ > 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
