Re: Finished the reading of all the BMRB model-free data - necessary corrections to the database entries.Re: Finished the reading of all the BMRB model-free data - necessary corrections to the database entries.Hi,Another important item which came to my mind this morning concerns recycle delays and saturation times in NOE experiments.
As most studies will use a fixed total delay for the reference and saturated experiments (i.e. recycle delay of reference spectrum = [recycle delay of saturated spectrum + saturation delay]), some will not...
This is best explained by citing [Morin (In press) A practical guide to protein dynamics from 15N spin relaxation in solution. Prog. NMR Spec. http://dx.doi.org/10.1016/j.pnmrs.2010.12.003]:
===========[...] in order to measure reliable NOE data for very flexible residues (or in the case of small proteins) at high magnetic fields, extended recovery and saturation delays might be needed [L.E. Kay, D.A. Torchia, A. Bax, Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease, Biochemistry 28 (1989) 8972–8979. ; C. Renner, M. Schleicher, L. Moroder, T.A. Holak, Practical aspects of the 2D 15N–[1H]–NOE experiment, J. Biomol. NMR 23 (2002) 23–33. ; Q. Gong, R. Ishima, 15N–{1H} NOE experiment at high magnetic field strengths, J. Biomol. NMR 37 (2007) 147–157.].
Indeed, two different experiments are used for measuring the steady-state NOE (with and without saturation). In these two different experiments, the magnetisation does not behave identically. As a consequence, the recovery time in the absence of saturation needs to be longer, whereas for the experiment with saturation, the recovery delay can be shorter since it is followed by the saturation delay [C. Renner, M. Schleicher, L. Moroder, T.A. Holak, Practical aspects of the 2D 15N–[1H]–NOE experiment, J. Biomol. NMR 23 (2002) 23–33.]. If delays for both recovery and saturation are too short, then the measured NOE will be overestimated [C. Renner, M. Schleicher, L. Moroder, T.A. Holak, Practical aspects of the 2D 15N–[1H]–NOE experiment, J. Biomol. NMR 23 (2002) 23–33.]. This problem is most important at high magnetic fields since both 1H and 15N T1 increase with increasing magnetic field, hence increasing the time needed for return of magnetisation parallel to the z axis, especially for flexible segments. Renner et al. [C. Renner, M. Schleicher, L. Moroder, T.A. Holak, Practical aspects of the 2D 15N–[1H]–NOE experiment, J. Biomol. NMR 23 (2002) 23–33.] proposed a recovery delay of 10 s (or more) for the experiment without saturation and of 1 s for the experiment with saturation, where a saturation delay of 5 s should follow. Hence, when suspecting higher flexibility (either by comparison with a similar protein, or by estimation of order parameters from methods such as the contact model [F. Zhang, R. Brüschweiler, Contact model for the prediction of NMR N–H order parameters in globular proteins, J. Am. Chem. Soc. 124 (2002) 12654–12655.] or the random coil index [M.V. Berjanskii, D.S. Wishart, A simple method to predict protein flexibility using secondary chemical shifts, J. Am. Chem. Soc. 127 (2005) 14970–14971. ; M. Berjanskii, D.S. Wishart, Nmr: prediction of protein flexibility, Nat. Protocols 1 (2006) 683–688. ; M.V. Berjanskii, D.S. Wishart, The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts, Nucleic Acids Res. 35 (2007) W531– W537. ; M.V. Berjanskii, D.S. Wishart, Application of the random coil index to studying protein flexibility, J. Biomol. NMR 40 (2008) 31–48.]), special care should be taken and the above guidelines followed for the recording of reliable NOE data.
===========Thus, the possibility for two different recycle delays should be taken into account for NOE data entry. Of course, the saturation delay should also be included in the deposited data.
Best regards, Séb :) On 11-03-08 1:49 PM, Edward d'Auvergne wrote:
Seb, we should discuss and make a list of the necessary tags. We can have relax ask the user to input the required data, this will be the easiest for the user and BMRB input. Adding new tags appears to be quite a lot easier with the BMRB than modifying existing designs, but we should be certain of these tags and design the list to be the highest quality possible.How should we write this list ? By exchanging emails in a new thread ? Or by svn ?It would be best by email, as Eldon will need to add the tags and his input will be needed.* the number of different relaxation delays (including some information on duplicates) * the order with which the different relaxation delays were recorded (and the use of interleaving) This is a good idea, but is hard to implement as a strict definition. Maybe a single tag with free-formatted text could be used. For example: _Auto_relaxation.Delay_interleaving where the free text could be something like "300, 20, 1000, 10, 1500, 200". Eldon, is there another way of storing this info?This is a good idea, although maybe free text could be replaced by, first, a question on the number of delays, then tags for each delays (where the total number would have been specified earlier). This would avoid having different formatting in the free text list...We can do this on the relax-side with one or two user functions. Adding the number is not necessary as we can easily count the elements of a list. In relax I would have 2 structures, a dictionary for storing the delay times per experiment, and a list storing the order. This will probably require 2 user functions. Storing this data in the BMRB is a different question. The tags are fixed, so you can't have one tag per delay. It might be possible to create a new looping tag category, but this is not the best way to store an ordered list. Maybe Eldon knows a better way. We can always dump the information into the _Auto_relaxation_list.Details tag if we have no interest in using it for automatic parsing of the BMRB, but I think to make this type of information parsable would be a good idea. What do you think?* the number of samples used (if not a single one) A single Auto_relaxation or Heteronuc_NOE saveframe should really come from a single sample. If there are different samples for different experiments, then _Auto_relaxation_list.Sample_condition_list_ID should point to the different samples for each saveframe.Currently, the name of the sample used for a single experiment is shown. Although, for model-free analysis results, it would be nice to have, in addition to the list of samples (as it is currently), the number of samples directly written. This would make it easier for quick lookup of the data as you could search for the tag and know directly if the analysis was made from data with one or multiple samples. It would help judge consistency and inconsistency issues...This should be easy enough to see in the _Order_parameter_experiment.Sample_ID tag. You just have to count the number of different IDs. I think this information is already in the model-free saveframes. I'm not sure how capable relax is of handling this though. Regards, Edward
-- Sébastien Morin, Ph.D. Postdoctoral fellow S. Grzesiek NMR Laboratory Biozentrum, Universität Basel Basel, Switzerland