Hello Edward and relax users, I have been recently using relax to carry out model free analyses on two different states of my protein at 600 and 800 MHz. I am working with a LOV domain (132 residues) which exists in a ground "dark" state and a photoactive "light" state. Both states exist as a symmetric homodimer in solution. For the analysis I have been using the crystal structures, one monomer at a time. Also, the resonances showing overlap have not been included in the analyses. There is no difference in the backbone as such between the two crystal structures. Along with model-free I have also carried out reduced spectral density mapping. The J(0)s of both the states agree well between the two fields. Hence there is nothing wrong with the data as such. Also both the J(w) agree well with my het-NOE and R1 with respect to regions in the protein showing fast timescale backbone motion.
The model free analysis of the "dark" state goes fine. The S2 values show same regions having fast timescale motions as observed from the raw relaxation data and rSDM. Both the monomers individually give me approximately comparable results. For e.g., a loop between residues 100 and 110 shows flexibility on fast time scale according to the raw data, rSDM as well as relax S2 values. However, for the "light" state the results from model free appear quite bizarre for both the monomers. The average S2 for the "dark" state was ~ 0.8. As per my raw data and rSDM, I expected the S2 values to be slightly elevated in "light" state. However, my "light" state S2 values are on an average 0.17! Also the same loop is now with higher than average S2 values in the "light" state whereas the raw data and rSDM showed the loop to be flexible, albeit less flexible compared to the "dark" state. The internal motions (Te) are less than 5 ps and seen only in 7 residues. No Ts or Tf. I have attached figures from the spectral density mapping as well as the "dark" and "light" state S2 values to illustrate better what I am trying to say. Also, I repeated the "dark" state model free analysis with "dark" state structures. thinking that there might be some bug somewhere and got results just like earlier. But not with the "light" state. Since the backbones between two states are near identical, I used the "dark" state structure to run with relax on the "light" state data. I again get these bizarre results. I am about to run model free with "light" state structure and "dark" state relaxation data. However, I am not sure where the problem lies, whether it is the structure, my data or some bug somewhere. Since the J(0)s add up nicely, I do not think it is the data. It is unlikely that it is bug since the "dark" state ran fine. It is also unlikely that the structure is strange since dark and light states have near identical backbones and there are no missing residues in either of the structures. I must also add that the correlation time obtained from relax are actually comparable with the ones extracted from R2/R1 ratio for both the "dark" and the "light" states. It is only the motion parameters which are weird for the "light" state. Has anyone encountered something like this recently? Any help/advice here will be very helpful. At this moment the data is only with two fields but I do plan to run relaxation at 900 MHz and use the three fields for model-free as soon as I get time on the magnet. Regards, Vineet Panwalkar Institute of Complex Systems-6: Strukturbiochemie (ICS-6) Building 05.8v, Room 2022 Forschungszentrum Jülich 52425 Jülich Germany ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
