Trusted, Bureaucrats
4,223
edits
Changes
→Parameter name space in relax: Included a number of code tags.
The Davis et al., 1994 2-site off-resonance fast exchange relaxation dispersion model for [[R1rho-type data]]. It extends the [[M61]] model to off-resonance data, hence it collapses to this model for on-resonance data. The model is labelled as '''DPL94''' in [[Relaxation dispersion citation for relax|relax]].
== Parameters ==
The DPL94 model has the parameters {$R_{1\rho{:R1rhoprime}}'$, $...$, $\Phi_{ex{:Phiex}}$, $k_{ex{:kex}}$}.
<source lang="python">
relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_values.txt', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
== Parameter name space in relax ==
{{collapsible script| type = relax script| title = At time of writing (March 2014) the parameters in relax was were stored as:demonstrated in this script.<source | lang ="python">| script =
# Load the outcome from an analysis
state.load(state="results.bz2", dir="results/final")
else:
print(mol_name, res_num, res_name, spin_id, curspin.r2, curspin.phi_ex, curspin.kex)
}}
Which means:
# $R_{1\rho{:R1rhoprime}}'$ = <code>spin.r2 </code> (Fitted)# $R_{1\rho{:R1rho}}$ = <code>spin.r2eff </code> (Back calculated)# $\Phi_{ex{:Phiex}}$ = <code>spin.phi_ex </code> (Fitted)# $k_{ex{:kex}}$ = <code>spin.kex </code> (Fitted)# $R_{1{:R1}}$ = <code>spin.ri_data['R1'] </code> (Loaded)
Please also see this thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5164
Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207
* {{#lst:Citations|Evenäs01}}* {{# Evenäs, J., Malmendal, A. & Akke, M. (2001). lst:Citations|KempfLoria04}}* {{#lst:Citations|Massi05}}* {{#lst:Citations|Palmer01}}* {{#lst:Citations|PalmerMassi06}}* {{# Dynamics lst:Citations|TrottPalmer02}} Different graphs. == The {{:R1rho}}: {{:R2}} or {{:R2eff}} as function of effective field in rotating frame: {{:omegaeff}} == === Discussion ===It is clear that there is no real name for the transition between open and closed conformations in a calmodulin Cpseudo-terminal domain mutantparameter. Structure 9, 185–195 http It looks like that {{:Reff}} was Art's original way of denoting this and that he has now changed to {{://dx.doi.org/10R2}} instead.1016/S0969-2126(01)00575-5<br># KempfBut if one look at the reference for the [[TP02|TP02 dispersion model]], J.Gone will see yet another notation: Here {{:R2}} does not contain the {{:Rex}} contribution. & Loria Also, J.P{{:Reff}} is absent of {{:Rex}}. <br>But in Art's Protein Science paper (2004Ref [5]). ## Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 httpthe definition {{://dxR2}} = {{:R2zero}} + {{:Rex}} is used.doi The [[MP05|MP05 model reference]] also does not use {{:Reff}}.org/10 The {{:Reff}} parameter name is confusing and it seems to have been dropped from 2005 onwards.1385/1-59259-809-9 The {{:185# Reff}} name appears to be specific to Art Palmer's group and as he himself has dropped it, Athen it would be best to avoid it too.G. & Massi Ref [2], FEquation 27. Here the calculated value is noted as: R_eff: <math>R_{\text{eff}} = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex} = R_{1\rho} / \sin^2(2006\theta).## Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 http:R_1 /\tan^2(\theta)</dx.doi.org/10.1021/cr0404287math> <br># PalmerRef [3], A.GEquation 20.Figure 11+16, Kroenke, C.D. & Loria, J.Pwould be the reference. Here the calculated value is noted as: R_2: <math>R_{2} = R_{1\rho} / \sin^2(2001\theta).## Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Meth. Enzymol. 339 http:R_1 /\tan^2(\theta)</dxmath>.doi<br>Ref [4], Equation 43.org<math>R_{\text{eff}} = R_{1\rho} /10.1016\sin^2(\theta) - R_1 /S0076-6879\tan^2(01\theta)39315-1</math> <br># Francesca MassiRef [5], Material and Methods, Michael Jpage 740. Grey, Arthur GFigure 4 would be the wished graphs. Palmer III* (2005)Here the calculated value is noted as: R_2: <math>R_{2} = R^{0}_2 + R_{ex}</math> ## Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experimentsThe following suggestions for the definition of the pseudo-parameters, which can be extracted, Protein science httpis then:<math>R_2 = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex} = R_{1\rho} /\sin^2(\theta) - R_1 /dx.doi.org\tan^2(\theta) = \frac{R_{1\rho} - R_1\cos^2(\theta)}{\sin^2(\theta)}</10.1110/ps.041139505math>
== Reference ==
The reference for the DPL94 model is:
* Davis, D., Perlman, M., and London, R. (1994). Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1rho and T2 (CPMG) methods. ''J. Magn. Reson.'', '''104'''(3), 266–275. ([http{{#lst://dx.doi.org/10.1006/jmrb.1994.1084 10.1006/jmrb.1994.1084])Citations|Davis94}}
== Related models ==
The [[Relaxation dispersion citation for relax|implementation of the DPL94 model in relax]] can be seen in the:
* [http://www.nmr-relax.com/manual/DPL94_2_site_fast_exchange_R1_modelThe_DPL94_2_site_fast_exchange_R1_rho_model.html relax manual],
* [http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html API documentation],
* [http://www.nmr-relax.com/analyses/relaxation_dispersion.html#DPL94 relaxation dispersion page of the relax website].
== See also ==
[[Category:Relaxation_dispersionModels]][[Category:Dispersion models]][[Category:Relaxation dispersion analysis]]