Changes

The DPL94 model has the parameters <math>\{R_{1\rho{:R1rhoprime}}', ..., \Phi_{ex{:Phiex}}, k_{ex{:kex}}\}</math>.

=== Essentials === {{note|{{:R1}} should be provided in rad/s, the SI default unit for this relaxation rate.}} It is essential to read in <math>R_{1{:R1}}</math> values before starting a calculation:<br>Note, R1 should be provided in rad/s.

 {{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 =

# <math>R_{1\rho{:R1rhoprime}'} = </mathcode> = spin.r2 </code> (Fitted)# <math>R_{1\rho{:R1rho}} = </mathcode> = spin.r2eff </code> (Back calculated)# <math>\Phi_{ex{:Phiex}}= </mathcode> = spin.phi_ex </code> (Fitted)# <math>k_{ex{:kex}} = </mathcode> = spin.kex </code> (Fitted)# <math>R_{1{:R1}} = </mathcode> = spin.ri_data['R1'] </code> (Loaded)

=== Equation - re-writed written forms ===

* {{# Evenäs, J., Malmendal, A. & Akke, M. (2001). Dynamics of the transition between open and closed conformations in a calmodulin C-terminal domain mutant. Structure 9, 185–195 httplst://dx.doi.org/10.1016/S0969-2126(01)00575-5Citations|Evenäs01}}* {{# Kempf, J.G. & Loria, J.P. (2004). Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 http://dx.doi.org/10.1385/1-59259-809-9lst:185Citations|KempfLoria04}}* {{# Palmer, A.G. & Massi, F. (2006). Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 httplst://dx.doi.org/10.1021/cr0404287Citations|Massi05}}* {{# Palmer, A.G., Kroenke, C.D. & Loria, J.P. (2001). Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Meth. Enzymol. 339 httplst://dx.doi.org/10.1016/S0076-6879(01)39315-1Citations|Palmer01}}* {{# Francesca Massi, Michael J. Grey, Arthur G. Palmer III* (2005). Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experiments, Protein science httplst://dx.doi.org/10.1110/ps.041139505Citations|PalmerMassi06}}* {{# Trott, O. and Palmer, 3rd, A. G. (2002). R1rho relaxation outside of the fast-exchange limit. J. Magn. Reson., 154(1), 157–160. (httplst://dx.doi.org/10.1006/jmre.2001.2466).Citations|TrottPalmer02}}

==== The {{:R1rho}}: {{: R2 }} or {{:R2eff }} as function of effective field in rotating frame: w_eff {{:omegaeff}} == ==='''Discussion:''' <br>===It is clear that there is no real name for the pseudo-parameter. It looks like that $R_{\text{eff:Reff}}$ was Art's original way of denoting this and that he has now changed to $R_{2{:R2}}$ instead. <br>But if one look at the reference for the [[TP02|TP02 dispersion model [[TP02]], one will see yet another notation:

Here $R_{2{:R2}}$ does not contain the $R_{ex{:Rex}}$ contribution. Also, $R_{\text{eff:Reff}}$ is absent of $R_{ex{:Rex}}$. <br>But in Art's Protein Science paper (Ref [5]), the definition $R_{2{:R2}} = R^{0{:R2zero}}_2 + R_{ex{:Rex}}$ is used. The [[MP05|MP05 model reference ]] also does not use $R_{\text{eff:Reff}}$ [[MP05]].

The $R_{\text{eff:Reff}}$ parameter name is confusing and it seems to have been dropped from 2005 onwards. The $R_{\text{eff:Reff}}$ name appears to be specific to Art Palmer's group and as he himself has dropped it, then it would be best to avoid it too.

Ref [2], Equation 27. Here the calculated value is noted as: R_eff: $<math>R_{\text{eff}} = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)$ </math> <br>Ref [3], Equation 20. Figure 11+16, would be the reference. Here the calculated value is noted as: R_2: $<math>R_{2} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)$</math>. <br>Ref [4], Equation 43. $<math>R_{\text{eff}} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)$ </math> <br>Ref [5], Material and Methods, page 740. Figure 4 would be the wished graphs. Here the calculated value is noted as: R_2: $<math>R_{2} = R^{0}_2 + R_{ex}$</math>

# $: <math>R_2 = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta) = \frac{R_{1\rho} - R_1\cos^2(\theta)}{\sin^2(\theta)}$</math>

* 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}}

[[Category:Relaxation_dispersion Models]][[Category:Dispersion models]][[Category:Relaxation dispersion analysis]]