Difference between revisions of "NS R1rho 2-site"

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For this model, the equations from Korzhnev05 have been used.
 
For this model, the equations from Korzhnev05 have been used.
 +
The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as
 +
\begin{equation}
 +
    \mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}}  \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right),
 +
\end{equation}
 +
 +
For this model, the equations from \citet{Korzhnev05a} have been used.
 
The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as
 
The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as
 
\begin{equation}
 
\begin{equation}
Line 34: Line 40:
 
\begin{equation}
 
\begin{equation}
 
     R = \begin{pmatrix}
 
     R = \begin{pmatrix}
           -\mathrm{R}_{1\rho}prime-\kAB & -\delta_A          & 0          & \kBA                & 0                  & 0 \\
+
           -\mathrm{R}_{1\rho}{`}-\kAB & -\delta_A          & 0          & \kBA                & 0                  & 0 \\
           \delta_A            & -\mathrm{R}_{1\rho}prime-\kAB & -\omega_1  & 0                  & \kBA                & 0 \\
+
           \delta_A            & -\mathrm{R}_{1\rho}{`}-\kAB & -\omega_1  & 0                  & \kBA                & 0 \\
 
           0                  & \omega_1          & -\Rone-\kAB & 0                  & 0                  & \kBA \\
 
           0                  & \omega_1          & -\Rone-\kAB & 0                  & 0                  & \kBA \\
           \kAB                & 0                  & 0          & -\mathrm{R}_{1\rho}prime-\kBA & -\delta_B          & 0 \\
+
           \kAB                & 0                  & 0          & -\mathrm{R}_{1\rho}{`}-\kBA & -\delta_B          & 0 \\
           0                  & \kAB                & 0          & \delta_B            & -\mathrm{R}_{1\rho}prime-\kBA & -\omega_1 \\
+
           0                  & \kAB                & 0          & \delta_B            & -\mathrm{R}_{1\rho}{`}-\kBA & -\omega_1 \\
 
           0                  & 0                  & \kAB        & 0                  & \omega_1          & -\Rone-\kBA \\
 
           0                  & 0                  & \kAB        & 0                  & \omega_1          & -\Rone-\kBA \\
 
         \end{pmatrix},
 
         \end{pmatrix},

Revision as of 10:18, 5 March 2014

The relaxation dispersion model for the numeric solution (NS) to the Bloch-McConnell equations for 2-site exchange for R1rho-type data. This model is labelled as NS R1rho 2-site in relax.

Equation

This is the numerical model for 2-site exchange using 3D magnetisation vectors. It is selected by setting the model to NS R1rho 2-site. The simple constraint $\textrm{pA} > \textrm{pB}$ is used to halve the optimisation space, as both sides of the limit are mirror image spaces.

For this model, the equations from Korzhnev05 have been used. The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as \begin{equation}

   \mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}}  \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right),

\end{equation}

For this model, the equations from \citet{Korzhnev05a} have been used. The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as \begin{equation}

   \mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}}  \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right),

\end{equation}

For this model, the equations from \citet{Korzhnev05a} have been used. The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as \begin{equation}

   \mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}}  \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right),

\end{equation}

For this model, the equations from \citet{Korzhnev05a} have been used. The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as \begin{equation}

   \mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}}  \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right),

\end{equation}

where \begin{align}

   M_0    &= \begin{pmatrix} \sin{\theta} \\ 0 \\ \cos{\theta} \\ 0 \\ 0 \\ 0  \end{pmatrix}, \\
   \theta &= \arctan \left( \frac{\omega_1}{\Omega_\textrm{A}} \right).

\end{align}

The relaxation evolution matrix is defined as \begin{equation}

   R = \begin{pmatrix}
         -\mathrm{R}_{1\rho}{`}-\kAB & -\delta_A           & 0           & \kBA                & 0                   & 0 \\
         \delta_A            & -\mathrm{R}_{1\rho}{`}-\kAB & -\omega_1  & 0                   & \kBA                & 0 \\
         0                   & \omega_1           & -\Rone-\kAB & 0                   & 0                   & \kBA \\
         \kAB                & 0                   & 0           & -\mathrm{R}_{1\rho}{`}-\kBA & -\delta_B           & 0 \\
         0                   & \kAB                & 0           & \delta_B            & -\mathrm{R}_{1\rho}{`}-\kBA & -\omega_1 \\
         0                   & 0                   & \kAB        & 0                   & \omega_1           & -\Rone-\kBA \\
       \end{pmatrix},

\end{equation}

Parameters

The NS R1rho 2-site model has the parameters {$R_{1\rho}'$, $...$, $p_A$, $\Delta\omega$, $k_{ex}$}.

Reference

The reference for the NS R1rho 2-site model is:

  • Korzhnev, D. M., Orekhov, V. Y., and Kay, L. E. (2005). Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock fields: an application to a Fyn SH3 domain. J. Am. Chem. Soc., 127(2), 713-721. (10.1021/ja0446855).

Links

The implementation of the NS R1rho 2-site model in relax can be seen in the:

See also