Difference between revisions of "DPL94"
| Line 75: | Line 75: | ||
=== Equation - re-writed forms === | === Equation - re-writed forms === | ||
Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207 | Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207 | ||
| + | |||
| + | # 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 http://dx.doi.org/10.1016/S0969-2126(01)00575-5 | ||
| + | # Kempf, J.G. & Loria, J.P. (2004). | ||
| + | ## Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 http://dx.doi.org/10.1385/1-59259-809-9:185 | ||
| + | # Palmer, A.G. & Massi, F. (2006). | ||
| + | ## Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 http://dx.doi.org/10.1021/cr0404287 | ||
| + | # 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 http://dx.doi.org/10.1016/S0076-6879(01)39315-1 | ||
| + | # 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 http://dx.doi.org/10.1110/ps.041139505 | ||
== Reference == | == Reference == | ||
Revision as of 08:37, 25 July 2014
Contents
Intro
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 relax.
Equation
[math] \mathrm{R}_{1\rho}= \mathrm{R}_1\cos^2\theta + \left( \mathrm{R}_{1\rho}{´} + \frac{\Phi_\textrm{ex} \textrm{k}_\textrm{ex}}{\textrm{k}_\textrm{ex}^2 + \omega_\textrm{e}^2} \right) \sin^2\theta [/math]
Parameters
The DPL94 model has the parameters {$R_{1\rho}'$, $...$, $\Phi_{ex}$, $k_{ex}$}.
Essentials
It is essential to read in $R_{1}$ values before starting a calculation:
Note, R1 should be provided in rad/s.
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)
Where the data could be stored like
# mol_name res_num res_name spin_num spin_name value error
None 13 L None N 1.323940 0.146870
None 15 R None N 1.344280 0.140560
None 16 T None N 1.715140 0.136510
Parameter name space in relax
At time of writing (March 2014) the parameters in relax was stored as:
# Load the outcome from an analysis
state.load(state="results.bz2", dir="results/final")
# import spin functions
from pipe_control.mol_res_spin import return_spin, spin_loop
# Alias one spin
s13 = return_spin(":13@N")
# See attributes
dir(s13)
# See parameters
print(s13.params)
['r2', 'phi_ex', 'kex']
# Print parameters
print(s13.r2)
{'R1rho - 799.77739910 MHz': xx.yy}
print(s13.phi_ex)
print(s13.kex)
# See Ri data (ri_type: The relaxation data type, i.e. 'R1', 'R2', 'NOE', or 'R2eff'. )
print(s13.ri_data)
{'R1': 1.3239399999999999}
# Print all spin id
for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False):
if curspin.select == False:
print(mol_name, res_num, res_name, spin_id)
else:
print(mol_name, res_num, res_name, spin_id, curspin.r2, curspin.phi_ex, curspin.kex)
Which means:
- $R_{1\rho}'$ = spin.r2 (Fitted)
- $R_{1\rho}$ = spin.r2eff (Back calculated)
- $\Phi_{ex}$ = spin.phi_ex (Fitted)
- $k_{ex}$ = spin.kex (Fitted)
- $R_{1}$ = spin.ri_data['R1'] (Loaded)
Please also see this thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5164
Equation - re-writed forms
Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207
- 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 http://dx.doi.org/10.1016/S0969-2126(01)00575-5
- Kempf, J.G. & Loria, J.P. (2004).
- Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 http://dx.doi.org/10.1385/1-59259-809-9:185
- Palmer, A.G. & Massi, F. (2006).
- Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 http://dx.doi.org/10.1021/cr0404287
- 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 http://dx.doi.org/10.1016/S0076-6879(01)39315-1
- 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 http://dx.doi.org/10.1110/ps.041139505
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. (10.1006/jmrb.1994.1084)
Related models
The DPL94 model is simply the extension of the M61 model for off-resonance data.
Links
The implementation of the DPL94 model in relax can be seen in the:
