Chemistry Reference
In-Depth Information
3 Extending Relaxation Measurements Beyond
R
1
,
R
2
, and
15
N-{
1
H}NOE.............. 107
4 Relaxation Dispersion Experiments . . ...................................................... 108
4.1 Relaxation Dispersion in General . . . . . . .............................................. 108
4.2
15
N CT-CPMG Relaxation Dispersion Experiment . . . .............................. 109
4.3
15
N Off-Resonance
R
1
r
Experiment . ................................................ 111
4.4 Bloch-McConnell Equation and Related Equations . . . . . . . . . ....................... 112
4.5 Practical Aspects Parameter Optimization ........................................... 112
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
1 NMR Relaxation to Detect Protein Dynamics
In this chapter, we describe mainly
15
N relaxation experiments to characterize
protein backbone dynamics in solution. NMR spin-relaxation is a phenomenon in
which perturbed magnetization is restored to statistical equilibrium by random
fluctuations of local magnetic fields. The major local magnetic fields in diamagnetic
proteins are generated by the amide
1
H-
15
N dipolar interaction and
15
N chemical
shift anisotropy (CSA). Interchange among different chemical shift environments
by chemical exchange or conformational exchange also contributes to the spin
relaxation. In this section, we review the types of
15
N relaxation experiments that
are used to characterize protein backbone dynamics.
The model-free approach is the most frequently applied protocol to extract
information about overall and fast (faster than overall) dynamics in proteins. In
this approach the spectral density function characterizing the randomly fluctuating
local fields is written in terms of correlation times for overall and internal motion and
a generalized order parameter (the model free parameters). These parameters are
obtained from the model-free analysis using
15
N longitudinal relaxation rate (
R
1
),
transverse relaxation rate (
R
2
), and
15
N-{
1
H} nuclear Overhauser effect (NOE)
measurements. Measuring at least four relaxation rates, at two or more static
magnetic field strengths, improves determination of the model-free parameters.
Alternatively,
15
N-{
1
H} NOE alone may be used to evaluate the high-frequency
spectral density function,
J
(
o
H
o
N
), instead of derivation of model-free
parameters. However this approach is not straightforward at high magnetic field
strength for proteins with significant mobility as described in Sect.
2.3
.
Although relaxation of nuclei other than
15
N can be used to characterize back-
bone dynamics,
15
N relaxation experiments have been the most widely applied, and
for this reason are the focuses of this chapter.
2 Recent Improvements in the
15
N
R
1
,
R
2
, and
15
N-{
1
H} NOE
Experiments
A set of
15
N
R
1
,
R
2
, and
15
N-{
1
H} NOE observations is typically analyzed using
model-free analysis to obtain the generalized-order parameter,
S
2
, that characterizes
degree of internal motion [
1
,
2
]. Since a set of
15
N
R
1
,
R
2
, and {
1
H}-
15
N NOE
