Comparing to NMR data
• NMR does not directly result in 3D structures
• What can we compare?
• 3D shapes (Scalar coupling constants, a.k.a. J-values,
nuclear Overhauser effects)
• Atomic motions (RMSF, Order Parameters)
Structure-related NMR Observables
H
HO
O
NOE
HO
O
HOHO
H
H
HO
HO
O
HO
OH
O
NOE
O
HOHO
H
JCH
HO
NOE intensities may be used to estimate the distance between
hydrogen atoms, separated by less than 4 Å
J-couplings may be used to estimate the torsion angles between
the rings
Sparse, complex data!
NMR J-values Depend on Torsion Angles
NMR – measure J-value
from spectrum then
derive angle
MD – compute angle
from trajectory then
derive J-value
NMR nOes Depend on Inter-Proton Distances
The nuclear Overhauser effect (NOE) identifies pairs of
protons (i,j) that are in close proximity. (A) Schematic
representation of a polypeptide chain highlighting five
particular protons. Protons 2 and 5 are in close proximity
Rij
j
i
Under certain NMR conditions: the magnitude of the NOE
intensity is proportional to 1/ Rij6, where Rij is the distance
between the protons.
Therefore, NOEs can also be computed from MD data (by
computing 1/Rij6)
(A) NOESY observations show that protons
(connected by dotted red lines) are close to one
another in space. (B) A three-dimensional
structure calculated with these proton pairs
constrained to be close together
http://www.ncbi.nlm.nih.gov/books/NBK22393/
J-values and n3D Structures from NMR
Collect NMR Data
Interpret NMR Data (assign all the intensities)
Determine J-vales and nOe restraints
Estimate 3D structure
Check for agreement with NMR data
Improve 3D Structure (Refine with Energy
Function and Restraints)
NMR J-values (i.e. torsion angles) and nOes (i.e. distances) provide limits
(restraints) on the range of possible 3D structures.
The best 3D model will violate the fewest J-value and nOe limits
http://www.nmr.chem.uu.nl/~abonvin/tutorials/Structcalc -Data/overview.html
NMR structure of CCHF virus Gn tail zinc finger.
NMR structure of CCHF virus Gn tail zinc finger.
Stereoview of the superposition of 20 lowest energy NMR
structures of CCHF virus Gn zinc finger (A).
Estrada D F , De Guzman R N J. Biol. Chem. 2011;286:21678-21686
For example
– when comparing to x-ray data, it is possible to compare theoretical
atomic positions or interatomic distances with experimental values – but
remember the x-ray data were not measured under the same conditions
as the simulation
– when comparing to NMR data, remember, 3D structures reported from
NMR studies are all models based on fitting to the measured NMR
observables (NOE intensities and couplings).
It may be preferable to compute these NMR observables from the
theoretical data, rather than comparing to a 3D model derived from the
NMR data
Property
X-Ray
NMR
MD Simulation
Atomic Positions
Well Defined
Not Defined
Well Defined
Bond Lengths and
Angles
Well Defined
Not Defined
Well Defined
Inter Atomic
Distances
Well Defined
Partially Defined
by NOEs
Well Defined
Torsion Angles
Well Defined
Partially Defined
by J-values
Well Defined
Internal Motions
Not Defined
Partially Defined
by correlation
times
Well Defined