Structure Calculations Using NMR Data • Development began in the middle of the 1980s. • Most of the early structures were of very small proteins or peptides. • You do not determine a single structure as in crystallography, but rather an ensemble of structures that satisfy a group of restraints. • In general, the more experimental restraints that are used, the better the precision of the structures calculated. • Advancements (new experiments, bigger magnets, faster computers) have not only increased the size of the molecule that can be studied, but they have improved the quality of the structures calculated
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Structure Calculations Using NMR Data• Development began in the middle of the 1980s.
• Most of the early structures were of very small
proteins or peptides.
• You do not determine a single structure as in
crystallography, but rather an ensemble of
structures that satisfy a group of restraints.
• In general, the more experimental restraints
that are used, the better the precision of the
structures calculated.
• Advancements (new experiments, bigger
magnets, faster computers) have not only
increased the size of the molecule that can be
studied, but they have improved the quality of
the structures calculated
Principles of NMR-based Structure Calculations
• The goal of all NMR structure calculation
protocols is to find the global minimum region
of a target function Etot.
Etot = Ecov + Evdw + ENMR
Ecov = covalent geometry terms for: bonds, angles
planarity and chirality.
Evdw = nonbonded contacts.
ENMR = experimental NMR restraints.
Algorithms used in NMR structure calculations
• Simulated annealing (SA) in both cartesian and
torsion angle space.
• Metric matrix distance geometry (DG).
• Minimization with a variable target function in
torsion angle space.
Ecov
• Depending on the algorithm used systematic
biasing may arise when calculating the
structure.
• Deviations from ideal geometry must be kept to
a minimum since the value of bond lengths,
angles, planes and chirality are known to very
high accuracy.
Evdw
• This term is associated with more uncertainty.
• It may be represented as a simple van der Waalsrepulsion term.
• It may also be a complete energy function thatincludes an electrostatic and a hydrogenbonding potential.
• All structures must display good non-bondedcontacts.
• Uncertainties associated with Ecov and Evdw canintroduce errors in the range of 0.3 Å.
Steps in NMR-based Structure Calculations
1) Data Input
2) Structure Determination Protocol
3) Acceptance Tests
4) Analysis of NMR structure.
Types of NMR Experimental Restraints
1) Noe-derived distance restraints.
2) Torsion angle restraints.
3) Chemical shift restraints.
4) Hydrogen bond restraints.
5) Residual Dipolar Coupling Angular restraints.
Outline of structure calculation protocol
Nuclear Overhauser Effect (NOE)
NOEs in solution structure determinations• NOEs provide the main source of geometric
information from the experimental data.
• NOEs are short in distance (~ 5Å) but they areconformationally very restrictive when they arefar apart in the primary sequence.
• At short mixing times, NOE signal isproportional to the inverse sixth power of thedistance between two protons.
• NOE intensities are converted to approximateinterproton distant restraints with lower andupper bounds.