Mengjuei - Blog

擬真 :: Refinement of NMR Structures

These are how would you refine an NMR structure if you were an NMR experimentist. This is just an introduction.

1. Resolving Assignment Ambiguities: This method uses the preliminary 3D structure to check the assignment ambiguities due to the cross peak of chemical shifts. By doing this, NMR guys can determine more long distance restraints.
2. Restrained Energy Minimization: Physics-based force-field is used to perform energy minimization and the distance restraints would be applied to the simulation if necessary. A simple energy minimization might not be able to relax the structures, that's why we need the following method.
3. Molecular Dynamics Simulation: This is calculated with explicit water to simulate solution enviroment and the distance restraints would be applied to the simulation if necessary. An 1ns simulation might not be enough to reach the equilibrium. See [my future blog] for detail.
4. Time- or Ensemble-Averaged Conformational Restraints: Because the restraints are all time-averaged, they can be just applied to the structure in a period of time or an ensemble of structures. That means you either do a simulation or do a series of simulation simultaneously.
5. Relaxation Matrix Refinement: The basis for the refinement is the calculation of the volume of a cross-peak between spins i and j, from the atomic coordinates by means of the relaxation matrix R. The relaxation matrix R is a function of the transition rates which are determined by spectral densities and dipolar coupling strengths.