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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
Trajectory analysis of NMR structure calculations
1Department of Molecular Physiology, the Tokyo Metropolitan Institute of Medical Science, 18-22, Honkomagome 3-chome, Bunkyo-ku, 113, Tokyo, Japan.
Journal of Biomolecular NMR
|August 23, 2012
Summary
Analyzing NMR structure calculations reveals how molecular structures move in conformational space. This trajectory analysis helps understand random sampling and optimize calculation protocols for better macromolecular structure determination.
Area of Science:
- Biophysics
- Structural Biology
- Computational Chemistry
Background:
- Nuclear Magnetic Resonance (NMR) and X-ray crystallography determine macromolecular structures at atomic resolution.
- NMR structure calculation uses initial random structures to generate coordinates compatible with experimental data.
Purpose of the Study:
- To analyze the conformational space trajectories of structures during NMR structure calculation.
- To assess the utility of trajectory analysis for understanding random sampling and optimizing calculation protocols.
Main Methods:
- Employed metric multidimensional scaling to obtain coordinates of structures in conformational space.
- Calculated root-mean-square deviation (RMSD) to measure distances between structures.
- Analyzed trajectories using a simulated annealing protocol with XPLOR on μ-Conotoxin GIIIA.
Main Results:
- The 3D solution from multidimensional scaling adequately describes overall trajectory configurations.
- Comparing full and converged calculation trajectories clearly distinguishes random sampling.
- Individual trajectory examination aids in optimizing NMR structure calculation protocols.
Conclusions:
- Trajectory analysis provides insights into the conformational landscape explored during NMR structure calculations.
- This method can identify random sampling and guide the refinement of computational protocols for improved structural accuracy.
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