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Updated: Nov 26, 2025
14:55
Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
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Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion
R Bryn Fenwick1, David Oyen1, Henry van den Bedem2
1Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California.
Biophysical Journal
|December 10, 2020
Summary
This study introduces a new method using unsigned chemical shift data to model alternative protein conformations. This approach successfully characterized a minor conformational state of Escherichia coli dihydrofolate reductase (DHFR).
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- NMR relaxation dispersion studies reveal protein dynamics on the microsecond to millisecond timescale.
- Chemical shifts from relaxation dispersion can model weakly populated conformational states.
- Determining the signs of chemical shift changes is often challenging.
Purpose of the Study:
- To develop a method for generating structural models of alternative protein conformations using only unsigned chemical shift changes.
- To characterize a minor conformational state of Escherichia coli dihydrofolate reductase (DHFR).
Main Methods:
- Utilized a "sample and select" approach combined with CS-Rosetta.
- Employed unsigned chemical shift changes for backbone amides and carbonyls (1H, 15N, and 13C').
- Generated diverse structures to represent alternative conformations.
Main Results:
- Successfully generated structural models of DHFR's C-terminal region using unsigned chemical shift data.
- Identified a minor conformational state differing in secondary structure from the ground state.
- Validated findings with existing chemical shift hypersurface predictions and X-ray crystallography.
Conclusions:
- Fragment modeling with sparse, unsigned chemical shift data can determine structures of μs-ms timescale alternative conformations.
- This method is valuable for characterizing transient states for drug screening and understanding biological roles.
- Advances the study of protein dynamics and conformational heterogeneity.
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