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NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
Published on: November 1, 2024
Domain mobility in proteins from NMR/SRLS.
Yury E Shapiro1, Edith Kahana, Eva Meirovitch
1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel. shapiro@nmrsgi4.ls.biu.ac.il
The Journal of Physical Chemistry. B
|August 14, 2009
Summary
This study reveals that simplified models inaccurately describe protein domain motion. Re-evaluating adenylate kinase’s internal dynamics provides a more accurate picture of enzyme flexibility and function.
Area of Science:
- Biochemistry and Molecular Biology
- Structural Biology
- Protein Dynamics
Background:
- Protein internal mobility is crucial for function, particularly in enzyme catalysis.
- Adenylate kinase (AK) exhibits nanosecond domain motion in its AMP-binding (AMPbd) and lid (LID) domains, as suggested by experimental data.
- Previous analyses using the mode-coupling slowly relaxing local structure (MCLSRS) approach yielded physically unrealistic parameters for local ordering and geometry.
Purpose of the Study:
- To re-evaluate the internal dynamics of E. coli adenylate kinase by refining the analysis of (15)N spin relaxation data.
- To address limitations of previous MCLSRS analyses by removing assumptions of axial local ordering and diffusion.
- To obtain a physically sound description of domain motion and its contribution to enzyme function.
Main Methods:
- Analysis of experimental (15)N spin relaxation data from E. coli adenylate kinase.
- Application of the mode-coupling slowly relaxing local structure (MCLSRS) approach without simplified axial symmetry assumptions.
- Determination of rhombic local ordering parameters and potential coefficients.
- Calculation of correlation times for domain and global motions at different temperatures.
- Assessment of temperature dependence using Arrhenius-type analysis to determine activation energies.
Main Results:
- Eliminating simplified axial symmetry assumptions resolved unrealistic local ordering and geometry issues.
- A physically sound picture of domain motion was obtained, characterized by rhombic local ordering (
= 0.471, = -0.952, = 0.481). - Average correlation times for domain motion were determined as 10.4 ns (288 K) and 6.4 ns (302 K), with global motion times of 20.6 ns (288 K) and 14.9 ns (302 K).
- Domain motion exhibited Arrhenius-type temperature dependence with activation energies of 63.8 ± 7.0 kJ/mol (AMPbd) and 53.0 ± 9.1 kJ/mol (LID).
- Traditional model-free analysis, ignoring mode-coupling, incorrectly suggested a largely rigid backbone.
Conclusions:
- The refined MCLSRS analysis provides a physically interpretable description of adenylate kinase domain motion.
- Rhombic local ordering and diffusion are essential for accurately characterizing protein internal dynamics.
- The determined motional parameters and activation energies offer insights into the functional flexibility of adenylate kinase.
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