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Population shuffling between ground and high energy excited states
T Michael Sabo1, John O Trent1, Donghan Lee1,2
1Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202.
Protein Science : a Publication of the Protein Society
|August 29, 2015
Summary
This study extends population shuffling to analyze protein dynamics in excited states, revealing how fast side-chain movements influence slow conformational changes in SH3 domains. This provides new insights into protein functionality and structural dynamics.
Area of Science:
- Biophysics
- Structural Biology
- Protein Dynamics
Background:
- Proteins utilize thermal energy-driven dynamics across various timescales for essential functions like catalysis and allostery.
- A hierarchy of motion is proposed to link fast and slow protein dynamics.
- Population shuffling, a model for temporal hierarchy, was previously limited to ground-state interconversions.
Purpose of the Study:
- To extend the population shuffling framework to systems interconverting between ground and excited states.
- To investigate the role of high-energy excited states in protein dynamics.
- To analyze the structural dynamics of SH3 domain mutants.
Main Methods:
- Application of the population shuffling model to systems involving excited states.
- Utilizing SH3 domain mutants (G48M and A39V/N53P/V55L) from Fyn tyrosine kinase.
- Performing unrestrained molecular dynamics (MD) simulations.
Main Results:
- The gauche-rotameric state of the leucine χ2 dihedral angle significantly impacts rotameric state distributions in both major and minor SH3 domain forms.
- High correlations were observed between experimental and back-calculated leucine χ2 rotameric populations from MD simulations.
- Fast timescale rotameric side-chain population distributions were successfully extracted from slow timescale conformational exchange data.
Conclusions:
- The extended population shuffling model provides a new tool for studying the structural dynamics of high-energy excited states.
- This work demonstrates the significant contribution of specific rotameric states to overall protein dynamics.
- The findings highlight the interplay between fast side-chain dynamics and slow conformational exchange in proteins.
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