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Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random
Ivan Peran1, Alex S Holehouse2, Isaac S Carrico1
1Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.
Summary
Unfolded proteins rapidly contract upon dilution but remain expanded, exhibiting random coil properties despite sequence-specific preferences. This provides insights into protein folding dynamics and conformational ensembles.
Area of Science:
- Biophysics
- Protein folding dynamics
- Molecular biology
Background:
- Proteins are marginally stable and exist in folded and unfolded states.
- Understanding unfolded states is crucial for comprehending protein folding mechanisms.
Purpose of the Study:
- To provide a high-resolution description of unfolded states for the N-terminal domain of the L9 protein (NTL9) under refolding conditions.
- To investigate the conformational properties and dynamics of unfolded proteins.
Main Methods:
- Time-resolved Förster resonance energy transfer (FRET) with multiple label pairs.
- Time-resolved small-angle X-ray scattering (SAXS).
- All-atom simulations and polymer theory.
Main Results:
- Unfolded NTL9 rapidly contracts upon dilution from denaturant.
- The contracted unfolded state remains expanded compared to the folded state.
- Unfolded states show sequence-specific preferences but ensemble-averaged properties resemble random coils.
Conclusions:
- Unfolded protein states possess complex conformational ensembles with residual structure and interactions.
- Ensemble-averaged properties align with random coil models, consistent with polymer theory.
- Findings support theoretical predictions and single-molecule experimental inferences on unfolded protein behavior.
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