Defining a length scale for millisecond-timescale protein conformational exchange

Area of Science:

• Biochemistry and Molecular Biology
• Structural Biology
• Biophysics

Background:

• Protein folding mechanisms, particularly interconversion between native and intermediate states, are not fully understood.
• The FF domain, a four-helix bundle, folds through a transient compact intermediate (I).
• Previous studies used NMR spectroscopy to determine the structure of the FF intermediate and identified water dynamics as key to I-N conformational exchange.

Purpose of the Study:

• To define the length scale of the FF domain's intermediate (I) to native (N) state transition.
• To investigate the size of structural units involved in the I-N conformational exchange.
• To understand the role of water dynamics in the FF domain's folding pathway.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy.
• Relaxation dispersion NMR spectroscopy.
• Measurement of effective hydrodynamic radius (EHR).

Main Results:

• The effective hydrodynamic radius (EHR) for the FF I-N transition was determined to be less than 4 Å.
• This EHR is significantly smaller than the FF domain's overall hydrodynamic radius (13 Å).
• The small EHR indicates that the I-N transition involves the movement of only one to two amino acid side chains at a time.

Conclusions:

• The FF domain I-N transition occurs through the localized exposure or burial of a few amino acid side chains.
• This transition does not involve large-scale protein conformational changes or significant disruption of the surrounding water structure.
• The findings suggest that water dynamics play a crucial role in facilitating protein conformational changes through small, localized events.