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Updated: Jul 17, 2026
10:03
Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
Published on: June 27, 2014
Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy
Ilya J Finkelstein1, Haruto Ishikawa, Seongheun Kim
1Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Summary
Substrate binding to horseradish peroxidase (HRP) alters its structural dynamics, reducing fluctuations and locking the enzyme into a specific conformation. This dynamic quenching optimizes HRP for its enzymatic functions.
Area of Science:
- Biochemistry
- Enzymology
- Protein Dynamics
Background:
- Enzyme structural dynamics are crucial for substrate binding and biological function.
- The impact of substrate binding on enzyme dynamics at fast timescales remains under-explored.
Purpose of the Study:
- To investigate the picosecond dynamics of horseradish peroxidase (HRP) isoenzyme C in its free and substrate-bound states.
- To understand how substrate ligation influences HRP's structural dynamics using advanced spectroscopic techniques.
Main Methods:
- Utilized 2D-IR vibrational echo spectroscopy to probe picosecond dynamics.
- Employed carbon monoxide (CO) bound to the heme active site as a spectroscopic marker for protein dynamics.
Main Results:
- Free HRP exists in two distinct conformations with picosecond fluctuations.
- Substrate binding restricts HRP to a single conformation with reduced dynamics.
- Observed decreased CO frequency fluctuations, linked to restricted motion of distal histidine and arginine residues.
Conclusions:
- Substrate binding significantly alters HRP's structural dynamics, reducing flexibility.
- This dynamic quenching stabilizes a conformation favorable for subsequent enzymatic steps.
- Key residues like distal histidine and arginine play a role in substrate-induced dynamic changes.
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