Mass-dependent bond vibrational dynamics influence catalysis by HIV-1 protease

Area of Science:

• Biochemistry
• Enzymology
• Chemical Physics

Background:

• Protein motions on microsecond-millisecond timescales correlate with enzymatic turnover rates.
• Femtosecond timescale enzyme motions (bond vibrations) are hypothesized to influence transition state formation.
• The role of ultrafast protein dynamics in enzyme catalysis remains an active area of investigation.

Purpose of the Study:

• To investigate the role of femtosecond protein motions in enzyme catalysis.
• To determine if altering vibrational frequencies affects enzymatic reaction rates.
• To explore the dynamic link between enzyme bond vibrations and the reaction coordinate.

Main Methods:

• Isotopic substitution: replacing nonexchangeable atoms (carbon, nitrogen, hydrogen) with heavier isotopes ((13)C, (15)N, (2)H) to perturb femtosecond motion.
• Enzyme studied: Human Immunodeficiency Virus type 1 (HIV-1) protease.
• Reaction monitoring: using a fluorescent peptide substrate to track multiple reaction steps.

Main Results:

• HIV-1 protease with heavy isotopes exhibited significantly reduced catalytic rates compared to the native (light) enzyme.
• Isotopic substitution altered vibrational frequencies without changing electrostatic properties, consistent with the Born-Oppenheimer approximation.
• The observed rate reduction provides experimental evidence for the influence of ultrafast dynamics on enzyme function.

Conclusions:

• Enzyme bond vibrations on the femtosecond timescale are dynamically linked to events along the reaction coordinate.
• Mass-dependent vibrational properties of the enzyme play a crucial role in determining catalytic efficiency.
• These findings challenge previous assumptions and highlight the importance of ultrafast dynamics in enzymatic catalysis.