Conformational substates modulate hydride transfer in dihydrofolate reductase

Area of Science:

• Biochemistry
• Enzymology
• Computational Biology

Background:

• Dihydrofolate reductase (DHFR) is crucial for folate metabolism.
• Previous studies identified protein features correlating with hydride-transfer reaction barriers.
• Understanding enzyme dynamics is key to elucidating catalytic mechanisms.

Purpose of the Study:

• To determine the hydride-transfer barrier in wild-type DHFR and G121V/G121S mutants using simulations.
• To investigate the full reaction pathway and reactive event.
• To correlate protein dynamics and fluctuations with hydride-transfer barrier heights.

Main Methods:

• Potential of Mean Force (PMF) simulations were performed.
• Analysis of free energy barriers and structural ensembles.
• Investigation of protein fluctuations and vibrational modes.

Main Results:

• PMF calculations confirmed trends from earlier studies on reaction barriers.
• Simulation fluctuations correlated with hydride-transfer barrier heights.
• Vibrational modes promoting hydride transfer showed larger amplitudes in simulations with lowered barriers.

Conclusions:

• Discrete enzyme substates on the potential energy landscape yield distinct hydride-transfer barriers.
• Mutations at position 121 in DHFR exert long-range effects via preorganized protein environments and substate distributions.
• Enzyme dynamics are intrinsically linked to catalytic efficiency and mutation effects.