Substrate-Dependent Mobile Loop Conformational Changes in Alkanesulfonate Monooxygenase from Accelerated Molecular...

Area of Science:

• Biochemistry
• Enzymology
• Computational Biology

Background:

• Alkanesulfonate monooxygenase (SsuD) catalyzes crucial reactions.
• Enzyme catalysis is often regulated by substrate-induced conformational changes.
• Understanding these dynamics is key to enzyme mechanism elucidation.

Purpose of the Study:

• To investigate substrate-induced conformational changes in SsuD using accelerated molecular dynamics (aMD) simulations.
• To correlate these conformational dynamics with enzyme activity and catalytic intermediates.
• To identify key residues and interactions involved in SsuD conformational regulation.

Main Methods:

• Accelerated molecular dynamics (aMD) simulations.
• Wild-type and variant SsuD enzyme systems.
• Simulations with reduced flavin (FMNH2), C4a-peroxyflavin intermediate (FMNOO-), and octanesulfonate (OCS).

Main Results:

• Identified three distinct mobile loop conformations: "open", "closed", and "semiclosed".
• Substrate-free SsuD exhibits an open conformation for substrate entry.
• FMNH2 binding induces a closed conformation, stabilized by salt bridges (Asp111-Arg263, Glu205-Arg271).
• A semiclosed conformation, stabilized by a His124-Phe261 pi-pi interaction, is formed with FMNH2 and OCS bound, potentially facilitating O2 binding.
• FMNOO- and OCS bound state shows an open loop, suggesting alternative flavin intermediates.

Conclusions:

• SsuD conformational flexibility, particularly the mobile loop, is critical for its catalytic mechanism.
• Specific loop conformations are dictated by the binding of different substrates and intermediates.
• Key salt bridges and pi-pi interactions play vital roles in stabilizing distinct SsuD conformations, influencing catalytic efficiency and substrate processing.