The open state of human topoisomerase I as probed by molecular dynamics simulation

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Human topoisomerase I is crucial for managing DNA topology during replication and transcription.
• Understanding the enzyme's conformational dynamics, particularly the transition to its open state, is key to its function.

Purpose of the Study:

• To investigate the conformational changes of human topoisomerase I when transitioning from a closed to an open state using molecular dynamics simulations.
• To analyze the stability of secondary and tertiary structures and the active site during this transition.

Main Methods:

• Molecular dynamics simulation initiated from a closed human topoisomerase I-DNA complex structure.
• Introduction of a brief repulsion force to destabilize the closed state, followed by 10 ns of unperturbed simulation.
• Electrostatic potential calculations on the simulated open protein structure.

Main Results:

• The protein undergoes significant domain rearrangements, moving as a coherent unit while preserving secondary and tertiary structures.
• Despite large domain movements (80-90 Å), the catalytic pentad remains preassembled, with minimal backbone deviation (1.7 Å) in the active site.
• Electrostatic analysis reveals a large positive region in the open state, positioning the active site optimally for interaction with supercoiled DNA.

Conclusions:

• Human topoisomerase I can adopt an open conformation through coordinated domain movements that maintain catalytic site integrity.
• The open state presents an electrostatically favorable surface for binding negatively charged DNA, facilitating its enzymatic function.