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Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome bc(1) complex
S Izrailev1, A R Crofts, E A Berry
1Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, USA.
Biophysical Journal
|October 8, 1999
Summary
The Rieske iron-sulfur protein (ISP) in the cytochrome bc(1) complex can rotate, enabling quinol oxidation. Simulations reveal a proton conduction pathway, clarifying a key step in mitochondrial respiration.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biophysics
Background:
- Mitochondrial ubiquinol/cytochrome c oxidoreductase (cytochrome bc(1) complex) is crucial for cellular respiration.
- Crystallographic data suggest significant movement of the Rieske iron-sulfur protein (ISP) during quinol oxidation.
Purpose of the Study:
- To investigate the feasibility and mechanism of Rieske ISP head domain rotation within the cytochrome bc(1) complex.
- To characterize the interactions stabilizing ISP conformations during rotation.
- To identify proton conduction pathways.
Main Methods:
- Steered molecular dynamics simulations of a solvated cytochrome bc(1) complex in a phospholipid bilayer.
- Construction of a large-scale molecular model (206,720 atoms).
- Force field parametrization for heme and Fe(2)S(2) cluster.
Main Results:
- Demonstrated the feasibility of a 56-degree rotation of the ISP soluble domain within 1 ns.
- Identified several metastable conformations of the ISP during rotation.
- Characterized stabilizing interactions for different ISP positions.
- Discovered a proton conduction pathway from the Q(o) site to the solvent via a water channel.
Conclusions:
- The rotation of the Rieske ISP head domain is a viable mechanism in quinol oxidation.
- The study provides insights into the dynamic conformational changes of the bc(1) complex.
- A novel proton conduction pathway has been elucidated, contributing to understanding energy transduction.
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