Possible pathway for ubiquinone shuttling in Rhodospirillum rubrum revealed by molecular dynamics simulation

Area of Science:

• Photosynthetic apparatus
• Purple bacteria
• Molecular assembly

Background:

• Structure of photosynthetic components in purple bacteria resolved.
• Assembly of reaction center (RC) and light-harvesting 1 (LH1) complexes is key.
• LH1 ring structure varies (open in Rhodobacter sphaeroides, closed in Rhodospirillum rubrum).

Purpose of the Study:

• Investigate ubiquinone diffusion through a closed LH1 ring.
• Determine how ubiquinone overcomes the LH1 barrier for electron transport.
• Model the diffusion pathway in Rhodospirillum rubrum.

Main Methods:

• Modeling the LH1 structure of Rhodospirillum rubrum.
• Steered molecular-dynamics simulations to determine potential of mean force.
• Fluctuation theorem and stiff spring approximation for potential reconstruction.

Main Results:

• Calculated an upper limit for ubiquinone diffusion time through the LH1 ring.
• Mean first-passage time estimated at ~8 x 10(-3) s.
• Diffusion time is compatible with known turnover rates of RC and RC-LH1 complexes (~1000 Hz).

Conclusions:

• Ubiquinone can efficiently diffuse through the closed LH1 ring.
• The modeled diffusion pathway supports observed photosynthetic efficiency.
• This mechanism explains electron transport in bacteria with closed LH1 rings.