Paper Citing NAMD - Abstract
Autenrieth, F.; Tajkhorshid, E.; Schulten, K.; Luthey-Schulten, Z.
Role of water in transient cytochrome c(2) docking
JOURNAL OF PHYSICAL CHEMISTRY B, 108:20376-20387, DEC 30 2004
Cytochrome c (cyt c) is a small water-soluble redox protein that facilitates electron transfer in photosynthesis and respiration by alternately docking to integral membrane proteins such as the photosynthetic reaction center (RC). Recently, a high-resolution X-ray structure was solved for the RC-cyt c(2) complex of Rhodobacter sphaeroides, revealing important contacts between the RC in its ground state and reduced cyt c(2) mediated by bridging water molecules. In this article, we compare the variations in these contacts and in the interface in general for both redox states of cyt c(2) that resulted from full-atom simulations of the complexes embedded in a membrane with explicit water molecules. Molecular dynamics simulations of the two redox states of the RC-cyt c(2) system were performed using the CHARMM27 parameters developed for the oxidized and reduced forms of the heme prosthethic group. In its overall dynamics, the encounter complex was found to be very similar in both redox states, exhibiting at the interface a stable hydrophobic tunneling domain and a broad basin of attraction. The differences between the redox states are subtle and involve the formation of a structured cluster of water molecules in the reduced cyt c(2) system. Fluctuations of water and residues at the interface increase upon oxidation and probably mediate the undocking process. The observed differences between the two redox states of the system can only be attributed to the different electrostatic potentials generated by heme in the interface region, as no other modifications were introduced. As the time scale of the undocking process is beyond the time scales reachable by full atomic molecular dynamics simulation of the system, we employed steered molecular dynamics to investigate and compare the energetics associated with the unbinding of RC-cyt c(2) in the reduced and oxidized forms.
