Paper Citing NAMD - Abstract
Pogorelov, Taras V.; Autenrieth, Felix; Roberts, Elijah; Luthey-Schulten, Zaida A.
Cytochrome c(2) exit strategy: Dissociation studies and evolutionary implications
JOURNAL OF PHYSICAL CHEMISTRY B, 111:618-634, JAN 25 2007
Small, water-soluble, type c cytochromes form a transient network connecting major bioenergetic membrane protein complexes in both photosynthesis and respiration. In the photosynthesis cycle of Rhodobacter sphaeroides, cytochrome c(2) (cyt c(2)) docks to the reaction center (RC), undergoes electron transfer, and exits for the cytochrome bc(1) complex. Translations of cyt c(2) about the RC-cyt c(2) docking interface and surrounding membrane reveal possible exit pathways. A pathway at a minimal elevation allowed by the architecture of the RC is analyzed using both an all-atom steered molecular dynamics simulation of the RC-cyt c(2) complex and a bioinformatic analysis of the structures and sequences of cyt c. The structure-based phylogenetic analysis allows for the identification of structural elements that have evolved to satisfy the requirements of having multiple functional partners. The patterns of evolutionary variation obtained from the phylogenetic analysis of both docking partners of cyt c(2) reveal conservation of key residues involved in the interaction interfaces that would be candidates for further experimental studies. Additionally, using the molecular mechanics Poisson-Boltzmann surface area method we calculate that the binding free energy of reduced cyt c(2) to the RC is nearly 6 kcal/mol more favorable than with oxidized cyt c(2). The redox-dependent variations lead to changes in structural flexibility, behavior of the interfacial water molecules, and eventually changes in the binding free energy of the complex.
