Paper Citing NAMD - Abstract
Salsbury, Freddie R., Jr.; Yuan, Ye; Knaggs, Michael H.; Poole, Leslie B.; Fetrow, Jacquelyn S.
Structural and Electrostatic Asymmetry at the Active Site in Typical and Atypical Peroxiredoxin Dimers
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6832-6843, JUN 14 2012
The peroxiredoxins (Prx) are ubiquitous peroxidases involved in important biological processes; however, details of their enzymatic mechanism remain elusive. To probe potential dynamics function relationships, molecular dynamics simulations and electrostatic calculations were performed on the atypical 2-cysteine thiol peroxidase (Tpx) from Streptococcus pneumoniae and results compared to a previous study of a typical 2-cysteine Prx from Trypanosoma cruzi. The analyses indicate a commonality between both typical and atypical Prx: dynamic asymmetry. Asymmetry is observed in structure, fluctuations, and active site electrostatics. Key residues, including Glu150 and Phe153, play roles in the developing asymmetry; furthermore, in the atypical 2-Cys Tpx, Glu150 exhibits conformation fluctuations suggesting involvement in a proton shuttle. The existence of a pathway of connected residues appears to propagate the asymmetry. The commonality of asymmetry and coupling pathways in both typical and atypical Prxs suggests a driving force toward dimer asymmetry as a common feature that plays a functional role in creating one active site with a lower cysteine pK(a).
