Paper Citing NAMD - Abstract
Khrenova, Maria; Domratcheva, Tatiana; Grigorenko, Bella; Nemukhin, Alexander
Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1
JOURNAL OF MOLECULAR MODELING, 17:1579-1586, JUL 2011
The first biochemical and structural characterization of the full-length active photoreceptor BlrP1 from Klebsiella pneumoniae was recently reported by Barends et al. [Nature 459:1015-1018, (2009)]. The light-regulated catalytic function of its C-terminal c-di-guanosine monophosphate phosphodiesterase, the EAL (Glu-Ala-Leu) domain, is activated by the N-terminal sensor of blue light using the flavin adenine dinucleotide (BLUF) domain. We performed molecular dynamics simulations on the dimeric BlrP1 protein in order to examine the coupling regions that are presumably involved in transmitting light-induced structural changes which occur in the BLUF domain to the EAL domain. According to the results of simulations and an analysis of the hydrogen bonding between the respective polypeptide chains, the region containing the site on the alpha 3 alpha 4 loop of BLUF is responsible for communication between the photosensing and catalytic domains in the dimeric BlrP1 protein.
