Paper Citing NAMD - Abstract
Rogacheva, Olga N.; Stefanov, Vasiliy E.; Shchegolev, Boris F.; Vershinina, Elena A.; Savvateeva-Popova, Elena V.
Role of arginine 209 in the conformational transition of the protein kinase A regulatory subunit RI alpha A-domain
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 12 Art. No. 1441005, APR 2014
Using the combination of molecular dynamics (MD) simulations and geometric clustering we analyzed the role of arginine at 209 position in the transition of protein kinase A I alpha (PKA I alpha) regulatory subunit A-domain from H- to B-conformation and stabilization of the latter. The mechanism underlying the role of the residue at position 209 in the realization of B-conformation includes: (1) possibility to bind the ligand tightly (if transition happens in the presence of cAMP), (2) capability to hold beta 2 beta 3-loop in the correct conformation, (3) tendency of residue at 209 position to stabilize B-conformation in the absence and in presence of the ligand. In terms of the effect produced on transition of A-domain from H- to B-conformation in the presence of cAMP, mutational substitutions for R209 can be arranged in the following order: Glu(Gly)> Lys>Ile. In the absence of cAMP the order is different Lys>Gly>Glu>Ile. Thus, our results allow us to presume that the role of arginine at 209 position can be important though not crucial.
