Paper Citing NAMD - Abstract
Rogacheva, O. N.; Shchegolev, B. F.; Stefanov, V. E.; Zakharov, G. A.; Savvateeva-Popova, E. V.
Initiation of the 3 ':5 '-AMP-Induced Protein Kinase A I alpha Regulatory Subunit Conformational Transition. Part I. A202 and A326 are Critical Residues
BIOCHEMISTRY-MOSCOW, 77:456-464, MAY 2012
Protein-ligand docking and molecular dynamics studies have shown that the key event initiated by 3':5'-AMP binding to the A- and B-domains of protein kinase A I alpha regulatory subunit is formation of a hydrogen bond between 3':5'-AMP and A202(A326) (the residue in parentheses being from the B-domain). The A202(A326) amide group movement associated with the bond formation leads to reorganization of the phosphate binding cassette (PBC) (the short 3(10)-helix becomes the long alpha-helix). This process results in L203(L327) displacement and finally causes hinge (B-helix) rotation. The L203(L327) displacement and packing into the hydrophobic pocket formed by the PBC and beta 2 beta 3-loop also depends on the beta 2 beta 3-loop conformation. The correct conformation is maintained by R, I, E, but not K at position 209(333) of the A- and B-domains. So, the R209K and R333K mutants have problems with reaching B-conformation. The apo-form of the 3':5'-AMP-binding domain also undergoes transition from H- to B-conformation. In this case, the movement of A202(A326) amide group seems to be a result of reorganization of the PBC into a more stable alpha-helix.
