Probing the Structural Dynamics of the Catalytic Domain of Human Soluble Guanylate Cyclase
Date
2020-01-01
Journal Title
Journal ISSN
Volume Title
Publisher
NATURE PUBLISHING GROUP
Abstract
In the nitric oxide (NO) signaling pathway, human soluble guanylate cyclase (hsGC) synthesizes cyclic guanosine monophosphate (cGMP)
responsible for the regulation of cGMP-specific protein kinases (PKGs) and phosphodiesterases (PDEs). The crystal structure of the inactive hsGC cyclase dimer is known, but there is still a lack of information regarding the substrate-specific internal motions that are essential for the catalytic mechanism of the hsGC. In the current study, the hsGC cyclase heterodimer complexed with guanosine triphosphate (GTP) and cGMP was subjected to molecular dynamics simulations, to investigate the conformational dynamics that have functional implications on the catalytic activity of hsGC. Results revealed that in the GTP-bound complex of the hsGC heterodimer, helix 1 of subunit alpha (alpha:h1) moves slightly inwards and comes close to helix 4 of subunit beta (beta:h4). This conformational change brings loop 2 of subunit beta (beta:L2) closer to helix 2 of subunit alpha (alpha:h2). Likewise, loop 2 of subunit alpha (alpha:L2) comes closer to helix 2 of subunit beta (beta:h2). These structural events stabilize and lock GTP within the closed pocket for cyclization. In the cGMP-bound complex, alpha:L2 detaches from beta:h2 and establishes interactions with beta:L2, which results in the loss of global structure compactness. Furthermore, with the release of pyrophosphate, the interaction between alpha:h1 and beta:L2 weakens, abolishing the tight packing of the binding pocket. This study discusses the conformational changes induced by the binding of GTP and cGMP to the hsGC catalytic domain, valuable in designing new therapeutic strategies for the treatment of cardiovascular diseases.
responsible for the regulation of cGMP-specific protein kinases (PKGs) and phosphodiesterases (PDEs). The crystal structure of the inactive hsGC cyclase dimer is known, but there is still a lack of information regarding the substrate-specific internal motions that are essential for the catalytic mechanism of the hsGC. In the current study, the hsGC cyclase heterodimer complexed with guanosine triphosphate (GTP) and cGMP was subjected to molecular dynamics simulations, to investigate the conformational dynamics that have functional implications on the catalytic activity of hsGC. Results revealed that in the GTP-bound complex of the hsGC heterodimer, helix 1 of subunit alpha (alpha:h1) moves slightly inwards and comes close to helix 4 of subunit beta (beta:h4). This conformational change brings loop 2 of subunit beta (beta:L2) closer to helix 2 of subunit alpha (alpha:h2). Likewise, loop 2 of subunit alpha (alpha:L2) comes closer to helix 2 of subunit beta (beta:h2). These structural events stabilize and lock GTP within the closed pocket for cyclization. In the cGMP-bound complex, alpha:L2 detaches from beta:h2 and establishes interactions with beta:L2, which results in the loss of global structure compactness. Furthermore, with the release of pyrophosphate, the interaction between alpha:h1 and beta:L2 weakens, abolishing the tight packing of the binding pocket. This study discusses the conformational changes induced by the binding of GTP and cGMP to the hsGC catalytic domain, valuable in designing new therapeutic strategies for the treatment of cardiovascular diseases.