title: A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation.
abstract: Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses. How exactly compartmentation is achieved, however, has remained a mystery for more than 40 years. In this study, we developed computational and mathematical models to represent a subcellular sarcomeric space in a cardiac myocyte with varying detail. We then used these models to predict the contributions of various mechanisms that establish subcellular cAMP microdomains. We used the models to test the hypothesis that phosphodiesterases act as functional barriers to diffusion, creating discrete cAMP signaling domains. We also used the models to predict the effect of a range of experimentally measured diffusion rates on cAMP compartmentation. Finally, we modeled the anatomical structures in a cardiac myocyte diad, to predict the effects of anatomical diffusion barriers on cAMP compartmentation. When we incorporated experimentally informed model parameters to reconstruct an in silico subcellular sarcomeric space with spatially distinct cAMP production sites linked to caveloar domains, the models predict that under realistic conditions phosphodiesterases alone were insufficient to generate significant cAMP gradients. This prediction persisted even when combined with slow cAMP diffusion. When we additionally considered the effects of anatomic barriers to diffusion that are expected in the cardiac myocyte dyadic space, cAMP compartmentation did occur, but only when diffusion was slow. Our model simulations suggest that additional mechanisms likely contribute to cAMP gradients occurring in submicroscopic domains. The difference between the physiological and pathological effects resulting from the production of cAMP may be a function of appropriate compartmentation of cAMP signaling. Therefore, understanding the contribution of factors that are responsible for coordinating the spatial and temporal distribution of cAMP at the subcellular level could be important for developing new strategies for the prevention or treatment of unfavorable responses associated with different disease states.
authors.affiliation: Department of Pharmacology, University of California Davis, Davis, California, United States of America.
authors.forename: Pei-Chi
authors.initials: PC
authors.lastname: Yang
authors.affiliation: Department of Biomedical Engineering, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Britton W
authors.initials: BW
authors.lastname: Boras
authors.affiliation: Department of Pharmacology, University of California Davis, Davis, California, United States of America.
authors.forename: Mao-Tsuen
authors.initials: MT
authors.lastname: Jeng
authors.affiliation: Department of Pharmacology, University of California Davis, Davis, California, United States of America.|Department of Mathematics, University of California Davis, Davis, California, United States of America.
authors.forename: Steffen S
authors.identifier: 0000-0003-3771-5504
authors.initials: SS
authors.lastname: Docken
authors.affiliation: Department of Mathematics, University of California Davis, Davis, California, United States of America.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Lewis
authors.affiliation: Department of Biomedical Engineering, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: McCulloch
authors.affiliation: Department of Pharmacology, Center for Molecular Medicine, School of Medicine, University of Nevada Reno, Reno, Nevada, United States of America.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Harvey
authors.affiliation: Department of Pharmacology, University of California Davis, Davis, California, United States of America.
authors.forename: Colleen E
authors.initials: CE
authors.lastname: Clancy
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D019295:Computational Biology; D003198:Computer Simulation; D000242:Cyclic AMP / Q000737:chemistry* / Q000378:metabolism*; D042541:Intracellular Space / Q000737:chemistry* / Q000378:metabolism*; D051379:Mice; D032383:Myocytes, Cardiac / Q000737:chemistry / Q000166:cytology / Q000378:metabolism; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D000242:Cyclic AMP; D010727:Phosphoric Diester Hydrolases