title: Computational analyses of synergism in small molecular network motifs.
abstract: Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically) to alter the responses of the motifs to stimuli. Synergism (or antagonism) was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.
authors.affiliation: Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America.
authors.forename: Yili
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America.
authors.forename: Paul
authors.initials: P
authors.lastname: Smolen
authors.affiliation: Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America.
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Baxter
authors.affiliation: Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, Texas, United States of America.
authors.forename: John H
authors.initials: JH
authors.lastname: Byrne
mesh_terms: D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000378:metabolism; D050882:CREB-Binding Protein / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D017362:Cyclic AMP Response Element-Binding Protein / Q000378:metabolism; D004359:Drug Therapy, Combination / Q000379:methods; D025461:Feedback, Physiological; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D006801:Humans; D012984:Software; D049490:Systems Biology; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; C115163:CREB1 protein, human; D017362:Cyclic AMP Response Element-Binding Protein; D050882:CREB-Binding Protein; C494363:CREBBP protein, human