@article{ahmed_grant_edwards_rahman_cirit_goshe_haugh_2014, title={Data-driven modeling reconciles kinetics of ERK phosphorylation, localization, and activity states}, volume={10}, ISSN={["1744-4292"]}, DOI={10.1002/msb.134708}, abstractNote={Abstract}, number={1}, journal={MOLECULAR SYSTEMS BIOLOGY}, publisher={Wiley-Blackwell}, author={Ahmed, Shoeb and Grant, Kyle G. and Edwards, Laura E. and Rahman, Anisur and Cirit, Murat and Goshe, Michael B. and Haugh, Jason M.}, year={2014}, month={Jan} }
 @article{cirit_haugh_2012, title={Data-driven modelling of receptor tyrosine kinase signalling networks quantifies receptor-specific potencies of PI3K-and Ras-dependent ERK activation}, volume={441}, ISSN={["0264-6021"]}, DOI={10.1042/bj20110833}, abstractNote={Signal transduction networks in mammalian cells, comprising a limited set of interacting biochemical pathways, are accessed by various growth factor and cytokine receptors to elicit distinct cell responses. This raises the question as to how specificity of the stimulus–response relationship is encoded at the molecular level. It has been proposed that specificity arises not only from the activation of unique signalling pathways, but also from quantitative differences in the activation and regulation of shared receptor-proximal signalling proteins. To address such hypotheses, data sets with greater precision and coverage of experimental conditions will need to be acquired, and rigorous frameworks that codify and parameterize the inherently non-linear relationships among signalling activities will need to be developed. In the present study we apply a systematic approach combining quantitative measurements and mathematical modelling to compare the signalling networks accessed by FGF (fibroblast growth factor) and PDGF (platelet-derived growth factor) receptors in mouse fibroblasts, in which the ERK (extracellular-signal-regulated kinase) cascade is activated by Ras- and PI3K (phosphoinositide 3-kinase)-dependent pathways. We show that, whereas the FGF stimulation of PI3K signalling is relatively weak, this deficiency is compensated for by a more potent Ras-dependent activation of ERK. Thus, as the modelling would predict, the ERK pathway is activated to a greater extent in cells co-stimulated with FGF and PDGF, relative to the saturated levels achieved with either ligand alone. It is envisaged that similar approaches will prove valuable in the elucidation of quantitative differences among other closely related receptor signalling networks.}, number={1}, journal={BIOCHEMICAL JOURNAL}, publisher={Portland Press Ltd.}, author={Cirit, Murat and Haugh, Jason M.}, year={2012}, month={Jan}, pages={77–85} }
 @article{cirit_grant_haugh_2012, title={Systemic Perturbation of the ERK Signaling Pathway by the Proteasome Inhibitor, MG132}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0050975}, abstractNote={Inhibition of the ubiquitin-proteasome protein degradation pathway has been identified as a viable strategy for anti-tumor therapy based on its broad effects on cell proliferation. By the same token, the variety of elicited effects confounds the interpretation of cell-based experiments using proteasome inhibitors such as MG132. It has been proposed that MG132 treatment reduces growth factor-stimulated phosphorylation of extracellular signal-regulated kinases (ERKs), at least in part through upregulation of dual specificity phosphatases (DUSPs). Here, we show that the effects of MG132 treatment on ERK signaling are more widespread, leading to a reduction in activation of the upstream kinase MEK. This suggests that MG132 systemically perturbs the intracellular phosphoproteome, impacting ERK signaling by reducing phosphorylation status at multiple levels of the kinase cascade.}, number={11}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Cirit, Murat and Grant, Kyle G. and Haugh, Jason M.}, editor={Buday, LaszloEditor}, year={2012}, month={Nov} }
 @article{buhrman_kumar_cirit_haugh_mattos_2011, title={Allosteric Modulation of Ras-GTP Is Linked to Signal Transduction through RAF Kinase}, volume={286}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m110.193854}, abstractNote={Ras is a key signal transduction protein in the cell. Mutants of Gly12 and Gln61 impair GTPase activity and are found prominently in cancers. In wild type Ras-GTP, an allosteric switch promotes disorder to order transition in switch II, placing Gln61 in the active site. We show that the “on” and “off” conformations of the allosteric switch can also be attained in RasG12V and RasQ61L. Although both mutants have similarly impaired active sites in the on state, RasQ61L stabilizes an anti-catalytic conformation of switch II in the off state of the allosteric switch when bound to Raf. This translates into more potent activation of the MAPK pathway involving Ras, Raf kinase, MEK, and ERK (Ras/Raf/MEK/ERK) in cells transfected with RasQ61L relative to RasG12V. This differential is not observed in the Raf-independent pathway involving Ras, phosphoinositide 3-kinase (PI3K), and Akt (Ras/PI3K/Akt). Using a combination of structural analysis, hydrolysis rates, and experiments in NIH-3T3 cells, we link the allosteric switch to the control of signaling in the Ras/Raf/MEK/ERK pathway, supporting a GTPase-activating protein-independent model for duration of the Ras-Raf complex.}, number={5}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Buhrman, Greg and Kumar, V. S. Senthil and Cirit, Murat and Haugh, Jason M. and Mattos, Carla}, year={2011}, month={Feb}, pages={3323–3331} }
 @article{wang_cirit_haugh_2011, title={PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk (vol 5, pg 246, 2009)}, volume={7}, ISSN={["1744-4292"]}, DOI={10.1038/msb.2011.61}, number={1}, journal={MOLECULAR SYSTEMS BIOLOGY}, publisher={Wiley-Blackwell}, author={Wang, Chun-Chao and Cirit, Murat and Haugh, Jason M.}, year={2011}, month={Aug} }
 @article{cirit_krajcovic_choi_welf_horwitz_haugh_2010, title={Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells}, volume={6}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.1000688}, abstractNote={Productive cell migration requires the spatiotemporal coordination of cell adhesion, membrane protrusion, and actomyosin-mediated contraction. Integrins, engaged by the extracellular matrix (ECM), nucleate the formation of adhesive contacts at the cell's leading edge(s), and maturation of nascent adhesions to form stable focal adhesions constitutes a functional switch between protrusive and contractile activities. To shed additional light on the coupling between integrin-mediated adhesion and membrane protrusion, we have formulated a quantitative model of leading edge dynamics combining mechanistic and phenomenological elements and studied its features through classical bifurcation analysis and stochastic simulation. The model describes in mathematical terms the feedback loops driving, on the one hand, Rac-mediated membrane protrusion and rapid turnover of nascent adhesions, and on the other, myosin-dependent maturation of adhesions that inhibit protrusion at high ECM density. Our results show that the qualitative behavior of the model is most sensitive to parameters characterizing the influence of stable adhesions and myosin. The major predictions of the model, which we subsequently confirmed, are that persistent leading edge protrusion is optimal at an intermediate ECM density, whereas depletion of myosin IIA relieves the repression of protrusion at higher ECM density.}, number={2}, journal={PLOS COMPUTATIONAL BIOLOGY}, publisher={Public Library of Science (PLoS)}, author={Cirit, Murat and Krajcovic, Matej and Choi, Colin K. and Welf, Erik S. and Horwitz, Alan F. and Haugh, Jason M.}, editor={Asthagiri, Anand R.Editor}, year={2010}, month={Feb} }
 @article{cirit_wang_haugh_2010, title={Systematic Quantification of Negative Feedback Mechanisms in the Extracellular Signal-regulated Kinase (ERK) Signaling Network}, volume={285}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m110.148759}, abstractNote={Cell responses are actuated by tightly controlled signal transduction pathways. Although the concept of an integrated signaling network replete with interpathway cross-talk and feedback regulation is broadly appreciated, kinetic data of the type needed to characterize such interactions in conjunction with mathematical models are lacking. In mammalian cells, the Ras/ERK pathway controls cell proliferation and other responses stimulated by growth factors, and several cross-talk and feedback mechanisms affecting its activation have been identified. In this work, we take a systematic approach to parse the magnitudes of multiple regulatory mechanisms that attenuate ERK activation through canonical (Ras-dependent) and non-canonical (PI3K-dependent) pathways. In addition to regulation of receptor and ligand levels, we consider three layers of ERK-dependent feedback: desensitization of Ras activation, negative regulation of MEK kinase (e.g. Raf) activities, and up-regulation of dual-specificity ERK phosphatases. Our results establish the second of these as the dominant mode of ERK self-regulation in mouse fibroblasts. We further demonstrate that kinetic models of signaling networks, trained on a sufficient diversity of quantitative data, can be reasonably comprehensive, accurate, and predictive in the dynamical sense.}, number={47}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Cirit, Murat and Wang, Chun-Chao and Haugh, Jason M.}, year={2010}, month={Nov}, pages={36736–36744} }