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Pajoh-Casco M, Vinujudson A, Enciso G. Bounds on the Ultrasensitivity of Biochemical Reaction Cascades. Bull Math Biol 2024; 86:59. [PMID: 38637362 DOI: 10.1007/s11538-024-01287-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
The ultrasensitivity of a dose response function can be quantifiably defined using the generalized Hill coefficient of the function. We examined an upper bound for the Hill coefficient of the composition of two functions, namely the product of their individual Hill coefficients. We proved that this upper bound holds for compositions of Hill functions, and that there are instances of counterexamples that exist for more general sigmoidal functions. Additionally, we tested computationally other types of sigmoidal functions, such as the logistic and inverse trigonometric functions, and we provided computational evidence that in these cases the inequality also holds. We show that in large generality there is a limit to how ultrasensitive the composition of two functions can be, which has applications to understanding signaling cascades in biochemical reactions.
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Affiliation(s)
- Marcello Pajoh-Casco
- Department of Physics and Astronomy, University of California, Irvine, 92697, USA
| | | | - German Enciso
- Department of Mathematics, University of California, Irvine, 92697, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, 92697, USA.
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Sun YH, Wu YL, Liao BY. Phenotypic heterogeneity in human genetic diseases: ultrasensitivity-mediated threshold effects as a unifying molecular mechanism. J Biomed Sci 2023; 30:58. [PMID: 37525275 PMCID: PMC10388531 DOI: 10.1186/s12929-023-00959-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023] Open
Abstract
Phenotypic heterogeneity is very common in genetic systems and in human diseases and has important consequences for disease diagnosis and treatment. In addition to the many genetic and non-genetic (e.g., epigenetic, environmental) factors reported to account for part of the heterogeneity, we stress the importance of stochastic fluctuation and regulatory network topology in contributing to phenotypic heterogeneity. We argue that a threshold effect is a unifying principle to explain the phenomenon; that ultrasensitivity is the molecular mechanism for this threshold effect; and discuss the three conditions for phenotypic heterogeneity to occur. We suggest that threshold effects occur not only at the cellular level, but also at the organ level. We stress the importance of context-dependence and its relationship to pleiotropy and edgetic mutations. Based on this model, we provide practical strategies to study human genetic diseases. By understanding the network mechanism for ultrasensitivity and identifying the critical factor, we may manipulate the weak spot to gently nudge the system from an ultrasensitive state to a stable non-disease state. Our analysis provides a new insight into the prevention and treatment of genetic diseases.
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Affiliation(s)
- Y Henry Sun
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
| | - Yueh-Lin Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wei-Gong Memorial Hospital, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institute, Zhunan, Miaoli, Taiwan
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Sun X, Zhang J, Zhao Q, Chen X, Zhu W, Yan G, Zhou T. Stochastic modeling suggests that noise reduces differentiation efficiency by inducing a heterogeneous drug response in glioma differentiation therapy. BMC SYSTEMS BIOLOGY 2016; 10:73. [PMID: 27515956 PMCID: PMC4982223 DOI: 10.1186/s12918-016-0316-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/06/2016] [Indexed: 12/23/2022]
Abstract
Background Glioma differentiation therapy is a novel strategy that has been used to induce glioma cells to differentiate into glia-like cells. Although some advances in experimental methods for exploring the molecular mechanisms involved in differentiation therapy have been made, a model-based comprehensive analysis is still needed to understand these differentiation mechanisms and improve the effects of anti-cancer therapeutics. This type of analysis becomes necessary in stochastic cases for two main reasons: stochastic noise inherently exists in signal transduction and phenotypic regulation during targeted therapy and chemotherapy, and the relationship between this noise and drug efficacy in differentiation therapy is largely unknown. Results In this study, we developed both an additive noise model and a Chemical-Langenvin-Equation model for the signaling pathways involved in glioma differentiation therapy to investigate the functional role of noise in the drug response. Our model analysis revealed an ultrasensitive mechanism of cyclin D1 degradation that controls the glioma differentiation induced by the cAMP inducer cholera toxin (CT). The role of cyclin D1 degradation in human glioblastoma cell differentiation was then experimentally verified. Our stochastic simulation demonstrated that noise not only renders some glioma cells insensitive to cyclin D1 degradation during drug treatment but also induce heterogeneous differentiation responses among individual glioma cells by modulating the ultrasensitive response of cyclin D1. As such, the noise can reduce the differentiation efficiency in drug-treated glioma cells, which was verified by the decreased evolution of differentiation potential, which quantified the impact of noise on the dynamics of the drug-treated glioma cell population. Conclusion Our results demonstrated that targeting the noise-induced dynamics of cyclin D1 during glioma differentiation therapy can increase anti-glioma effects, implying that noise is a considerable factor in assessing and optimizing anti-cancer drug interventions. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0316-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoqiang Sun
- Zhong-shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510089, China. .,School of Mathematical and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Jiajun Zhang
- School of Mathematical and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qi Zhao
- School of Mathematics, Liaoning University, Shenyang, 110036, China.,Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Shenyang, 110036, China
| | - Xing Chen
- School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, China
| | - Wenbo Zhu
- Zhong-shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510089, China.
| | - Guangmei Yan
- Zhong-shan School of Medicine, Sun Yat-Sen University, Guangzhou, 510089, China
| | - Tianshou Zhou
- School of Mathematical and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, China.
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Sun X, Xian H, Tian S, Sun T, Qin Y, Zhang S, Cui J. A Hierarchical Mechanism of RIG-I Ubiquitination Provides Sensitivity, Robustness and Synergy in Antiviral Immune Responses. Sci Rep 2016; 6:29263. [PMID: 27387525 PMCID: PMC4937349 DOI: 10.1038/srep29263] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/13/2016] [Indexed: 12/12/2022] Open
Abstract
RIG-I is an essential receptor in the initiation of the type I interferon (IFN) signaling pathway upon viral infection. Although K63-linked ubiquitination plays an important role in RIG-I activation, the optimal modulation of conjugated and unanchored ubiquitination of RIG-I as well as its functional implications remains unclear. In this study, we determined that, in contrast to the RIG-I CARD domain, full-length RIG-I must undergo K63-linked ubiquitination at multiple sites to reach full activity. A systems biology approach was designed based on experiments using full-length RIG-I. Model selection for 7 candidate mechanisms of RIG-I ubiquitination inferred a hierarchical architecture of the RIG-I ubiquitination mode, which was then experimentally validated. Compared with other mechanisms, the selected hierarchical mechanism exhibited superior sensitivity and robustness in RIG-I-induced type I IFN activation. Furthermore, our model analysis and experimental data revealed that TRIM4 and TRIM25 exhibited dose-dependent synergism. These results demonstrated that the hierarchical mechanism of multi-site/type ubiquitination of RIG-I provides an efficient, robust and optimal synergistic regulatory module in antiviral immune responses.
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Affiliation(s)
- Xiaoqiang Sun
- Zhong-shan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China
- School of Life Science, Sun Yat-sen University, Guangzhou, 510275, China
- School of Mathematical and Computational Science, Sun Yat-sen University, Guangzhou, 510000, China
| | - Huifang Xian
- School of Life Science, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shuo Tian
- School of Life Science, Sun Yat-sen University, Guangzhou, 510275, China
| | - Tingzhe Sun
- School of Life Sciences, AnQing Normal University, AnQing, 246011, China
| | - Yunfei Qin
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Shoutao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Jun Cui
- School of Life Science, Sun Yat-sen University, Guangzhou, 510275, China
- Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China
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Enciso GA, Ryerson S. The effect of site-to-site variability in ultrasensitive dose responses. J Math Biol 2016; 74:23-41. [DOI: 10.1007/s00285-016-1013-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 04/11/2016] [Indexed: 11/28/2022]
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Salakhieva DV, Sadreev II, Chen MZQ, Umezawa Y, Evstifeev AI, Welsh GI, Kotov NV. Kinetic regulation of multi-ligand binding proteins. BMC SYSTEMS BIOLOGY 2016; 10:32. [PMID: 27090530 PMCID: PMC4835871 DOI: 10.1186/s12918-016-0277-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND Second messengers, such as calcium, regulate the activity of multisite binding proteins in a concentration-dependent manner. For example, calcium binding has been shown to induce conformational transitions in the calcium-dependent protein calmodulin, under steady state conditions. However, intracellular concentrations of these second messengers are often subject to rapid change. The mechanisms underlying dynamic ligand-dependent regulation of multisite proteins require further elucidation. RESULTS In this study, a computational analysis of multisite protein kinetics in response to rapid changes in ligand concentrations is presented. Two major physiological scenarios are investigated: i) Ligand concentration is abundant and the ligand-multisite protein binding does not affect free ligand concentration, ii) Ligand concentration is of the same order of magnitude as the interacting multisite protein concentration and does not change. Therefore, buffering effects significantly influence the amounts of free ligands. For each of these scenarios the influence of the number of binding sites, the temporal effects on intermediate apo- and fully saturated conformations and the multisite regulatory effects on target proteins are investigated. CONCLUSIONS The developed models allow for a novel and accurate interpretation of concentration and pressure jump-dependent kinetic experiments. The presented model makes predictions for the temporal distribution of multisite protein conformations in complex with variable numbers of ligands. Furthermore, it derives the characteristic time and the dynamics for the kinetic responses elicited by a ligand concentration change as a function of ligand concentration and the number of ligand binding sites. Effector proteins regulated by multisite ligand binding are shown to depend on ligand concentration in a highly nonlinear fashion.
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Affiliation(s)
- Diana V. Salakhieva
- />Kazan (Volga Region) Federal University, 18 Kremlyovskaya St., 420008 Kazan, Russia
| | - Ildar I. Sadreev
- />Centre for Systems, Dynamics and Control, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Harrison Building, North Park Road, Exeter, EX4 4QF UK
| | - Michael Z. Q. Chen
- />Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yoshinori Umezawa
- />Department of Dermatology, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461 Japan
| | - Aleksandr I. Evstifeev
- />Biophysics & Bionics Lab, Institute of Physics, Kazan Federal University, Kazan, 420008 Russia
| | - Gavin I. Welsh
- />Academic Renal Unit, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY UK
| | - Nikolay V. Kotov
- />Biophysics & Bionics Lab, Institute of Physics, Kazan Federal University, Kazan, 420008 Russia
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Lengyel IM, Soroldoni D, Oates AC, Morelli LG. Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations. PAPERS IN PHYSICS 2014; 6:060012. [PMID: 34267827 PMCID: PMC7611245 DOI: 10.4279/pip.060012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
We study the effects of multiple binding sites in the promoter of a genetic oscillator. We evaluate the regulatory function of a promoter with multiple binding sites in the absence of cooperative binding, and consider different hypotheses for how the number of bound repressors affects transcription rate. Effective Hill exponents of the resulting regulatory functions reveal an increase in the nonlinearity of the feedback with the number of binding sites. We identify optimal configurations that maximize the nonlinearity of the feedback. We use a generic model of a biochemical oscillator to show that this increased nonlinearity is reflected in enhanced oscillations, with larger amplitudes over wider oscillatory ranges. Although the study is motivated by genetic oscillations in the zebrafish segmentation clock, our findings may reveal a general principle for gene regulation.
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Affiliation(s)
- Ivan M. Lengyel
- Departamento de F’sica, FCEyN UBA and IFIBA, CONICET; Pabellon 1, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Daniele Soroldoni
- MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Andrew C. Oates
- MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Luis G. Morelli
- Departamento de F’sica, FCEyN UBA and IFIBA, CONICET; Pabellon 1, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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Flockerzi D, Holstein K, Conradi C. N-Site phosphorylation systems with 2n-1 steady states. Bull Math Biol 2014; 76:1892-916. [PMID: 25033781 DOI: 10.1007/s11538-014-9984-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/03/2014] [Indexed: 11/28/2022]
Abstract
Multisite protein phosphorylation plays a prominent role in intracellular processes like signal transduction, cell-cycle control and nuclear signal integration. Many proteins are phosphorylated in a sequential and distributive way at more than one phosphorylation site. Mathematical models of n-site sequential distributive phosphorylation are therefore studied frequently. In particular, in Wang and Sontag (J Math Biol 57:29–52, 2008), it is shown that models of n-site sequential distributive phosphorylation admit at most 2n - 1 steady states.Wang and Sontag furthermore conjecture that for odd n, there are at most n and that, for even n, there are at most n + 1 steady states. This, however, is not true: building on earlier work in Holstein et al. (BullMath Biol 75(11):2028–2058, 2013), we present a scalar determining equation for multistationarity which will lead to parameter values where a 3-site system has 5 steady states and parameter values where a 4-site system has 7 steady states. Our results therefore are counterexamples to the conjecture of Wang and Sontag.We furthermore study the inherent geometric properties of multistationarity in n-site sequential distributive phosphorylation: the complete vector of steady state ratios is determined by the steady state ratios of free enzymes and unphosphorylated protein and there exists a linear relationship between steady state ratios of phosphorylated protein.
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Affiliation(s)
- Dietrich Flockerzi
- Max Planck Institute Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 , Magdeburg, Germany,
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