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Manna RK, Shklyaev OE, Balazs AC. Chemically Driven Multimodal Locomotion of Active, Flexible Sheets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:780-789. [PMID: 36602946 DOI: 10.1021/acs.langmuir.2c02666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The inhibitor-promoter feedback loop is a vital component in regulatory pathways that controls functionality in living systems. In this loop, the production of chemical A at one site promotes the production of chemical B at another site, but B inhibits the production of A. In solution, differences in the volumes of the reactants and products of this reaction can generate buoyancy-driven fluid flows, which will deform neighboring soft material. To probe the intrinsic interrelationship among chemistry, hydrodynamics, and fluid-structure interactions, we model a bio-inspired system where a flexible sheet immersed in solution encompasses two spatially separated catalytic patches, which drive the A-B inhibitor-promotor reaction. The convective rolls of fluid generated above the patches can circulate inward or outward depending on the chemical environment. Within the regime displaying chemical oscillations, the dynamic fluid-structure interactions morph the shape of the sheet to periodically "fly", "crawl", or "swim" along the bottom of the confining chamber, revealing an intimate coupling between form and function in this system. The oscillations in the sheet's motion in turn affect the chemical oscillations in the solution. In the regime with non-oscillatory chemistry, the induced flow still morphs the shape of the sheet, but now, the fluid simply translates the sheet along the length of the chamber. The findings reveal the potential for enzymatic reactions in the body to generate hydrodynamic behavior that modifies the shape of neighboring soft tissue, which in turn modifies both the fluid dynamics and the enzymatic reaction. The findings indicate that this non-linear dynamic behavior can be playing a critical role in the functioning of regulatory pathways in living systems.
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Affiliation(s)
- Raj Kumar Manna
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania15260, United States
| | - Oleg E Shklyaev
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania15260, United States
| | - Anna C Balazs
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania15260, United States
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2
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Spatial scales of living cells and their energetic and informational capacity. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:515-521. [DOI: 10.1007/s00249-017-1267-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/27/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022]
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3
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Zhdanov VP. Three-dimensional Monte Carlo simulations of intracellular diffusion and reaction of signaling proteins. J Chem Phys 2007; 127:035101. [PMID: 17655463 DOI: 10.1063/1.2753159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We show that the Monte Carlo technique makes it possible to perform three-dimensional simulations of intracellular protein-mediated signal transduction with realistic ratio of the rates of protein diffusion and association with genes. Specifically, we illustrate that in the simplest case when the protein degradation and phosphorylation/dephosphorylation are negligible the distribution of the first passage time for this process is close to exponential provided that the number of target genes is between 1 and 100.
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Affiliation(s)
- Vladimir P Zhdanov
- Department of Applied Physics, Chalmers University of Technology, S-41296 Göteborg, Sweden.
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Kindzelskii AL, Petty HR. Apparent role of traveling metabolic waves in oxidant release by living neutrophils. Proc Natl Acad Sci U S A 2002; 99:9207-12. [PMID: 12082178 PMCID: PMC123119 DOI: 10.1073/pnas.132630999] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2001] [Indexed: 11/18/2022] Open
Abstract
Cell metabolism self-organizes into two types of dissipative structures: chemical oscillations and traveling metabolic waves. In the present study we test the hypothesis that traveling NAD(P)H waves within neutrophils are associated spatially and temporally with the release of reactive oxygen metabolites (ROMs). Using high-speed optical microscopy and taking advantage of the autofluorescence of NAD(P)H, we have observed the propagation of NAD(P)H waves within cells. When NAD(P)H waves reach the lamellipodium of morphologically polarized neutrophils, a diffusing plume of superoxide is released as evidenced by the conversion of hydroethidine in the extracellular environment to ethidium bromide. Parallel results were obtained by using high-speed emission microspectrophotometry. These experiments indicate that the spatial and temporal properties of NAD(P)H waves are transformed into ROM pulses in the extracellular environment. Propagating NAD(P)H waves allow neutrophils to specifically deliver substrate to the lamellipodium at high concentrations, thus facilitating the local and periodic release of ROMs in the direction of cell movement and/or a target.
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Affiliation(s)
- Andrei L Kindzelskii
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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Petty HR, Kindzelskii AL. Dissipative metabolic patterns respond during neutrophil transmembrane signaling. Proc Natl Acad Sci U S A 2001; 98:3145-9. [PMID: 11248046 PMCID: PMC30621 DOI: 10.1073/pnas.061014298] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2000] [Accepted: 01/08/2001] [Indexed: 11/18/2022] Open
Abstract
Self-organization is a common theme in biology. One mechanism of self-organization is the creation of chemical patterns by the diffusion of chemical reactants and their nonlinear interactions. We have recently observed sustained unidirectional traveling chemical redox [NAD(P)H - NAD(P)(+)] waves within living polarized neutrophils. The present study shows that an intracellular metabolic wave responds to formyl peptide receptor agonists, but not antagonists, by splitting into two waves traveling in opposite directions along a cell's long axis. Similar effects were noted with other neutrophil-activating substances. Moreover, when cells were exposed to an N-formyl-methionyl-leucyl-phenylalanine (FMLP) gradient whose source was perpendicular to the cell's long axis, cell metabolism was locally perturbed with reorientation of the pattern in a direction perpendicular to the initial cellular axis. Thus, extracellular activating signals and the signals' spatial cues are translated into distinct intracellular dissipative structures.
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Affiliation(s)
- H R Petty
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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Kozak JJ, Nicolis C, Nicolis G. Efficiency of encounter-controlled reaction between diffusing reactants in a finite lattice. J Chem Phys 2000. [DOI: 10.1063/1.1315322] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Petty HR, Worth RG, Kindzelskii AL. Imaging sustained dissipative patterns in the metabolism of individual living cells. PHYSICAL REVIEW LETTERS 2000; 84:2754-2757. [PMID: 11017317 DOI: 10.1103/physrevlett.84.2754] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/1999] [Indexed: 05/23/2023]
Abstract
Theoretical studies have predicted spatiotemporal organization of cell metabolism. Using a rapidly gated CCD camera, we demonstrate for the first time sustained traveling waves of NAD(P)H autofluorescence and protons in individual morphologically polarized living cells. Chemical concentration fronts moved in the direction of cell orientation, thus correlating dissipative structures with cell shape.
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Affiliation(s)
- H R Petty
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, USA.
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Stange P, Mikhailov AS, Hess B. Coherent Intramolecular Dynamics of Enzymic Reaction Loops in Small Volumes. J Phys Chem B 2000. [DOI: 10.1021/jp992641q] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pedro Stange
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Dahlem), Germany, and Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
| | - Alexander S. Mikhailov
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Dahlem), Germany, and Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
| | - Benno Hess
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Dahlem), Germany, and Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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Stange P, Mikhailov AS, Hess B. Mutual Synchronization of Molecular Turnover Cycles in Allosteric Enzymes II. Product Inhibition. J Phys Chem B 1999. [DOI: 10.1021/jp9900640] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Stange
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4−6, D-14195 Berlin, Germany, and Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11 D-44227 Dortmund, Germany2
| | - A. S. Mikhailov
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4−6, D-14195 Berlin, Germany, and Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11 D-44227 Dortmund, Germany2
| | - B. Hess
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4−6, D-14195 Berlin, Germany, and Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11 D-44227 Dortmund, Germany2
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Stange P, Mikhailov AS, Hess B. Mutual Synchronization of Molecular Turnover Cycles in Allosteric Enzymes. J Phys Chem B 1998. [DOI: 10.1021/jp9813185] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pedro Stange
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Dahlem), Germany, and Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Alexander S. Mikhailov
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Dahlem), Germany, and Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Benno Hess
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Dahlem), Germany, and Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
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11
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Abstract
Strong diffusional mixing and short delivery times typical for micrometer and sub-micrometer reaction volumes lead to a special situation where the turnover times of individual enzyme molecules become the largest characteristic time scale of the chemical kinetics. Under these conditions, populations of cross-regulating allosteric enzymes form molecular networks that exhibit various kinds of self-organized coherent collective dynamics.
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Affiliation(s)
- P Stange
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
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Wyskovsky W. Enzymatic reactions in small spatial volumes: comment on a model of Hess and Mikhailov. Biophys Chem 1998; 71:73-81; discussion 83-5. [PMID: 17027453 DOI: 10.1016/s0301-4622(98)00091-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/1997] [Revised: 09/29/1997] [Accepted: 12/05/1997] [Indexed: 10/17/2022]
Abstract
Recently Hess and Mikhailov pointed out that in small subcellular compartments diffusion is so fast that mixing is instantaneous on the time scale of many enzymatic reactions. This opens the possibility for synchronizing individual reaction events. To illustrate this fact they discuss as example an irreversible enzymatic reaction with allosteric product activation. Under appropriate conditions their model shows coherent spiking in the number of product molecules, caused by the strong correlation between reaction events. In this model only substrate binding is an indeterministic process, all other subsequent transitions between different enzyme states being deterministic, contrary to real processes. The purpose of the present paper was to investigate this interesting phenomenon by means of a more realistic modification of the original model, with only probabilistic transitions. In an attempt to obtain spiking, which was not observed under these conditions, the model was extended to make a clear distinction between allosteric high and low affinity substrate binding, in contrast to the original model using a product dependent mean binding probability. However no periodic signal was detectable in the indeterministic version of the Hess Mikhailov model or the extended version, either by means of direct visualization or on autocorrelation or Fourier analysis. Reasons why spiking is not observed in indeterministic enzyme models are discussed.
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Affiliation(s)
- W Wyskovsky
- Pharmakologisches Institut der Universität Wien Währingerstr. 13 A, A-1090 Vienna, Austria
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Mikhailov A, Hess B. Fluctuations of molecular turnover times in enzymatic reactions: reply to W. Wyskovsky. Biophys Chem 1998. [DOI: 10.1016/s0301-4622(98)00092-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hess B, Mikhailov A. Transition from molecular chaos to coherent spiking of enzymic reactions in small spatial volumes. Biophys Chem 1996; 58:365-8. [PMID: 17023363 DOI: 10.1016/0301-4622(95)00109-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/1995] [Revised: 07/05/1995] [Accepted: 07/12/1995] [Indexed: 11/24/2022]
Abstract
Theoretical study of an irreversible enzymic reaction with allosteric product activation reveals that, in small spatial volumes, it can undergo a transition to coherent spiking regime characterized by the presence of strong correlations between reaction events and the states of individual enzyme molecules.
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Affiliation(s)
- B Hess
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
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