Kinetic model for a threshold filter in an enzymatic system for bioanalytical and biocomputing applications

Journal of Physical Chemistry B

Volumn 118, Issue 43, 2014, Pages 12435-12443

  Privman, Vladimir ^a   Domanskyi, Sergii ^a   Mailloux, Shay ^a   Holade, Yaovi ^a,b   Katz, Evgeny ^a  

^a CLARKSON UNIVERSITY   (United States)

^b UNIVERSITÉ DE POITIERS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-COMPUTING; BIOANALYTICAL; ENZYMATIC SYSTEM; KINETIC MODELING; THRESHOLD FILTER;

ENZYME INHIBITOR; MALATE DEHYDROGENASE;

ANTAGONISTS AND INHIBITORS; BIOCATALYSIS; BIOLOGICAL MODEL; ENZYME ACTIVATION; GENETIC PROCEDURES; KINETICS; METABOLISM; MOLECULAR COMPUTER;

BIOCATALYSIS; BIOSENSING TECHNIQUES; COMPUTERS, MOLECULAR; ENZYME ACTIVATION; ENZYME INHIBITORS; KINETICS; MALATE DEHYDROGENASE; MODELS, BIOLOGICAL;

EID: 84908584016     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp508224y     Document Type: Article

References (90)

1. de Silva, A. P. Molecular Computing-A Layer of Logic Nature 2008, 454, 417-418
2. de Silva, A. P. Molecular Logic and Computing Nat. Nanotechnol. 2007, 2, 399-410
3. Pischel, U.; Andreasson, J.; Gust, D.; Pais, V. F. Information Processing with Molecules-Quo Vadis? ChemPhysChem 2013, 14, 28-46
4. Pischel, U. Advanced Molecular Logic with Memory Function Angew. Chem., Int. Ed. 2010, 49, 1356-1358
5. Benenson, Y. Biocomputers: From Test Tubes to Live Cells Mol. BioSyst. 2009, 5, 675-685
6. Benenson, Y. Biomolecular Computing Systems: Principles, Progress and Potential Nat. Rev. Genet. 2012, 13, 455-468
7. Stojanovic, M. N.; Stefanovic, D.; Rudchenko, S. Exercises in Molecular Computing Acc. Chem. Res. 2014, 47, 1845-1852
8. Stojanovic, M. N.; Stefanovic, D. Chemistry at a Higher Level of Abstraction J. Comput. Theor. Nanosci. 2011, 8, 434-440
9. Katz, E.; Privman, V. Enzyme-Based Logic Systems for Information Processing Chem. Soc. Rev. 2010, 39, 1835-1857
10. Liu, Y.; Kim, E.; White, I. M.; Bentley, W. E.; Payne, G. F. Information Processing Through a Bio-Based Redox Capacitor: Signatures for Redox-Cycling Bioelectrochemistry 2014, 98, 94-102
11. Jiang, H.; Riedel, M. D.; Parhi, K. K. Digital Signal Processing with Molecular Reactions IEEE Des. Test Comput. 2012, 29, 21-31
12. Hillenbrand, P.; Fritz, G.; Gerland, U. Biological Signal Processing with a Genetic Toggle Switch PLoS One 2013, 8, e68345
13. Bowsher, C. G. Information Processing by Biochemical Networks: A Dynamic Approach J. R. Soc., Interface 2011, 8, 186-200
14. Buisman, H. J.; ten Eikelder, H. M. M.; Hilbers, P. A. J.; Liekens, A. M. L. Computing Algebraic Functions with Biochemical Reaction Networks Artif. Life 2009, 15, 5-19
15. Jia, Y. M.; Duan, R. X.; Hong, F.; Wang, B. Y.; Liu, N. N.; Xia, F. Electrochemical Biocomputing: A New Class of Molecular-Electronic Logic Devices Soft Matter 2013, 9, 6571-6577
16. Zhou, M.; Dong, S. J. Bioelectrochemical Interface Engineering: Toward the Fabrication of Electrochemical Biosensors, Biofuel Cells, and Self-Powered Logic Biosensors Acc. Chem. Res. 2011, 44, 1232-1243
17. Zhou, M.; Zhou, N.; Kuralay, F.; Windmiller, J. R.; Parkhomovsky, S.; Valdés-Ramírez, G.; Katz, E.; Wang, J. A Self-Powered "Sense-Act-Treat" System That Is Based on a Biofuel Cell and Controlled by Boolean Logic Angew. Chem., Int. Ed. 2012, 51, 2686-2689
18. Katz, E. Bioelectronic Devices Controlled by Biocomputing Systems Isr. J. Chem. 2011, 51, 132-140
19. Katz, E.; Wang, J.; Privman, M.; Halámek, J. Multi-Analyte Digital Enzyme Biosensors with Built-in Boolean Logic Anal. Chem. 2012, 84, 5463-5469
20. Wang, J.; Katz, E. Digital Biosensors with Built-in Logic for Biomedical Applications-Biosensors Based on Biocomputing Concept Anal. Bioanal. Chem. 2010, 398, 1591-1603
21. Privman, V. Control of Noise in Chemical and Biochemical Information Processing Isr. J. Chem. 2011, 51, 118-131
22. Privman, V. Approaches to Control of Noise in Chemical and Biochemical Information and Signal Processing. In Molecular and Supramolecular Information Processing-From Molecular Switches to Unconventional Computing; Katz, E., Ed.; Wiley-VCH: Weinheim, Germany, 2012; Chapter 12, pp 281-303.
23. Katz, E.; Privman, V.; Wang, J. Towards Biosensing Strategies Based on Biochemical Logic Systems, E. In Proceedings of The Fourth International Conference on Quantum, Nano and Micro Technologies (ICQNM 2010); Ovchinnikov, V.; Privman, V., Eds.; IEEE Computer Society Conference Publishing Services: Los Alamitos, CA, 2010; pp 1-9.
24. Guz, N.; Halámek, J.; Rusling, J. F.; Katz, E. A Biocatalytic Cascade with Several Output Signals-Towards Biosensors with Different Levels of Confidence Anal. Bioanal. Chem. 2014, 406, 3365-3370
25. Mailloux, S.; Guz, N.; Zakharchenko, A.; Minko, S.; Katz, E. Majority and Minority Gates Realized in Enzyme-Biocatalyzed Systems Integrated with Logic Networks and Interfaced with Bioelectronic Systems J. Phys. Chem. B 2014, 118, 6775-6784
26. MacVittie, K.; Halámek, J.; Privman, V.; Katz, E. A Bioinspired Associative Memory System Based on Enzymatic Cascades Chem. Commun. 2013, 49, 6962-6964
27. Halámek, J.; Bocharova, V.; Chinnapareddy, S.; Windmiller, J. R.; Strack, G.; Chuang, M.-C.; Zhou, J.; Santhosh, P.; Ramirez, G. V.; Arugula, M. A. Multi-Enzyme Logic Network Architectures for Assessing Injuries: Digital Processing of Biomarkers Mol. BioSyst. 2010, 6, 2554-2560
28. Privman, V.; Arugula, M. A.; Halámek, J.; Pita, M.; Katz, E. Network Analysis of Biochemical Logic for Noise Reduction and Stability: A System of Three Coupled Enzymatic AND Gates J. Phys. Chem. B 2009, 113, 5301-5310
29. Strack, G.; Ornatska, M.; Pita, M.; Katz, E. Biocomputing Security System: Concatenated Enzyme-Based Logic Gates Operating as a Biomolecular Keypad Lock J. Am. Chem. Soc. 2008, 130, 4234-4235
30. Privman, V.; Zavalov, O.; Simonian, A. Extended Linear Response for Bioanalytical Applications Using Multiple Enzymes Anal. Chem. 2013, 85, 2027-2031
31. Zavalov, O.; Domanskyi, S.; Privman, V.; Simonian, A. Design of Biosensors with Extended Linear Response and Binary-Type Sigmoid Output Using Multiple Enzymes. In Proc. Conf. ICQNM 2013; ThinkMind Online Publishing: Red Hook, NY, 2013; pp 54-59.
32. Rinken, T.; Rinken, P.; Kivirand, K. Signal Analysis and Calibration of Biosensors for Biogenic Amines in the Mixtures of Several Substrates. In Biosensors-Emerging Materials and Applications; Serra, P. A., Ed.; InTech: Rijeka, Croatia, 2011; pp 3-16.
33. Bakker, E. Electrochemical Sensors Anal. Chem. 2004, 76, 3285-3298
34. Chen, X.; Zhu, J.; Tian, R.; Yao, C. Bienzymatic Glucose Biosensor Based on Three Dimensional Macroporous Ionic Liquid Doped Sol-Gel Organic-Inorganic Composite Sens. Actuators, B 2012, 163, 272-280
35. Coche-Guérente, L.; Cosnier, S.; Labbé, P. Sol-Gel Derived Composite Materials for the Construction of Oxidase/Peroxidase Mediatorless Biosensors Chem. Mater. 1997, 9, 1348-1352
36. De Benedetto, G. E.; Palmisano, F.; Zambonin, P. G. One-Step Fabrication of a Bienzyme Glucose Sensor Based on Glucose Oxidase and Peroxidase Immobilized onto a Poly(pyrrole) Modified Glassy Carbon Electrode Biosens. Bioelectron. 1996, 11, 1001-1008
37. Delvaux, M.; Walcarius, A.; Demoustier-Champagne, S. Bienzyme HRP-GOx-Modified Gold Nanoelectrodes for the Sensitive Amperometric Detection of Glucose at Low Overpotentials Biosens. Bioelectron. 2005, 20, 1587-1594
38. Ferri, T.; Maida, S.; Poscia, A.; Santucci, R. A Glucose Biosensor Based on Electro-Enzyme Catalyzed Oxidation of Glucose Using a HRP-GOD Layered Assembly Electroanalysis 2001, 13, 1198-1202
39. +- and Glutathione-Dependent Recombinant Formaldehyde Dehydrogenase and Diaphorase for Formaldehyde Assay Sens. Actuators, B 2007, 125, 1-9
40. Tian, F. M.; Zhu, G. Y. Bienzymatic Amperometric Biosensor for Glucose Based on Polypyrrole/Ceramic Carbon as Electrode Material Anal. Chim. Acta 2002, 451, 251-258
41. Zhu, L.; Yang, R.; Zhai, J.; Tian, C. Bienzymatic Glucose Biosensor Based on Co-Immobilization of Peroxidase and Glucose Oxidase on a Carbon Nanotubes Electrode Biosens. Bioelectron. 2007, 23, 528-535
42. Simonian, A. L.; Badalian, I. E.; Smirnova, I. P.; Berezov, T. T. Metabolite Alternative Splitting by Different Enzymes. In Biochemical Engineering-Stuttgart; Reuss, M., Ed.; G. Fisher Pub.: Stuttgart, New York, 1991; pp 344-347.
43. Simonian, A. L.; Khachatrian, G. E.; Tatikian, S. S.; Avakian, T. M.; Badalian, I. E. A Flow-Through Enzyme Analyzer for Determination of L-Lysine Concentration Biosens. Bioelectron. 1991, 6, 93-99
44. Simonian, A. L.; Badalian, I. E.; Berezov, T. T.; Smirnova, I. P.; Khaduev, S. H. Flow-Injection Amperometric Biosensor Based on Immobilized L-Lysine-a-Oxidase for L-Lysine Determination Anal. Lett. 1994, 27, 2849-2860
45. Biomolecular Information Processing-From Logic Systems to Smart Sensors and Actuators; Katz, E., Ed.; Wiley-VCH: Weinheim, Germany, 2012.
46. Unconventional Computation. Lecture Notes in Computer Science; Calude, C. S.; Costa, J. F.; Dershowitz, N.; Freire, E.; Rozenberg, G., Eds.; Springer: Berlin, 2009; Vol. 5715.
47. Unconventional Computing; Adamatzky, A.; De Lacy Costello, B.; Bull, L.; Stepney, S.; Teuscher, C., Eds.; Luniver Press: Frome, U.K., 2007.
48. Molecular and Supramolecular Information Processing-From Molecular Switches to Unconventional Computing; Katz, E., Ed.; Willey-VCH: Weinheim, Germany, 2012.
49. Lederman, H.; Macdonald, J.; Stefanovic, D.; Stojanovic, M. N. Deoxyribozyme-Based Three-Input Logic Gates and Construction of a Molecular Full Adder Biochemistry 2006, 45, 1194-1199
50. Baron, R.; Lioubashevski, O.; Katz, E.; Niazov, T.; Willner, I. Elementary Arithmetic Operations by Enzymes: A Model for Metabolic Pathway Based Computing Angew. Chem., Int. Ed. 2006, 45, 1572-1576
51. MacVittie, K.; Halámek, J.; Katz, E. Enzyme-Based D-Flip-Flop Memory System Chem. Commun. 2012, 48, 11742-11744
52. Pita, M.; Strack, G.; MacVittie, K.; Zhou, J.; Katz, E. Set-Reset Flip-Flop Memory Based on Enzyme Reactions: Towards Memory Systems Controlled by Biochemical Pathways J. Phys. Chem. B 2009, 113, 16071-16076
53. Privman, V.; Zavalov, O.; Halámková, L.; Moseley, F.; Halámek, J.; Katz, E. Networked Enzymatic Logic Gates with Filtering: New Theoretical Modeling Expressions and Their Experimental Application J. Phys. Chem. B 2013, 117, 14928-14939
54. Halámek, J.; Zavalov, O.; Halámková, L.; Korkmaz, S.; Privman, V.; Katz, E. Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid "Filter" Response J. Phys. Chem. B 2012, 116, 4457-4464
55. Zavalov, O.; Bocharova, V.; Privman, V.; Katz, E. Enzyme-Based Logic: OR Gate with Double-Sigmoid Filter Response J. Phys. Chem. B 2012, 116, 9683-9689
56. Zavalov, O.; Bocharova, V.; Halámek, J.; Halámková, L.; Korkmaz, S.; Arugula, M. A.; Chinnapareddy, S.; Katz, E.; Privman, V. Two-Input Enzymatic Logic Gates Made Sigmoid by Modifications of the Biocatalytic Reaction Cascades Int. J. Unconv. Comput. 2012, 8, 347-365
57. Bakshi, S.; Zavalov, O.; Halámek, J.; Privman, V.; Katz, E. Modularity of Biochemical Filtering for Inducing Sigmoid Response in Both Inputs in an Enzymatic AND Gate J. Phys. Chem. B 2013, 117, 9857-9865
58. Privman, V.; Fratto, B. E.; Zavalov, O.; Halámek, J.; Katz, E. Enzymatic AND Logic Gate with Sigmoid Response Induced by Photochemically Controlled Oxidation of the Output J. Phys. Chem. B 2013, 117, 7559-7568
59. Rafael, S. P.; Vallée-Bélisle, A.; Fabregas, E.; Plaxco, K.; Palleschi, G.; Ricci, F. Employing the Metabolic "Branch Point Effect" to Generate an All-or-None, Digital-Like Response in Enzymatic Outputs and Enzyme-Based Sensors Anal. Chem. 2012, 84, 1076-1082
60. Vallée-Bélisle, A.; Ricci, F.; Plaxco, K. W. Engineering Biosensors with Extended, Narrowed, or Arbitrarily Edited Dynamic Range J. Am. Chem. Soc. 2012, 134, 2876-2879
61. Kang, D.; Vallée-Bélisle, A.; Plaxco, K. W.; Ricci, F. Re-engineering Electrochemical Biosensors to Narrow or Extend Their Useful Dynamic Range Angew. Chem., Int. Ed. 2012, 51, 6717-6721
62. Halámek, J.; Zhou, J.; Halámková, L.; Bocharova, V.; Privman, V.; Wang, J.; Katz, E. Biomolecular Filters for Improved Separation of Output Signals in Enzyme Logic Systems Applied to Biomedical Analysis Anal. Chem. 2011, 83, 8383-8386
63. Pita, M.; Privman, V.; Arugula, M. A.; Melnikov, D.; Bocharova, V.; Katz, E. Towards Biochemical Filter with Sigmoidal Response to pH Changes: Buffered Biocatalytic Signal Transduction Phys. Chem. Chem. Phys. 2011, 13, 4507-4513
64. Privman, V.; Halámek, J.; Arugula, M. A.; Melnikov, D.; Bocharova, V.; Katz, E. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic J. Phys. Chem. B 2010, 114, 14103-14109
65. Domanskyi, S.; Privman, V. Design of Digital Response in Enzyme-Based Bioanalytical Systems for Information Processing Applications J. Phys. Chem. B 2012, 116, 13690-13695
66. Unger, R.; Moult, J. Towards Computing with Proteins Proteins 2006, 63, 53-64
67. Margolin, A. A.; Stojanovic, M. N. Boolean Calculations Made Easy (for Ribozymes) Nat. Biotechnol. 2005, 23, 1374-1376
68. Win, M. N.; Smolke, C. D. Higher-Order Cellular Information Processing with Synthetic RNA Devices Science 2008, 322, 456-460
69. Rinaudo, K.; Bleris, L.; Maddamsetti, R.; Subramanian, S.; Weiss, R.; Benenson, Y. A Universal RNAi-Based Logic Evaluator That Operates in Mammalian Cells Nat. Biotechnol. 2007, 25, 795-801
70. Simpson, M. L.; Sayler, G. S.; Fleming, J. T.; Applegate, B. Whole-Cell Biocomputing Trends Biotechnol. 2001, 19, 317-323
71. Li, Z.; Rosenbaum, M. A.; Venkataraman, A.; Tam, T. K.; Katz, E.; Angenent, L. T. Bacteria-Based AND Logic Gate: A Decision-Making and Self-Powered Biosensor Chem. Commun. 2011, 47, 3060-3062
72. Chuang, M.-C.; Windmiller, J. R.; Santhosh, P.; Valdés-Ramírez, G.; Katz, E.; Wang, J. High-Fidelity Simultaneous Determination of Explosives and Nerve Agent Threats via a Boolean Biocatalytic Cascade Chem. Commun. 2011, 47, 3087-3089
73. Halámek, J.; Windmiller, J. R.; Zhou, J.; Chuang, M.-C.; Santhosh, P.; Strack, G.; Arugula, M. A.; Chinnapareddy, S.; Bocharova, V.; Wang, J. Multiplexing of Injury Codes for the Parallel Operation of Enzyme Logic Gates Analyst 2010, 135, 2249-2259
74. Xia, F.; Zuo, X. L.; Yang, R. Q.; White, R. J.; Xiao, Y.; Kang, D.; Gong, X. O.; Lubin, A. A.; Vallee-Belisle, A.; Yuen, J. D. Label-Free, Dual-Analyte Electrochemical Biosensors: A New Class of Molecular-Electronic Logic Gates J. Am. Chem. Soc. 2010, 132, 8557-8559
75. Mailloux, S.; Halámek, J.; Katz, E. A Model System for Targeted Drug Release Triggered by Biomolecular Signals Logically Processed Through Enzyme Logic Networks Analyst 2014, 139, 982-986
76. Katz, E.; Bocharova, V.; Privman, M. Electronic Interfaces Switchable by Logically Processed Multiple Biochemical and Physiological Signals J. Mater. Chem. 2012, 22, 8171-8178
77. Privman, M.; Tam, T. K.; Bocharova, V.; Halámek, J.; Wang, J.; Katz, E. Responsive Interface Switchable by Logically Processed Physiological Signals-Towards "Smart" Actuators for Signal Amplification and Drug Delivery ACS Appl. Mater. Interfaces 2011, 3, 1620-1623
78. Electrochemical Sensors, Biosensors and their Biomedical Applications; Zhang, X.; Ju, H.; Wang, J., Eds.; Academic Press: New York, 2008.
79. Poghossian, A.; Malzahn, K.; Abouzar, M. H.; Mehndiratta, P.; Katz, E.; Schöning, M. J. Integration of Biomolecular Logic Gates with Field-Effect Transducers Electrochim. Acta 2011, 56, 9661-9665
80. Krämer, M.; Pita, M.; Zhou, J.; Ornatska, M.; Poghossian, A.; Schöning, M. J.; Katz, E. Coupling of Biocomputing Systems with Electronic Chips: Electronic Interface for Transduction of Biochemical Information J. Phys. Chem. C 2009, 113, 2573-2579
81. Mailloux, S.; Zavalov; Nataliia Guz, N.; Katz, E.; Bocharova, V. Enzymatic Filter for Improved Separation of Output Signals in Enzyme Logic Systems Towards 'Sense and Treat' Medicine Biomater. Sci. 2014, 2, 184-191
82. Silverstein, E.; Sulebele, G. Catalytic Mechanism of Pig Heart Mitochondrial Malate Dehydrogenase Studied by Kinetics at Equilibrium Biochemistry 1969, 8, 2543-2550
83. Marangoni, A. G. Enzyme Kinetics. A Modern Approach; John Wiley & Sons, Inc.: New York, 2003.
84. Ohshima, T.; Ito, Y.; Sakuraba, H.; Goda, S.; Kawarabayasi, Y. The Sulfolobus Tokodaii Gene ST1704 Codes Highly Thermostable Glucose Dehydrogenase J. Mol. Catal. B 2003, 23, 281-289
85. Strecker, H. J.; Korkes, S. Glucose Dehydrogenase J. Biol. Chem. 1952, 196, 769-784
86. Bhaumik, S. R.; Sonawat, H. M. Kinetic Mechanism of Glucose Dehydrogenase from Halobacterium Salinarum Indian J. Biochem. Biophys. 1999, 36, 143-149
87. Cunningham, M. A.; Ho, L. L.; Nguyen, D. T.; Gillilan, R. E.; Bash, P. A. Simulation of the Enzyme Reaction Mechanism of Malate Dehydrogenase Biochemistry 1997, 36, 4800-4816
88. Wolfe, R. G.; Neilands, J. B. Some Molecular and Kinetic Properties of Heart Malic Dehydrogenase J. Biol. Chem. 1956, 221, 61-70
89. Minárik, P.; Tomášková, N.; Kollárová, M.; Antalík, M. Malate Dehydrogenases-Structure and Function Gen. Physiol. Biophys. 2002, 21, 265-257
90. Cha, S. A Simple Method for Derivation of Rate Equations for Enzyme-Catalyzed Reactions under the Rapid Equilibrium Assumption or Combined Assumptions of Equilibrium and Steady State J. Biol. Chem. 1968, 243, 820-825