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Register a new userTheoretical Modeling Expressions for Networked Enzymatic Signal Processing Steps as Logic Gates Optimized by Filtering
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Authors
Vladimir Privman
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We describe modeling approaches to a network of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical expressions are derived that allow simple, few-parameter modeling of processes concatenated in such cascades, both with and without filtering. The modeling approach captures and explains features identified in earlier studies of enzymatic processes considered as potential network components for multi-step information/signal processing systems.
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We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic cascade. New theoretical expressions are derived to allow simple, few-parameter modeling of network components concatenated in such cascades, both with and without filtering. The derived expressions are tested against experimental data obtained for the realized networks responses, measured optically, to variations of its input chemicals concentrations with and without filtering processes. We also describe how the present modeling approach captures and explains several observations and features identified in earlier studies of enzymatic processes when they were considered as potential network components for multi-step information/signal processing systems.
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps (reactions) in a cascade are desirable in order to allow control of the systems response. Here we consider conversion of convex response to sigmoid by intensity filtering, as well as threshold filtering, and we offer a general overview of this field of research. Specifically, we survey rate equation modelling that has been used for enzymatic reactions. This allows us to design modified biochemical processes as network components with responses desirable in applications.
Computing based on biochemical processes is a newest rapidly developing field of unconventional information and signal processing. In this paper we present results of our research in the field of biochemical computing and summarize the obtained numerical and experimental data for implementations of the standard two-input OR and AND gates with double-sigmoid shape of the output signal. This form of response was obtained as a function of the two inputs in each of the realized biochemical systems. The enzymatic gate processes in the first system were activated with two chemical inputs and resulted in optically detected chromogen oxidation, which happens when either one or both of the inputs are present. In this case, the biochemical system is functioning as the OR gate. We demonstrate that the addition of a filtering biocatalytic process leads to a considerable reduction of the noise transmission factor and the resulting gate response has sigmoid shape in both inputs. The second system was developed for functioning as an AND gate, where the output signal was activated only by a simultaneous action of two enzymatic biomarkers. This response can be used as an indicator of liver damage, but only if both of these of the inputs are present at their elevated, pathophysiological values of concentrations. A kinetic numerical model was developed and used to estimate the range of parameters for which the experimentally realized logic gate is close to optimal. We also analyzed the system to evaluate its noise-handling properties.
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this complex problem are computationally assisted, the drafting of catalytic mechanisms, i.e. the specification of the chemical steps-and hence intermediate states-that the enzyme is meant to implement, is largely left to human expertise. The ability to capture specific chemistries of multi-step catalysis in a fashion that enables its computational construction and design is therefore highly desirable and would equally impact the elucidation of existing enzymatic reactions whose mechanisms are unknown. Results: We use the mathematical framework of graph transformation to express the distinction between rules and reactions in chemistry. We derive about 1000 rules for amino acid side chain chemistry from the M-CSA database, a curated repository of enzymatic mechanisms. Using graph transformation we are able to propose hundreds of hypothetical catalytic mechanisms for a large number of unrelated reactions in the Rhea database. We analyze these mechanisms to find that they combine in chemically sound fashion individual steps from a variety of known multi-step mechanisms, showing that plausible novel mechanisms for catalysis can be constructed computationally.
The first realization of a biomolecular OR gate function with double-sigmoid response (sigmoid in both inputs) is reported. Two chemical inputs activate the enzymatic gate processes resulting in the output signal: chromogen oxidation, which occurs when either one of the inputs or both are present (corresponding to the OR binary function), and can be optically detected. High-quality gate functioning in handling of sources of noise is enabled by filtering involving pH control with an added buffer. The resulting gate response is sigmoid in both inputs when proper system parameters are chosen, and the gate properties are theoretically analyzed within a model devised to evaluate its noise-handling properties.
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