scholarly journals Enzymes as Biocatalysts: Review on Investigations on Synthesis, Mechanism, Kinetics, Applications and Potential

2021 ◽  
Vol 11 (1) ◽  
pp. 3049-3064

Sustainable development is becoming the goal of many investigations carried out in chemistry and chemical engineering. Because of the waste generated by chemical reactions, there is a shift from traditional thinking about the catalyst's yield, selectivity, efficiency, and effectiveness. Mild, low temperature, highly selective alternative was found in biological reactions. Biocatalyst application fulfills the two important requirements. It does not deplete natural resources and does not have any significant environmental footprints. Modeling of biological reactions is a very important area of investigation on enzyme-catalyzed reactions. Monod and Moser growth kinetics can be applied to cell growth and substrate utilization. The discovery of new enzymes and optimization of the synthesis and application methods for biocatalysts are being investigated widely for better and industrially applicable technologies.

2018 ◽  
Author(s):  
Justin Eilertsen ◽  
Santiago Schnell

<div>As a case study, we consider a coupled enzyme assay of sequential enzyme reactions obeying the Michaelis--Menten reaction mechanism. The sequential reaction consists of a single-substrate, single-enzyme non-observable reaction followed by another single-substrate, single-enzyme observable reaction (indicator reaction). In this assay, the product of the non-observable reaction becomes the substrate of the indicator reaction. A mathematical analysis of the reaction kinetics is performed, and it is found that after an initial fast transient, the sequential reaction is described by a pair of interacting Michaelis--Menten equations. Timescales that approximate the respective lengths of the indicator and non-observable reactions, as well as conditions for the validity of the Michaelis--Menten equations are derived. The theory can be extended to deal with more complex sequences of enzyme catalyzed reactions.</div>


2018 ◽  
Author(s):  
Justin Eilertsen ◽  
Santiago Schnell

<div>As a case study, we consider a coupled enzyme assay of sequential enzyme reactions obeying the Michaelis-Menten reaction mechanism. The sequential reaction consists of a single-substrate, single enzyme non-observable reaction followed by another single-substrate, single enzyme observable reaction (indicator reaction). In this assay, the product of the non-observable reaction becomes the substrate of the indicator reaction. A mathematical analysis of the reaction kinetics is performed, and it is found that after an initial fast transient, the sequential reaction is described by a pair of interacting Michaelis-Menten equations. Timescales that approximate the respective lengths of the indicator and non-observable reactions, as well as conditions for the validity of the Michaelis-Menten equations are derived. The theory can be extended to deal with more complex sequences of enzyme catalyzed reactions.</div>


2018 ◽  
Author(s):  
Timothy Newhouse ◽  
Daria E. Kim ◽  
Joshua E. Zweig

The diverse molecular architectures of terpene natural products are assembled by exquisite enzyme-catalyzed reactions. Successful recapitulation of these transformations using chemical synthesis is hard to predict from first principles and therefore challenging to execute. A means of evaluating the feasibility of such chemical reactions would greatly enable the development of concise syntheses of complex small molecules. Herein, we report the computational analysis of the energetic favorability of a key bio-inspired transformation, which we use to inform our synthetic strategy. This approach was applied to synthesize two constituents of the historically challenging indole diterpenoid class, resulting in a concise route to (–)-paspaline A in 9 steps from commercially available materials and the first pathway to and structural confirmation of emindole PB in 13 steps. This work highlights how traditional retrosynthetic design can be augmented with quantum chemical calculations to reveal energetically feasible synthetic disconnections, minimizing time-consuming and expensive empirical evaluation.


2021 ◽  
Vol 13 (8) ◽  
pp. 4528
Author(s):  
Olga Lingaitienė ◽  
Juozas Merkevičius ◽  
Vida Davidavičienė

The World Bank, United Nations, the Organization for Economic Cooperation and Development, and others are in line with the governments of countries that are strongly interested in the sustainable development of countries, regions, and enterprises. One of the aspects that affects the indicators and prospects of sustainable development is the efficiency of energy source use. Nationwide reductions in the greenhouse gas emissions of motor vehicles could have a direct effect on ambient temperature and reducing the effects of global warming, which can affect future environmental, societal, and economic development. Significant reductions in fuel consumption can be achieved by increasing the efficiency of use, and the performance, of current cargo vehicles. This aspect is directly related to cargo delivery systems and supply chain efficiency and effectiveness. The article solves the problem of increasing the effectiveness of cargo delivery and proposes a model that would minimize transportation costs that are directly related to fuel consumption, shortening transportation time. The model addresses the problem of a lack of models evaluating the efficiency of cargo to Lithuania that is using several different modes of transportation. For the solution to this problem, the article examines the complexity of the rational use of land and water vehicles depending on the type of cargo transported, the technical capabilities of the vehicles (loading, speed, environmental pollution, fuel consumption, etc.), and the type (cars, railways, ships). The novelty of the findings is based on the availability to select the most appropriate vehicles, on a case-by-case basis, from the available options, depending on their environmental performance and energy efficiency. This model, later in this article, is used for calculations of Lithuanian companies for selecting the most rational vehicle by identifying the most appropriate route, as well as assessing the dynamics of the economic and physical indicators. The model allows for creating dependencies between the main indicators characterizing the transport process—the cost, the time of transport, and the safety, taking into account the dynamics of economic and physical indicators, that lead to a very important issue—reducing the amount of energy required to provide products and services.


Metabolites ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 48
Author(s):  
Marc Feuermann ◽  
Emmanuel Boutet ◽  
Anne Morgat ◽  
Kristian Axelsen ◽  
Parit Bansal ◽  
...  

The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences and functional annotation that covers genomes and proteomes from tens of thousands of taxa, including a broad range of plants and microorganisms producing natural products of medical, nutritional, and agronomical interest. Here we describe work that enhances the utility of UniProtKB as a support for both the study of natural products and for their discovery. The foundation of this work is an improved representation of natural product metabolism in UniProtKB using Rhea, an expert-curated knowledgebase of biochemical reactions, that is built on the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Knowledge of natural products and precursors is captured in ChEBI, enzyme-catalyzed reactions in Rhea, and enzymes in UniProtKB/Swiss-Prot, thereby linking chemical structure data directly to protein knowledge. We provide a practical demonstration of how users can search UniProtKB for protein knowledge relevant to natural products through interactive or programmatic queries using metabolite names and synonyms, chemical identifiers, chemical classes, and chemical structures and show how to federate UniProtKB with other data and knowledge resources and tools using semantic web technologies such as RDF and SPARQL. All UniProtKB data are freely available for download in a broad range of formats for users to further mine or exploit as an annotation source, to enrich other natural product datasets and databases.


ChemInform ◽  
2012 ◽  
Vol 43 (29) ◽  
pp. no-no
Author(s):  
Richard Lonsdale ◽  
Jeremy N. Harvey ◽  
Adrian J. Mulholland

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