scholarly journals Computational modelling of cobalamin-dependent enzymatic reactions : activation of Co-C bond in adenosylcobalamin-dependent mutases and cob(II)alamin/cob(I)alamin redox process in methyltransferases.

2012 ◽  
Author(s):  
Manoj Kumar
Keyword(s):  
Computational Modelling ◽  
Redox Process ◽  
Enzymatic Reactions

scholarly journals A Comparison of Finite Difference Schemes for Computational Modelling of Biosensors

2007 ◽  
Vol 12 (3) ◽  
pp. 359-369 ◽  
Author(s):  
E. Gaidamauskaitė ◽  
R. Baronas
Keyword(s):  
Finite Difference ◽  
Computational Modelling ◽  
Computation Time ◽  
Reaction Diffusion ◽  
Difference Schemes ◽  
Reaction Diffusion Equations ◽  
Finite Difference Schemes ◽  
Enzymatic Reactions ◽  
Calculation Results ◽  
Kinetics Of

This paper presents a one-dimensional-in-space mathematical model of an amperometric biosensor. The model is based on the reaction-diffusion equations containing a non-linear term related to Michaelis-Menten kinetics of the enzymatic reactions. The stated problem is solved numerically by applying the finite difference method. Several types of finite difference schemes are used. The numerical results for the schemes and couple mathematical software packages are compared and verified against known analytical solutions. Calculation results are compared in terms of the precision and computation time.

Development of 96 Multiple Injection-GC-MS Technique and Its Application in Protein Engineering of Natural and Non-Natural Enzymatic Reactions

2019 ◽  
Author(s):  
Anja Knorrscheidt ◽  
Pascal Püllmann ◽  
Eugen Schell ◽  
Dominik Homann ◽  
Erik Freier ◽  
...  
Keyword(s):  
Microtiter Plate ◽  
Axial Ligand ◽  
Cell System ◽  
Enzymatic Reactions ◽  
The Novel ◽  
Internal Standards ◽  
E Coli ◽  
Enzyme Screening ◽  
Plate Analysis ◽  
Microtiter Plate Analysis

Directed evolution requires the screening of enzyme libraries in biological matrices. Available assays are mostly substrate or enzyme specific. Chromatographic techniques like LC and GC overcome this limitation, but require long analysis times. The herein developed multiple injections in a single experimental run (MISER) using GC coupled to MS allows the injection of samples every 33 s resulting in 96-well microtiter plate analysis within 50 min. This technique is implementable in any GC-MS system with autosampling. Since the GC-MS is far less prone to ion suppression than LCMS, no chromatographic separation is required. This allows the utilisation of an internal standards and the detection of main and side-product. To prove the feasibility of the system in enzyme screening, two libraries were assessed: i) YfeX library in an E. coli whole cell system for the carbene-transfer reaction on indole revealing the novel axial ligand tryptophan, ii) a library of 616 chimeras of fungal unspecific peroxygenase (UPO) in S. cerevisiae supernatant for hydroxylation of tetralin resulting in novel constructs. The data quality and representation are automatically assessed by a new R-script.

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

2020 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Computational Modelling ◽  
Free Energy Calculations ◽  
Energy Estimates ◽  
Binding Affinities ◽  
Spherical Coordinates ◽  
Collective Variables ◽  
Guest Binding ◽  
Starting Point ◽  
Sampl Challenge

Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.

Modular Simulation to Determine the Optimal Operating Policy of a Batch Reactor for the Enzymatic Fructose Reduction to Mannitol with the in situ Continuous Enzymatic Regeneration of the NAD Cofactor

2017 ◽  
Vol 68 (9) ◽  
pp. 2196-2203 ◽  
Author(s):  
Mara Crisan ◽  
Gheorghe Maria
Keyword(s):  
Batch Reactor ◽  
Production Capacity ◽  
Optimization Procedure ◽  
Enzymatic Reactions ◽  
Mannitol Dehydrogenase ◽  
Optimal Operating ◽  
Operating Policy ◽  
Enzymatic Reduction ◽  
Optimal Operating Policy

Novel coupled enzymatic systems reported important applications in the industrial bio-catalysis. Multi-enzymatic reactions can successfully replace complex chemical syntheses, using milder reaction conditions, and generating less waste. For such systems acting simultaneously, the model-based engineering calculations (design, reactor operation optimization) are difficult tasks, because they must account for interacting reactions, differences in enzymes optimal activity domains and deactivation kinetics. The determination of the optimal operating mode (enzyme ratios, enzyme feeding policy, temperature, pH) often turns into a difficult multi-objective optimization problem with multiple constraints to be solved for every particular system. The paper focuses on applying a modular screening procedure that can identify the optimal operating policy of an enzymatic reactor, which minimizes the enzyme consumption, given the process kinetic model, and an imposed production capacity. Following an optimization procedure, the process effectiveness is evaluated in a systematic approach, by including simple batch reactor (BR), batch with intermittent addition of the key-enzyme following certain optimal policies (BRP). Exemplification is made for the case of the enzymatic reduction of D-fructose to mannitol by using suspended MDH (mannitol dehydrogenase) and NADH (Nicotinamide adenine dinucleotide) cofactor, with the in-situ continuous regeneration of the cofactor by the expense of formate degradation in the presence of suspended FDH (Formate dehydrogenase).

Synthesis of Rare Pentoses Using Microbial and Enzymatic Reactions

2016 ◽  
Vol 20 (14) ◽  
pp. 1456-1464 ◽  
Author(s):  
Zijie Li ◽  
Xiao-Dong Gao ◽  
Li Cai
Keyword(s):  
Enzymatic Reactions

Pollutants in Organic Chemistry and Medicinal Chemistry Education Laboratory. Experimental and Machine Learning Studies

2020 ◽  
Vol 20 (9) ◽  
pp. 720-730
Author(s):  
Iker Montes-Bageneta ◽  
Urtzi Akesolo ◽  
Sara López ◽  
Maria Merino ◽  
Eneritz Anakabe ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Machine Learning ◽  
Chemistry Education ◽  
Organic Waste ◽  
Computational Modelling ◽  
University Education ◽  
Academic Factors ◽  
Academic Year ◽  
Statistical Analysis Software

Aims: Computational modelling may help us to detect the more important factors governing this process in order to optimize it. Background: The generation of hazardous organic waste in teaching and research laboratories poses a big problem that universities have to manage. Methods: In this work, we report on the experimental measurement of waste generation on the chemical education laboratories within our department. We measured the waste generated in the teaching laboratories of the Organic Chemistry Department II (UPV/EHU), in the second semester of the 2017/2018 academic year. Likewise, to know the anthropogenic and social factors related to the generation of waste, a questionnaire has been utilized. We focused on all students of Experimentation in Organic Chemistry (EOC) and Organic Chemistry II (OC2) subjects. It helped us to know their prior knowledge about waste, awareness of the problem of separate organic waste and the correct use of the containers. These results, together with the volumetric data, have been analyzed with statistical analysis software. We obtained two Perturbation-Theory Machine Learning (PTML) models including chemical, operational, and academic factors. The dataset analyzed included 6050 cases of laboratory practices vs. practices of reference. Results: These models predict the values of acetone waste with R2 = 0.88 and non-halogenated waste with R2 = 0.91. Conclusion: This work opens a new gate to the implementation of more sustainable techniques and a circular economy with the aim of improving the quality of university education processes.

Recycling and Reuse in the Roman Economy

2020 ◽  
Keyword(s):  
Building Materials ◽  
Computational Modelling ◽  
Late Antique ◽  
Roman Economy ◽  
Wide Range ◽  
The Status ◽  
Recent Developments ◽  
Methodological Approaches ◽  
First Time ◽  
Site Types

The recycling and reuse of materials and objects were extensive in the past, but have rarely been embedded into models of the economy; even more rarely has any attempt been made to assess the scale of these practices. Recent developments, including the use of large datasets, computational modelling, and high-resolution analytical chemistry, are increasingly offering the means to reconstruct recycling and reuse, and even to approach the thorny matter of quantification. Growing scholarly interest in the topic has also led to an increasing recognition of these practices from those employing more traditional methodological approaches, which are sometimes coupled with innovative archaeological theory. Thanks to these efforts, it has been possible for the first time in this volume to draw together archaeological case studies on the recycling and reuse of a wide range of materials, from papyri and textiles, to amphorae, metals and glass, building materials and statuary. Recycling and reuse occur at a range of site types, and often in contexts which cross-cut material categories, or move from one object category to another. The volume focuses principally on the Roman Imperial and late antique world, over a broad geographical span ranging from Britain to North Africa and the East Mediterranean. Last, but not least, the volume is unique in focusing upon these activities as a part of the status quo, and not just as a response to crisis.

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