Biocatalytic reaction and recycling by using CO2-induced organic-aqueous tunable solvents.
Explore the source record for details and available documents.
Acetates↗
Biomedical subjects
Andreas S Bommarius
Publications and source records attributed to Andreas S Bommarius.
Simulation modeling of pooling for combinatorial protein engineering.
Pooling in directed-evolution experiments will greatly increase the throughput of screening systems, but important parameters such as the number of good mutants created and the activity level increase of the good mutants will depend highly on the protein being engineered. The authors developed and validated a Monte Carlo simulation model of pooling that allows the testing of various scenarios in silico before starting experimentation. Using a simplified test system of 2 enzymes, betagalactosidase (supermutant, or greatly improved enzyme) and beta-glucuronidase (dud, or enzyme with ancestral level of activity), the model accurately predicted the number of supermutants detected in experiments within a factor of 2. Additional simulations using more complex activity distributions show the versatility of the model. Pooling is most suited to cases such as the directed evolution of new function in a protein, where the background level of activity is minimized, making it easier to detect small increases in activity level. Pooling is most successful when a sensitive assay is employed. Using the model will increase the throughput of screening procedures for directed-evolution experiments and thus lead to speedier engineering of proteins.
Cells, Cultured↗
Support vector machines for learning to identify the critical positions of a protein.
A method for identifying the positions in the amino acid sequence, which are critical for the catalytic activity of a protein using support vector machines (SVMs) is introduced and analysed. SVMs are supported by an efficient learning algorithm and can utilize some prior knowledge about the structure of the problem. The amino acid sequences of the variants of a protein, created by inducing mutations, along with their fitness are required as input data by the method to predict its critical positions. To investigate the performance of this algorithm, variants of the beta-lactamase enzyme were created in silico using simulations of both mutagenesis and recombination protocols. Results from literature on beta-lactamase were used to test the accuracy of this method. It was also compared with the results from a simple search algorithm. The algorithm was also shown to be able to predict critical positions that can tolerate two different amino acids and retain function.
Algorithms↗
Crystallization and preliminary analysis of a water-forming NADH oxidase from Lactobacillus sanfranciscensis.
Single crystals have been obtained of NADH oxidase (Nox), a flavoenzyme cloned from Lactobacillus sanfranciscensis. The enzyme catalyzes the oxidation of two equivalents of NAD(P)H and reduces one equivalent of oxygen to yield two equivalents of water, without releasing hydrogen peroxide after the reduction of the first equivalent of NAD(P)H. The enzyme crystallizes in space group P2(1)2(1)2(1), with unit-cell parameters a = 59.6, b = 92.6, c = 163.5 A. The crystals diffract to 1.85 A resolution using synchrotron radiation. Matthews coefficient calculations suggest the presence of two molecules per asymmetric unit (V(M) = 2.3 A(3) Da(-1), 45.5% solvent content), which has been confirmed by the molecular-replacement solution using a search molecule derived from NADH peroxidase (PDB code 1f8w).
Crystallization↗
Accelerated biocatalyst stability testing for process optimization.
The deactivation of protein biocatalysts even at relatively low temperatures is one of the principal drawbacks to their use. To aid in the development of novel biocatalysts, we have derived an equation for both time- and temperature-dependent activity of the biocatalyst based on known concepts such as transition state theory and the Lumry-Eyring model. We then derived an analytical solution for the total turnover number (ttn), under isothermal operation, as a function of the catalytic constant kcat, the unfolding equilibrium constant K, and the intrinsic first-order deactivation rate constant(s) k(d,i). Employing an immobilized glucose isomerase biocatalyst in a CSTR and utilizing a linear temperature ramp beyond the Tm of the enzyme, we demonstrate an accelerated method for extracting the thermodynamic and kinetic constants describing the biocatalyst system. In addition, we demonstrate that the predicted biocatalyst behavior at different temperatures and reaction times is consistent with the experimental observations.
Aldose-Ketose Isomerases↗
Deactivation of formate dehydrogenase (FDH) in solution and at gas-liquid interfaces.
Enzymes, increasingly important in the synthesis of fine chemicals and pharmaceutical intermediates, are often insufficiently stable under reacting conditions. We have investigated the stability, in homogeneous aqueous solution and at gas-liquid interfaces, of formate dehydrogenase (FDH), important for cofactor regeneration, from Candida boidinii and overexpressed in E. coli. When exposed to mechanical stress, residual activity, [E](t)/[E](0), and residual protein were found to scale proportionally with gas-liquid surface area in the bubble column, verifying a surface-driven process, and with time and total throughput in a gear pump, but did not seem to be influenced much by shear in a Couette viscometer. All FDH variants are deactivated by chaotropes but not kosmotropes: the first-order deactivation constant k(d) correlates well with the Jones-Dole coefficient B but not well with the surface tension increment deltasigma of various concentrated ammonium salt solutions. This finding might provide guidance for focusing the search for quantitative theories of Hofmeister effects.
Bioreactors↗