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5 results for “Enzyme Design”
Plasmid Design for Tunable Two‐Enzyme Co‐Expression Promotes Whole‐Cell Production of Cellobiose
<p>We provide underlying data for the publication "Plasmid design for tunable two-enzyme co-expression promotes whole-cell production of cellobiose". Please find the abstract below.</p> <p>Catalyst development for biochemical cascade reactions often follows a “whole cell approach” in which a single microbial cell is made to express all of the required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux from substrate to product necessitates precise balancing between the individual activities. Here, we show effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors enabling tunable two‐enzyme co‐expression in <em>E. coli </em>, for the purpose of whole‐cell production of cellobiose. Flux efficiency in the transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co‐expression cope with large differences in the specific activity of cellobiose phosphorylase (14 U mg<sup>−1</sup>) and sucrose phosphorylase (122 U mg<sup>−1</sup>). Comparing mono‐ and bicistronic co‐expression strategies, we analyze genetic elements controlling transcription, transcription‐translation coupling or plasmid replication for effect on activity, and also stable producibility, of the whole cell catalyst. We discover a key role of the <em>bom </em>(basis of mobility) site for plasmid stability dependent on the origin of replication and demonstrate the importance of RBS (ribosome binding site) strength for balanced bicistronic co‐expression. Whole cell catalysts show high specific rates (460 μmol cellobiose min<sup>−1</sup> g<sup>−1</sup> dry cells) and performance metrics (30 g L<sup>−1</sup>; ∼82% yield; 3.8 g L<sup>−1</sup> h<sup>−1</sup> overall productivity) promising for cellobiose production.</p>
Computer-Aided Drug Design (CADD): To Screen Potential Antibiotics Against Klebsiella Pneumoniae Beta-Lactamase Enzyme
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Massively parallel, computationally-guided design of a pro-enzyme
<p>Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to re-design any chosen enzyme to be similarly stimulus-responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for pro-enzyme design. As a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of most effective designed variants shows that they are inhibited by approximately 80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98%, but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing pro-enzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the pro-domain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of pro-proteins with precise spatial regulation.</p>
Investigating the role of Pseudomonas dye-decolorizing peroxidases in quinone redox cycling for bio-design of a DypB-based lignin degrading enzyme cocktail
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Computational design of the temperature optimum of an enzyme reaction
<p>This repository accompanies the following publication: (added upon publication)</p> <p>EVB.zip contains input files for simulations performed with Q. It contains a topology file, a fep file and a input files used to perform minimization, equilibration and FEP/EVB simulations on a psychrophilic amylase. The version of Q used in this research is also available on Zenodo: <span>10.5281/zenodo.7940182</span></p> <p>Fig_2.zip contains raw data and python code used to generate the subplots shown in figure 2 in the publication. The python code is in the form of an ipython notebook.</p>
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