K. Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation. P Natl Acad Sci USA 103, 9879–9884, doi: 10.1073/pnas.0603557103 (2006). 31. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal ...
Such a trade-off has been observed for the LacI repressor, which regulates the lactose-metabolizing lac operon. Excessive binding affinity of LacI to its TFBS requires a higher concentration of the inducer to de-repress the system119. If the same applied to TetR, the necessary increase of ...
4). Here, modeling was conducted in the same manner as described above for Pr. In this case, we used the AlphaFold model of the DHp domain as a guide to manually extend its fit within the EM density. Placement of the observed CA domain into the density was then possible by manual ...
coli strains growing on glucose because it represses expression of the lac operon. Stoebel et al. [46] have in fact found that cells with the genomic copy of lacI show some residual lacA activity when grown in glucose, and estimated the cost of expressing lacA as 1.85% per generation [46...
Tentative modeling revealed a non-canonical turn within the root of domain IV (Fig. 5b, c), causing H61 to thread through the gap created by the absence of both uL22 and bL32 (Fig. 5d). As a result, the entire domain IV is positioned on the solvent side (back) of the subunit, ...
Using single-cell measurements and mathematical modeling, we found that the cAMP-CRP system modulates the expression of the large group of metabolic enzymes called the C-sector in response to stochastic variations within the metabolic network. Our quantitative approach allowed us to reveal the complex...
The first, SBML4 is a biological modeling standard that has been developed by the systems biology community to encode strains and pathways. The second, SBOL5, is a data exchange standard specific to synthetic biology. SBOL has been developed to document genetic components (DNA, RNA, protein, ...
Systems-based techniques play a key role in the analysis of GRNs as it is nearly impossible to understand the behavior of a moderately complex GRN that incorporates feedback loops without modeling. As it becomes increasingly practical to map the regulatory linkages in GRNs from large-scale ...
I co-host The Bioinformatics Lab podcast with @kevinlibuit.bsky.social and the other day we had a great chat about our job hunting experiences, the importance of professional networks and making genuine connections. Its on all the podcasting apps & youtube soundcloud.com/the_bioinfor…— Andr...
considered. Final operons on forward strand were required to be in front of the peak, and operons on reverse strand were required to be behind the peak. Genome-scale data were visualized using MetaScope to manually curate peaks (https://sites.google.com/view/systemskimlab/software?authuser=...