ATP-induced helicase slippage reveals highly coordinated subunits

This paper discusses the T7 helicase enzyme, which unwinds DNA using dTTP. The authors found that adding ATP would also allow unwinding but caused the helicase to 'slip' along the DNA. Enzyme kinetics were also discussed to determine the effect of slippage frequency. Further discussion on the binding of the enzyme to DNA is also included.

Control of tumor and microenvironment cross-talk by miR-15a and miR-16 in prostate cancer

In this paper, Musumeci and co-workers found new miR-15a/16 targets responsible for tumor promoting activity in non-neoplastic associated fibroblasts. They have shown miR-15a/16 are downregulated in fibroblast cells that are surrounded by tumor cells. Downregulation of these microRNAs induced the expression of growth factor FGF-2 which promotes tumor growth and progression via microenvironment cross talk. I found this article interesting that microRNAs are involved in cell-cell interactions.

Fluorescent DNA chemosensors: identification of bacterial species by their volatile metabolites

DNA-like fluorescent sensors are reported to identify M. tuberculosis, E. coli and P. putida bacterial strains in culture based on volatile metabolites. These DNA based chemosensors are able to differentiate bacterial strains of interest due to unique fluorescent profiles produced when exposed to the bacterial cultures. This method allows for quick detection of pathogenic bacteria in clinical samples through a fluorescent readout.

An efficient platform for genetic selection and screening of gene switches in Escherichia coli

In Gavin's class we discussed Gallivan's system for evolving a riboswitch using a motility selection. I raised the question whether a genetic selection would be better in this case. As described in the introduction of this paper, there are several problems with genetic selections for riboswitches. Two of these problems include the handling of hundreds of agar plates and the difficulty of quantitatively monitoring the selection. This paper describes a dual selection and screen that uses a TetA-GFP fusion protein to genetically select for riboswitches and quantitatively monitor the process.

Discovery of Pazopanib, a Novel and Potent Vascular Endothelial Growth Factor Receptor Inhibitor

In Alex's class we recently discussed small molecule inhibitors of DNA. One of the small molecules targeted the VEGF pathway in the hope of reducing tumor growth. As we discussed, DNA small molecule inhibitors must be able to not only penetrate the cell and nucleus, but also access the DNA wrapped around the histones.
Small molecules that can inhibit cellular receptors are the most widely used therapeutic on the market due to the easy accessibly of the receptor on the outside of the cell. This paper from GlaxoSmithKline (RTP) describes the discovery of a kinase inhibitor that targets a VEGF receptor, which has been approved by the FDA to treat renal cell carcinoma (RCC).

Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase

In contrast to this conventional concept, archaeal fructose-1,6-bisphosphate (FBP) aldolase/phosphatase (FBPA/P) consists of a single catalytic domain, but catalyses two chemically distinct reactions of gluconeogenesis: (1) the reversible aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to FBP; (2) the dephosphorylation of FBP to fructose-6-phosphate (F6P)². Thus, FBPA/P is fundamentally different from ordinary enzymes whose active sites are responsible for a specific reaction. However, the molecular mechanism by which FBPA/P achieves its unusual bifunctionality remains unknown. Here we report the crystal structure of FBPA/P at 1.5-Å resolution in the aldolase form, where a critical lysine residue forms a Schiff base with DHAP. A structural comparison of the aldolase form with a previously determined phosphatase form³ revealed a dramatic conformational change in the active site, demonstrating that FBPA/P metamorphoses its active-site architecture to exhibit dual activities. Thus, our findings expand the conventional concept that one enzyme catalyses one biochemical reaction.

Largazole and Analogues with Modified Metal-Binding Motifs Targeting Histone Deacetylases: Synthesis and Biological Evaluation

Inhibitors of Histone Deacetylases represent promising anti-cancer agents. HDAC proteins are a familly of 18 enzymes and they exhibit a high homology within their catalytic sites, rendering specific targeting of one protein really challenging. They developed an efficient route to largazole analogues. They investigated the properties of chelation with Zinc cation.
The compounds they made were less active than largazole, however they show some selectivity toward the class I of HDACs.

Chemical Tools for Studying Directed Cell Migration

This review discusses the use of controlling proteins through light or small molecule regulation, and how those tools can be used to study cellular migration. It goes over many topics we have discussed in class: chemical genetics approaches, protein dimerization/activation with SM, caging molecules, fluorescent reporters, sensors/switches, etc. I think it is a cool overview that links the material in a meaningful example.

NOTE: Contains shout-outs to Deiters for photochemical protein control, photocaged rapamycin, and engineered kinases.

Antibacterial lysine analogs that target lysine riboswitches

In Deiter's class today we talked about how riboswitches are good targets for small molecule inhibitors because they already endogenously bind to small molecules. In addition, because riboswitches often sense metabolites, the expression platform often contains genes that are essential to its survival. This then would make them good antibiotic targets. However, there are few examples of small molecule antibiotics that were designed to target riboswitches. Attached is one of those papers.
In this paper, Blount and co-workers target the bacterial lysine riboswitch which controls lysine biosynthesis. In most bacteria, the binding of lysine to the lysine riboswitch forms a transcription terminator, stopping the production of proteins that will produce more lysine and lysine intermediates. Therefore, finding an alternative small molecule that will bind to the lysine riboswitch, will halt lysine production and cause the bacteria to die. The way that this is done is by rational design, where the authors vary specific areas of the lysine side chain and determine dissociation constants by in-line probing. Below shows (a) the optical density of cultures grown in the presence of the analogs over time (b) this data was then plotted in a bar chart (c) shows the mininum concentrations of complete inhibition (MIC) and the switch attached to lacZ (d) that beta-galactosidase activity when the switch is attached to the lacZ gene is dose dependent.

Identification and Characterization of the Lysobactin Biosynthetic Gene Cluster Reveals Mechanistic Insights into an Unusual Termination Module Archit

Irina recently presented a non-ribosomal peptide synthetase-derived thioesterase which served to cleave a completed linear polypeptide chain from a solid-phase synthetic assembly line and induce macrocyclization to yield the desired macrocycle. This article highlights an unusual thioesterase action mediated by two independent thioesterase domains, where one is responsible for substrate cleavage and the other for macrocyclization. This interesting alternative highlights the importance of correct thioesterase activity, in that different thioesterases with distinct activities may be necessary for macrocyclization fidelity.