Catalytic DNA: Ligating with lambda

February 16th, 2016 by Terry L Sheppard

Nature Chemical Biology 12, 125 (2016). doi:10.1038/nchembio.2033

Author: Terry L Sheppard

RNA conformation: Lightening up invisible states

February 16th, 2016 by Yun-Xing Wang

Nature Chemical Biology 12, 126 (2016). doi:10.1038/nchembio.2030

Author: Yun-Xing Wang

The versatility of RNA is achieved in part through its ability to adopt various shapes of structures. A new technology called X-ray scattering interferometry enables the detection of 'invisible' states by lighting up gold pairs tagged to RNA molecules.

Development and application of bond cleavage reactions in bioorthogonal chemistry

February 16th, 2016 by Jie Li

Nature Chemical Biology 12, 129 (2016). doi:10.1038/nchembio.2024

Authors: Jie Li & Peng R Chen

  • Posted in Nat Chem Biol, Publications
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Optogenetics: Follow the PIF

February 16th, 2016 by Grant Miura

Nature Chemical Biology 12, 125 (2016). doi:10.1038/nchembio.2031

Author: Grant Miura

RNA modification: Translating for growth

February 16th, 2016 by Grant Miura

Nature Chemical Biology 12, 125 (2016). doi:10.1038/nchembio.2034

Author: Grant Miura

Molecular Modeling of the Structural and Dynamical Changes in Calcium Channel TRPV5 Induced by the African-Specific A563T Variation

February 15th, 2016 by Lingyun Wang, Ross P. Holmes and Ji-Bin Peng

TOC Graphic

Biochemistry
DOI: 10.1021/acs.biochem.5b00732

Allosteric substrate switching in a voltage-sensing lipid phosphatase

February 15th, 2016 by Sasha S Grimm

Nature Chemical Biology 12, 261 (2016). doi:10.1038/nchembio.2022

Authors: Sasha S Grimm & Ehud Y Isacoff

  • Posted in Nat Chem Biol, Publications
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Allostery: A lipid two-step

February 15th, 2016 by Liang Hong

Nature Chemical Biology 12, 202 (2016). doi:10.1038/nchembio.2037

Authors: Liang Hong & Francesco Tombola

A sensor of membrane depolarization controls the activity of a bound enzyme through a novel mechanism involving two sequential voltage-dependent transitions allosterically coupled to changes in the substrate specificity of the catalytic domain.

YihQ is a sulfoquinovosidase that cleaves sulfoquinovosyl diacylglyceride sulfolipids

February 15th, 2016 by Gaetano Speciale

Nature Chemical Biology 12, 215 (2016). doi:10.1038/nchembio.2023

Authors: Gaetano Speciale, Yi Jin, Gideon J Davies, Spencer J Williams & Ethan D Goddard-Borger

Sulfoquinovose is produced by photosynthetic organisms at a rate of 1010 tons per annum and is degraded by bacteria as a source of carbon and sulfur. We have identified Escherichia coli YihQ as the first dedicated sulfoquinovosidase and the gateway enzyme to sulfoglycolytic pathways. Structural and mutagenesis studies unveiled the sequence signatures for binding the distinguishing sulfonate residue and revealed that sulfoquinovoside degradation is widespread across the tree of life.

  • Posted in Nat Chem Biol, Publications
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Transcription elongation factor NusA is a general antagonist of Rho-dependent termination in Escherichia coli. [Microbiology]

February 12th, 2016 by Qayyum, M. Z., Dey, D., Sen, R.

NusA is an essential protein that binds to RNA polymerase (RNAP) and also to the nascent RNA, and influences transcription by inducing pausing and facilitating the process of transcription termination / antitermination. Its participation in Rho-dependent transcription termination has been perceived, but the molecular nature of this involvement is not known. We hypothesized that as both Rho and NusA are RNA-binding proteins and have the potential to target the same RNA, the latter is likely to influence the global pattern of the Rho-dependent termination. Analyses of the nascent RNA-binding properties and consequent effects on the Rho-dependent termination functions of specific NusA-RNA binding domain mutants revealed an existence of Rho-NusA direct competition for the overlapping nut (NusA-binding site) and rut (Rho-binding site) sites on the RNA. This leads to delayed entry of Rho at the rut site that inhibits the RNA release process of the latter. High density tiling micro-array profiles of these NusA mutants revealed that a significant number of genes, together with transcripts from intergenic regions are up-regulated. Interestingly, majority of these genes were also up-regulated when the Rho function was compromised. These are strong evidences for the existence of NusA-binding sites in different operons which are also the targets of Rho-dependent terminations. Our data strongly argue in favor of a direct competition between NusA and Rho for the access of specific sites on the nascent transcripts in different parts of the genome. We propose that this competition enables NusA to function as a global antagonist of the Rho function, which is unlike its role as a facilitator of hairpin-dependent termination.