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Nature Chemical Biology - April 2009 (Vol.5 N°4)
English | 80 pages | PDF | 10.46 MB
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C-H activation: New recipes for biocatalysis

C-H activation: New recipes for biocatalysis

[h=4]C-H activation: New recipes for biocatalysis[/h]
Eric M BrustadPublished online: 26 January 2014 | doi:10.1038/nchembio.1457The bacterial halogenase SyrB2 catalyzes selective installation of halogens in place of unactivated aliphatic C-H bonds. By substituting halide reagents with the nitrogenous anions N[SUB]3[/SUB][SUP]−[/SUP] and NO[SUB]2[/SUB][SUP]−[/SUP], SyrB2 can perform C-N bond formation reactions not previously observed in nature.
 

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Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

Michael J Hammerling, Jared W Ellefson, Daniel R Boutz, Edward M Marcotte, Andrew D Ellington & Jeffrey E Barrick
Published online: 02 February 2014 | doi:10.1038/nchembio.1450




Translational reprogramming, which enables site-specific incorporation of non-natural amino acids into proteins, offers practical tools for studying protein function but also provides insights into the genetic code. Bacteriophages engineered with a 21-amino-acid genetic code make use of the additional noncanonical amino acid during in vitro evolution.
 

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An orthogonal DNA replication system in yeast

An orthogonal DNA replication system in yeast

An orthogonal DNA replication system in yeast

Arjun Ravikumar, Adrian Arrieta & Chang C Liu
Published online: 02 February 2014 | doi:10.1038/nchembio.1439



A stable replication system, based on a DNA polymerase that replicates cytoplasmic plasmids with unique terminal proteins, decouples plasmid gene replication from host genom
 

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Negative selection and stringency modulation in phage-assisted continuous evolution

Negative selection and stringency modulation in phage-assisted continuous evolution

Negative selection and stringency modulation in phage-assisted continuous evolution

Jacob C Carlson, Ahmed H Badran, Drago A Guggiana-Nilo & David R Liu
Published online: 02 February 2014 | doi:10.1038/nchembio.1453



Phage-assisted continuous evolution (PACE) minimizes researcher intervention while maximizing rounds of protein evolution. New strategies now eliminate the need for intermediate substrate analogs and promote altered selectivity instead of promiscuity, exemplified by a 10,000-fold switch in polymerase specificity while retaining wild-type activity.
 

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Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase

Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase

Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase

Megan L Matthews, Wei-chen Chang, Andrew P Layne, Linde A Miles, Carsten Krebs & J Martin Bollinger Jr
Published online: 26 January 2014 | doi:10.1038/nchembio.1438


Halogenases differ from hydroxylases by coordination of a chloride ion at the reactive iron center, which is taken up by an activated substrate. Biochemical and spectroscopic evidence now show other anions can be used, resulting in the first enzymatic incorporation of nitrogen onto unactivated aliphatic carbons.
 

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Integrated RAS signaling defined by parallel NMR detection of effectors and regulators

Integrated RAS signaling defined by parallel NMR detection of effectors and regulators

Integrated RAS signaling defined by parallel NMR detection of effectors and regulators

Matthew J Smith & Mitsuhiko Ikura
Published online: 19 January 2014 | doi:10.1038/nchembio.1435



An NMR analysis of RAS-binding domains (effectors) placed under direct competition allows a systems-level view of effector binding and describes how oscillating concentrations can lead to effector switching. Deconvolution of effector binding to oncogenic RAS[SUP]G12V[/SUP] revealed a reordering of the effector hierarchy.
 

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Allostery in Ca2+ channel modulation by calcium-binding proteins

Allostery in Ca2+ channel modulation by calcium-binding proteins

Allostery in Ca[SUP]2+[/SUP] channel modulation by calcium-binding proteins

Philemon S Yang, Manu Ben Johny & David T Yue
Published online: 19 January 2014 | doi:10.1038/nchembio.1436



A tethered ligand approach reveals that calcium-binding proteins (CaBPs) act as allosteric modulators of calcium channel calmodulin regulation, shedding light on how trace CaBPs can prevail over an abundance of CaM.
 

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Designable DNA-binding domains enable construction of logic circuits in mammalian cells

Designable DNA-binding domains enable construction of logic circuits in mammalian cells

Designable DNA-binding domains enable construction of logic circuits in mammalian cells

Rok Gaber, Tina Lebar, Andreja Majerle, Branko Šter, Andrej Dobnikar, Mojca Benčina & Roman Jerala
Published online: 12 January 2014 | doi:10.1038/nchembio.1433


Synthetic biology requires orthogonal inputs and outputs to avoid undesired crosstalk between genetic constructs. Transcription activator–like effectors (TALEs), which bind diverse DNA sequences and can thus be orthogonal, are now employed to construct NOR gates and logic circuits in mammalian cells.
 

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An optogenetic gene expression system with rapid activation and deactivation kinetics

An optogenetic gene expression system with rapid activation and deactivation kinetics

An optogenetic gene expression system with rapid activation and deactivation kinetics

Laura B Motta-Mena, Anna Reade, Michael J Mallory, Spencer Glantz, Orion D Weiner, Kristen W Lynch & Kevin H Gardner
Published online: 12 January 2014 | doi:10.1038/nchembio.1430


Optogenetic systems permit the temporal and spatial control of gene expression using light. A variant of the LOV domain–containing EL222 protein displays responsive blue light–gated transcriptional control of genes in zebrafish and in mammalian cell lines.
 

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Allosteric Wip1 phosphatase inhibition through flap-subdomain interaction

Allosteric Wip1 phosphatase inhibition through flap-subdomain interaction

Allosteric Wip1 phosphatase inhibition through flap-subdomain interaction

Aidan G Gilmartin, Thomas H Faitg, Mark Richter, Arthur Groy, Mark A Seefeld, Michael G Darcy, Xin Peng, Kelly Federowicz, Jingsong Yang, Shu-Yun Zhang, Elisabeth Minthorn, Jon-Paul Jaworski, Michael Schaber, Stan Martens, Dean E McNulty, Robert H Sinnamon, Hong Zhang, Robert B Kirkpatrick, Neysa Nevins, Guanglei Cui, Beth Pietrak, Elsie Diaz, Amber Jones, Martin Brandt, Benjamin Schwartz, Dirk A Heerding & Rakesh Kumar
Published online: 05 January 2014 | doi:10.1038/nchembio.1427


Allosteric small-molecule inhibitors of the p53-induced oncogenic phosphatase Wip1 bind at a ‘flap’ subdomain near the catalytic site. Inhibitor GSK2830371 inhibits the phosphatase and oncogenic activities in cell lines and a xenograft tumor model.
 

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Opening of an alternative ion permeation pathway in a nociceptor TRP channel

Opening of an alternative ion permeation pathway in a nociceptor TRP channel

Opening of an alternative ion permeation pathway in a nociceptor TRP channel

Joris Vriens, Katharina Held, Annelies Janssens, Balázs István Tóth, Sara Kerselaers, Bernd Nilius, Rudi Vennekens & Thomas Voets
Published online: 05 January 2014 | doi:10.1038/nchembio.1428


Besides the canonical pore that allows passage of cations into the cell, the TRPM3 channel has an alternative ‘omega’ permeation pathway formed by the S1–S4 region of the protein. This peripheral pore is inwardly rectifying, whereas the canonical central axis pore is outwardly rectifying.
 

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