[NiFe]-Hydrogenase Maturation

March 13th, 2016 by Michael J. Lacasse and Deborah B. Zamble

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Biochemistry
DOI: 10.1021/acs.biochem.5b01328

Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays

March 8th, 2016 by Leandro Watanabe and Chris J. Myers

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ACS Synthetic Biology
DOI: 10.1021/acssynbio.5b00242

Survival of Phenotypic Information during Cellular Growth Transitions

March 7th, 2016 by J. Christian J. Ray

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ACS Synthetic Biology
DOI: 10.1021/acssynbio.5b00229

Probes of ubiquitin E3 ligases enable systematic dissection of parkin activation

March 7th, 2016 by Kuan-Chuan Pao

Nature Chemical Biology 12, 324 (2016). doi:10.1038/nchembio.2045

Authors: Kuan-Chuan Pao, Mathew Stanley, Cong Han, Yu-Chiang Lai, Paul Murphy, Kristin Balk, Nicola T Wood, Olga Corti, Jean-Christophe Corvol, Miratul M K Muqit & Satpal Virdee

  • Posted in Nat Chem Biol, Publications
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Enzyme Architecture: A Startling Role for Asn270 in Glycerol 3-Phosphate Dehydrogenase-Catalyzed Hydride Transfer

March 3rd, 2016 by Archie C. Reyes, Tina L. Amyes and John P. Richard

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Biochemistry
DOI: 10.1021/acs.biochem.6b00116

Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase

February 29th, 2016 by Lisa K. Schneider and Oliver Einsle

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Biochemistry
DOI: 10.1021/acs.biochem.5b01278

Motor proteins: Kinesin’s gait captured

February 29th, 2016 by Erwin J G Peterman

Nature Chemical Biology 12, 206 (2016). doi:10.1038/nchembio.2038

Author: Erwin J G Peterman

Kinesin is a motor protein that drives intracellular transport by stepping along microtubules in a hand-over-hand manner. Advanced dark-field microscopy has made it possible to capture the gait of this motor with unprecedented resolution.

Direct observation of intermediate states during the stepping motion of kinesin-1

February 29th, 2016 by Hiroshi Isojima

Nature Chemical Biology 12, 290 (2016). doi:10.1038/nchembio.2028

Authors: Hiroshi Isojima, Ryota Iino, Yamato Niitani, Hiroyuki Noji & Michio Tomishige

  • Posted in Nat Chem Biol, Publications
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The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases

February 29th, 2016 by Kristian E H Frandsen

Nature Chemical Biology 12, 298 (2016). doi:10.1038/nchembio.2029

Authors: Kristian E H Frandsen, Thomas J Simmons, Paul Dupree, Jens-Christian N Poulsen, Glyn R Hemsworth, Luisa Ciano, Esther M Johnston, Morten Tovborg, Katja S Johansen, Pernille von Freiesleben, Laurence Marmuse, Sébastien Fort, Sylvain Cottaz, Hugues Driguez, Bernard Henrissat, Nicolas Lenfant, Floriana Tuna, Amgalanbaatar Baldansuren, Gideon J Davies, Leila Lo Leggio & Paul H Walton

  • Posted in Nat Chem Biol, Publications
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Quantification of cooperativity in heterodimer-DNA binding improves the accuracy of binding specificity models [Computational Biology]

February 24th, 2016 by Isakova, A., Berset, Y., Hatzimanikatis, V., Deplancke, B.

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its impact on heterodimer DNA binding specificity models is still lacking. Here, we used a novel integrative approach, combining microfluidics-steered measurements of dimer-DNA assembly with mechanistic modeling of the implicated protein-protein-DNA interactions to quantitatively interrogate the cooperative DNA binding behavior of the adipogenic PPARγ:RXRα heterodimer. Using the high-throughput MITOMI platform, we derived equilibrium DNA binding data for PPARγ, RXRα, as well as the PPARγ:RXRα heterodimer to more than 300 target DNA sites and variants thereof. We then quantified cooperativity underlying heterodimer-DNA binding and derived an integrative heterodimer DNA binding constant. Using this cooperativity-inclusive constant, we were able to build a heterodimer DNA binding specificity model that has superior predictive power than the one based on a regular one-site equilibrium. Our data further revealed that individual nucleotide substitutions within the target site affect the extent of cooperativity in PPARγ:RXRα-DNA binding. Our study therefore emphasizes the importance of assessing cooperativity when generating DNA binding specificity models for heterodimers.