A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2

February 8th, 2016 by Jessika Valero-González

Nature Chemical Biology 12, 240 (2016). doi:10.1038/nchembio.2019

Authors: Jessika Valero-González, Christina Leonhard-Melief, Erandi Lira-Navarrete, Gonzalo Jiménez-Osés, Cristina Hernández-Ruiz, María Carmen Pallarés, Inmaculada Yruela, Deepika Vasudevan, Anabel Lostao, Francisco Corzana, Hideyuki Takeuchi, Robert S Haltiwanger & Ramon Hurtado-Guerrero

  • Posted in Nat Chem Biol, Publications
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Engineering nonphosphorylative metabolism to generate lignocellulose-derived products

February 8th, 2016 by Yi-Shu Tai

Nature Chemical Biology 12, 247 (2016). doi:10.1038/nchembio.2020

Authors: Yi-Shu Tai, Mingyong Xiong, Pooja Jambunathan, Jingyu Wang, Jilong Wang, Cole Stapleton & Kechun Zhang

  • Posted in Nat Chem Biol, Publications
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Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-Binding Protein (CBP) and p300 [Signal Transduction]

February 5th, 2016 by Dyson, H. J., Wright, P. E.

The transcriptional coactivators CBP and p300 undergo a particularly rich set of interactions with disordered and partly-ordered partners, as a part of their ubiquitous role in facilitating transcription of genes. CBP and p300 contain a number of small structured domains that provide scaffolds for the interaction of disordered transactivation domains from a wide variety of partners including p53, HIF-1&alpha, NF-&kappaB and STAT proteins, and are the targets for the interactions of disordered viral proteins that compete with cellular factors to disrupt signaling and subvert the cell cycle. The functional diversity of the CBP/p300 interactome provides an excellent example of the power of intrinsic disorder to facilitate the complexity of living systems.
  • Posted in Journal of Biological Chemistry, Publications
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Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-Dependent RNA Polymerase Allosterically Block the Transition from Initiation to Elongation [RNA]

February 5th, 2016 by Li, J., Johnson, K. A.

Replication of the Hepatitis C viral genome is catalyzed by the NS5B RNA-dependent RNA polymerase catalyzes, which is a major target of antiviral drugs currently in the clinic. Prior studies established that initiation of RNA replication could be facilitated by starting with a dinucleotide (pGG). Here we establish conditions for efficient initiation from GTP to form the dinucleotide and subsequent intermediates leading to highly processive elongation, and we examine the effects of four classes of nonnucleoside inhibitors on each step of the reaction. We show that palm site inhibitors block initiation starting from GTP but not when starting from pGG. In addition we show that nonnucleoside inhibitors binding to thumb site-2 (NNI2) lead to the accumulation of abortive intermediates 3-5 nucleotides in length. Our kinetic analysis shows that NNI2 do not significantly block initiation or elongation of RNA synthesis; rather they block the transition from initiation to elongation, which is thought to proceed with significant structural rearrangement of the enzyme-RNA complex including displacement of the ╬▓-loop from the active site. Direct measurement in single turnover kinetic studies show that pyrophosphate release is faster than the chemistry step, which appears to be rate-limiting during processive synthesis. These results reveal important new details to define the steps involved in initiation and elongation during viral RNA replication, establish the allosteric mechanisms by which NNI2 inhibitors act, and point the way to the design of more effective allosteric inhibitors that exploit this new information.
  • Posted in Journal of Biological Chemistry, Publications
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Design principles involving protein disorder facilitate specific substrate selection and degradation by the ubiquitin-proteasome system [Protein Synthesis and Degradation]

February 5th, 2016 by Guharoy, M., Bhowmick, P., Tompa, P.

The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss posttranslational modifications within disordered regions that regulate E3 ligase localization, conformation and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity. Next we review well-studied substrates and discuss that substrate elements (degrons) recognized by E3 ligases are highly disordered: short linear motifs recognized by many E3s constitute an important class of degrons and these are almost always present in disordered regions. Substrate lysines targeted for ubiquitination are also often located in neighboring regions of the E3 docking motifs and are therefore part of the disordered segment. Finally, biochemical experiments and predictions show that initiation of degradation at the 26S proteasome requires a partially unfolded region to facilitate substrate entry into the proteasomal core.
  • Posted in Journal of Biological Chemistry, Publications
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Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance

February 5th, 2016 by Yu-Shan Cheng and James C. Sacchettini

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Biochemistry
DOI: 10.1021/acs.biochem.5b00993

Expanding the Range of Protein Function at the Far end of the Order-Structure Continuum [Molecular Biophysics]

February 5th, 2016 by Burger, V. M., Nolasco, D. O., Stultz, C. M.

The traditional view of the structure-function paradigm is that a protein's function is inextricably linked to a well-defined, three-dimensional structure, which is determined by the protein's primary amino acid sequence. However, it is now accepted that a number of proteins do not adopt a unique tertiary structure in solution and that some degree of disorder is required for many proteins to perform their prescribed functions. In this review we highlight how a number of protein functions are facilitated by intrinsic disorder and introduce a new protein structure taxonomy that is based on quantifiable metrics of a protein's disorder.

A Stable Pyrophosphoserine Analog for Incorporation into Peptides and Proteins

February 5th, 2016 by Lisa M. Yates and Dorothea Fiedler

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ACS Chemical Biology
DOI: 10.1021/acschembio.5b00972

Sirtuins 1 and 2 Are Universal Histone Deacetylases

February 5th, 2016 by Willie W. Hsu, Bo Wu and Wenshe R. Liu

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ACS Chemical Biology
DOI: 10.1021/acschembio.5b00886

Probing Chromatin-modifying Enzymes with Chemical Tools

February 4th, 2016 by Wolfgang Fischle and Dirk Schwarzer

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ACS Chemical Biology
DOI: 10.1021/acschembio.5b01023