Journal Articles
Evidence for Functionally Relevant Encounter Complexes in Nitrogenase Catalysis
In Situ Probing of the Active Site Geometry of Ultrathin Nanowires for the Oxygen Reduction Reaction
From meso-Lactide to Isotactic Polylactide: Epimerization by B/N Lewis Pairs and Kinetic Resolution by Organic Catalysts
Post-translational Introduction of d-Alanine into Ribosomally Synthesized Peptides by the Dehydroalanine Reductase NpnJ
Kinetic Analysis as a Tool to Distinguish Pathway Complexity in Molecular Assembly: An Unexpected Outcome of Structures in Competition
Sulfur-Bridged Terthiophene Dimers: How Sulfur Oxidation State Controls Interchromophore Electronic Coupling
A Highly Selective Electrochemical DNA-Based Sensor That Employs Steric Hindrance Effects to Detect Proteins Directly in Whole Blood
Barrierless Photoisomerization of 11-cis Retinal Protonated Schiff Base in Solution
Tin(II) Sulfide (SnS) Nanosheets by Liquid-Phase Exfoliation of Herzenbergite: IV–VI Main Group Two-Dimensional Atomic Crystals
Controlled Release of an Anti-inflammatory Drug Using an Ultrasensitive ROS-Responsive Gas-Generating Carrier for Localized Inflammation Inhibition
Systematic noise degrades gene co-expression signals but can be corrected
2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib
STAP cells are derived from ES cells
STAP cells are derived from ES cells
Nature 525, 7570 (2015). doi:10.1038/nature15366
Authors: Daijiro Konno, Takeya Kasukawa, Kosuke Hashimoto, Takehiko Itoh, Taeko Suetsugu, Ikuo Miura, Shigeharu Wakana, Piero Carninci & Fumio Matsuzaki
arising fromH. Obokata et al.Nature505, 641–647 (2014) doi:10.1038/nature12968; retraction 511, 112 (2014) doi:10.1038/nature13598; and H. Obokata et al.Nature505, 676–680 (2014)
Failure to replicate the STAP cell phenomenon
Failure to replicate the STAP cell phenomenon
Nature 525, 7570 (2015). doi:10.1038/nature15513
Authors: Alejandro De Los Angeles, Francesco Ferrari, Yuko Fujiwara, Ronald Mathieu, Soohyun Lee, Semin Lee, Ho-Chou Tu, Samantha Ross, Stephanie Chou, Minh Nguyen, Zhaoting Wu, Thorold W. Theunissen, Benjamin E. Powell, Sumeth Imsoonthornruksa, Jiekai Chen, Marti Borkent, Vladislav Krupalnik, Ernesto Lujan, Marius Wernig, Jacob H. Hanna, Konrad Hochedlinger, Duanqing Pei, Rudolf Jaenisch, Hongkui Deng, Stuart H. Orkin, Peter J. Park & George Q. Daley
arising from H. Obokata et al.Nature505, 641–647 (2014) doi:10.1038/nature12968; retraction 511, 112 (2014) doi:10.1038/nature13598; and H. Obokata et al.Nature505, 676–680 (2014
The diurnal cycle of water ice on comet 67P/Churyumov–Gerasimenko
The diurnal cycle of water ice on comet 67P/Churyumov–Gerasimenko
Nature 525, 7570 (2015). doi:10.1038/nature14869
Authors: M. C. De Sanctis, F. Capaccioni, M. Ciarniello, G. Filacchione, M. Formisano, S. Mottola, A. Raponi, F. Tosi, D. Bockelée-Morvan, S. Erard, C. Leyrat, B. Schmitt, E. Ammannito, G. Arnold, M. A. Barucci, M. Combi, M. T. Capria, P. Cerroni, W.-H. Ip, E. Kuehrt, T. B. McCord, E. Palomba, P. Beck & E. Quirico
Observations of cometary nuclei have revealed a very limited amount of surface water ice, which is insufficient to explain the observed water outgassing. This was clearly demonstrated on comet 9P/Tempel 1, where the dust jets (driven by volatiles) were only partially correlated with the exposed ice regions. The observations of 67P/Churyumov–Gerasimenko have revealed that activity has a diurnal variation in intensity arising from changing insolation conditions. It was previously concluded that water vapour was generated in ice-rich subsurface layers with a transport mechanism linked to solar illumination, but that has not hitherto been observed. Periodic condensations of water vapour very close to, or on, the surface were suggested to explain short-lived outbursts seen near sunrise on comet 9P/Tempel 1. Here we report observations of water ice on the surface of comet 67P/Churyumov–Gerasimenko, appearing and disappearing in a cyclic pattern that follows local illumination conditions, providing a source of localized activity. This water cycle appears to be an important process in the evolution of the comet, leading to cyclical modification of the relative abundance of water ice on its surface.
htsint: a Python library for sequencing pipelines that combines data through gene set generation
Highly Regio- and Enantioselective Alkoxycarbonylative Amination of Terminal Allenes Catalyzed by a Spiroketal-Based Diphosphine/Pd(II) Complex
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
by Noah Ollikainen, René M. de Jong, Tanja Kortemme
Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.