Journal Articles
Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase
Large-Volume Self-Organization of Polymer/Nanoparticle Hybrids with Millimeter-Scale Grain Sizes Using Brush Block Copolymers
CH Bond Activation of Methane by a Transient η2-Cyclopropene/Metallabicyclobutane Complex of Niobium
Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11
We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy
Interactions between proteins and other molecules play essential roles in all biological processes. Although it is widely held that a protein's ligand specificity is determined primarily by its three-dimensional structure, the general principles by which structure determines ligand binding remain poorly understood. Here we use statistical analyses of a large number of protein−ligand complexes with associated binding-affinity measurements to quantitatively characterize how combinations of atomic interactions contribute to ligand affinity. We find that there are significant differences in how atomic interactions determine ligand affinity for proteins that bind small chemical ligands, those that bind DNA/RNA and those that interact with other proteins. Although protein-small molecule and protein-DNA/RNA binding affinities can be accurately predicted from structural data, models predicting one type of interaction perform poorly on the others. Additionally, the particular combinations of atomic interactions required to predict binding affinity differed between small-molecule and DNA/RNA data sets, consistent with the conclusion that the structural bases determining ligand affinity differ among interaction types. In contrast to what we observed for small-molecule and DNA/RNA interactions, no statistical models were capable of predicting protein−protein affinity with >60% correlation. We demonstrate the potential usefulness of protein-DNA/RNA binding prediction as a possible tool for high-throughput virtual screening to guide laboratory investigations, suggesting that quantitative characterization of diverse molecular interactions may have practical applications as well as fundamentally advancing our understanding of how molecular structure translates into function. Proteins 2015; 83:2100–2114. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Chiral Cationic CpxRu(II) Complexes for Enantioselective Yne-Enone Cyclizations
Chemoenzymatic Assembly of Bacterial Glycoconjugates for Site-Specific Orthogonal Labeling
Structural Adaptability Facilitates Histidine Heme Ligation in a Cytochrome P450
Subtype prediction in pediatric acute myeloid leukemia: classification using differential network rank conservation revisited
How Does Confinement Change Ligand–Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels
Pressure Modulation of the Enzymatic Activity of Phospholipase A2, A Putative Membrane-Associated Pressure Sensor
Erratum: Mechanism of phospho-ubiquitin-induced PARKIN activation
Erratum: Mechanism of phospho-ubiquitin-induced PARKIN activation
Nature 526, 7575 (2015). doi:10.1038/nature15531
Authors: Tobias Wauer, Michal Simicek, Alexander Schubert & David Komander
Nature524, 370–374 (2015); doi:10.1038/nature14879The print and PDF versions of this Letter are correct, but the wrong HTML versions of Figs 1–4 and ED Figs 1–10 were used initially, owing to an in-house error; these have been
Corrigendum: Cleavage of CAD inhibitor in CAD activation and DNA degradation during apoptosis
Corrigendum: Cleavage of CAD inhibitor in CAD activation and DNA degradation during apoptosis
Nature 526, 7575 (2015). doi:10.1038/nature15532
Authors: Hideki Sakahira, Masato Enari & Shigekazu Nagata
Nature391, 96–99 (1998); doi:10.1038/34214Recently, it has come to our attention that in Fig. 1a of this Letter, lanes 1 and 5 appear to be duplicated and lanes 6 and 10 appear to be duplicated. It is
Erratum: IgG1 protects against renal disease in a mouse model of cryoglobulinaemia
Erratum: IgG1 protects against renal disease in a mouse model of cryoglobulinaemia
Nature 526, 7575 (2015). doi:10.1038/nature15534
Authors: Richard T. Strait, Monica T. Posgai, Ashley Mahler, Nathaniel Barasa, Chaim O. Jacob, Jörg Köhl, Marc Ehlers, Keith Stringer, Shiva Kumar Shanmukhappa, David Witte, Md Monir Hossain, Marat Khodoun, Andrew B. Herr & Fred D. Finkelman
Nature517, 501–504 (2015); doi:10.1038/nature13868Owing to a production error, in Fig. 1b of this Letter, the key should have shown that the black bars corresponded to ‘WT’ and the red bars to ‘γ1−’, instead of
Power play
Power play
Nature 525, 7570 (2015). doi:10.1038/525425b
The replacement of mitochondria does not signal ethical problems.
STAP revisited
STAP revisited
Nature 525, 7570 (2015). doi:10.1038/525426a
Reanalysis of the controversy provides a strong example of the self-correcting nature of science.
Make academic job advertisements fair to all
Make academic job advertisements fair to all
Nature 525, 7570 (2015). http://www.nature.com/doifinder/10.1038/525427a
Author: Mathias Wullum Nielsen
Too many university posts are given to men without proper competition, says Mathias Wullum Nielsen.
Planetary science: Global ocean on Enceladus
Planetary science: Global ocean on Enceladus
Nature 525, 7570 (2015). doi:10.1038/525428a
Beneath an icy crust, Saturn's moon Enceladus (pictured) has an ocean that covers its entire globe.NASA's Cassini spacecraft measured wobbles in Enceladus's rotation over more than seven years. The data confirm that the crust is moving separately from the rocky core, meaning that there