Showing papers in "Structure in 2020"

TL;DR: The theoretical limits of accuracy when using established energy terms for scoring are explored, comparison with flexible docking algorithms are provided, and the historical performance of servers in the CAPRI docking experiment is reviewed.

TL;DR: In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARFAR2 recovers native-like structures more accurate than models submitted during the RNA- Puzzles trials, and preregistered blind models for adenovirus VA-I RNA and five riboswitch complexes predicted native- like folds with 3- to 14 Å root-mean-square deviation accuracies.

TL;DR: This work genetically and structurally characterized β-propiolactone-inactivated viruses from a propagated and purified clinical strain of SARS-CoV-2 and observed that the virus particles are roughly spherical or moderately pleiomorphic, thus resembling a postfusion state.

TL;DR: The enzyme active site cavity reveals a high degree of malleability, allowing aldehyde leupeptin and hepatitis C clinical protease inhibitors to bind and inhibit SARS-CoV-2 3CL Mpro.

TL;DR: It is shown in atomic detail that phalloidin, a mushroom toxin that is routinely used to stabilize and label actin filaments, suspends the structural changes in actin, likely influencing its interaction with actin-binding proteins.

TL;DR: A reimplementation of the Rama-Z score is described in the Computational Crystallography Toolbox along with an algorithm to estimate its uncertainty for individual models; final implementations are available in Phenix and PDB-REDO.

TL;DR: A general mode of recognition for phosphorylated Rab GTPases by this family of phospho-specific effector RILPL2 is proposed, which proposes that X-cap residues critical for pRab8a binding are conserved in JIP3 and JIP4, which also interact with LRRK2-phosphorylation Rab10.

TL;DR: The crystal and NMR structures of branched K11/K48-linked tri-ubiquitin are determined and a previously unobserved inter domain interface between the distal ubiquitins is discovered, suggesting a functional impact of this interdomain interface and pinpointing the mechanistic site of enhanced degradation.

TL;DR: It is demonstrated that reducing time between sample application and vitrification is just one tool to improve cryoEM grid quality, but that it is unlikely to be a generic “silver bullet” for improving the quality of everyCryoEM sample preparation.

TL;DR: This workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could be used for large-scale phenotypic studies of frozen-hydrated specimens in a variety of healthy and diseased conditions with and without treatments.

TL;DR: GemSpot is presented, an automated pipeline of computational chemistry methods that take into account EM map potentials, quantum mechanics energy calculations, and water molecule site prediction to generate candidate poses and provide a measure of the degree of confidence.

TL;DR: Two X-ray structures of human AQP7 at 1.9 and 2.2 Å resolution combined with molecular dynamics simulations suggest that AQP 7 is a channel selective for Glycerol and that glycerol may hamper water permeation through the channel.

TL;DR: It is demonstrated that massive T cell deformation and death are linked with PSM α3 aggregation and co-localization with cell membranes, and hypothesize that PSMα3 cytotoxicity is governed by the ability to form cross-α fibrils and involves a dynamic process of co-aggregation with the cell membrane, rupturing it.

TL;DR: Cryo-EM structures of AcRB and the AcrBZ complex in lipid environments are reported and comparisons suggest that conformational changes occur in the drug-binding pocket as a result of AcrZ binding, suggesting that AcRZ and lipid cooperate to allosterically modulate Acr B activity.

TL;DR: Glycan networks underpin the conservation of bnAb epitopes and are an important parameter in immunogen design and it is shown that the PG9 and PG16 glycan-based epitopes at the trimer apex are dependent on the presence of the highly conserved surrounding glycans.

TL;DR: It is investigated here how information about complementarity-determining regions and binding epitopes can be used to drive the modeling process, and a comparative study of four different docking software suites providing specific options for antibody-antigen modeling.

TL;DR: The results provide a structural basis for understanding the 3D configuration of CENP-A-containing chromatin, and may explain how centromeric proteins can specifically target the CENp-A nucleosome buried in robust amounts of H3 nucleosomes in centromeres.

TL;DR: It is shown that the death domains of human MyD88 spontaneously and reversibly associate to form helical filaments in vitro, suggesting that intracellularly, the MyD 88 scaffold may be pre-formed and poised for recruitment of IRAKs on receptor activation and TIR engagement.

TL;DR: It is proposed that this workflow provides a decision-free solution for cryo-EM, making data preprocessing more generalized and robust in the high-throughput era as well as more convenient for users from a range of backgrounds.

TL;DR: The crystal structure of human AT2R bound to AngII and its specific antibody at 3.2-Å resolution is solved and will inform the design of more effective ligands for ATRs.

TL;DR: Novel atomic and interactomic insights are provided into phosphorylatable dual specificity motifs and the differential effects of phosphorylation and phosphomimetic approaches and the structural basis of PBM capture by 14-3-3 proteins are elucidated.

TL;DR: The protocol developed in this work provides a means to refine open-like structures of the whole pentameric ligand-gated ion channel superfamily and reconciles the previous issues with the cryo-EM structure.

TL;DR: An ensemble model of httex1 was derived that identified both flanking regions as opposing poly-Q secondary structure promoters and showed that these structural traits are present in many human glutamine-rich proteins and that they are more prevalent in proteins with longerpoly-Q tracts.

TL;DR: The data suggest the metazoan retromer is an adaptable and plastic scaffold that accommodates interactions with different sorting nexins to sort multiple cargoes from endosomes their final destinations.

TL;DR: A 2.3-Å crystal structure of βarr2 in complex with a phosphopeptide (C7pp) derived from the carboxyl terminus of CXCR7 is presented and key differences from the previously determined active conformation ofβarr1 are revealed.

TL;DR: Single-molecule fluorescence spectroscopy with the β2-adrenergic receptor in the ligand-free state showed that TM VII spontaneously fluctuates between one inactive and one active-like conformation, suggesting that ligands can induce signaling bias by modulating the kinetics of receptor conformational exchange.

TL;DR: Cryoelectron microscopy analysis of the structure of insulin-like growth factor II bound to a leucine-zipper-stabilized IGF-1R ectodomain reveals long-suspected differences in the way in which the critical C domain of the respective growth factors interact with IGF- 1R.

TL;DR: The structure of Tel1 is presented using cryoelectron microscopy and molecular details of key residues surrounding the nucleotide binding site are revealed, which provides a structural and molecular basis for its intrinsically low basal activity.

TL;DR: Stability prediction tools often favor mutations that increase stability at the expense of solubility, and making multiple mutations markedly improves the prospects for achieving a stabilization target, and modest improvements in the precision of future tools may yield disproportionate gains.

TL;DR: This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Cross-linking MS for which guidelines should be developed as part of a Cross- linking MS standards initiative.