A protein export pathway involving Escherichia coli porins

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Highlights? The porin OmpF is a required element for the secretion of YebF ? YebF interacts with OmpF and OmpC channels at their periplasmic face ? YebF exhibits a dynamic surface that is involved in the secretion process ? Proposed model of YebF secretion mediated by OmpF     

Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor

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Highlights? Bacteriophytochrome structure containing photosensory and output transducing domain ? RpBphP1 binds to the cognate repressor RpPpsR2 on illumination with far-red light ? HOS domain is distantly related to Dhp and is essential for binding to the repressor ? Light-induced protomer swapping mechanism between dimers     

Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection

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Highlights? Complexes of MetRS from T. brucei with its substrate, intermediate, and inhibitors ? In crystals, substrate-bound MetRS undergoes extensive changes with inhibitor binding ? The inhibitor-bound conformation is surprisingly similar to the ligand-free state ? This indicates inhibitor binding occurs via conformational selection not by induced fit     

DAD2 Is an α/β Hydrolase Likely to Be Involved in the Perception of the Plant Branching Hormone,Strigolactone

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Highlights? DAD2 gene, identified by transposon tagging, encodes an α/β hydrolase fold protein ? DAD2 acts in the shoot; mutants are insensitive to strigolactones ? DAD2 crystal structure shows an internal cavity capable of binding strigolactones ? DAD2 can hydrolyze the strigolactone GR24     

Structure of AAV-DJ, a Retargeted Gene Therapy Vector: Cryo-Electron Microscopy at 4.5 Å Resolution

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Highlights? The 4.5 Å cryo-EM structure of AAV-DJ fully resolves the polypeptide backbone ? Liver tropism selected for in AAV-DJ has not changed the heparin binding site ? Changed conformation in an antigenic loop blocks binding of a neutralizing mAb ? Changed in vivo tropism may result from changed immune interactions     

An Autoinhibited State in the Structure of Thermotoga maritima NusG

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Highlights? Thermotoga maritima NusG shows a dynamic intramolecular NTD-CTD interaction ? The NTD-CTD interaction hides the binding surfaces for RNA polymerase, S10, and Rho ? Domain interaction contributes to thermostability ? Thermotoga maritima NusG does not complement a NusG-deficient E. coli strain     

Host cell autophagy activated by antibiotics is required for their effective antimycobacterial drug action

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Highlights? Antimycobacterial antibiotics activate autophagy in Mtb-infected host cells ? Autophagy activation depends on cellular and mitochondrial reactive oxygen species ? Host cell autophagy is essential for antimycobacterial drug action in infected macrophages and flies ? Antibiotic-induced autophagy dampened proinflammatory responses in infected macrophages     

Finding Protein Targets for Small Biologically Relevant Ligands across Fold Space Using Inverse Ligand Binding Predictions

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Highlights? Inverse ligand binding prediction is implemented with modern binding site predictors ? Use of just one protein-ligand complex allows accurate identification of other protein targets ? Inverse prediction is effective in finding structurally distant protein targets ? Consensus approach provides improvements     

Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement

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Highlights? A protein-ligand binding method combining structure and evolutionary insights ? Large-scale test and validation on both benchmark and blind experiments ? Comprehensive and deep analysis on what works and what does not ? Ligand binding prediction with accuracy higher than the state-of-the-art methods     

Targeting the Cell Wall of Mycobacterium tuberculosis: Structure and Mechanism of L,D-Transpeptidase 2

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Highlights? The structure of Mtb Ldt_Mt2 shows the binding of a peptidoglycan fragment ? The structure of the complex maps the interaction between acyl donor and enzyme ? Ldts show a conserved C-terminal ykuD domain with a divergent N-terminal domain ? Based on the structure of this complex, a reaction mechanism is proposed     

Organism-Scale Modeling of Early Drosophila Patterning via Bone Morphogenetic Proteins

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Highlights? Capturing 3D spatiotemporal content of expression data increases model utility ? Embryo geometry shapes signaling; prepatterns compensate in misshapen embryos ? Cell-surface binding proteins compensate for weak ligand/inhibitor/receptor binding ? BMP-mediated patterning is “nearly” scale-invariant     

Leukemia Fusion Target AF9 Is an Intrinsically Disordered Transcriptional Regulator that Recruits Multiple Partners via Coupled Folding and Binding

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Highlights? The AF9 AHD is intrinsically disordered ? The AHD recruits AF4, BCoR, Dot1L, and hPC3 by coupled folding and binding ? AF9 binding partners compete for binding to a common site ? Dynamics of the AF4-AF9 complex may facilitate exchange between partners     

Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly

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Highlights? Initial nucleotide binding occurs in the open polymerase complex ? Correct and incorrect nucleotides undergo metal-dependent conformational changes ? Watson-Crick base pairing is sampled upon nucleotide binding ? The stabilization of the correct, but not incorrect, nucleotide deters misinsertion     

Structures of adnectin/protein complexes reveal an expanded binding footprint

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Highlights? Adnectins interact with targets using multiple binding modes ? Residues outside of the diversified loops can interact with ligand ? Some fixed scaffold residues contribute to the binding energy ? Adnectins can interact with epitopes that may be inaccessible to antibodies     

Solution Conformations of Prototype Foamy Virus Integrase and Its Stable Synaptic Complex with U5 Viral DNA

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Highlights? Missing domains in PFV intasome revealed by SAXS/SANS ? PFV IN undergoes dramatic changes in conformation and oligomerization upon binding DNA ? Strand transfer inhibitors do not alter quaternary structure of PFV intasome     

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

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Highlights? The gut microbiome is highly active, similar to nutrient-rich productive systems ? Firmicutes dominate the active and damaged subsets of the gut microbiome ? Both antibiotics and host-targeted drugs rapidly alter the active gut microbiome ? Xenobiotics induce genes for drug metabolism, drug resistance, and stress response     

Design of a Phosphorylatable PDZ Domain with Peptide-Specific Affinity Changes

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Highlights? Successful design of phosphorylation sites into a globular protein ? Redesigned PDZ domain phosphorylation is associated with local destabilization ? Phosphorylation switches peptide binding function ? Phosphorylation switches peptide recognition specificity     

Structural and functional analysis of HtrA1 and its subdomains

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Highlights? IGFBP-like domain structure suggests that it is incompetent for IGF binding ? Kazal-like domain structure shows distorted “P1” loop incompetent for inhibition ? Protease domain shows catalytic readiness in apo form ? SAXS envelope for full-length HtrA1     

The Crystal Structures of the Eukaryotic Chaperonin CCT Reveal Its Functional Partitioning

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Highlights? CCT subunit types can be identified in crystallographic data, even at low resolutions ? Actin and tubulin both bind around CCT6 ? ATP hydrolysis and substrate binding are partitioned in the CCT particle