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Journal of Molecular Biology

Badreddine Douzi, Laureen Logger, Silvia Spinelli, Stéphanie Blangy, Christian Cambillau, Eric Cascales
The Type VI secretion system (T6SS) is a specialized macromolecular complex dedicated to the delivery of protein effectors into both eukaryotic and bacterial cells. The general mechanism of action of the T6SS is similar to the injection of DNA by contractile bacteriophages. The cytoplasmic portion of the T6SS is evolutionarily, structurally and functionally related to the phage tail complex. It is composed of an inner tube made of stacked Hcp hexameric rings, engulfed within a sheath and built on a baseplate...
December 6, 2017: Journal of Molecular Biology
Moritz M Gaidt, Veit Hornung
NLRP3 is the most studied inflammasome sensor due to its crucial involvement in sterile and infection-triggered inflammation. Although its molecular mode of activation remains to be defined, it is well established that low intracellular potassium concentrations result in its activation. This functionality allows the classical NLRP3 pathway to serve as a highly sensitive, but non-specific surveillance mechanism responding to any type of perturbation that breaches plasma membrane integrity and the associated potassium-gradient across the membrane...
December 1, 2017: Journal of Molecular Biology
Darius Kazlauskas, Guennadi Sezonov, Nicole Charpin, Česlovas Venclovas, Patrick Forterre, Mart Krupovic
Cellular organisms in different domains of life employ structurally unrelated, non-homologous DNA primases for synthesis of a primer for DNA replication. Archaea and eukaryotes encode enzymes of the archaeo-eukaryotic primase (AEP) superfamily, whereas bacteria uniformly use primases of the DnaG family. However, AEP genes are widespread in bacterial genomes raising questions regarding their provenance and function. Here, using an archaeal primase-polymerase PolpTN2 encoded by pTN2 plasmid as a seed for sequence similarity searches, we recovered over 800 AEP homologs from bacteria belonging to twelve highly diverse phyla...
November 30, 2017: Journal of Molecular Biology
Christophe Bignon, Francesca Troilo, Stefano Gianni, Sonia Longhi
Intrinsically disordered proteins (IDPs) recognize their partners through molecular recognition elements (MoREs). The MoRE of the C-terminal intrinsically disordered domain of the measles virus nucleoprotein (NTAIL) is partly pre-configured as an α-helix in the free form and undergoes α-helical folding upon binding to the X domain (XD) of the viral phosphoprotein. Beyond XD, NTAIL also binds the major inducible heat shock protein 70 (hsp70). So far, no structural information is available for the NTAIL/hsp70 complex...
November 29, 2017: Journal of Molecular Biology
Yao Fang, Xiao Xiao, Shuxing Li, Aaron Wolfe, Xiaojiang S Chen
The single-stranded DNA (ssDNA) cytidine deaminase APOBEC3F (A3F) deaminates cytosine (C) to uracil (U) and is a known restriction factor of HIV-1. Its C-terminal catalytic domain (CD2) alone is capable of binding single-stranded nucleic acids and is important for deamination. However, little is known about how the CD2 interacts with single-stranded DNA (ssDNA). Here we report a crystal structure of A3F-CD2 in complex with a 10 nucleotide (nt) ssDNA composed of poly-thymine, which reveals a novel positively-charged nucleic acid binding site distal to the active center that plays a key role in substrate DNA binding and catalytic activity...
November 27, 2017: Journal of Molecular Biology
Ryan L Kelly, Doris Le, Jessie Zhao, K Dane Wittrup
Successful antibody development requires both functional binding and desirable biophysical characteristics. In the current study we analyze the causes of one hurdle to clinical development, off-target reactivity or nonspecificity. We used a high-throughput nonspecificity assay to isolate panels of nonspecific antibodies from two synthetic scFv libraries expressed on the surface of yeast, identifying both individual amino acids and motifs within the complementarity determining regions (CDRs) which contribute to the phenotype...
November 25, 2017: Journal of Molecular Biology
Pedro F Teixeira, Geoffrey Masuyer, Catarina M Pinho, Rui M M Branca, Beata Kmiec, Cecilia Wallin, Sebastian K T S Wärmländer, Ronnie P-A Berntsson, Maria Ankarcrona, Astrid Gräslund, Janne Lehtiö, Pål Stenmark, Elzbieta Glaser
Proteolysis plays an important role in mitochondrial biogenesis, from the processing of newly imported precursor proteins to the degradation of mitochondrial targeting peptides. Disruption of peptide degradation activity in yeast, plant and mammalian mitochondria is known to have deleterious consequences for organism physiology, highlighting the important role of mitochondrial peptidases. In the present work, we show that the human mitochondrial peptidase neurolysin (hNLN) can degrade mitochondrial presequence peptides as well as other fragments up to 19 amino acids long...
November 25, 2017: Journal of Molecular Biology
Daniel L Winter, Gene Hart-Smith, Marc R Wilkins
Protein methylation is one of the major post-translational modifications (PTMs) in the cell. In Saccharomyces cerevisiae, over twenty protein methyltransferases (MTases) and their respective substrates have been identified. However, the way in which these MTases are modified, and potentially subject to regulation, remains poorly understood. Here, we investigated six overexpressed S. cerevisiae protein MTases (Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1) to identify PTMs of potential functional relevance. We identified 48 PTM sites across the six MTases, including phosphorylation, acetylation and methylation...
November 25, 2017: Journal of Molecular Biology
Nikolai N Sluchanko
14-3-3 proteins are well-known universal regulators binding a vast number of partners by recognizing their phosphorylated motifs, typically located within the intrinsically disordered regions (IDRs). The abundance of such phosphomotifs ensures the involvement of 14-3-3 proteins in sophisticated protein-protein interaction networks that govern vital cellular processes. Thousands of 14-3-3 partners have been either experimentally identified or predicted, but the spatiotemporal hierarchy of the processes based on 14-3-3 interactions is not clearly understood...
November 24, 2017: Journal of Molecular Biology
Stephanie Seveau, Joanne Turner, Mikhail A Gavrilin, Jordi B Torrelles, Luanne Hall-Stoodley, Jacob Yount, Amal O Amer
Autophagy and inflammasome complex assembly are physiological processes that control homeostasis, inflammation, and immunity. Autophagy is a ubiquitous pathway that degrades cytosolic macromolecules or organelles, as well as intracellular pathogens. Inflammasomes are multi-protein complexes that assemble in the cytosol of cells upon detection of pathogen- or danger-associated molecular patterns. A critical outcome of inflammasome assembly is the activation of the serine protease caspase-1, which activates the pro-inflammatory cytokine precursors pro-IL-1β and pro-IL-18...
November 18, 2017: Journal of Molecular Biology
Sangmi Lee, Dale E A Lewis, Sankar Adhya
Bacteriophage λ of Escherichia coli has two alternative life cycles after infection-host survival with lysogen formation, or host lysis and phage production. In a lysogen, CI represses the two lytic promoters, pR and pL, and activates its own transcription from the auto-regulated pRM promoter. During induction from the lysogenic to lytic state, CI is inactivated, and the two lytic promoters are de-repressed allowing expression of Cro from pR. Cro is known to repress transcription of CI from pRM to prevent lysogeny...
November 17, 2017: Journal of Molecular Biology
Roman Sloutsky, Kristen M Naegle
No abstract text is available yet for this article.
November 13, 2017: Journal of Molecular Biology
Ivan Andreas Stancik, Martin Sebastijan Šestak, Boyang Ji, Marina Axelson-Fisk, Damjan Franjevic, Carsten Jers, Tomislav Domazet-Lošo, Ivan Mijakovic
The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988. It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim...
November 11, 2017: Journal of Molecular Biology
Loïc Salmon, Frederick Stull, Sabrina Sayle, Claire Cato, Şerife Akgül, Linda Foit, Logan S Ahlstrom, Elan Z Eisenmesser, Hashim M Al-Hashimi, James C A Bardwell, Scott Horowitz
HdeA is a periplasmic chaperone that is rapidly activated upon shifting the pH to acidic conditions. This activation is thought to involve monomerization of HdeA. There is evidence that monomerization and partial unfolding allow the chaperone to bind to proteins denatured by low pH thereby protecting them from aggregation. We analyzed the acid-induced unfolding of HdeA using NMR spectroscopy and fluorescence measurements, and obtained experimental evidence suggesting a complex mechanism in HdeA's acid-induced unfolding pathway, as previously postulated from molecular dynamics simulations...
November 11, 2017: Journal of Molecular Biology
Menglong Zeng, Fei Ye, Jia Xu, Mingjie Zhang
DLG MAGUKs are abundantly expressed in glutamatergic synapses, crucial for synaptic transmission and plasticity by anchoring various postsynaptic components including glutamate receptors, downstream scaffold proteins and signaling enzymes. Different DLG members have shared structures and functions, but also contain unique features. How DLG family proteins function individually and cooperatively are largely unknown. Here, we report that PSD-95 PDZ3 directly couples with SH3-GK tandem in a PDZ ligand binding-dependent manner, and the coupling can promote PSD-95 dimerization and multimerization...
November 11, 2017: Journal of Molecular Biology
Georg Krainer, Andreas Hartmann, Abhinaya Anandamurugan, Pablo Gracia, Sandro Keller, Michael Schlierf
Proteins fold on timescales from hours to microseconds. In addition to protein size, sequence, and topology, the environment represents an equally important factor in determining folding speed. This is particularly relevant for proteins that require a lipid membrane or a membrane mimic to fold. However, only little is known about how properties of such a hydrophilic/hydrophobic interface modulate the folding landscape of membrane-interacting proteins. Here, we studied the influence of different membrane-mimetic micellar environments on the folding and unfolding kinetics of the helical-bundle protein Mistic...
November 8, 2017: Journal of Molecular Biology
May Daher, Julia R Widom, Wendy Tay, Nils G Walter
Living cells contain diverse biopolymers, creating a heterogeneous crowding environment, the impact of which on RNA folding is poorly understood. Here, we have used single-molecule fluorescence resonance energy transfer to monitor tertiary structure formation of the hairpin ribozyme as a model to probe the effects of polyethylene glycol (PEG) and yeast cell extract as crowding agents. As expected, PEG stabilizes the docked, catalytically active state of the ribozyme, in part through excluded volume effects; unexpectedly, we found evidence that it additionally displays soft, non-specific interactions with the ribozyme...
November 8, 2017: Journal of Molecular Biology
Yufan Wu, Annemarie Honegger, Alexander Batyuk, Peer R E Mittl, Andreas Plückthun
To untangle the complex signaling of the c-Jun N-terminal kinase (JNK) isoforms we need tools which can selectively detect and inhibit individual isoforms. Because of the high similarity between JNK1, JNK2 and JNK3, it is very difficult to generate small-molecule inhibitors with this discriminatory power. Thus, we have recently selected protein binders from the designed ankyrin repeat protein (DARPin) library which were indeed isoform-specific inhibitors of JNK1 with low nanomolar potency. Here we provide the structural basis for their isotype discrimination and their inhibitory action...
November 7, 2017: Journal of Molecular Biology
Timothy D Frouws, Philip D Barth, Timothy J Richmond
We engineered nucleosome core particles (NCPs) with two site-specific cysteine crosslinks that increase the stability of the particle. The first disulfide was introduced between the two copies of H2A via a H2A-N38C point mutation, effectively crosslinking the two H2A/H2B heterodimers together to stabilize the histone octamer against H2A/H2B dimer dissociation. The second crosslink was engineered between a R40C point mutation on the N-terminal tail of H3 and the NCP DNA ends by the introduction of a convertible nucleotide...
November 4, 2017: Journal of Molecular Biology
Vitaliya Sagulenko, Nazarii Vitak, Parimala Vajjhala, James E Vince, Katryn J Stacey
Canonical inflammasomes are multiprotein complexes that can activate both caspase-1 and caspase-8. Caspase-1 drives rapid lysis of cells by pyroptosis and maturation of IL-1β and IL-18. In caspase-1-deficient cells, inflammasome formation still leads to caspase-3 activation and slower apoptotic death, dependent on caspase-8 as an apical caspase. A role for caspase-8 directly upstream of caspase-1 has also been suggested, but here we show that caspase-8-deficient macrophages have no defect in AIM2 inflammasome-mediated caspase-1 activation, pyroptosis and IL-1β release...
October 31, 2017: Journal of Molecular Biology
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