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Journal of Molecular Biology

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https://www.readbyqxmd.com/read/30419243/structural-variability-of-espg-chaperones-from-mycobacterial-esx-1-esx-3-and-esx-5-type-vii-secretion-systems
#1
Anne T Tuukkanen, Diana Freire, Sum Chan, Mark A Arbing, Robert W Reed, Timothy J Evans, Grasilda Zenkeviciutė, Jennifer Kim, Sara Kahng, Michael R Sawaya, Catherine T Chaton, Matthias Wilmanns, David Eisenberg, Annabel H A Parret, Konstantin V Korotkov
Type VII secretion systems (ESX) are responsible for transport of multiple proteins in mycobacteria. How different ESX systems achieve specific secretion of cognate substrates remains elusive. In the ESX systems, the cytoplasmic chaperone EspG forms complexes with heterodimeric PE-PPE substrates that are secreted from the cells or remain associated with the cell surface. Here we report the crystal structure of the EspG1 chaperone from the ESX-1 system determined using a fusion strategy with T4 lysozyme. EspG1 adopts a quasi 2-fold symmetric structure that consists of a central β-sheet and two α-helical bundles...
November 9, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30419242/biovisualization-of-the-genome-from-data-analysis-and-hypothesis-generation-to-communication-and-learning
#2
REVIEW
Mike N Goodstadt, Marc A Marti-Renom
Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space...
November 9, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414967/a-membrane-protein-complex-docking-benchmark
#3
Panagiotis I Koukos, Inge Faro, Charlotte W van Noort, Alexandre M J J Bonvin
We report the first membrane protein-protein docking benchmark consisting of 37 targets of diverse functions and folds. The structures were chosen based on a set of parameters such as the availability of unbound structures, the modelling difficulty and their uniqueness. They have been cleaned and consistently numbered to facilitate their use in docking. Using this benchmark, we establish the baseline performance of HADDOCK, without any specific optimization for membrane proteins, for two scenarios: True interface-driven docking and ab-initio docking...
November 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414966/contacts-in-death-the-role-of-the-er-mitochondria-axis-in-acetic-acid-induced-apoptosis-in-yeast
#4
Vítor M Martins, Tânia R Fernandes, Catarina B Afonso, Diana Lopes, Maria R M Domingues, Manuela Côrte-Real, Maria J Sousa
Endoplasmic reticulum-mitochondria contact sites (ER-MCS) have been a subject of increasing scientific interest since the discovery that these structures are disrupted in several pathologies. Due to the emerging data that correlates ER-MCS function to known events of the apoptotic program, we aimed to dissect this interplay using our well-established model of acetic acid-induced apoptosis in Saccharomyces cerevisiae. Until recently, the only known tethering complex between ER and mitochondria in this organism was the ER-mitochondria encounter structure (ERMES)...
November 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414965/biochemical-studies-provide-insights-into-the-necessity-for-multiplearabidopsis-thalianaprotein-only-rnase-p-isoenzymes
#5
Tien-Hao Chen, Marcos Sotomayor, Venkat Gopalan
RNase P catalyzes removal of the 5' leader from precursor tRNAs (pre-tRNAs) in all three domains of life. Some eukaryotic cells contain multiple forms of the protein-only RNase P (PRORP) variant, prompting efforts to unravel this seeming redundancy. Previous studies concluded that there were only modest differences in the processing of typical pre-tRNAs by the three isoforms inArabidopsis thaliana[AtPRORP1 (organellar), AtPRORP2 and AtPRORP3 (nuclear)]. Here, we investigated if different physical attributes of the three isoforms might engender payoffs under specific conditions...
November 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414964/controlling-liquid-liquid-phase-separation-of-cold-adapted-crystallin-proteins-from-the-antarctic-toothfish
#6
Jan C Bierma, Kyle W Roskamp, Aaron P Ledray, Andor J Kiss, C-H Christina Cheng, Rachel W Martin
Liquid-liquid phase separation (LLPS) of proteins is important to a variety of biological processes both functional and deleterious, including the formation of membraneless organelles, molecular condensations that sequester or release molecules in response to stimuli, and the early stages of disease-related protein aggregation. In the protein-rich, crowded environment of the eye lens, LLPS manifests as cold cataract. We characterize the LLPS behavior of six structural γ-crystallins from theeye lens of the Antarctic toothfish Dissostichus mawsoni, whose intact lenses resist cold cataract in subzero waters...
November 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414963/rna-mediated-dimerization-of-the-human-deoxycytidine-deaminase-apobec3h-influences-enzyme-activity-and-interaction-with-nucleic-acids
#7
Yuqing Feng, Lai Wong, Michael Morse, Ioulia Rouzina, Mark C Williams, Linda Chelico
Human APOBEC3H is a single-stranded (ss)DNA deoxycytidine deaminase that inhibits replication of retroelements and HIV-1 in CD4+ T cells. When aberrantly expressed in lung or breast tissue APOBEC3H can contribute to cancer mutagenesis. These different activities are carried out by different haplotypes of APOBEC3H. Here we studied APOBEC3H haplotype II, which is able to restrict HIV-1 replication and retroelements. We determined how the dimerization mechanism, which is mediated by a double-stranded RNA molecule, influenced interactions with and activity on ssDNA...
November 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414962/the-antibody-light-chain-linker-regulates-domain-orientation-and-amyloidogenicity
#8
Benedikt Weber, Manuel Hora, Pamina Kazman, Christoph Göbl, Carlo Camilloni, Bernd Reif, Johannes Buchner
The antibody light chain (LC) consists of two domains and is essential for antigen binding in mature immunoglobulins. The two domains are connected by a highly conserved linker which comprises the structurally important Arg108 residue. In antibody light chain (AL) amyloidosis, a severe protein amyloid disease, the LC and its N-terminal variable domain (VL ) convert to fibrils deposited in the tissues causing organ failure. Understanding the factors shaping the architecture of the LC, is important for basic science, biotechnology and for deciphering the principles that lead to fibril formation...
November 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414407/hiv-1-protease-uses-bi-specific-s2-s2-subsites-to-optimize-cleavage-of-two-classes-of-target-sites
#9
Marc Potempa, Sook-Kyung Lee, Nese KurtYilmaz, Ellen A Nalivaika, Amy Rogers, Ean Spielvogel, Charles W Carter, Celia A Schiffer, Ronald Swanstrom
Retroviral proteases (PR) have a unique specificity that allows cleavage of sites with or without a P1' proline. A P1' proline is required at the MA/CA cleavage site due to its role in a post-cleavage conformational change in the capsid protein. However, the HIV-1 PR prefers to have large hydrophobic amino acids flanking the scissile bond, suggesting PR recognizes two different classes of substrate sequences. We analyzed the cleavage rate of over 150 combinations of six different HIV-1 cleavage sites to explore rate determinants of cleavage...
November 7, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30414406/cooperative-dna-binding-of-the-plasmid-partitioning-protein-tubr-from-the-bacillus-cereus-pxo1-plasmid
#10
Ikuko Hayashi, Takashi Oda, Mamoru Sato, Sotaro Fuchigami
Tubulin/FtsZ-like GTPase TubZ is responsible for maintaining the stability of pXO1-like plasmids in virulent Bacilli. TubZ forms a filament in a GTP-dependent manner, and like other partitioning systems of low-copy-number plasmids, it requires the centromere-binding protein TubR that connects the plasmid to the TubZ filament. Systems regulating TubZ partitioning have been identified in Clostridium prophages as well as virulent Bacillus species, in which TubZ facilitates partitioning by binding and towing the segrosome: the nucleoprotein complex composed of TubR and the centromere...
November 7, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30412706/an-n-terminal-extension-to-uba5-adenylation-domain-boosts-ufm1-activation-isoform-specific-differences-in-ubiquitin-like-protein-activation
#11
Nadine Soudah, Prasanth Padala, Fouad Hassouna, Manoj Kumar, Bayan Mashahreh, Andrey A Lebedev, Michail N Isupov, Einav Cohen-Kfir, Reuven Wiener
Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding, but also affects how the adenylation domain interacts with ATP...
November 6, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30391297/proteins-knotty-problems
#12
Aleksandra I Jarmolinska, Agata P Perlinska, Robert Runkel, Benjamin Trefz, Helen M Ginn, Peter Virnau, Joanna I Sulkowska
Knots in proteins are increasingly being recognized as an important structural concept, and the folding of these peculiar structures still poses considerable challenges. From a functional point of view, most protein knots discovered so far are either enzymes or DNA-binding proteins. Our comprehensive topological analysis of the Protein Data Bank reveals several novel structures including knotted mitochondrial proteins and the most deeply embedded protein knot discovered so far. For the latter we propose a novel folding pathway based on the idea that a loose knot forms at a terminus and slides to its native position...
October 31, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30342933/differential-activities-of-dna-polymerases-in-processing-ribonucleotides-during-dna-synthesis-in-archaea
#13
Mélanie Lemor, Ziqing Kong, Etienne Henry, Raphaël Brizard, Sébastien Laurent, Audrey Bossé, Ghislaine Henneke
Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex...
October 31, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30389436/the-two-component-system-zrapsr-is-a-novel-esr-that-contributes-to-intrinsic-antibiotic-tolerance-in-escherichia-coli
#14
Kévin Rome, Céline Borde, Raleb Taher, Erwan Gueguen, Eve De Rosny, Agnès Rodrigue
During their lifecycle bacteria are exposed to continuous changes in their environment, some of which are stressful and can be harmful. The cell envelope is the first line of defense against a hostile environment but it is also the first target for damage. To deal with this problem, bacteria have evolved systems collectively called "Envelope Stress Response" or ESR, dedicated to the detection and repair of damaged components. Here we decided to investigate whether the atypical two-component system ZraP-SR is a novel ESR...
October 30, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30389435/elamipretide-promotes-mitophagosome-formation-and-prevents-its-reduction-induced-by-nutrient-excess-in-ins1-%C3%AE-cells
#15
Anton Petcherski, Kyle M Trudeau, Dane M Wolf, Mayuko Segawa, Jennifer Lee, Evan P Taddeo, Jude T Deeney, Marc Liesa
Elamipretide is a tetrapeptide that restores defects in mitochondrial function, binds to cardiolipin and is being tested in clinical trials for mitochondria-related diseases. However, whether Elamipretide modulates mitochondrial quality control and dynamics, processes essential to preserve mitochondrial function, is unclear. Thus, we tested the effects of Elamipretide on mitochondrial morphology, mitophagosome formation and their early disruption induced by excess nutrients in INS1 β-cells. Elamipretide treatment was sufficient to increase engulfment of mitochondria into autophagosomes in control INS1 β-cells, without inducing widespread changes in mitochondrial morphology or membrane potential...
October 30, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30385240/mitochondrial-dna-purifying-selection-in-mammals-and-invertebrates
#16
REVIEW
Jonathan M Palozzi, Swathi P Jeedigunta, Thomas R Hurd
Numerous mitochondrial quality control mechanisms exist within cells, but none have been shown to effectively assess and control the quality of mitochondrial DNA (mtDNA). One reason such mechanisms have yet to be elucidated is that they do not appear to be particularly active in most somatic cells, where many studies are conducted. The female germline, the cell lineage that gives rise to eggs, appears to be an exception. In the germline, strong purifying selection pathways act to eliminate deleterious mtDNA...
October 29, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30381149/conformational-flexibility-of-ubiquitin-modified-and-sumo-modified-pcna-shown-by-full-ensemble-hybrid-methods
#17
Kyle T Powers, Emily D Lavering, M Todd Washington
Ubiquitin-modified PCNA (Ub-PCNA) and SUMO-modified PCNA (SUMO-PCNA) regulate DNA damage tolerance pathways. X-ray crystal structures of these proteins suggested that they do not have much conformational flexibility, because the modifiers have preferred binding sites on the surface of PCNA. By contrast, small-angle X-ray scattering (SAXS) analyses of these proteins suggested that they have different degrees of conformational flexibility with SUMO-PCNA being more flexible. These conclusions were based upon minimal ensemble hybrid approaches, which produce unrealistic models by representing flexible proteins with only a few static structures...
October 28, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30381148/the-interaction-between-the-drosophila-eag-potassium-channel-and-the-protein-kinase-camkii-involves-an-extensive-interface-at-the-active-site-of-the-kinase
#18
Artur F Castro-Rodrigues, Yaxian Zhao, Fátima Fonseca, Guillaume Gabant, Martine Cadene, Gail A Robertson, João H Morais-Cabral
The Drosophila EAG (dEAG) potassium channel is the founding member of the superfamily of KNCH channels, which are involved in cardiac repolarization, neuronal excitability and cellular proliferation. In flies, dEAG is involved in regulation of neuron firing and assembles with CaMKII to form a complex implicated in memory formation. We have characterized the interaction between the kinase domain of CaMKII and a 53-residue fragment of the dEAG channel that includes a canonical CaMKII recognition sequence. Crystal structures together with biochemical/biophysical analysis show a substrate-kinase complex with an unusually tight and extensive interface that appears to be strengthened by phosphorylation of the channel fragment...
October 28, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30367843/evolutionary-morphing-of-tryptophan-synthase-functional-mechanisms-for-the-enzymatic-channeling-of-indole
#19
Jennifer R Fleming, Michael Schupfner, Florian Busch, Arnaud Baslé, Alexander Ehrmann, Reinhard Sterner, Olga Mayans
Tryptophan synthase (TrpS) is a heterotetrameric αββα enzyme that exhibits complex substrate channeling and allosteric mechanisms and is a model system in enzymology. In this work, we characterize proposed early and late evolutionary states of TrpS and show that they have distinct quaternary structures, caused by insertions-deletions of sequence segments (indels) in the β-subunit. Remarkably, indole hydrophobic channels that connect α and β active sites have re-emerged in both TrpS types, yet they follow different paths through the β-subunit fold...
October 24, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30367842/bip-grp78-mediates-erad-targeting-of-proteins-produced-by-membrane-bound-ribosomes-stalled-at-the-stop-codon
#20
Francesca Cesaratto, Linda Sasset, Michael P Myers, Angela Re, Gianluca Petris, Oscar R Burrone
Translational stalling of ribosome bound to ER membrane requires an accurate clearance of the associated polypeptides, which is not completely understood in mammals. We characterised in mammalian cells the model of ribosomal stalling at the STOP-codon based on proteins tagged at the C-terminus with the picornavirus 2A peptide followed by a termination codon instead of the Proline (2A*). We exploited the 2A* stalling model to characterise the pathway of degradation of ER-targeted polypeptides. We report that the ER chaperone BiP/GRP78 is a new main factor involved...
October 24, 2018: Journal of Molecular Biology
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