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Journal of Molecular Biology

G Logan Draughn, Morgan E Milton, Erik A Feldmann, Benjamin G Bobay, Braden M Roth, Andrew L Olson, Richele J Thompson, Luis A Actis, Christopher Davies, John Cavanagh
The rise of drug-resistant bacterial infections coupled with decreasing antibiotic efficacy poses a significant challenge to global healthcare. Acinetobacter baumannii is an insidious, emerging bacterial pathogen responsible for severe nosocomial infections aided by its ability to form biofilms. The response regulator BfmR, from the BfmR/S two-component system, is the master regulator of biofilm initiation in A. baumannii and is a tractable therapeutic target. Here we present the structure of A. baumannii BfmR using a hybrid approach combining X-ray crystallography, nuclear magnetic resonance spectroscopy, chemical crosslinking mass spectrometry, and molecular modeling...
February 10, 2018: Journal of Molecular Biology
Jelger A Lycklama A Nijeholt, Ruslan Vietrov, Gea K Schuurman-Wolters, Bert Poolman
Solute transport via ABC importers involves receptor-mediated substrate binding, which is followed by ATP-driven translocation of the substrate across the membrane. How these steps are exactly initiated and coupled, and how much ATP it takes to complete a full transport cycle, are subject of debate. Here, we reconstitute the ABC importer GlnPQ in nanodiscs and in proteoliposomes and determine substrate-(in)dependent ATP hydrolysis and transmembrane transport. We determined the conformational states of the substrate-binding domains (SBDs) by single-molecule FRET measurements...
February 9, 2018: Journal of Molecular Biology
Gustavo Martínez-Noël, Katja Luck, Simone Kühnle, Alice Desbuleux, Patricia Szajner, Jeffrey T Galligan, Diana Rodriguez, Leon Zheng, Kathleen Boyland, Flavian Leclere, Quan Zhong, David E Hill, Marc Vidal, Peter M Howley
Perturbations in activity and dosage of the UBE3A ubiquitin-ligase have been linked to Angelman Syndrome and autism spectrum disorders. UBE3A was initially identified as the cellular protein hijacked by the human papillomavirus E6 protein to mediate the ubiquitylation of p53, a function critical to the oncogenic potential of these viruses. Although a number of substrates have been identified, the normal cellular functions and pathways affected by UBE3A are largely unknown. Previously we showed that UBE3A associates with HERC2, NEURL4, and MAPK6/ERK3 in a high molecular weight complex of unknown function that we refer to as the HUN complex (HERC2, UBE3A, and NEURL4)...
February 6, 2018: Journal of Molecular Biology
Ivana G Molina, Sebastian A Esperante, Cristina Marino-Buslje, Lucía B Chemes, Gonzalo de Prat-Gay
RNA transcription of mononegavirales decreases gradually from the 3' leader promoter towards the 5' end of the genome, due to a decay in polymerase processivity. In the respiratory syncytial virus (RSV) and metapneumovirus, the M2-1 protein ensures transcription anti-termination. Despite being a homotetramer, RSV M2-1 binds two molecules of RNA of 13mer or longer per tetramer, and temperature sensitive secondary structure in the RNA ligand is unfolded by stoichiometric interaction with M2-1. Fine quantitative analysis shows positive cooperativity, indicative of conformational asymmetry in the tetramer...
February 4, 2018: Journal of Molecular Biology
Rhys M Williams, Barbara Franke, Mark Wilkinson, Jennifer R Fleming, Daniel J Rigden, Guy M Benian, Patrick A Eyers, Olga Mayans
Titin-like kinases are muscle-specific kinases that regulate mechanical sensing in the sarcomere. Twitchin kinase (TwcK) is the best-characterized member of this family, both structurally and enzymatically. TwcK activity is auto-inhibited by a dual intrasteric mechanism, in which N- and C-terminal tail extensions wrap around the kinase domain, blocking the hinge region, the ATP binding pocket and the peptide substrate binding groove. Physiologically, kinase activation is thought to occur by a stretch-induced displacement of the inhibitory tails from the kinase domain...
February 3, 2018: Journal of Molecular Biology
Yilin Meng, Lalima G Ahuja, Alexandr P Kornev, Susan S Taylor, Benoît Roux
Tyrosine kinases are enzymes playing a critical role in cellular signaling. Molecular dynamics (MD) umbrella sampling potential of mean force (PMF) computations are used to quantify the impact of activating and inactivating mutations of c-Src kinase. The PMF computations predict that a specific double-mutant can stabilize c-Src kinase into an active-like conformation while disabling the binding of ATP in the catalytic active site. The active-like conformational equilibrium of this catalytically-dead kinase is affected by a hydrophobic unit that connects to the hydrophobic spine network via the C-helix...
February 2, 2018: Journal of Molecular Biology
Abraham Rimon, Manish Dwivedi, Assaf Friedler, Etana Padan
Na+/H+ antiporters have a crucial role in pH- and Na+ homeostasis in cells. The crystal structure of NhaA, the main antiporter of Escherichia coli, has provided general insights into antiporter mechanisms and revealed a previously unknown structural fold, which has since been identified in several secondary active transporters. This unique structural fold is very delicately electrostatically balanced. Asp133 and Lys 300 have been ascribed essential roles in this balance, and, more generally, in the structure and function of the antiporter...
February 1, 2018: Journal of Molecular Biology
Andrey G Tereshchenkov, Malgorzata Dobosz-Bartoszek, Ilya A Osterman, James Marks, Vasilina A Sergeeva, Pavel Kasatsky, Ekaterina S Komarova, Andrey A Stavrianidi, Igor A Rodin, Andrey L Konevega, Petr V Sergiev, Natalia V Sumbatyan, Alexander S Mankin, Alexey A Bogdanov, Yury S Polikanov
Antibiotic chloramphenicol (CHL) binds with a moderate affinity at the peptidyl transferase center of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving properties of this inhibitor, we explored ribosome binding and inhibitory activity of a number of amino-acid analogues of CHL. The L-histidyl analogue binds to the ribosome with the affinity exceeding that of CHL by 10 fold. Several of the newly synthesized analogues were able to inhibit protein synthesis and exhibited the mode of action that was distinct from the action of CHL...
February 1, 2018: Journal of Molecular Biology
David C Bode, Helen F Stanyon, Trisha Hirani, Mark D Baker, Jon Nield, John H Viles
Central to Alzheimer's disease (AD) pathology is the assembly of monomeric amyloid-β peptide (Aβ) into oligomers and fibres. The most abundant protein in the blood plasma and cerebrospinal fluid (CSF) is human serum albumin (HSA). Albumin can bind to Aβ and is capable of inhibiting the fibrillisation of Aβ at physiological (μM) concentrations. The ability of albumin to bind Aβ has recently been exploited in a phase-II clinical trial, which showed a reduction in cognitive decline in Alzheimer's disease patients undergoing albumin plasma-exchange...
February 1, 2018: Journal of Molecular Biology
Nir Hecht, Ofir Regev, Daniel Dovrat, Amir Aharoni, Eyal Gur
The Pup-proteasome system (PPS) is a prokaryotic tagging and degradation system analogous in function to the ubiquitin-proteasome system (UPS). Like ubiquitin, Pup is conjugated to proteins, tagging them for proteasomal degradation. However, in the PPS, a single Pup-ligase, PafA, conjugates Pup to a wide variety of proteins. PafA couples ATP hydrolysis to formation of an isopeptide bond between Pup and a protein lysine via a mechanism similar to that used by glutamine synthetase (GS) to generate glutamine from ammonia and glutamate...
February 1, 2018: Journal of Molecular Biology
Aaron H Phillips, Ou Li, Alexandre Gay, Arnaud Besson, Richard W Kriwacki
p27 mediates cell cycle arrest by binding to and inhibiting cyclin-dependent kinase (Cdk)/cyclin complexes, but p27 can also contribute to pro-oncogenic signaling upon mislocalization to the cytoplasm. Cytoplasmic p27 stimulates cell migration by associating with RhoA and interfering with the exchange of GDP from RhoA stimulated by guanine nucleotide exchange factors (GEFs). We used biophysical methods to show that the N-terminus of p27 directly interacts with RhoA in vitro. The affinity of p27 for RhoA is low, with an equilibrium dissociation constant of hundreds of micromolar; however, at high concentrations, p27 interfered with GEF-mediated nucleotide exchange from RhoA...
January 30, 2018: Journal of Molecular Biology
Rebecca Stephens, Krystle Lim, Marta Portela, Marc Kvansakul, Patrick O Humbert, Helena E Richardson
The Scribble cell polarity module, comprising Scribbled (Scrib), Discs-large (Dlg) and Lethal-2-giant larvae (Lgl), has a tumor suppressive role in mammalian epithelial cancers. The Scribble module proteins play key functions in the establishment and maintenance of different modes of cell polarity, as well as in the control of tissue growth, differentiation and directed cell migration, and therefore are major regulators of tissue development and homeostasis. Whilst molecular details are known regarding the roles of Scribble module proteins in cell polarity regulation, their precise mode of action in the regulation of other key cellular processes remains enigmatic...
January 30, 2018: Journal of Molecular Biology
Matthew T Mawhinney, Runcong Liu, Fang Lu, Jasna Maksimoska, Kevin Damico, Ronen Marmorstein, Paul M Lieberman, Brigita Urbanc
The CTCF protein has emerged as a key architectural protein involved in genome organization. Although hypothesized to initiate DNA looping, direct evidence of CTCF-induced DNA loop formation is still missing. Several studies have shown that the eleven zinc finger (11 ZF) domain of CTCF is actively involved in DNA binding. We here use atomic force microscopy (AFM) to examine the effect of the 11 zinc finger (ZF) domain comprising residues 266-579 (11 ZF CTCF) and the 3 ZF domain comprising residues 402-494 (6-8 ZF CTCF) of human CTCF on the DNA morphology...
January 30, 2018: Journal of Molecular Biology
Jungmin Yoon, Seung Joong Kim, Sojin An, Saehyun Cho, Alexander Leitner, Taeyang Jung, Ruedi Aebersold, Hans Hebert, Uhn-Soo Cho, Ji-Joon Song
Importin4 transports histone H3/H4 in complex with Asf1a to the nucleus for chromatin assembly. Importin4 recognizes the nuclear localization sequence located at the N-terminal tail of histones. Here, we analyzed the structures and interactions of human Importin4, histones and Asf1a by cross-linking mass spectrometry (XL-MS), X-ray crystallography, negative-stain electron microscopy, small-angle X-ray scattering and integrative modeling. The XL-MS data showed that the C-terminal region of Importin4 was extensively crosslinked with the histone H3 tail...
January 30, 2018: Journal of Molecular Biology
Christopher R Reynolds, Suhail A Islam, Michael J E Sternberg
EzMol is a molecular visualisation web server in the form of a software wizard, located at It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualisation system. EzMol allows the upload of molecular structure files in PDB format to generate a web page including a representation of the structure that the user can manipulate...
January 29, 2018: Journal of Molecular Biology
Matteo Serino
Alterations of both ecology and functions of gut microbiota are conspicuous traits of several inflammatory pathologies, notably metabolic diseases such as obesity and type 2 diabetes. Moreover, the proliferation of enterobacteria, subdominant members of the intestinal microbial ecosystem, has been shown to be favoured by western diet, the strongest inducer of both metabolic diseases and gut microbiota dysbiosis. The inner interdependence between the host and the gut microbiota is based on a plethora of molecular mechanisms by which host and intestinal microbes modify each other...
January 25, 2018: Journal of Molecular Biology
Egor Svidritskiy, Andrei A Korostelev
Understanding the mechanisms of inhibitors of translation termination may inform development of new antibacterials and therapeutics for premature-termination diseases. We report the crystal structure of the potent termination inhibitor BlaS bound to the ribosomal 70S•RF1 termination complex. BlaS shifts the catalytic domain 3 of RF1 and restructures the peptidyl transferase center. Universally conserved uridine 2585 in the peptidyl transferase center occludes the catalytic backbone of the GGQ motif of RF1, explaining the structural mechanism of inhibition...
January 19, 2018: Journal of Molecular Biology
Marissa L Smith, Weidong Cui, Ashleigh J Jackobel, Nancy Walker-Kopp, Knutson
RNA polymerase I (Pol I) transcription in Saccharomyces cerevisiae requires four separate factors that recruit Pol I to the promoter to form a pre-initiation complex (PIC). Upstream Activating Factor (UAF) is one of two multi-subunit complexes that regulate PIC formation by binding to the ribosomal DNA promoter and by stimulating recruitment of downstream Pol I factors. UAF is composed of Rrn9, Rrn5, Rrn10, Uaf30, and histones H3 and H4. We developed a recombinant E. coli based system to coexpress and purify transcriptionally active UAF complex and to investigate the importance of each subunit in complex formation...
January 18, 2018: Journal of Molecular Biology
Marie-Theres Vielberg, Verena C Bauer, Michael Groll
The 20S proteasome is a key player in eukaryotic and archaeal protein degradation, but its progenitor in eubacteria is unknown. Recently, the ancestral β-subunit protein (Anbu) was predicted to be the evolutionary precursor of the proteasome. We crystallised Anbu from Hyphomicrobium sp. strain MC1 in four different space groups and solved the structures by SAD-phasing and Patterson search calculation techniques. Our data reveal that Anbu adopts the classical fold of Ntn-hydrolases, but its oligomeric state differs from that of barrel-shaped proteases...
January 17, 2018: Journal of Molecular Biology
Katarzyna E Zawada, Kenta Okamoto, Peter M Kasson
Influenza viral entry into the host cell cytoplasm is accomplished by a process of membrane fusion mediated by the viral hemagglutinin protein. Hemagglutinin acts in a pH-triggered fashion, inserting a short fusion peptide into the host membrane followed by refolding of a coiled-coil structure to draw the viral envelope and host membranes together. Mutations to this fusion peptide provide an important window into viral fusion mechanisms and protein-membrane interactions. Here, we show that a well-described fusion peptide mutant, G1S, has a phenotype that depends strongly on the viral membrane context...
January 16, 2018: Journal of Molecular Biology
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