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https://www.readbyqxmd.com/read/28340332/super-elongation-complex-promotes-early-hiv-transcription-and-its-function-is-modulated-by-p-tefb
#1
Alona Kuzmina, Simona Krasnopolsky, Ran Taube
Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear...
February 17, 2017: Transcription
https://www.readbyqxmd.com/read/28338942/structure-and-mechanism-of-benzaldehyde-dehydrogenase-from-pseudomonas-putida-atcc-12633-a-member-of-the-class-3-aldehyde-dehydrogenase-superfamily
#2
Megan P D Zahniser, Shreenath Prasad, Malea M Kneen, Cheryl A Kreinbring, Gregory A Petsko, Dagmar Ringe, Michael J McLeish
Benzaldehyde dehydrogenase from Pseudomonas putida (PpBADH) belongs to the Class 3 aldehyde dehydrogenase (ALDH) family. The Class 3 ALDHs are unusual in that they are generally dimeric (rather than tetrameric), relatively non-specific and utilize both NAD+ and NADP+. To date, X-ray structures of three Class 3 ALDHs have been determined, of which only two have cofactor bound, both in the NAD+ form. Here we report the crystal structure of PpBADH in complex with NADP+ and a thioacyl intermediate adduct. The overall architecture of PpBADH resembles that of most other members of the ALDH superfamily, and the cofactor binding residues are well conserved...
March 9, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28338703/theoretical-investigation-of-proton-collisions-on-prebiotic-candidates-hydrogen-cyanide-polymers
#3
Marie-Christine Bacchus-Montabonel
One of the major concerns in prebiotic chemistry is the formation and destruction routes of prebiotic compounds in space. As detected for a long time, hydrogen cyanide (HCN) has been suggested to be a feedstock molecule at the origin of life driving easy oligomerization, in particular to form adenine. This may focus on its first oligomers because its dimer cyanomethanimine was recently observed in star-forming regions, or its trimer aminomalononitrile. With regard to the assumption of an extra-terrestrial origin of life, the stability of such species under ultraviolet radiation or in ion-collisions is an open question...
March 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28338331/an-in-silico-study-on-the-isomers-of-pentacene-the-case-for-air-stable-and-alternative-c22h14-acenes-for-organic-electronics
#4
Leighton Jones, Long Lin
Pentacene is one of the most investigated candidates for organic thin film transistor (OTFT) applications over the last few decades even though it unstable in air (Eg = 1.80 eV), owing in part to its planar nature and high charge-transfer mobilities as both a single crystal (35 cm2 V 1 s 1) and as a thin-film (3.0 cm2 V 1 s 1). Until now, picene is the only isomer of pentacene to be investigated for organic electronic applications, due to its greater stability (Eg = 4.21 eV) and high charge transfer mobility (3...
March 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28338015/simultaneously-measuring-multiple-protein-interactions-and-their-correlations-in-a-cell-by-protein-interactome-footprinting
#5
Si-Wei Luo, Zhi Liang, Jia-Rui Wu
Quantitatively detecting correlations of multiple protein-protein interactions (PPIs) in vivo is a big challenge. Here we introduce a novel method, termed Protein-interactome Footprinting (PiF), to simultaneously measure multiple PPIs in one cell. The principle of PiF is that each target physical PPI in the interactome is simultaneously transcoded into a specific DNA sequence based on dimerization of the target proteins fused with DNA-binding domains. The interaction intensity of each target protein is quantified as the copy number of the specific DNA sequences bound by each fusion protein dimers...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337996/protein-interaction-evolution-from-promiscuity-to-specificity-with-reduced-flexibility-in-an-increasingly-complex-network
#6
T Alhindi, Z Zhang, P Ruelens, H Coenen, H Degroote, N Iraci, K Geuten
A key question regarding protein evolution is how proteins adapt to the dynamic environment in which they function and how in turn their evolution shapes the protein interaction network. We used extant and resurrected ancestral plant MADS-domain transcription factors to understand how SEPALLATA3, a protein with hub and glue properties, evolved and takes part in network organization. Although the density of dimeric interactions was saturated in the network, many new interactions became mediated by SEPALLATA3 after a whole genome triplication event...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337497/dimerization-and-conformation-related-free-energy-landscapes-of-dye-tagged-amyloid-%C3%AE-12-28-linked-to-fret-experiments
#7
Alexander Kulesza, Steven Daly, Philippe Dugourd
We have investigated the free energy landscape of Aβ-peptide dimer models in connection to gas-phase FRET experiments. We use a FRET-related distance coordinate and one conformation-related coordinate per monomer for accelerated structural exploration with well-tempered metadynamics in solvent and in vacuo. The free energy profiles indicate that FRET under equilibrium conditions should be significantly affected by the de-solvation upon the transfer of ions to the gas-phase. In contrast, a change in the protonation state is found to be less impacting once de-solvated...
March 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28337319/bifunctional-inhibitors-as-a-new-tool-to-reduce-cancer-cell-invasion-by-impairing-mmp-9-homodimerization
#8
Elisa Nuti, Lea Rosalia, Doretta Cuffaro, Caterina Camodeca, Chiara Giacomelli, Eleonora Da Pozzo, Tiziano Tuccinardi, Barbara Costa, Claudia Antoni, Laura Vera, Lidia Ciccone, Elisabetta Orlandini, Susanna Nencetti, Vincent Dive, Claudia Martini, Enrico A Stura, Armando Rossello
Protein homodimers play important roles in physiological and pathological processes, including cancer invasion and metastasis. Recently, MMP-9 natural homodimerization via the PEX domain has been correlated with high migration rates of aggressive cancer cells. Here we propose that bifunctional MMP-9 inhibitors designed to impair natural MMP-9 homodimerization promoted by PEX-PEX interactions might be an effective tool to fight cancer cell invasion. Elaborating a previously described dimeric hydroxamate inhibitor 1, new ligands were synthesized with different linker lengths and branch points...
March 9, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28337214/crystal-structure-of-the-chloroplastic-oxoene-reductase-ceqorh-from-arabidopsis-thaliana
#9
Sarah Mas Y Mas, Gilles Curien, Cécile Giustini, Norbert Rolland, Jean-Luc Ferrer, David Cobessi
Enzymatic and non-enzymatic peroxidation of polyunsaturated fatty acids give rise to accumulation of aldehydes, ketones, and α,β-unsaturated carbonyls of various lengths, known as oxylipins. Oxylipins with α,β-unsaturated carbonyls are reactive electrophile species and are toxic. Cells have evolved several mechanisms to scavenge reactive electrophile oxylipins and decrease their reactivity such as by coupling with glutathione, or by reduction using NAD(P)H-dependent reductases and dehydrogenases of various substrate specificities...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28336776/apoptosis-inhibitor-5-is-an-endogenous-inhibitor-of-caspase-2
#10
Gergely Imre, Jean Berthelet, Jan Heering, Sebastian Kehrloesser, Inga Maria Melzer, Byung Il Lee, Bernd Thiede, Volker Dötsch, Krishnaraj Rajalingam
Caspases are key enzymes responsible for mediating apoptotic cell death. Across species, caspase-2 is the most conserved caspase and stands out due to unique features. Apart from cell death, caspase-2 also regulates autophagy, genomic stability and ageing. Caspase-2 requires dimerization for its activation which is primarily accomplished by recruitment to high molecular weight protein complexes in cells. Here, we demonstrate that apoptosis inhibitor 5 (API5/AAC11) is an endogenous and direct inhibitor of caspase-2...
March 23, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28336771/dimerization-in-lbd16-and-lbd18-transcription-factors-is-critical-for-lateral-root-formation
#11
Han Woo Lee, Na Young Kang, Shashank Pandey, Chuloh Cho, Sung Haeng Lee, Jungmook Kim
LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD)/ASYMMETRIC LEAVES2-LIKE (ASL)s (hereafter referred to as LBD) are plant-specific transcription factors that play important roles in a plethora of plant growth and development. The leucine-zipper-like coiled-coil motif in the LOB domain of the class I LBD proteins has been proposed to mediate protein dimerization, but it has not been experimentally assessed yet. LBD16 and LBD18 have been well characterized to play important roles in lateral root development in Arabidopsis...
March 23, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28336533/critical-residues-and-motifs-for-homodimerization-of-the-first-transmembrane-domain-of-the-plasma-membrane-glycoprotein-cd36
#12
Peng Wei, Fu-de Sun, Li-Min Zuo, Jing Qu, Peng Chen, Li-da Xu, Shi-Zhong Luo
The plasma transmembrane (TM) glycoprotein CD36 is critically involved in many essential signaling processes, especially the binding /uptake of long-chain fatty acids and oxidized low-density lipoproteins. The association of CD36 potentially activates cytosolic protein tyrosine kinases that are thought to associate with the C-terminal cytoplasmic tail of CD36. To understand the mechanisms by which CD36 mediates ligand binding and signal transduction, we have characterized the homo- oligomeric interaction of CD36 TM domains in membrane environments and with molecular dynamics (MD) simulations...
March 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28336060/recent-advances-in-development-of-genetically-encoded-fluorescent-sensors
#13
Lynn Sanford, Amy Palmer
Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28335714/testis-specific-atp-synthase-peripheral-stalk-subunits-required-for-tissue-specific-mitochondrial-morphogenesis-in-drosophila
#14
Eric M Sawyer, Elizabeth C Brunner, Yihharn Hwang, Lauren E Ivey, Olivia Brown, Megan Bannon, Dennis Akrobetu, Kelsey E Sheaffer, Oshauna Morgan, Conroy O Field, Nishita Suresh, M Grace Gordon, E Taylor Gunnell, Lindsay A Regruto, Cricket G Wood, Margaret T Fuller, Karen G Hales
BACKGROUND: In Drosophila early post-meiotic spermatids, mitochondria undergo dramatic shaping into the Nebenkern, a spherical body with complex internal structure that contains two interwrapped giant mitochondrial derivatives. The purpose of this study was to elucidate genetic and molecular mechanisms underlying the shaping of this structure. RESULTS: The knotted onions (knon) gene encodes an unconventionally large testis-specific paralog of ATP synthase subunit d and is required for internal structure of the Nebenkern as well as its subsequent disassembly and elongation...
March 23, 2017: BMC Cell Biology
https://www.readbyqxmd.com/read/28335612/thrombin-generation-in-patients-with-suspected-venous-thromboembolism
#15
Fredrik Wexels, Ola E Dahl, Are H Pripp, Ingebjørg Seljeflot
Increasing number of patients with clinically suspected venous thromboembolism is referred to radiological departments for definitive diagnosis. A simple assay to exclude the diagnosis and avoid radiological examinations is needed. We have reported correlations between D-dimer and prothrombin fragment 1 + 2 measured in plasma and urine. To further develop an analysis based on urine, more understanding of thrombin generation in these patients is needed. The aim of this study was to compare ex vivo thrombin generation with in vivo markers in plasma and urine in patients with and without venous thromboembolism...
January 1, 2017: Clinical and Applied Thrombosis/hemostasis
https://www.readbyqxmd.com/read/28335602/local-structure-and-dynamics-of-water-absorbed-in-polyetherimide-a-hydrogen-bonding-anatomy
#16
Antonio De Nicola, Andrea Correa, Giuseppe Milano, Pietro La Manna, Pellegrino Musto, Giuseppe Mensitieri, Giuseppe Scherillo
Hydrogen Bonding (HB) interactions play a major role in determining the behavior of macromolecular systems absorbing water. In fact, functional and structural properties of polymer-water mixtures are affected by the amount and type of these interactions. This contribution aims at a molecular level understanding of the interactional scenario for the technologically relevant case of the polyetherimide-water system. The problem has been tackled by combining different experimental and theoretical approaches which, taken together, provide a comprehensive physical picture...
March 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28335523/-2-2-photodimerization-of-naphthylvinylpyridines-through-cation-%C3%AF-interactions-in-acidic-solution
#17
Shinji Yamada, Yuka Nojiri
Irradiation of (E)-4-(2-(2-naphthyl)vinyl)pyridine (1a) and (E)-4-(2-(1-naphthyl)vinyl)pyridine (1b) with a 250 W high-pressure mercury lamp in acidic solution afforded synHT dimers in high stereoselectivities. Similar results were obtained by visible light irradiation. On the other hand, when the reactions were carried out under neutral conditions, the stereoselectivities were very low, and the yields were decreased by visible light irradiation. Comparison of the UV-vis spectra between the acidic and the neutral conditions elucidated that the red shift was observed in acidic solutions...
March 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335037/lrsam1-mediated-ubiquitylation-is-disrupted-in-axonal-charcot-marie-tooth-disease-2p
#18
Johanna E Hakonen, Vincenzo Sorrentino, Rossella Avagliano Trezza, Marit B de Wissel, Marlene van den Berg, Boris Bleijlevens, Fred van Ruissen, Ben Distel, Frank Baas, Noam Zelcer, Marian A J Weterman
Charcot-Marie-Tooth (CMT) disease type 2 is a genetically heterogeneous group of inherited neuropathies characterized by motor and sensory deficits as a result of peripheral axonal degeneration. We recently reported a frameshift mutation in the RING domain of LRSAM1 (c.2121_2122dup, p.Leu708Argfs) that encodes an E3 ubiquitin ligase, as the cause of axonal type CMT (CMT2P). However, the frequency of LRSAM1 mutations in CMT2 and the functional basis for their association with disease remains unknown. In this study we evaluated LRSAM1 mutations in two large Dutch cohorts...
March 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28335002/handcuffing-reversal-is-facilitated-by-proteases-and-replication-initiator-monomers
#19
Katarzyna Bury, Katarzyna Wegrzyn, Igor Konieczny
Specific nucleoprotein complexes are formed strictly to prevent over-initiation of DNA replication. An example of those is the so-called handcuff complex, in which two plasmid molecules are coupled together with plasmid-encoded replication initiation protein (Rep). In this work, we elucidate the mechanism of the handcuff complex disruption. In vitro tests, including dissociation progress analysis, demonstrate that the dimeric variants of plasmid RK2 replication initiation protein TrfA are involved in assembling the plasmid handcuff complex which, as we found, reveals high stability...
March 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334941/rna-protein-interactions-govern-antiviral-specificity-and-encapsidation-of-broad-spectrum-anti-hiv-reverse-transcriptase-aptamers
#20
Margaret J Lange, Phuong D M Nguyen, Mackenzie K Callaway, Marc C Johnson, Donald H Burke
RNA aptamers that bind HIV-1 reverse transcriptase (RT) inhibit HIV-1 replication, but little is known about potential aptamer-specific viral resistance. During replication, RT interacts with diverse nucleic acids. Thus, the genetic threshold for eliciting resistance may be high for aptamers that make numerous contacts with RT. To evaluate the impact of RT-aptamer binding specificity on replication, we engineered proviral plasmids encoding diverse RTs within the backbone of HIV-1 strain NL4-3. Viruses inhibited by pseudoknot aptamers were rendered insensitive by a naturally occurring R277K variant, providing the first demonstration of aptamer-specific resistance in cell culture...
March 6, 2017: Nucleic Acids Research
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