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Andrea Fagagnini, Riccardo Montioli, Andra Caloiu, Marc Ribó, Douglas V Laurents, Giovanni Gotte
Bovine pancreatic ribonuclease A (RNase A) is the monomeric prototype of the so-called secretory 'pancreatic-type' RNase super-family. Like the naturally domain-swapped dimeric bovine seminal variant, BS-RNase, and its glycosylated RNase B isoform, RNase A forms N- and C-terminal 3D domain-swapped oligomers after lyophilization from acid solutions, or if subjected to thermal denaturation at high protein concentration. All mentioned RNases can undergo deamidation at Asn67, forming Asp or isoAsp derivatives that modify the protein net charge and consequently its enzymatic activity...
October 23, 2016: Biochimica et Biophysica Acta
Zhengrong Yang, Qingxian Zhou, Leo Mok, Anukriti Singh, Douglas J Swartz, Ina L Urbatsch, Christie G Brouillette
Structural changes in mouse P-glycoprotein (Pgp) induced by thermal unfolding were studied by differential scanning calorimetry (DSC), circular dichroism and fluorescence spectroscopy to gain insight into the solution conformation(s) of this ABC transporter that may not be apparent from current crystal structures. DSC of reconstituted Pgp showed two thermal unfolding transitions in the absence of MgATP, suggesting that each transition involved the cooperative unfolding of two or more interacting structural domains...
October 23, 2016: Biochimica et Biophysica Acta
Eileen K Jaffe
Porphobilinogen synthase (PBGS), also known as 5-aminolevulinate dehydratase, is an essential enzyme in the biosynthesis of all tetrapyrroles, which function in respiration, photosynthesis, and methanogenesis. Throughout evolution, PBGS adapted to a diversity of cellular niches and evolved to use an unusual variety of metal ions both for catalytic function and to control protein multimerization. With regard to the active site, some PBGSs require Zn(2+); a subset of those, including human PBGS, contain a constellation of cysteine residues that acts as a sink for the environmental toxin Pb(2+)...
October 26, 2016: Accounts of Chemical Research
Morten Beck Trelle, Shona H Pedersen, Eva Christina Østerlund, Jeppe Buur Madsen, Søren Risom Kristensen, Thomas J D Jørgensen
Antithrombin deficiency is associated with increased risk of venous thrombosis. In certain families this condition is caused by pathogenic polymerization of mutated antithrombin in the blood. To facilitate future development of pharmaceuticals against antithrombin polymerization an improved understanding of the polymerogenic intermediates is crucial. However, X-ray crystallography of these intermediates is severely hampered by the difficulty in obtaining well-diffracting crystals of transient and heterogeneous noncovalent protein assemblies...
October 26, 2016: Analytical Chemistry
Kerry Marie Goodman, Rotem Rubinstein, Chan Aye Thu, Seetha Mannepalli, Fabiana Bahna, Göran Ahlsén, Chelsea Rittenhouse, Tom Maniatis, Barry Honig, Lawrence Shapiro
Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealing trans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depict cis-interacting regions in monomeric form. Together these structures span the entire Pcdhγ ectodomain...
October 26, 2016: ELife
Marta Tarkanovskaja, Kuno Kooser, Helena Levola, Ergo Nõmmiste, Edwin Kukk
Photofragmentation of small gas-phase acetamide clusters (CH3CONH2)n (n ≤ 10) produced by a supersonic expansion source has been studied using time-of-flight ion mass spectroscopy combined with tunable vacuum-ultraviolet (VUV) synchrotron radiation. Fragmentation channels of acetamide clusters under VUV photoionization resulting in protonated and ammoniated clusters formation were identified with the discussion about the preceding intramolecular rearrangements. Acetamide-2,2,2-d3 clusters were also studied in an experiment with a gas discharge lamp as a VUV light source; comparison with the main experiment gave insights into the mechanism of formation of protonated acetamide clusters, indicating that proton transfer from amino group plays a dominant role in that process...
September 28, 2016: Journal of Chemical Physics
DeCarlos E Taylor, János G Ángyán, Giulia Galli, Cui Zhang, Francois Gygi, Kimihiko Hirao, Jong Won Song, Kar Rahul, O Anatole von Lilienfeld, Rafał Podeszwa, Ireneusz W Bulik, Thomas M Henderson, Gustavo E Scuseria, Julien Toulouse, Roberto Peverati, Donald G Truhlar, Krzysztof Szalewicz
In the past decade, a number of approaches have been developed to fix the failure of (semi)local density-functional theory (DFT) in describing intermolecular interactions. The performance of several such approaches with respect to highly accurate benchmarks is compared here on a set of separation-dependent interaction energies for ten dimers. Since the benchmarks were unknown before the DFT-based results were collected, this comparison constitutes a blind test of these methods.
September 28, 2016: Journal of Chemical Physics
Anirban Ghosh, Rajat K Chaudhuri, Sudip Chattopadhyay
A four-component (4c) relativistic state specific multireference coupled cluster (4c-SSMRCC) method has been developed and applied to compute the ground state spectroscopic constants of Ag2, Cu2, Au2, and I2. The reference functions used in these calculations are obtained using computationally inexpensive improved virtual orbital-complete active space configuration interaction scheme. Rigorous size-extensivity and insensitivity towards the intruder state problem make our method an interesting choice for the calculation of the dissociation energy surface...
September 28, 2016: Journal of Chemical Physics
Christian Urban, Roberto Otero, David Écija, Marta Trelka, Nazario Martín, José M Gallego, Rodolfo Miranda
We have measured STM movies to study the diffusion of individual vacancies in a self-assembled layer of a tetrathiafulvalene derivative (exTTF) on Au(111) at room temperature. The diffusion is anisotropic, being faster along the compact direction of the molecular lattice. A detailed analysis of the anisotropic displacement distribution of the single vacancies shows that the relative abundance of double jumps (that is, the collective motion of molecular dimers) with respect to single jumps is rather large, the number of double jumps being more than 20% of the diffusion events...
October 21, 2016: Journal of Chemical Physics
Jérôme F Gonthier, C David Sherrill
Symmetry-Adapted Perturbation Theory (SAPT) is one of the most popular approaches to energy component analysis of non-covalent interactions between closed-shell systems, yielding both accurate interaction energies and meaningful interaction energy components. In recent years, the full open-shell equations for SAPT up to second-order in the intermolecular interaction and zeroth-order in the intramolecular correlation (SAPT0) were published [P. S. Zuchowski et al., J. Chem. Phys. 129, 084101 (2008); M. Hapka et al...
October 7, 2016: Journal of Chemical Physics
Maurizio Baldassarre, Marco Domenicali, Marina Naldi, Maristella Laggetta, Ferdinando A Giannone, Maurizio Biselli, Daniela Patrono, Carlo Bertucci, Mauro Bernardi, Paolo Caraceni
Decompensated cirrhosis is associated to extensive post-transcriptional changes of human albumin (HA). This study aims to characterize the occurrence of HA homodimerization in a large cohort of patients with decompensated cirrhosis and to evaluate its association with clinical features and prognosis. HA monomeric and dimeric isoforms were identified in peripheral blood by using a HPLC-ESI-MS technique in 123 cirrhotic patients hospitalized for acute decompensation and 50 age- and sex-comparable healthy controls...
October 26, 2016: Scientific Reports
Matthew Wiens, Yi Shen, Xi Li, Mohammad Salem, Nick Smisdom, Wei Zhang, Alex Brown, Robert E Campbell
The tetrameric red fluorescent protein from Discosoma sp. coral (DsRed) has previously been engineered to produce dimeric and monomeric fluorescent variants with excitation and emission profiles that span the visible spectrum. The brightest of the effectively monomeric DsRed variants is tdTomato - a tandem fusion of a dimeric DsRed variant. Here we describe the engineering of brighter red (RRvT), green (GGvT), and green-red heterodimeric (GRvT), tdTomato variants. GRvT exhibits 99% intramolecular Förster resonance energy transfer (FRET) efficiency, resulting in long Stokes shift red fluorescence...
October 26, 2016: Chembiochem: a European Journal of Chemical Biology
José L Zafra, Lili Qiu, Naoyuki Yanai, Takamichi Mori, Masahiro Nakano, Miriam Peña Alvarez, Juan T López Navarrete, Carlos J Gómez-García, Miklos Kertesz, Kazuo Takimiya, Juan Casado
Conducting polymers can be synthesized by irreversible diradical monomer polymerization. A reversible version of this reaction consisting of the formation/dissociation of σ-dimers and σ-polymers from a stable quinonoidal diradical precursor is described. The reaction reversibility is made by a quinonoidal molecule which changes its structure to an aromatic species by forming weak and long intermolecular C-C single bonds. The reaction provokes a giant chromic effect of about 2.5 eV. The two opposite but complementary quinonoidal and aromatic tautomers provide the Janus faces of the reactants and products which produces the observed chromic effect...
October 26, 2016: Angewandte Chemie
Marlene Møller Madsen, Nykola C Jones, Steen Brøndsted Nielsen, Søren Vrønning Hoffmann
Solar mutagenesis via the formation of thymine dimer photoproducts is a primary cause of skin cancer. The aim of this study is to provide a direct method for following the development of photolesions in thymine single strands and to determine how the formation of these photoproducts depends on the excitation wavelength in the ultraviolet (UV) between 210 nm and 325 nm. Experiments were performed both with a 20 Hz pulsed, intense, tunable laser as well as UV lamps (at 254 nm and 302 nm), but we find that only the dose matters at these wavelengths for the yield of photoproducts...
October 26, 2016: Physical Chemistry Chemical Physics: PCCP
Xiangyu Cai, Yandong Zhou, Robert M Nwokonko, Natalia A Loktionova, Xianming Wang, Ping Xin, Mohamed Trebak, Youjun Wang, Donald L Gill
Orai channels mediate store-operated Ca2+ signals crucial in regulating transcription in many cell types, and implicated in numerous immunological and inflammatory disorders. Despite their central importance, controversy surrounds the basic subunit structure of Orai channels, several biochemical and biophysical studies suggesting a tetrameric structure yet crystallographic evidence indicating a hexamer. We systematically investigated the subunit configuration of the functional Orai1 channel, generating a series of tdTomato-tagged concatenated Orai1 channel constructs (dimers to hexamers) expressed in CRISPR-derived Orai1-knockout HEK cells, stably expressing STIM1-YFP...
October 25, 2016: Journal of Biological Chemistry
Shicheng Lei, Minhao Xie, Bing Hu, Li Zhou, Yi Sun, Muhammad Saeeduddin, Hongcheng Zhang, Xiaoxiong Zeng
In the present study, pear polyphenol oxidase (PPO) was purified, immobilized and applied for the synthesis of theaflavin-3,3'-digallate (TF3). Firstly, PPO of pear (Pyrus bretschneideri Rehd cv. Huangguan) was purified 24.36-fold in specific activity with a recovery of 6.77% by sequential use of precipitation with 70% saturated ammonium sulfate and chromatography of DEAE-Sepharose Fast Flow column. The purified pear PPO, found to be a dimer of identical subunits of molecular mass 35kDa, was then successfully immobilized onto Fe3O4/chitosan nanoparticles via glutaraldehyde coupling reaction...
October 22, 2016: International Journal of Biological Macromolecules
Emilie Ramberg, Maria Olausson, Tem Bendix Salkvist Jørgensen, Malene Lindholmer Nepper, Priya Bhardwaj, Tomas Sorm Binko, Jan Roland Petersen, Gitte Gleerup Fornitz
AIMS: Assessment of right ventricular (RV) function in acute pulmonary embolism (PE) has prognostic significance. The aim of this study was to evaluate right atrium (RA) and RV myocardial damage with 2-dimensional speckle-tracking in patients with an acute central vs an acute peripheral PE. METHODS AND RESULTS: Twenty-six patients with acute PE and 10 controls were retrospectively enrolled. Right atrium and RV myocardial deformation was analyzed using speckle-tracking imaging echocardiography...
September 29, 2016: American Journal of Emergency Medicine
Johnathan Ho, Christin Pelzel, Andreas Begitt, Maureen Mee, Hany M Elsheikha, David J Scott, Uwe Vinkemeier
STAT2 is the quintessential transcription factor for type 1 interferons (IFNs), where it functions as a heterodimer with STAT1. However, the human and murine STAT2-deficient phenotypes suggest important additional and currently unidentified type 1 IFN-independent activities. Here, we show that STAT2 constitutively bound to STAT1, but not STAT3, via a conserved interface. While this interaction was irrelevant for type 1 interferon signaling and STAT1 activation, it precluded the nuclear translocation specifically of STAT1 in response to IFN-γ, interleukin-6 (IL-6), and IL-27...
October 2016: PLoS Biology
Rong Fu, Yinping Meng, Yihao Wang, Hui Liu, Yi Liu, Lijuan Li, Shaoxue Ding, Guojin Wang, Jia Song, Zonghong Shao
INTRODUCTION: Thrombosis is a dangerous complication of paroxysmal nocturnal hemoglobinuria (PNH) and has a high mortality rate. However, the mechanism underlying the development of thrombosis in PNH remains unclear. To explore this, platelet function and serum complement activity were investigated in 14 patients with classical PNH, 11 with PNH aplastic anemia (AA) and 30 healthy controls. MATERIAL AND METHODS: Serum concentrations of the terminal complement complex (sC5b-9) were determined by enzyme-linked immunofluorescence assay (ELISA), and the levels of C5b-9, CD61 and CD62p on platelet membranes were determined by flow cytometry...
July 22, 2016: Thrombosis Research
Benoît Silvestre de Ferron, Catherine Vilpoux, Myriam Kervern, Alexandre Robert, Johan Antol, Mickael Naassila, Olivier Pierrefiche
Low to moderate perinatal ethanol exposure (PEE) may have disastrous consequences for the central nervous system resulting notably in permanent cognitive deficits. Learning and memory are mediated in the hippocampus by long-term potentiation (LTP) and long term depression (LTD), two forms of synaptic plasticity. PEE decreases LTP but also abnormally facilitates LTD (Kervern et al. ) through a presently unknown mechanism. We studied in rat hippocampus slice, the involvement of the chloride co-transporters NKCC1 and KCC2, in the role of GABAA inhibitions in facilitated LTD after moderate PEE...
October 25, 2016: Addiction Biology
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