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https://www.readbyqxmd.com/read/29786960/the-atomic-resolution-structure-of-a-class-c-%C3%AE-lactamase-and-of-its-complex-with-avibactam
#1
Stefano Mangani, Cecilia Pozzi, Flavio Di Pisa, Filomena De Luca, Manuela Benvenuti, Jean-Denis Docquier
β-lactamases (BLs) are important antibiotic resistance determinants that significantly compromise the efficacy of valuable β-lactam antibacterial drugs. For that reason, combinations with β-lactamase inhibitor were developed. Avibactam is the first non-β-lactam BL inhibitor introduced in clinical practice. Ceftazidime-avibactam represents one of the few last-resort antibiotics available for the treatment of infections caused by near pandrug-resistant bacteria. TRU-1 is a chromosomally-encoded AmpC-type BL of Aeromonas enteropelogenes, related to the FOX-type BLs and constitutes a good model for class C BLs...
May 22, 2018: ChemMedChem
https://www.readbyqxmd.com/read/29786756/backbone-nmr-assignments-of-hypf-n-under-conditions-generating-toxic-and-non-toxic-oligomers
#2
Jayneil R Patel, Yingqi Xu, Claudia Capitini, Fabrizio Chiti, Alfonso De Simone
The HypF protein is involved in the maturation and regulation of hydrogenases. The N-terminal domain of HypF (HypF-N) has served as a key model system to study the pathways of protein amyloid formation and the nature of the toxicity of pre-fibrilar protein oligomers. This domain can aggregate into two forms of oligomers having significantly different toxic effects when added to neuronal cultures. Here, NMR assignments of HypF-N backbone resonances are presented in its native state and under the conditions favouring the formation of toxic and non-toxic oligomers...
May 21, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29786745/histone-modifications-in-fatty-acid-synthase-modulated-by-carbohydrate-responsive-element-binding-protein-are-associated-with-non%C3%A2-alcoholic-fatty-liver-disease
#3
Can Cai, Huihong Yu, Guangming Huang, Xuan Du, Xiaoqing Yu, Youping Zhou, Wei Shen
Non‑alcoholic fatty liver disease (NAFLD) is a manifestation of metabolic syndrome in the liver and is closely associated with diabetes; however, its pathogenesis remains to be elucidated. Carbohydrate responsive element binding protein (ChREBP), the hub of glucolipid metabolism, regulates the induction of fatty acid synthase (FASN), the key enzyme of de novo lipogenesis, by directly binding to carbohydrate response element (ChoRE) in its promoter. Investigations of histone modifications on NAFLD remain in their infancy...
May 22, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786739/synthesis-of-pure-silica-mfi-zeolites-using-imidazolium-based-long-dications-a-comparative-study-of-structure-directing-effects-derived-from-a-further-spacer-length-increase
#4
Peng Lu, Luis Gómez-Hortigüela, Miguel A Camblor
Length-dependent structure direction of linear methylimidazolium-based dications towards MFI zeolite, previously known only for the tetramethylene spacer, has also been found for octamethylene and decamethylene spacers. This works only under highly concentrated conditions, whereas dilution always tends to favor TON, a default structure that is the only zeolite obtained with the other reported dications (with tri-, penta-, and hexamethylene spacers). The locations and conformations of the dications have been studied by molecular mechanics simulations...
May 22, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29786696/crystal-structure-of-dihydrodipicolinate-reductase-padhdpr-from-paenisporosarcina-sp-tg-14-structural-basis-for-nadph-preference-as-a-cofactor
#5
Chang Woo Lee, Sun-Ha Park, Sung Gu Lee, Hyun Ho Park, Hak Jun Kim, HaJeung Park, Hyun Park, Jun Hyuck Lee
Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29786430/galaxygpcrloop-template-based-and-ab-initio-structure-sampling-of-the-extracellular-loops-of-g-protein-coupled-receptors
#6
Jonghun Won, Gyu Rie Lee, Hahnbeom Park, Chaok Seok
The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed...
May 22, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29785948/-genetics-of-fertility-restoration-in-the-isocytoplasm-allonuclear-c-group-of-cytoplasmic-male-sterility-in-maize
#7
Zhuo Fan Zhao, Ling Huang, Yong Ming Liu, Peng Zhang, Gui Wei, Mo Ju Cao
Maize is one of the first crops to produce hybrids using cytoplasmic male sterile lines. The C-type cytoplasmic male sterile (CMS-C) line is vital for hybrid seed production, and the fertility-restoration reaction along with its stability has a direct bearing on its applications. However, fertility restoration mechanism of CMS-C is complex and is still not clear so far. To further explore the factors affecting the fertility restoration of maize CMS, a series of test crosses were carried out by pollinating the isocytoplasm allonuclear CMS-C lines C48-2, Chuangzaosi and C478 with the test lines 18 bai, zi 330, 5022 and the restorer line A619, respectively...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29785941/life-style-and-risk-of-atypical-eating-disorders-in-university-students-reality-versus-perception
#8
Olga Castelao-Naval, Ascensión Blanco-Fernández, Carmen Marina Meseguer-Barros, Israel J Thuissard-Vasallo, Begoña Cerdá, Mar Larrosa
OBJECTIVE: The objectives of this paper were to determine weight status, eating, and alcohol drinking and smoking habits of university students, to determine the association between these variables with negative self-perception of their eating habits and to assess the risk of developing eating disorders. METHOD: A cross-sectional study was carried out on 422 university students. The parameters analyzed were: nutritional status, eating habits, alcohol/ tobacco consumption, and risk of eating disorder...
May 18, 2018: Enfermería Clínica
https://www.readbyqxmd.com/read/29785642/differential-binding-of-active-and-inactive-integrin-to-talin
#9
Dongchuan Wang, Qiang Guo, Ailin Wei, Ang Li
Bi-directional signaling of integrins plays an important role in platelet and leukocyte function. Talin plays a key role in integrin bi-directional signaling and its binding to integrin is highly regulated. The precise regulation of the recruitment and binding of talin to integrin is still being elucidated. In particular, the recruitment of talin to integrin is controlled by the RAP-1 and RIAM/lamellipodin signaling axis and the affinity between talin and integrin is regulated by the conformation or protease cleavage of talin...
May 21, 2018: Protein Journal
https://www.readbyqxmd.com/read/29785435/assessing-the-performance-of-mm-pbsa-and-mm-gbsa-methods-7-entropy-effects-on-the-performance-of-end-point-binding-free-energy-calculation-approaches
#10
Huiyong Sun, Lili Duan, Fu Chen, Hui Liu, Zhe Wang, Peichen Pan, Feng Zhu, John Z H Zhang, Tingjun Hou
Entropy effects play an important role in drug-target interactions, but the entropic contribution to ligand-binding affinity is often neglected by end-point binding free energy calculation methods, such as MM/GBSA and MM/PBSA, due to the expensive computational cost of normal mode analysis (NMA). Here, we systematically investigated entropy effects on the prediction power of MM/GBSA and MM/PBSA using >1500 protein-ligand systems and six representative AMBER force fields. Two computationally efficient methods, including NMA based on truncated structures and the interaction entropy approach, were used to estimate the entropic contributions to ligand-target binding free energies...
May 22, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29785088/insight-into-resistance-mechanism-of-anaplastic-lymphoma-kinase-to-alectinib-and-jh-viii-157-02-caused-by-g1202r-solvent-front-mutation
#11
Han Wang, Yao Wang, Wentao Guo, Bin Du, Xiaobing Huang, Riping Wu, Baoyu Yang, Xiaoyan Lin, Yilan Wu
Background: Mutated anaplastic lymphoma kinase (ALK) drives the development of advanced non-small cell lung cancer (NSCLC). Most reported small-molecule inhibitors targeting the ALK domain do not display good inhibition of the G1202R solvent front mutation. The solvent front mutation was assumed to hinder drug binding. However, a different fact could be uncovered by the simulations reported in this study through a structural analog of alectinib (JH-VIII-157-02), which demonstrated potent effects against the G1202R mutation...
2018: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/29784991/a-new-fundamental-type-of-conformational-isomerism
#12
Peter J Canfield, Iain M Blake, Zheng-Li Cai, Ian J Luck, Elmars Krausz, Rika Kobayashi, Jeffrey R Reimers, Maxwell J Crossley
Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1 , which we term 'akamptisomerization'...
June 2018: Nature Chemistry
https://www.readbyqxmd.com/read/29784972/comprehensive-analysis-of-the-mouse-cytochrome-p450-family-responsible-for-omega-3-epoxidation-of-eicosapentaenoic-acid
#13
Yosuke Isobe, Mai Itagaki, Yuko Ito, Satoko Naoe, Kotoe Kojima, Mitsunori Ikeguchi, Makoto Arita
Metabolites generated via oxygenation of the omega-3 double bond (omega-3 oxygenation) in eicosapentaenoic acid (EPA) have recently been identified as novel anti-inflammatory lipid mediators. Therefore, oxygenase(s) responsible for this metabolic pathway are of particular interest. We performed genome-wide screening of mouse cytochrome P450 (CYP) isoforms to explore enzymes involved in omega-3 oxygenation of EPA. As a result, 5 CYP isoforms (mouse Cyp1a2, 2c50, 4a12a, 4a12b, and 4f18) were selected and identified to confer omega-3 epoxidation of EPA to yield 17,18-epoxyeicosatetraenoic acid (17,18-EpETE)...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784877/adapting-to-oxygen-3-hydroxyanthrinilate-3-4-dioxygenase-employs-loop-dynamics-to-accommodate-two-substrates-with-disparate-polarities
#14
Yu Yang, Fange Liu, Aimin Liu
3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O2 and inserts both O atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O2, even though local O2 concentrations and diffusion rates are relatively low. Here, a close inspection of the HAO structures revealed that substrate- and inhibitor-bound structures exhibit a closed conformation with three hydrophobic loop regions moving toward the catalytic iron center, whereas the ligand-free structure is open...
May 21, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29784778/extant-fold-switching-proteins-are-widespread
#15
Lauren L Porter, Loren L Looger
A central tenet of biology is that globular proteins have a unique 3D structure under physiological conditions. Recent work has challenged this notion by demonstrating that some proteins switch folds, a process that involves remodeling of secondary structure in response to a few mutations (evolved fold switchers) or cellular stimuli (extant fold switchers). To date, extant fold switchers have been viewed as rare byproducts of evolution, but their frequency has been neither quantified nor estimated. By systematically and exhaustively searching the Protein Data Bank (PDB), we found ∼100 extant fold-switching proteins...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784777/structure-of-an-eiic-sugar-transporter-trapped-in-an-inward-facing-conformation
#16
Zhenning Ren, Jumin Lee, Mahdi Muhammad Moosa, Yin Nian, Liya Hu, Zhichun Xu, Jason G McCoy, Allan Chris M Ferreon, Wonpil Im, Ming Zhou
The phosphoenolpyruvate-dependent phosphotransferase system (PTS) transports sugar into bacteria and phosphorylates the sugar for metabolic consumption. The PTS is important for the survival of bacteria and thus a potential target for antibiotics, but its mechanism of sugar uptake and phosphorylation remains unclear. The PTS is composed of multiple proteins, and the membrane-embedded Enzyme IIC (EIIC) component transports sugars across the membrane. Crystal structures of two members of the glucose superfamily of EIICs, bcChbC and bcMalT, were solved in the inward-facing and outward-facing conformations, and the structures suggest that sugar translocation could be achieved by movement of a structured domain that contains the sugar-binding site...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784647/regulation-of-rabgaps-involved-in-insulin-action
#17
REVIEW
Samaneh Mafakheri, Alexandra Chadt, Hadi Al-Hasani
Rab (Ras-related proteins in brain) GTPases are key proteins responsible for a multiplicity of cellular trafficking processes. Belonging to the family of monomeric GTPases, they are regulated by cycling between their active GTP-bound and inactive GDP-bound conformations. Despite possessing a slow intrinsic GTP hydrolysis activity, Rab proteins rely on RabGAPs (Rab GTPase-activating proteins) that catalyze GTP hydrolysis and consequently inactivate the respective Rab GTPases. Two related RabGAPs, TBC1D1 and TBC1D4 (=AS160) have been described to be associated with obesity-related traits and type 2 diabetes in both mice and humans...
May 21, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29784539/revisiting-antithrombin-in-health-and-disease-congenital-deficiencies-and-genetic-variants-and-laboratory-studies-on-%C3%AE-and-%C3%AE-forms
#18
REVIEW
Jean Amiral, Jerard Seghatchian
Antithrombin [AT] is the main inhibitor for activated plasma coagulation serine esterases, inhibiting thrombin, Factors Xa and IXa, but also Factors XIIa, XIa, VIIa, kallicrein, and plasmin. Its activity is highly enhanced by heparin, through binding to the pentasaccharide sequences, for inhibition of all coagulation proteases, except thrombin, which inhibition requires its additional binding to the heparin polysaccharide chain. However, AT is the major inhibitor of thrombin in the blood circulation. Congenital or acquired deficiencies of AT expose affected patients to an increased risk of developing unprovoked and recurrent thrombo-embolic diseases...
April 19, 2018: Transfusion and Apheresis Science
https://www.readbyqxmd.com/read/29784465/-proper-use-of-fluoroquinolones-in-hospitalized-elderly-patients-realisation-of-a-clinical-audit-in-geriatric-hospitals-of-lyon-university-hospital
#19
C Papailhau, S Gaujard, R Girard, L Bourguignon, C Mouchoux
INTRODUCTION: Fluoroquinolones (FQ) are widely used because of their broad spectrum and their ease of use, especially in the elderly. Nevertheless, their misuse is behind the development and the emergence of bacterial resistances. The objective of this study was to evaluate the compliance of FQ prescriptions in the elderly hospitalized, before and after pharmaceutical interventions (PI). METHODS: A prospective clinical audit was conducted for three months in three geriatric hospitals...
May 18, 2018: La Revue de Médecine Interne
https://www.readbyqxmd.com/read/29784393/interactions-of-pyrene-and-or-1-hydroxypyrene-with-bovine-serum-albumin-based-on-eem-parafac-combined-with-molecular-docking
#20
Jing Zhang, Linfeng Chen, Dan Liu, Yaxian Zhu, Yong Zhang
The interactions of pyrene (Pyr) and/or 1-hydroxypyrene (1-OHPyr) with bovine serum albumin (BSA) in binary and ternary systems were investigated using the excitation-emission matrix (EEM)-parallel factor analysis (PARAFAC) method combined with fluorescence quenching analysis and the molecular docking method. The results showed that the PARAFAC approach could be used to decompose the EEM spectra of Pyr, 1-OHPyr, and BSA in the binary and ternary systems. The binding constants of Pyr and 1-OHPyr with BSA increased from 1...
August 15, 2018: Talanta
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