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https://www.readbyqxmd.com/read/28723955/crystal-structure-and-functional-characterization-of-an-isoaspartyl-dipeptidase-cpsiada-from-colwellia-psychrerythraea-strain-34h
#1
Sun-Ha Park, Chang Woo Lee, Sung Gu Lee, Seung Chul Shin, Hak Jun Kim, Hyun Park, Jun Hyuck Lee
Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site...
2017: PloS One
https://www.readbyqxmd.com/read/28719051/the-binding-mechanism-between-azoles-and-fgcyp51b-sterol-14%C3%AE-demethylase-of-fusarium-graminearum
#2
Hengwei Qian, Meilin Duan, Xiaomei Sun, Mengyu Chi, Ying Zhao, Wenxing Liang, Juan Du, Jinguang Huang, Baodu Li
BACKGROUND: Fusarium graminearum is the main pathogen of Fusarium Head Blight (FHB), a worldwide plant disease and one of the major wheat diseases in China. The control of the FHB is mainly dependent on the application of DMIs fungicides. Fungal sterol 14α-demethylase enzymes (CYP51) are the main target for DMIs fungicides. In order to investigate the binding mechanism between azoles and CYP51B in F.graminearum, the molecular modeling study and biological evaluation were performed. RESULTS: Firstly, the homology model based on the crystal structure of Aspergillus fumigatus was built...
July 18, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28718012/implant-decontamination-with-phosphoric-acid-during-surgical-peri-implantitis-treatment-a-rct
#3
Diederik F M Hentenaar, Yvonne C M De Waal, Hans Strooker, Henny J A Meijer, Arie-Jan Van Winkelhoff, Gerry M Raghoebar
BACKGROUND: Peri-implantitis is known as an infectious disease that affects the peri-implant soft and hard tissue. Today, scientific literature provides very little evidence for an effective intervention protocol for treatment of peri-implantitis. The aim of the present randomized controlled trial is to evaluate the microbiological and clinical effectiveness of phosphoric acid as a decontaminating agent of the implant surface during surgical peri-implantitis treatment. METHODS: Peri-implantitis lesions were treated with resective surgical treatment aimed at peri-implant granulation tissue removal, bone recontouring, and pocket elimination...
December 2017: International Journal of Implant Dentistry
https://www.readbyqxmd.com/read/28716949/biochemical-regulatory-features-of-aid-remain-conserved-from-lamprey-to-humans
#4
Emma M Quinlan, Justin J King, Chris T Amemiya, Ellen Hsu, Mani Larijani
Activation induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to non-specific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation...
July 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28716734/crystal-structure-analysis-of-3-6-anhydro-l-galactonate-cycloisomerase-suggests-emergence-of-novel-substrate-specificity-in-the-enolase-superfamily
#5
Saeyoung Lee, Kyoung Heon Kim, Hye-Yeon Kim, In-Geol Choi
3,6-Anydro-l-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-l-galactonic acid (AHGA) known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 Å and 2.6 Å resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common β-elimination reactions by α-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism...
July 14, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28715793/monitoring-in-vivo-metabolic-flux-with-a-designed-whole-cell-metabolite-biosensor-of-shikimic-acid
#6
Heng Li, Chaoning Liang, Wei Chen, Jian-Ming Jin, Shuang-Yan Tang, Yong Tao
Knowledge of intracellular metabolite levels is important for the understanding of metabolic flux distributions. Whole-cell biosensors of key metabolites are ideal for the monitoring of carbon flow in important metabolic pathways, thus guiding metabolic engineering for microbial improvement. However, lack of biosensors for metabolites of interests has limited their applications. In this study, a genetically encoded whole-cell biosensor specifically responding to shikimic acid has been developed by screening a site-saturation mutagenesis library of the binding pocket of a uric acid-responsive regulatory protein...
July 11, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28715213/probing-the-hydrophobic-binding-pocket-of-g-protein-coupled-lysophosphatidylserine-receptor-gpr34-lps1-by-docking-aided-structure-activity-analysis
#7
Misa Sayama, Asuka Inoue, Sho Nakamura, Sejin Jung, Masaya Ikubo, Yuko Otani, Akiharu Uwamizu, Takayuki Kishi, Kumiko Makide, Junken Aoki, Takatsugu Hirokawa, Tomohiko Ohwada
The ligands of certain G-protein-coupled receptors (GPCRs) have been identified as endogenous lipids, such as lysophosphatidylserine (LysoPS). Here, we analyzed the molecular basis of the structure-activity relationship of ligands of GPR34, one of the LysoPS receptor subtypes, focusing on recognition of the long-chain fatty acid moiety by the hydrophobic pocket. By introducing benzene ring(s) into the fatty acid moiety of 2-deoxy-LysoPS, we explored the binding site's preference for the hydrophobic shape. A tribenzene-containing fatty acid surrogate with modifications of the terminal aromatic moiety showed potent agonistic activity toward GPR34...
July 17, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28712809/near-atomic-resolution-structure-of-a-plant-geminivirus-determined-by-electron-cryomicroscopy
#8
Katharina Hipp, Clemens Grimm, Holger Jeske, Bettina Böttcher
African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure...
July 5, 2017: Structure
https://www.readbyqxmd.com/read/28705120/qsar-docking-admet-system-pharmacology-studies-on-tormentic-acid-derivatives-for-anticancer-activity
#9
Sarfaraz Alam, Feroz Khan
To explore the anticancer compounds from tormentic acid derivatives, a quantitative structure-activity relationship (QSAR) model was developed by the multiple linear regression methods. The developed QSAR model yielded a high activity-descriptors relationship accuracy of 94% referred by regression coefficient (r(2)= 0.94) and a high activity prediction accuracy of 91%. The QSAR study indicates that chemical descriptors, chiV5, T_T_Cl_7, T_2_T_4, SsCH3count, and Epsilon3 are significantly correlated with anticancer activity...
July 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28696463/xanthine-oxidase-product-complexes-probe-the-importance-of-substrate-product-orientation-along-the-reaction-coordinate
#10
Jing Yang, Chao Dong, Martin L Kirk
A combination of reaction coordinate computations, resonance Raman spectroscopy, spectroscopic computations, and hydrogen bonding investigations have been used to understand the importance of substrate orientation along the xanthine oxidase reaction coordinate. Specifically, 4-thiolumazine and 2,4-dithiolumazine have been used as reducing substrates for xanthine oxidase to form stable enzyme-product charge transfer complexes suitable for spectroscopic study. Laser excitation into the near-infrared molybdenum-to-product charge transfer band produces rR enhancement patterns in the high frequency in-plane stretching region that directly probe the nature of this MLCT transition and provide insight into the effects of electron redistribution along the reaction coordinate between the transition state and the stable enzyme-product intermediate, including the role of the covalent Mo-O-C linkage in facilitating this process...
July 11, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28692513/viability-and-biomechanics-of-diced-cartilage-blended-with-platelet-rich-plasma-and-wrapped-with-poly-lactic-co-glycolic-acid-membrane
#11
Jun-Lin Liao, Jia Chen, Bin He, Yong Chen, Jia-Qun Xu, Hong-Ju Xie, Feng Hu, Ai-Jun Wang, ChengQun Luo, Qing-Feng Li, Jian-Da Zhou
OBJECTIVES: The objective of this study was to investigate the viability and biomechanics of diced cartilage blended with platelet-rich plasma (PRP) and wrapped with poly (lactic-co-glycolic) acid (PLGA) membrane in a rabbit model. METHODS: A total of 10 New Zealand rabbits were used for the study. Cartilage grafts were harvested from 1 side ear. The grafts were divided into 3 groups for comparison: bare diced cartilage, diced cartilage wrapped with PLGA membrane, and diced cartilage blended with PRP and wrapped with PLGA membrane...
July 7, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28692281/structural-and-biophysical-characterization-of-the-mycobacterium-tuberculosis-protein-rv0577-a-protein-associated-with-neutral-red-staining-of-virulent-tuberculosis-strains-and-homolog-of-the-streptomyces-coelicolor-protein-kbpa
#12
Garry W Buchko, Nathanial Echols, E Megan Flynn, Ho Ng, Sam Stephenson, Heung-Bok Kim, Peter J Myler, Thomas C Terwilliger, Tom Alber, Chang-Yub Kim
The 261-residue Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the responsible component for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has 36% amino acid sequence identity to Streptomyces coelicolor AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomycetes genus from which many commercial antibiotics are derived...
July 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28691247/crystal-structure-of-the-ubr-box-from-ubr6-fbxo11-reveals-a-domain-swapping-mediated-by-zinc-binding
#13
Juliana Muñoz-Escobar, Guennadi Kozlov, Kalle Gehring
The UBR-box is a 70-residue zinc finger domain present in the UBR family of E3 ubiquitin ligases that directly binds N-terminal degradation signals in substrate proteins. UBR6, also called FBXO11, is an UBR-box containing E3 ubiquitin ligase that does not bind N-terminal signals. Here, we present the crystal structure of the UBR-box domain from human UBR6. The dimeric crystal structure reveals a unique form of domain swapping mediated by zinc coordination, where three independent protein chains come together to regenerate the topology of the monomeric UBR-box fold...
July 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28689968/the-ribosomal-protein-ul22-modulates-the-shape-of-the-protein-exit-tunnel
#14
Itai Wekselman, Ella Zimmerman, Chen Davidovich, Matthew Belousoff, Donna Matzov, Miri Krupkin, Haim Rozenberg, Anat Bashan, Gilgi Friedlander, Jette Kjeldgaard, Hanne Ingmer, Lasse Lindahl, Janice M Zengel, Ada Yonath
Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the β hairpin of uL22 that renders resistance to erythromycin...
June 21, 2017: Structure
https://www.readbyqxmd.com/read/28688388/liberation-of-h2-from-o-c6h4me-3p-h-h-b-p-c6f4h-3-ion-pair-a-transition-state-in-the-minimum-energy-path-versus-the-transient-species-in-born-oppenheimer-molecular-dynamics
#15
Maoping Pu, Mojgan Heshmat, Timofei Privalov
Using Born-Oppenheimer molecular dynamics (BOMD) with density functional theory, transition-state (TS) calculations, and the quantitative energy decomposition analysis (EDA), we examined the mechanism of H2-liberation from LB-H((+)) + ((-))H-LA ion-pair, 1, in which the Lewis base (LB) is (o-C6H4Me)3P and the Lewis acid (LA) is B(p-C6F4H)3. BOMD simulations indicate that the path of H2 liberation from the ion-pair 1 goes via the short-lived transient species, LB⋯H2⋯LA, which are structurally reminiscent of the TS-structure in the minimum-energy-path describing the reversible reaction between H2 and (o-C6H4Me)3P/B(p-C6F4H)3 frustrated Lewis pair (FLP)...
July 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28688220/assessment-of-the-protein-interaction-between-coagulation-factor-xii-and-corn-trypsin-inhibitor-by-molecular-docking-and-biochemical-validation
#16
Badraldin K Hamad, Monika Pathak, Rosa Manna, Peter M Fischer, Jonas Emsley, Lodewijk V Dekker
BACKGROUND: Corn trypsin inhibitor (CTI) has selectivity for serine proteases coagulation factor XII (FXII) and trypsin. CTI is in widespread use as a reagent that specifically inhibits the intrinsic pathway of blood coagulation but not the extrinsic pathway. OBJECTIVES: To investigate the molecular basis of FXII inhibition by CTI. METHODS: We performed molecular docking of CTI, using its known crystal structure, with a model of the activated FXII (FXIIa) protease domain...
July 8, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28687529/design-synthesis-and-biological-evaluation-of-2-4-dihydropyrano-2-3-c-pyrazole-derivatives-as-autotaxin-inhibitors
#17
Tatu Pantsar, Prosanta Singha, Tapio J Nevalainen, Igor Koshevoy, Jukka Leppänen, Antti Poso, Juha M A Niskanen, Sanna Pasonen-Seppänen, Juha R Savinainen, Tuomo Laitinen, Jarmo T Laitinen
Inhibition of Autotaxin (ATX) is a potential treatment strategy for several diseases, including tumors with elevated ATX-lysophosphatidic acid (LPA) signaling. Combining structure-based virtual screening together with hen egg-white Autotaxin (ewATX) activity assays enabled the discovery of novel small-molecule ATX inhibitors with a 2,4-dihydropyrano[2,3-c]pyrazole scaffold. These compounds are suggested to bind to the lipophilic pocket, leaving the active site unrestrained. Our most potent compound, (S)-6-amino-4-(3,4-dichlorophenyl)-3-(4-[(4-fluorobenzyl)oxy]phenyl)-2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile [(S)-25], inhibited human ATX (hATX) with an IC50-value of 134nM...
July 5, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28686246/an-inhibition-mechanism-of-dihydromyricetin-on-tyrosinase-and-the-joint-effects-of-vitamins-b6-d3-or-e
#18
Meihui Fan, Guowen Zhang, Junhui Pan, Deming Gong
Dihydromyricetin (DMY), a natural flavonoid, was found to effectively inhibit tyrosinase activity in a mixed-type manner with an IC50 value of (3.66 ± 0.14) × 10(-5) mol L(-1). DMY combined with the dietary vitamin D3 at lower concentrations exhibited a synergistic effect on the inhibition of tyrosinase. The formation of a DMY-tyrosinase complex led to fluorescence quenching and conformational changes of tyrosinase, which was driven mainly by hydrophobic interactions and hydrogen bonds. The molecular simulation further found that DMY inserted into the active pocket of tyrosinase interacted with amino acid residues Tyr78, His85, and Ala323, occupying the catalytic center of tyrosinase to hinder entrance of the substrate, leading to the inhibition of tyrosinase...
July 19, 2017: Food & Function
https://www.readbyqxmd.com/read/28683334/in%C3%A2-vitro-assessment-of-phthalate-acid-esters-trypsin-complex-formation
#19
Zhenxing Chi, Jing Zhao, Weiguo Li, Arash Araghi, Songwen Tan
In this work, interactions of three phthalate acid esters (PAEs), including dimethyl phthalate (DMP), diethyl phthalate (DEP) and dibutyl phthalate (DBP), with trypsin have been studied in vitro, under simulated physiological conditions using multi-spectroscopic techniques and molecular modeling. The results show that these PAEs can bind to the trypsin, forming trypsin-PAEs complexes, mainly via hydrophobic interactions, with the affinity order of DMP > DEP > DBP. Binding to the PAEs is found to result in molecular deformation of trypsin...
July 1, 2017: Chemosphere
https://www.readbyqxmd.com/read/28680153/disruption-of-key-nadh-binding-pocket-residues-of-the-mycobacterium-tuberculosis-inha-affects-dd-coa-binding-ability
#20
Daniel J Shaw, Kirsty Robb, Beatrice V Vetter, Madeline Tong, Virginie Molle, Neil T Hunt, Paul A Hoskisson
Tuberculosis (TB) is a global health problem that affects over 10 million people. There is an urgent need to develop novel antimicrobial therapies to combat TB. To achieve this, a thorough understanding of key validated drug targets is required. The enoyl reductase InhA, responsible for synthesis of essential mycolic acids in the mycobacterial cell wall, is the target for the frontline anti-TB drug isoniazid. To better understand the activity of this protein a series of mutants, targeted to the NADH co-factor binding pocket were created...
July 5, 2017: Scientific Reports
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