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Biochemistry

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https://www.readbyqxmd.com/read/28549218/exosite-2-directed-ligands-attenuate-protein-c-activation-by-the-thrombin-thrombomodulin-complex
#1
Kai Chen, Alan R Stafford, Chengliang Wu, Calvin Yeh, Paul Y Kim, James C Fredenburgh, Jeffrey I Weitz
Thrombin activity, inhibition, and localization are regulated by two exosites that flank the active site. Substrates, cofactors and inhibitors bind to exosite 1 to promote active site access, whereas exosite 2 interactions retain thrombin on cells, platelets, and proteins. The exosites also serve allosteric roles, whereby ligand binding alters thrombin activity. Previously, we showed that ligands that bind exosite 2 attenuate the exosite 1-mediated interaction of thrombin with fibrin, demonstrating allosteric connection between the exosites...
May 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28549213/binding-of-copper-and-cisplatin-to-atox1-is-mediated-by-glutathione-through-the-formation-of-metal-sulfur-clusters
#2
Nataliya V Dolgova, Corey Yu, John P Cvitkovic, Miroslav Hodak, Kurt Nienaber, Kelly Lynn Summers, Julien Cotelesage, Jerzy Bernholc, George A Kaminski, Ingrid J Pickering, Graham N George, Oleg Y Dmitriev
Copper is an essential nutrient required for many biological processes involved in primary metabolism, but free cop-per is toxic due to its ability to catalyze formation of free radicals. To prevent toxic effects, in the cell copper is bound to proteins and low molecular weight compounds, such as glutathione, at all times. The widely used chemotherapy agent cisplatin is known to bind to copper-transporting proteins, including copper chaperone Atox1. Cisplatin interac-tions with Atox1 and other copper transporters are linked to cancer resistance to platinum-based chemotherapy...
May 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28548844/two-dynamical-regimes-of-the-substrate-radical-rearrangement-reaction-in-b12-dependent-ethanolamine-ammonia-lyase-resolve-contributions-of-native-protein-configurations-and-collective-configurational-fluctuations-to-catalysis
#3
Meghan Kohne, Chen Zhu, Kurt Warncke
The kinetics of the substrate radical rearrangement reaction step in B12-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium are measured over a 92 K temperature range. The observed first-order rate constants display a piecewise-continuous Arrhenius dependence, with linear regions over 295→220 K (monoexponential) and 214→203 K (biexponential) that are delineated by a kinetic bifurcation and kinks at 219 and 217 K, respectively. The results are interpreted by using a free energy landscape model and derived microscopic kinetic mechanism...
May 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28547993/conformational-heterogeneity-and-dna-recognition-by-the-morphogen-bicoid
#4
Ramkrishna Adhikary, Yun Xuan Tan, Jian Liu, Jörg Zimmermann, Matthew Holcomb, Carolyn Yvellez, Philip E Dawson, Floyd E Romesberg
The morphogenic activity of the Drosophila transcription factor bicoid (Bcd), the first morphogenic protein identified, is controlled by its DNA binding homeodomain. Homeodomains mediate developmental processes in all multicellular organisms, but the Bcd homeodomain appears to be unique as it can bind multiple DNA sequences and even RNA. All homeodomain proteins adopt a three-helix fold, with residues of the third helix mediating recognition of the nucleic acid target via interactions with the major groove...
May 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28539047/identifying-the-protein-interactions-of-the-cytosolic-iron-sulfur-cluster-targeting-complex-essential-for-its-assembly-and-recognition-of-apo-targets
#5
Amanda Thuy Van Vo, Nicholas M Fleischman, Mary J Froehlich, Claudia Y Lee, Jessica A Cosman, Calina A Glynn, Zanub O Hassan, Deborah L Perlstein
The cytosolic iron sulfur cluster assembly (CIA) system assembles iron sulfur (FeS) cluster cofactors and inserts them into >20 apo-protein targets residing in the cytosol and nucleus. Three CIA proteins, called Cia1, Cia2, and Met18 in yeast, form the targeting complex responsible for apo-target recognition. There is little information about the structure of this complex or its mechanism of CIA substrate recognition. Herein, we exploit affinity co-purification and size exclusion chromatography to determine the subunit connectivity and stoichiometry of the CIA targeting complex...
May 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28516764/an-autoinhibitory-role-for-the-pleckstrin-homology-domain-of-interleukin-2-inducible-tyrosine-kinase-and-its-interplay-with-canonical-phospholipid-recognition
#6
Sujan Devkota, Raji E Joseph, Scott E Boyken, D Bruce Fulton, Amy H Andreotti
Pleckstrin homology (PH) domains are well-known as phospholipid binding modules, yet evidence that PH domain function extends beyond lipid recognition is mounting. In this work, we characterize a protein binding function for the PH domain of interleukin-2-inducible tyrosine kinase (ITK), an immune cell specific signaling protein that belongs to the TEC family of nonreceptor tyrosine kinases. Its N-terminal PH domain is a well-characterized lipid binding module that localizes ITK to the membrane via phosphatidylinositol 3,4,5-trisphosphate (PIP3) binding...
May 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28513152/a-molecular-mechanism-for-nonphotochemical-quenching-in-cyanobacteria
#7
Yue Lu, Haijun Liu, Rafael Saer, Veronica L Li, Hao Zhang, Liuqing Shi, Carrie Goodson, Michael L Gross, Robert E Blankenship
The cyanobacterial orange carotenoid protein (OCP) protects photosynthetic cyanobacteria from photodamage by dissipating excess excitation energy collected by phycobilisomes (PBS) as heat. Dissociation of the PBS-OCP complex in vivo is facilitated by another protein known as the fluorescence recovery protein (FRP), which primarily exists as a dimeric complex. We used various mass spectrometry (MS)-based techniques to investigate the molecular mechanism of this FRP-mediated process. FRP in the dimeric state (dFRP) retains its high affinity for the C-terminal domain (CTD) of OCP in the red state (OCP(r))...
May 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28538097/biochemical-characterization-of-the-functional-roles-of-residues-in-the-active-site-of-the-%C3%AE-galactosidase-from-bacillus-circulans-atcc-31382
#8
Huifang Yin, Tjaard Pijning, Xiangfeng Meng, Lubbert Dijkhuizen, Sander Sebastiaan van Leeuwen
The β-galactosidase enzyme from Bacillus circulans ATCC 31382 BgaD is widely used in the food industry to produce prebiotic galactooligosaccharides (GOS). Recently, the crystal structure of a C-terminally truncated version of the enzyme (BgaD-D) has been elucidated. The roles of active site amino acid residues in β-galactosidase enzyme reaction and product specificity have remained unknown. Based on a structural alignment of the β-galactosidase enzymes BgaD-D from Bacillus circulans and BgaA from Streptococcus pneumoniae, and the complex of BgaA with LacNAc, we identified 8 active site amino acid residues (Arg185, Asp481, Lys487, Tyr511, Trp570, Trp593, Glu601, and Phe616) in BgaD-D...
May 24, 2017: Biochemistry
https://www.readbyqxmd.com/read/28535337/overall-structural-model-of-ns5a-protein-from-hepatitis-c-virus-and-modulation-by-mutations-confering-resistance-of-virus-replication-to-cyclosporin-a
#9
Aurelie Badillo, Veronique Brechot, Stephane Sarrazin, François-Xavier Cantrelle, Frederic Delolme, Marie-Laure Fogeron, Jennifer Molle, Roland Montserret, Anja Bockmann, Ralf Bartenschlager, Volker Lohmann, Guy Lippens, Sylvie Ricard-Blum, Xavier Hanoulle, Francois Penin
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a RNA-binding phosphoprotein composed of a N-terminal membrane anchor (AH), a structured domain 1 (D1) and two intrinsically disordered domains (D2 and D3). The knowledge of the functional architecture of this multifunctional protein remains limited. We report here that NS5A-D1D2D3 produced in a wheat germ cell-free system is obtained under a highly phosphorylated state. Its NMR analysis revealed that these phosphorylations do not change the disordered nature of D2 and D3 domains but increase the number of conformers due to partial phosphorylations...
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28535029/the-quaternary-structure-of-the-r-state-of-escherichia-coli-aspartate-transcarbamoylase-in-solution-is-different-from-that-in-the-crystal-and-is-modified-by-mg-2-%C3%A2-atp-binding
#10
https://www.readbyqxmd.com/read/28534615/origins-of-water-molecules-in-the-photosystem-ii-crystal-structure
#11
Naoki Sakashita, Hiroshi C Watanabe, Takuya Ikeda, Keisuke Saito, Hiroshi Ishikita
The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region...
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28534610/application-of-the-halogen-bond-in-protein-systems
#12
Máté Erdélyi
No abstract text is available yet for this article.
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28514140/properties-of-intermediates-in-the-catalytic-cycle-of-oxalate-oxidoreductase-and-its-suicide-inactivation-by-pyruvate
#13
Elizabeth Pierce, Steven O Mansoorabadi, Mehmet Can, George H Reed, Stephen W Ragsdale
Oxalate:ferredoxin oxidoreductase (OOR) is an unusual member of the thiamine pyrophosphate (TPP)-dependent 2-oxoacid:ferredoxin oxidoreductase (OFOR) family in that it catalyzes the coenzyme A (CoA)-independent conversion of oxalate into 2 equivalents of carbon dioxide. This reaction is surprising because binding of CoA to the acyl-TPP intermediate of other OFORs results in formation of a CoA ester, and in the case of pyruvate:ferredoxin oxidoreductase (PFOR), CoA binding generates the central metabolic intermediate acetyl-CoA and promotes a 10(5)-fold acceleration of the rate of electron transfer...
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28509550/sugars-require-rigid-multivalent-displays-for-activation-of-mouse-sperm-acrosomal-exocytosis
#14
He Huang, Maria T Rodolis, Surita R Bhatia, Nicole S Sampson
As a prerequisite to mammalian fertilization, the sperm acrosomal vesicle fuses with the plasma membrane and the acrosome contents are exocytosed. Induction occurs through engagement of the sperm receptors by multiple sugar residues. Multivalent polymers displaying mannose, fucose, or GlcNAc are effective synthetic inducers of mouse sperm acrosomal exocytosis (AE). Each carbohydrate is proposed to have a distinct binding site on the sperm cell surface. To determine the role of the scaffold structure in the efficiency of AE induction, different polymer backbones were employed to display the different activating sugar residues...
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28530801/hydrogen-bonding-environment-of-the-n3-h-group-of-fmn-in-the-lov-domains-of-phototropins
#15
Tatsuya Iwata, Dai Nozaki, Atsushi Yamamoto, Takayuki Koyama, Yasuzo Nishina, Kiyoshi Shiga, Satoru Tokutomi, Masashi Unno, Hideki Kandori
LOV (light-oxygen-voltage) domain is a flavin-binding blue-light receptor domain originally found in plant phototropin, a photoreceptor for phototropism, chloroplast movement and stomata opening. LOV domains are available as optogenetics tools for photosensory domain of fusion proteins. Therefore, it is important to investigate how LOV domains show light-induced structural changes not only for the elucidation of regulation mechanism of kinase domain but also for the appropriate activation of other functional domains by LOV domain...
May 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28530393/structural-factors-that-alter-the-redox-potential-of-quinones-in-cyanobacterial-and-plant-photosystem-i
#16
Keisuke Kawashima, Hiroshi Ishikita
Using the cyanobacterial and plant photosystem I (PSI) crystal structures and by considering the protonation states of all titratable residues, redox potentials (Em) of the two phylloquinones--A1A and A1B--were calculated. The calculated Em values were Em(A1A) = -773 mV and Em(A1B) = -818 mV for the plant PSI structure and Em(A1A) = -612 mV and Em(A1B) = -719 mV for the cyanobacterial PSI structure. Our analysis of the PSI crystal structures suggested that the side-chain orientations of Lys-B542 and Gln-B678 in the cyanobacterial crystal structure differ from these side-chain orientations in the plant crystal structure...
May 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28530384/divalent-metal-ion-activation-of-a-guanine-general-base-in-the-hammerhead-ribozyme-insights-from-molecular-simulations
#17
Haoyuan Chen, Timothy J Giese, Barbara L Golden, Darrin M York
The hammerhead ribozyme is a well-studied nucleolytic ribozyme that catalyzes the self-cleavage of the RNA phosphodiester backbone. Despite experimental and theoretical efforts, there remain key questions about details of the mechanism with regard to the activation of the nucleophile by the putative general base guanine (G12). Straight-forward interpretation of the measured activity-pH data implies the pKa value of the N1 position in the G12 nucleobase is significantly shifted by the ribozyme environment. Recent crystallographic and biochemical work has identified pH-dependent divalent metal ion binding at the N7/O6 position of G12, leading to the hypothesis that this binding mode could induce a pKa shift of G12 towards neutrality...
May 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28530094/troponin-c-mutations-partially-stabilize-the-active-state-of-regulated-actin-and-fully-stabilize-the-active-state-when-paired-with-%C3%AE-14-tnt
#18
Tamatha Baxley, Dylan Johnson, Jose Renato Pinto, Joseph Michael Chalovich
Striated muscle contraction is regulated by the actin associated proteins tropomyosin and troponin. Activation of myosin ATPase activity is lowest in the absence of both Ca2+ and activating crossbridges (i.e. S1-ADP or rigor S1). Binding of activating species of myosin to actin at saturating Ca2+ stabilizes the most active state (M state) of actin-tropomyosin-troponin (regulated actin). Ca2+ binding alone produces partial stabilization of the active state. The extent of stabilization at saturating Ca2+ depends on the isoform of the troponin subunits, the phosphorylation state of troponin and, in the case of cardiac muscle, the presence of hypertrophic cardiomyopathy producing mutants of troponin T and troponin I...
May 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28494585/induced-fit-is-a-special-case-of-conformational-selection
#19
Pradipta Chakraborty, Enrico Di Cera
Conformational selection (CS) and induced fit (IF) are two widely used interpretations of binding of a ligand to biological macromolecules. Both mechanisms envision a two-step reaction in which a conformational transition either precedes (CS) or follows (IF) the binding step. Under pseudo-first-order conditions where the ligand is in excess compared to the macromolecule, both mechanisms produce two relaxations. A fast one eventually increases linearly with ligand concentration and reflects the binding interaction...
May 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28525271/electron-spin-relaxation-and-biochemical-characterization-of-the-hydrogenase-maturase-hydf-insights-into-2fe-2s-and-4fe-4s-cluster-communication-and-hydrogenase-activation
#20
Eric M Shepard, Amanda S Byer, Priyanka Aggarwal, Jeremiah N Betz, Anna G Scott, Krista Shisler, Robert J Usselman, Gareth R Eaton, Sandra S Eaton, Joan B Broderick
Nature utilizes [FeFe]-hydrogenase enzymes to catalyze the interconversion between H2 and protons and electrons. Catalysis occurs at the H-cluster, a carbon monoxide, cyanide, and dithiomethylamine-coordinated 2Fe subcluster bridged via a cysteine to a [4Fe-4S] cluster. Biosynthesis of this unique metallocofactor is accomplished by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG belong to the radical S-adenosylmethionine superfamily of enzymes and synthesize the nonprotein ligands of the H-cluster...
May 19, 2017: Biochemistry
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