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Biochemistry

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https://www.readbyqxmd.com/read/29350905/ampulexins-a-new-family-of-peptides-in-venom-of-the-emerald-jewel-wasp-ampulex-compressa
#1
Eugene Moore, Ryan Arvidson, Christopher Banks, Jean Urenda, Elizabeth Duong, Haroun Mohammad, Michael E Adams
The parasitoid wasp Ampulex compressa injects venom directly into the brain and subesophageal ganglion of the cockroach Periplaneta americana, inducing a seven to ten day lethargy termed hypokinesia. Hypokinesia presents as a significant reduction in both escape response and spontaneous walking. We examined aminergic and peptidergic components of milked venom with HPLC and MALDI-TOF mass spectrometry. HPLC coupled with electrochemical detection confirmed presence of dopamine in milked venom, while mass spectrometry revealed that the venom gland and venom sac have distinct peptide profiles, with milked venom predominantly composed of venom sac peptides...
January 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29350031/microbiota-regulated-outcomes-of-human-cancer-immunotherapy-via-the-pd-1-pd-l1-axis
#2
Jaymin Patel, Jason M Crawford
No abstract text is available yet for this article.
January 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29346724/structural-and-biophysical-characterization-of-human-extl3-domain-organisation-glycosylation-and-solution-structure
#3
Wael Awad, Sven Kjellstrom, Gabriel Svensson Birkedal, Katrin Mani, Derek Thomas Logan
Heparan sulfate proteoglycans are proteins substituted with one or more heparan sulfate (HS) polysaccharides, found in abundance at cell surfaces. HS chains influence the activity of many biologically important molecules involved in cellular communication and signaling. The exostosin (EXT) proteins are glycosyltransferases in the Golgi apparatus that assemble HS chains on HSPGs. The EXTL3 enzyme mainly works as an initiator in HS biosynthesis. In this work, human lumenal N-glycosylated EXTL3 (EXTL3ΔN) was cloned, expressed in human embryonic kidney cells and purified...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345922/efficient-fusion-at-neutral-ph-by-human-immunodeficiency-virus-gp41-trimers-containing-the-fusion-peptide-and-transmembrane-domain
#4
Shuang Liang, Punsisi Ratnayake, Craig Keinath, Lihui Jia, Robert Wolfe, Ahinsa Ranaweera, David P Weliky
Human immunodeficiency virus (HIV) is membrane-enveloped and an initial infection step is joining/fusion of viral and cell membranes. This step is catalyzed by gp41 which is a single-pass integral viral membrane protein. The protein contains a ~170-residue ectodomain located outside the virus that is important for fusion, and includes the fusion peptide (FP), N-helix, loop, C-helix, and viral membrane-proximal external region (MPER). The virion initially has non-covalent complexes between three gp41 ectodomains and three gp120 proteins...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345921/molecular-mechanisms-in-the-selectivity-of-non-steroidal-anti-inflammatory-drugs
#5
Yasmin Shamsudin Khan, Hugo Gutiérrez de Terán, Johan Åqvist
Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX) 1 and 2 with varying degrees of selectivity. A group of COX-2 selective inhibitors - coxibs - bind in a time-dependent manner through a three-step mechanism, utilizing a side-pocket in the binding site. Coxibs have been extensively probed to identify the structural features regulating the slow tight-binding mechanism responsible for COX-2 selectivity. In this study, we further probe a structurally and kinetically diverse data set of COX inhibitors in COX-2 by molecular dynamics and free energy simulations...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345920/acetylation-by-eis-and-deacetylation-by-rv1151c-of-mycobacterium-tuberculosis-hupb-biochemical-and-structural-insight
#6
Keith D Green, Tapan Biswas, Allan H Pang, Melisa J Willby, Matthew S Reed, Olga Stuchlik, Jan Pohl, James E Posey, Oleg V Tsodikov, Sylvie Garneau-Tsodikova
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345912/a-re-discovery-of-the-fom3-substrate
#7
Anthony J Blaszczyk, Squire J Booker
No abstract text is available yet for this article.
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345911/role-of-glycanation-and-convertase-maturation-of-the-soluble-glypican-3-in-inhibiting-proliferation-of-hepatocellular-carcinoma-cells
#8
Ahmad Saad, Benjamin Liet, Gilles Joucla, Xavier Santarelli, Justine Charpentier, Stéphane Claverol, Christophe F Grosset, Véronique Trézéguet
Glypican 3 (GPC3) is a complex heparan sulfate proteoglycan associated with the outer surface of the plasma membrane by a glycosyl-phosphatidylinositol anchor (GPI). It is also N-glycosylated and processed by a furine-like convertase. GPC3 has numerous biological functions. While undetectable in normal liver tissue, it is abnormally and highly overexpressed in hepatocellular carcinoma (HCC). Interestingly, proliferation of HCC cells such as HepG2 and HuH7 is inhibited when they express a soluble form of GPC3 after lentiviral transduction...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345908/a-small-molecule-inhibitor-of-human-dna-polymerase-eta-potentiates-the-effects-of-cisplatin-in-tumor-cells
#9
Maroof K Zafar, Leena Maddukuri, Amit Ketkar, Narsimha Penthala, Megan R Reed, Sarah D Eddy, Peter A Crooks, Robert L Eoff
Translesion DNA synthesis (TLS) performed by human DNA polymerase eta (hpol η) allows tolerance of damage from cis-diamminedichloroplatinum(II) (CDDP or cisplatin). We have developed hpol η inhibitors derived from N-aryl-substituted indole barbituric acid (IBA), indole thiobarbituric acid (ITBA), and indole quinuclidine scaffolds and identified 5-((5-chloro-1-(naphthalen-2-ylmethyl)-1H-indol-3-yl)methylene)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione (PNR-7-02), an ITBA derivative that inhibited hpol η activity with an IC50 value of 8 μM and exhibited five- to ten-fold specificity for hpol η over replicative pols...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345906/prediction-of-hot-spots-at-myeloid-cell-leukemia-1-inhibitors-interface-using-energy-estimation-and-alanine-scanning-mutagenesis
#10
Parthiban Marimuthu, Kalaimathy Singaravelu
Myeloid cell leukemia 1 (Mcl1) is an anti-apoptotic protein that plays central role in apoptosis regulation. Also, Mcl1 has the potency to resist apoptotic cues resulting in up-regulation and cancer cell protection. A molecular probe that has the potential to specifically target Mcl1, and thereby provoke its down-regulatory activity is very essential. The aim of the current study is to probe the internal conformational dynamics of protein motions and potential binding mechanism in response to a series of picomolar range Mcl1 inhibitors using explicit-solvent molecular dynamics (MD) simulations...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29341606/hogg1-removes-solution-accessible-8-oxog-lesions-from-globally-substituted-nucleosomes-except-at-the-dyad-region
#11
Katharina Bilotti, Mary E Tarantino, Sarah Delaney
Persistent DNA damage is responsible for mutagenesis, aging, and disease. Repair of the prototypic oxidatively damaged guanine lesion 8-oxo-7,8-dihydroguanine (8-oxoG) is initiated by oxoguanine glycosylase (hOGG1 in humans). In this work, we examine hOGG1 activity on DNA packaged as it is in chromatin, in a nucleosome core particle (NCP). We use synthetic methods to generate a population of NCPs with G to 8-oxoG substitutions and evaluate the global profile of hOGG1 repair in packaged DNA. For several turns of the helix, we observe that solution-accessible 8-oxoG are sites of activity for hOGG1...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29341605/prediction-of-active-site-and-distal-residues-in-e-coli-dna-polymerase-iii-alpha-polymerase-activity
#12
Ramya Parasuram, Timothy A Coulther, Judith M Hollander, Elise Keston-Smith, Mary Jo Ondrechen, Penny J Beuning
The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA Pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue Pol III alpha subunit is responsible for the polymerase activity and copies DNA accurately, making one error per 105 nucleotide incorporations. The goal of this research is to determine the residues that contribute to the activity of the polymerase subunit...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29341603/pokmt1-from-the-polyketomycin-biosynthetic-machinery-of-streptomyces-diastatochromogenes-t%C3%A3-6028-belongs-to-the-emerging-family-of-c-methyltransferases-that-act-on-coa-activated-aromatic-substrates
#13
Xun Guo, Ivana Crnovcic, Chin-Yuan Chang, Jun Luo, Jeremy R Lohman, Monica Papinski, Andreas Bechthold, Geoffrey P Horsman, Ben Shen
Recent biochemical characterizations of the MdpB2 CoA ligase and MdpB1 C-methyltransferase (C-MT) from the maduropeptin (MDP, 2) biosynthetic machinery revealed unusual pathway logic involving C-methylation occurring on a CoA-activated aromatic substrate. Here we confirmed this pathway logic for the biosynthesis of polyketomycin (POK, 3). Biochemical characterization unambiguously established that PokM3 and PokMT1 catalyze the sequential conversion of 6-methylsalicylic acid (6-MSA, 4) to form 3,6-dimethylsalicylyl-CoA (3,6-DMSA-CoA, 6), which serves as the direct precursor for the 3,6-dimethylsalicylic acid (3,6-DMSA) moiety in the biosynthesis of 3...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29341597/the-wyl-domain-of-the-pif1-helicase-from-the-thermophilic-bacterium-thermotoga-elfii-is-an-accessory-single-stranded-dna-binding-module
#14
Nicholas M Andis, Christopher W Sausen, Ashna Alladin, Matthew Bochman
PIF1 family helicases are conserved from bacteria to man. With the exception of the well-studied yeast PIF1 helicases (e.g., ScPif1 and ScRrm3), however, very little is known about how these enzymes help maintain genome stability. Indeed, we lack a basic understanding of the protein domains found N- and C-terminal to the characteristic central PIF1 helicase domain in these proteins. Here, using chimeric constructs, we show that the ScPif1 and ScRrm3 helicase domains are interchangeable and that the N-terminus of ScRrm3 is important for its function in vivo...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29341594/designing-flavoprotein-gfp-fusion-probes-for-analyte-specific-ratiometric-fluorescence-imaging
#15
Devin A Hudson, Jeffrey L Caplan, Colin Thorpe
The development of genetically encoded fluorescent probes for analyte-specific imaging has revolutionized our understanding of intracellular processes. Current classes of intracellular probes depend on the selection of binding domains that either undergo conformational changes on analyte binding or can be linked to thiol redox chemistry. Here we have designed novel probes by fusing a flavoenzyme, whose fluorescence is quenched on reduction by the analyte of interest, with a GFP domain to allow for rapid and specific ratiometric sensing...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29341593/analysis-of-cellular-tyrosine-phosphorylation-via-chemical-rescue-of-conditionally-active-abl-kinase
#16
Zhihong Wang, Min-Sik Kim, Isabel Martinez Ferrando, Anthony John Koleske, Akhilesh Pandey, Philip Arthur Cole
Identifying direct substrates targeted by protein kinases is important in understanding cellular physiology and intracellular signal transduction. Mass-spectrometry based quantitative proteomics provides a powerful tool for comprehensively characterizing the downstream substrates of protein kinases. This approach is efficiently applied to receptor kinases which can be precisely, directly, and rapidly activated by some agent, such as a growth factor. However, non-receptor tyrosine kinase Abl lacks the experimental advantage of extracellular growth factors as immediate and direct stimuli...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29338257/a-dynamic-protein-protein-coupling-between-the-tonb-dependent-transporter-fhua-and-tonb
#17
Jessica Sarver, Michael Zhang, Lishan Liu, David Nyenhuis, David S Cafiso
Bacterial outer membrane TonB-dependent transporters function by executing cycles of binding and unbinding to the inner membrane protein TonB. In the vitamin B12 transporter BtuB and the ferric citrate transporter FecA, substrate binding increases the periplasmic exposure of the Ton box, an energy-coupling segment. This increased exposure appears to enhance the affinity of the transporter for TonB. Here, continuous wave and pulse EPR spectroscopy were used to examine the state of the Ton box in the Escherichia coli ferrichrome transporter, FhuA...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29337541/enzyme-architecture-the-role-of-a-flexible-loop-in-activation-of-glycerol-3-phosphate-dehydrogenase-for-catalysis-of-hydride-transfer
#18
Rui He, Archie C Reyes, Tina L Amyes, John Richard
The side chain of Q295 of glycerol-3-phosphate dehydrogenase from human liver (hlGPDH) lies in a flexible loop. This loop folds over the phosphodianion of substrate dihydroxyacetone phosphate (DHAP), where Q295 interacts with the side chain cation from R269, which is ion-paired to the substrate phosphodianion. Kinetic parameters kcat/Km (M-1 s-1) and kcat/KGAKHPi (M-2 s-1) were determined, respectively, for catalysis of the reduction of DHAP and for dianion activation of catalysis of reduction of glycolaldeyde (GA) catalyzed by wildtype, Q295G, Q295S, Q295A, and Q295N mutants of hlGPDH...
January 16, 2018: Biochemistry
https://www.readbyqxmd.com/read/29336553/catalytic-mechanism-of-cruzain-from-trypanosoma-cruzi-as-determined-from-solvent-kinetic-isotope-effects-of-steady-state-and-pre-steady-state-kinetics
#19
Xiang Zhai, Thomas D Meek
Cruzain, an important drug target for Chagas disease, is a member of Clan CA of the cysteine proteases. Understanding the catalytic mechanism of cruzain is vital to the design of new inhibitors. To this end, we have performed pH-rate profiles for substrates and affinity agents, and have determined solvent kinetic isotope effects in pre-steady-state and steady-state modes using three substrates: Cbz-Phe-Arg-AMC, Cbz-Arg-Arg-AMC and Cbz-Arg-Ala-AMC. The pH-rate profile of kcat/Km for Cbz-Arg-Arg-AMC indicated groups of pK1 = 6...
January 16, 2018: Biochemistry
https://www.readbyqxmd.com/read/29334465/design-of-mini-nucleic-acid-probe-for-cooperative-binding-of-rna-repeated-transcript-associated-with-myotonic-dystrophy-type-1
#20
Wei-Che Hsieh, Raman Bahal, Shivaji Thadke, Kirti Bhatt, Krzysztof Sobczak, Charles A Thornton, Danith H Ly
Toxic RNAs containing expanded trinucleotide repeats are the cause of many neuromuscular disorders, one being myotonic dystrophy type 1 (DM1). DM1 is triggered by CTG-repeat expansion in the 3'-UTR of the DMPK gene, resulting in toxic-gain of RNA function through sequestration of MBNL1 protein, among others. Herein we report the development of a relatively short MPPNA probe, two triplet-repeats in length, containing terminal pyrene moieties, that is capable of binding rCUG-repeats in a sequence-specific and selective manner...
January 15, 2018: Biochemistry
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