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Biochemistry

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https://www.readbyqxmd.com/read/29792689/selectivity-within-a-family-of-bacterial-phosphothreonine-lyases
#1
Kaitlin A Chambers, Nile S Abularrage, Rebecca A Scheck
Phosphothreonine lyases are bacterial effector proteins secreted into host cells to facilitate the infection process. This enzyme family catalyzes an irreversible elimination reaction that converts phosphothreonine or phosphoserine to dehydrobutyrine or dehydroalanine, respectively. Herein we report a study of substrate selectivity for each of the four known phosphothreonine lyases. This was accomplished using a combination of mass spectrometry and enzyme kinetics assays for a series of phosphorylated peptides derived from the mitogen activated protein kinase (MAPK) activation loop...
May 24, 2018: Biochemistry
https://www.readbyqxmd.com/read/29792687/co-mobility-of-gabarap-and-phosphatidylinositol-4-kinase-2a-on-cytoplasmic-vesicles
#2
Yan Chen, Hui-Qiao Sun, John P Eichorst, Joseph P Albanesi, Helen Yin, Joachim D Mueller
We previously reported that recruitment of the Type IIA phosphatidylinositol 4-kinase (PI4K2A) to autophagosomes by GABARAP, a member of the Atg8 family of autophagy-related proteins, is important for autophagosome-lysosome fusion. Because both PI4K2A and GABARAP have also been implicated in the intracellular trafficking of plasma membrane receptors in the secretory/endocytic pathway, we characterized their interaction in cells under non-autophagic conditions. Fluorescence fluctuation spectroscopy measurements revealed that GABARAP exists predominantly as a cytosolic monomer in live cells, but is recruited to small cytoplasmic vesicles upon overexpression of PI4K2A...
May 24, 2018: Biochemistry
https://www.readbyqxmd.com/read/29792686/high-throughput-screens-for-cis-acting-rna-sequence-elements-that-promote-nuclear-retention
#3
Kathi Zarnack, Michaela Müller-McNicoll
No abstract text is available yet for this article.
May 24, 2018: Biochemistry
https://www.readbyqxmd.com/read/29792023/fern-9-11-ene-2%C3%AE-3%C3%AE-diol-action-on-insulin-secretion-in-hyperglycemic-conditions
#4
Allisson Jhonatan Gomes Castro, Luisa Helena Cazarolli, Gabrielle Da Luz, Delsi Altenhofen, Hemily Batista Da Silva, Francieli Kanumfre Carvalho, Moacir Geraldo Pizzolatti, Fátima Rmb Silva
The objective of this study was to investigate the effect and the mechanism of action of fernenediol as insulin secretagogue. Wistar rats were treated with 0.1; 1 and 10 mg/kg fernenediol and then induced hyperglycemia by oral glucose. The glycaemia, insulin, LDH, calcium and hepatic glycogen were analyzed. Considering the intestine and pancreas as targets for the triterpene action, the duodenum was used to verify the influence of fernenediol on intestinal glycosidases. Additionally, pancreatic islets were used for studies of 14 C-deoxyglucose uptake and influx of 45 Ca2+ in hyperglycemic medium with/without fernenediol in the presence/absence of an inhibitor/activator of KATP channels, glibenclamide, diazoxide, nifedipine, calcium chelator (BAPTA- AM) and H-89 and ST the inhibitors of the PKA and PKC enzymes...
May 24, 2018: Biochemistry
https://www.readbyqxmd.com/read/29791793/assays-for-nucleotide-competitive-reversible-and-irreversible-inhibitors-of-ras-gtpases
#5
Sadasivam Jeganathan, Matthias Philipp Müller, Ali Imtiaz, Roger S Goody
Although the Ras protein has been seen as a potential target for cancer therapy for the past 30 years, there was a tendency to consider it undruggable until recently. This has changed with the demonstration that small molecules with specifcity for (disease related mutants of) Ras can indeed be found, and some of these molecules form covalent adducts. A subgroup of these molecules can be characterized as competing with binding of the natural ligands GTP and GDP. Because of the distinct properties of Ras and related GTPases, in particular the very high nucleotide affinities and associated very low dissociation rates, assays for characterizing such molecules are not trivial...
May 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29791145/slow-starter-enzymes-role-of-active-site-architecture-in-the-catalytic-control-in-the-biosynthesis-of-taxadiene-by-taxadiene-synthase
#6
Tamar Ansbacher, Yehoshua Freud, Dan Thomas Major
Taxadiene synthase (TXS) catalyzes the formation of the natural product Taxa-4(5),11(12)-diene (henceforth Taxadiene). Taxadiene is the precursor in the formation of Taxol, which is an important natural anti-cancer agent. In the current study, we present a detailed mechanistic view of the biosynthesis of Taxadiene by TXS, using a hybrid quantum mechanics-molecular mechanics potential in conjunction with free energy simulation methods. The obtained free energy landscape displays initial endergonic steps followed by a step-wise downhill profile, which is an emerging free energy fingerprint for type I terpene synthases...
May 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29791142/reassessment-of-the-transport-mechanism-of-the-human-zinc-transporter-slc39a2
#7
Marie Christine Franz, Jonai Pujol-Gimenez, Nicolas Montalbetti, Miguel Fernandez-Tenorio, Timothy R DeGrado, Ernst Niggli, Michael F Romero, Matthias A Hediger
The human zinc transporter SLC39A2, also known as ZIP2, was shown to mediate zinc transport that could be inhibited at pH values below 7.0 and stimulated by HCO3-, suggesting a Zn2+/HCO3- cotransport mechanism (1). In contrast, recent experiments in our laboratory indicated that the functional activity of ZIP2 increases at acidic pH (2). The present study was therefore designed to reexamine the findings on the pH-dependence and to extend the functional characterization of ZIP2. Our current results show that ZIP2-mediated transport is modulated by extracellular pH, but independent of the H+ driving force...
May 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29791133/design-construction-and-validation-of-histone-binding-effectors-in-vitro-and-in-cells
#8
Stefan J Tekel, Cassandra M Barrett, Daniel A Vargas, Karmella A Haynes
Chromatin is a system of nuclear proteins and nucleic acids that plays a pivotal role in gene expression and cell behavior, and is therefore the subject of intense study for cell development and cancer research. Biochemistry, crystallography, and reverse genetics have elucidated the macromolecular interactions that drive chromatin regulation. One of the central mechanisms is the recognition of post translational modifications (PTMs) on histone proteins by a family of nuclear proteins known as "readers...
May 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29790347/hydrophobic-collapse-of-ubiquitin-generates-rapid-protein-water-motions
#9
Hanna Wirtz, Sarah Schaefer, Claudius Hoberg, Korey M Reid, David M Leitner, Martina Havenith
We report time resolved measurements of the coupled protein-water modes of solvated ubiquitin during protein folding. Kinetic terahertz absorption (KITA) spectroscopy serves as a label-free technique to monitor large-scale conformational changes and folding of proteins subsequent to a sudden T-jump. Our KITA measurements reveal a significant change in the coupled ubiquitin-solvent dynamics even in the initial phase of hydrophobic collapse. Complementary equilibrium experiments and molecular simulations of ubiquitin solutions were carried out to clarify non-equilibrium contributions and reveal the molecular picture upon structural change, respectively...
May 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29787249/structure-function-relationships-in-the-oligomeric-nadph-dependent-assimilatory-sulfite-reductase
#10
Isabel Askenasy, Daniel Murray, Rachel M Andrews, Vladimir N Uversky, Huan He, M Elizabeth Stroupe
The central step in the assimilation of sulfur is a six-electron reduction of sulfite to sulfide, catalyzed by the oxidoreductase NADPH-dependent assimilatory Sulfite Reductase (SiR). SiR is composed of two subunits. One is a multi-domain flavin-binding reductase (SiRFP) and the other an iron-containing oxidase (SiRHP). Both enzymes are primarily globular, as expected from their functions as redox enzymes. Consequently, we know a fair amount about their structures but not how they assemble. Curiously, both structures have conspicuous regions that are structurally undefined, leaving questions about their functions and raising the possibility that they are critical in forming the larger complex...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29787246/investigation-of-solvent-hydron-exchange-in-the-reaction-catalyzed-by-the-antibiotic-resistance-protein-cfr
#11
Matthew R Bauerle, Tyler L Grove, Squire J Booker
Cfr is a radical S-adenosylmethionine (RS) methylase that appends methyl groups to C8 and C2 of adenosine 2503 in 23S ribosomal RNA. Methylation of C8 confers resistance to several classes of antibiotics that bind in or near the peptidyl transferase center of the bacterial ribosome, including the synthetic antibiotic linezolid. The Cfr reaction requires the action of five conserved cysteines, three of which ligate a required [4Fe-4S] cluster cofactor. The two remaining cysteines play a more intricate role in the reaction, one of which (Cys338) becoming transiently methylated during catalysis...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29787243/benchmark-analysis-of-native-and-artificial-nad-dependent-enzymes-generated-by-a-sequence-based-design-method-with-or-without-phylogenetic-data
#12
Shogo Nakano, Tomoharu Motoyama, Yurina Miyashita, Yuki Ishizuka, Naoya Matsuo, Hiroaki Tokiwa, Suguru Shinoda, Yasuhisa Asano, Sohei Ito
The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full consensus design (FCD) and ancestral sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial L-threonine 3-dehydrogenase (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1 and AncTDH, using FCD and ASR, respectively...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29787242/membrane-topology-of-trafficking-regulator-of-glut4-1-trarg1
#13
Xiaowen Duan, James Krycer, Kristen Cooke, Guang Yang, David E James, Daniel Fazakerley
Trafficking regulator of GLUT4 1 (TRARG1) was recently identified to localise to glucose transporter type 4 (GLUT4) storage vesicles (GSVs) and to positively regulate GLUT4 trafficking. Our knowledge of TRARG1 structure and membrane topology is limited to predictive models, hampering efforts to further our mechanistic understanding of how it carries out its functions. Here, we use a combination of bioinformatics prediction tools and biochemical assays to define the membrane topology of the 173-amino acid mouse TRARG1...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29787240/sulfonium-ion-condensation-the-burden-borne-by-sam-synthetase
#14
Charles A Lewis, Richard Wolfenden
S-Adenosylmethionine (SAM+) serves as the prin-cipal methylating agent in biological systems, but the thermodynamic basis of its reactivity does not appear to have been established. Here, we show that methionine, methanol and H+ combine to form S-methylmethionine (SMM+) with a temperature-independent equilibrium constant of 9.9 M-2. The corresponding group transfer potential of SMM+, i. e. its free energy of hydrolysis at pH 7, is -8.2 kcal/mol. The "energy-rich" nature of sulfonium ions is related to the extreme acidity (pKa -5...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29787239/catalytic-bases-and-stereo-control-in-lamiaceae-class-ii-diterpene-cyclases
#15
Samuel Schulte, Kevin Potter, Cody Lemke, Reuben J Peters
Plants from the widespread Lamiaceae family produce many labdane-related diterpenoids, a number of which serve medicinal roles, and whose biosynthesis is initiated by class II diterpene cyclases (DTCs). These enzymes utilize a general acid-base catalyzed cyclo-isomerization reaction to produce various stereoisomers of the eponymous labdaenyl carbocation intermediate, which can then undergo rearrangement and/or the addition of water prior to terminating deprotonation. Identification of the pair of residues that cooperatively serve as the catalytic base in the DTCs that produce ent-copalyl diphosphate (CPP) required for gibberellin phytohormone biosynthesis in all vascular plants has led to insight into the addition of water as well as rearrangement...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29787228/cyanylated-cysteine-reports-site-specific-changes-at-protein-protein-binding-interfaces-without-perturbation
#16
Shannon R Dalton, Alice R Vienneau, Shana R Burstein, Rosalind J Xu, Sara Linse, Casey H Londergan
To investigate the cyanylated cysteine vibrational probe group's ability to report on binding-induced changes along a protein-protein interface, the probe group was incorporated at several sites in a peptide of the calmodulin (CaM) binding domain of skeletal muscle myosin light chain kinase. Isothermal titration calorimetry was used to determine the binding thermodynamics between calmodulin and each peptide. For all probe positions, the binding affinity was nearly identical to that of the unlabeled peptide...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29782795/rna-modulates-the-interaction-between-influenza-a-virus-ns1-and-human-pabp1
#17
Bryan H Arias-Mireles, Cyrus M de Rozieres, Kevin Ly, Simpson Joseph
Non-Structural Protein 1 (NS1) is a multifunctional protein involved in preventing host-interferon response in Influenza A Virus (IAV). Previous studies have indicated that NS1 also stimulates the translation of viral mRNA by binding to conserved sequences in the viral 5'-UTR. Additionally, NS1 binds to Poly (A) Binding Protein (PABP1) and eukaryotic Initiation Factor 4G (eIF4G). The interaction of NS1 with the viral 5'-UTR, PABP1, and eIF4G has been suggested to specifically enhance the translation of viral mRNAs...
May 21, 2018: Biochemistry
https://www.readbyqxmd.com/read/29775292/entropy-as-a-driver-of-selectivity-for-inhibitor-binding-to-histone-deacetylase-6
#18
Nicholas J Porter, Florence F Wagner, David W Christianson
Among the metal-dependent histone deacetylases, the class IIb isozyme HDAC6 is remarkable because of its role in the regulation of microtubule dynamics in the cytosol. Selective inhibition of HDAC6 results in microtubule hyperacetylation, leading to cell cycle arrest and apoptosis, which is a validated strategy for cancer chemotherapy and the treatment of other disorders. HDAC6 inhibitors generally consist of a Zn2+ -binding group such as a hydroxamate, a linker, and a capping group; the capping group is a critical determinant of isozyme selectivity...
May 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29771536/selective-removal-of-b800-bacteriochlorophyll-a-from-light-harvesting-complex-2-of-the-purple-photosynthetic-bacterium-phaeospirillum-molischianum
#19
Yoshitaka Saga, Keiya Hirota, Sayaka Matsui, Hitoshi Asakawa, Hiroshi Ishikita, Keisuke Saito
The selective removal of B800 bacteriochlorophyll (BChl) a from light-harvesting complex 2 (LH2) in purple photosynthetic bacteria is a clue about elucidation of the mechanism for the transfer of energy from these pigments to B850 BChl a and their roles in the LH2 protein structure. We demonstrated that the kinetics of the removal of B800 BChl a from two representative LH2 proteins derived from Phaeospirillum molischianum and Rhodoblastus acidophilus differed significantly, in contrast to the calculated binding enthalpy...
May 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29771508/comparison-of-kinetics-toxicity-oligomers-formation-and-membrane-binding-capacity-of-%C3%AE-synuclein-familial-mutations-at-a53-site-including-newly-discovered-a53v-mutation
#20
Ganesh M Mohite, Rakesh Kumar, Rajlaxmi Panigrahi, Ambuja Navalkar, Nitu Singh, Debalina Datta, Surabhi Mehra, Soumik Ray, Laxmikant G Gadhe, Subhadeep Das, Namrata Singh, Debdeep Chatterjee, Ashutosh Kumar, Samir K Maji
The involvement of α-synuclein (α-Syn) amyloid formation in Parkinson's disease (PD) pathogenesis is supported by the discovery of α-Syn gene (SNCA) mutations linked with familial PD, which are known to modulate the oligomerization and aggregation of α-Syn. Recently, the A53V mutation has been discovered, which leads to the late-onset PD. In the present study, we characterized for the first time the biophysical properties including the aggregation propensities, toxicity of aggregated species and membrane binding capability of A53V along with all familial mutations at A53 position...
May 17, 2018: Biochemistry
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