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Elena Sugrue, Paul D Carr, Colin Scott, Colin J Jackson
The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little is known regarding how enzymes can naturally evolve active sites with highly reactive and desolvated charges. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214, Tyr215), whereas TrzN from Nocardioides sp...
October 21, 2016: Biochemistry
Purva P Bhojane, Michael R Duff, Khushboo Bafna, Gabriella P Rimmer, Pratul K Agarwal, Elizabeth E Howell
Folate, or vitamin B9, is an important compound in one carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium towards the free ligand and protein species. This study uses vapor pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value)...
October 21, 2016: Biochemistry
Allison B Norvil, Christopher J Petell, Lama Abdullah Alabdi, Lanchen Wu, Sandra Rossie, Humaira Gowher
The catalytic domains of the de novo DNA methyltransferases, Dnmt3a-C and Dnmt3b-C are highly homologous. However their unique biochemical properties could potentially contribute to differences in the substrate preferences or biological functions of these enzymes. Dnmt3a-C forms tetramers through interactions at the dimer interface, which also promote multimerization on DNA and cooperativity. Similar to processive enzymes, cooperativity allows Dnmt3a-C to methylate multiple sites on the same DNA molecule, however it is unclear whether Dnmt3b-C methylates DNA by cooperative or processive mechanism...
October 21, 2016: Biochemistry
Hongwei Yao, Myungwoon Lee, Shu Y Liao, Mei Hong
The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of the parainfluenza virus 5 (PIV5) fusion protein F using solid-state NMR...
October 21, 2016: Biochemistry
Gokul Turaga, Stephen P Edmondson, Kelley Smith, John William Shriver
The structure of Archaeal chromatin or nucleoid is believed to have characteristics similar to that found in both eukaryotes and bacteria. Recent comparative studies have suggested that DNA compaction in Archaea requires a bridging protein (e.g. Alba) along with either a wrapping protein (e.g. a histone) or a bending protein such as Sac7d. While x-ray crystal structures demonstrate that Sac7d binds as a monomer to create a significant kink in duplex DNA, the structure of a multiprotein-DNA complex has not been established...
October 21, 2016: Biochemistry
Ryo Amano, Kenta Takada, Yoichiro Tanaka, Yoshikazu Nakamura, Gota Kawai, Tomoko Kozu, Taiichi Sakamoto
AML1 (RUNX1) protein is an essential transcription factor involved in the development of hematopoietic cells. Several genetic aberrations that disrupt the function of AML1 have been frequently observed in human leukemia. AML1 contains a DNA-binding domain known as the Runt domain (RD), which recognizes the RD-binding double-stranded DNA element of target genes. In this study, we identified high-affinity RNA aptamers that bind to RD by SELEX. The binding assay using surface plasmon resonance indicated that a shortened aptamer retained the ability to bind to RD when 1 M potassium acetate was used...
October 21, 2016: Biochemistry
Susith Wickramaratne, Douglas M Banda, Shaofei Ji, Amelia H Manlove, Bhaskar Malayappan, Nicole N Nuñez, Leona Samson, Colin Campbell, Sheila S David, Natalia Tretyakova
The important industrial and environmental carcinogen 1,3-butadiene (BD) forms a range of adenine adducts in DNA, including N(6)-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine (N(6)-HB-dA), 1,N(6)-(2-hydroxy-3-hydroxymethylpropan-1,3-diyl)-2'-deoxyadenosine (1,N(6)-HMHP-dA), and N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine (N(6),N(6)-DHB-dA). If not removed prior to DNA replication, these lesions can contribute to A → T and A → G mutations commonly observed following exposure to BD and its metabolites...
October 21, 2016: Biochemistry
Xiaohua Zhang, Sami Caner, Emily Kwan, Chunmin Li, Gary D Brayer, Stephen G Withers
Starch provides the major source of caloric intake in many diets. Cleavage of starch into malto-oligosaccharides in the gut is catalyzed by pancreatic alpha-amylase. These oligosaccharides are then further cleaved by gut wall alpha-glucosidases to release glucose, which is absorbed into the bloodstream. Potential surface binding sites for starch on the pancreatic amylase, distinct from the active site of the amylase, have been identified through X-ray crystallographic analyses. The role of these sites in the degradation of both starch granules and soluble starch was probed by the generation of a series of surface variants modified at each site to disrupt binding...
October 19, 2016: Biochemistry
Adam E Brummett, Mishtu Dey
The marine microbial catabolism of dimethylsulfoniopropionate (DMSP) by the lyase pathway liberates ~300 million tons of dimethylsulfide (DMS) per year, which plays a major role in the biogeochemical cycling of sulfur. Recent biochemical and structural studies of some DMSP lyases, including DddQ reveal the importance of divalent transition metal ions in assisting DMSP cleavage. While DddQ is believed to be zinc-dependent primarily based on structural studies, excess zinc inhibits the enzyme. We examine the importance of iron in regulating the DMSP β-elimination reaction catalyzed by DddQ as our as-isolated purple-colored enzyme possesses ~0...
October 18, 2016: Biochemistry
Karan Kapoor, Michael R Duff, Amit Upadhyay, Joel C Bucci, Arnold M Saxton, Robert J Hinde, Elizabeth E Howell, Jerome Yves Baudry
The dynamics of anion-quadrupole (or anion-) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (PDB: 1EP0), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-anion--) are formed by the protein during the simulated trajectory which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1...
October 18, 2016: Biochemistry
Tiernan Thomas O'Malley, William M Wittbold, Sara Linse, Dominic M Walsh
Extracts of Alzheimer's disease (AD) brain that contain what appear to be SDS-stable amyloid β-protein (Aβ) dimers potently block LTP and impair memory consolidation. Brain-derived dimers can be physically separated from Aβ monomer, consist primarily of Aβ42 and resist denaturation by powerful chaotropic agents. In nature, covalently cross-linked Aβ dimers could be generated in only one of two different ways - either by the formation of a dityrosine (DiY) or an isopeptide ε-(γ-glutamyl)-lysine (Q-K) bond...
October 17, 2016: Biochemistry
L Tyler Mix, Julia Kirpich, Masato Kumauchi, Jie Ren, Mikas Vengris, Wouter D Hoff, Delmar S Larsen
We explored the photoisomerization mechanisms in novel homologs of Photoactive Yellow Protein (PYP) from Leptospira biflexa to identify conserved features and functional diversity in the primary photochemistry of this family of photoreceptors. In close agreement with the prototypical PYP from Halorhodospira halophila, we observe excited state absorbance near 375 nm and stimulated emission near 500 nm, with triphasic excited state decay. While the excited state decay for Lbif PYP is the slowest among known PYPs due to the redistribution of the amplitudes of the three decay components, the quantum yield for productive photocycle entry is very similar to that of Hhal PYP...
October 17, 2016: Biochemistry
Simone Morra, Mariaconcetta Arizzi, Francesca Valetti, Gianfranco Gilardi
The newly isolated Clostridium beijerinckii [FeFe]-hydrogenase CbA5H was characterized by Fourier transform infrared spectroscopy coupled to enzymatic activity assays. This showed for the first time that in this enzyme the oxygen-sensitive active state Hox can be simply and reversibly converted to the oxygen-stable inactive Hinact state. This suggests that oxygen sensitivity is not an intrinsic feature of the catalytic center of [FeFe]-hydrogenases (H-cluster), opening new challenging perspectives on the oxygen sensitivity mechanism as well as new possibilities for exploitation in industrial applications...
October 17, 2016: Biochemistry
Salette Martinez, Robert P Hausinger
The ethylene-forming enzyme (EFE) from Pseudomonas syringae pv. phaseolicola PK2 is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. This enzyme is reported to simultaneously catalyze the conversion of 2OG into ethylene plus three CO2 and the Cδ hydroxylation of L-arginine (L-Arg) while oxidatively decarboxylating 2OG to form succinate and carbon dioxide. A new plasmid construct for expression in recombinant Escherichia coli cells allowed for the purification of large amounts of EFE with greater activity than previously recorded...
October 17, 2016: Biochemistry
Ian M Robertson, Sandra E Pineda-Sanabria, Ziqian Yan, Thomas Kampourakis, Yin-Biao Sun, Brian D Sykes, Malcolm Irving
The binding of Ca(2+) to cardiac troponin C (cTnC) triggers contraction in heart muscle. In the diseased heart, the myocardium is often desensitized to Ca(2+), which leads to impaired contractility. Therefore, compounds that sensitize cardiac muscle to Ca(2+) (Ca(2+)-sensitizers) have therapeutic promise. The only Ca(2+)-sensitizer used regularly in clinical settings is levosimendan. While the primary target of levosimendan is thought to be cTnC, the molecular details of this interaction are not well understood...
October 17, 2016: Biochemistry
Elizaveta A Kovrigina, Brian Pattengale, Chuanwu Xia, Azamat R Galiakhmetov, Jier Huang, Jung-Ja P Kim, Evgenii L Kovrigin
NADPH-cytochrome P450 oxidoreductase (CYPOR) was demonstrated to undergo large conformational rearrangements in its functional cycle. Using a new FRET approach based on femtosecond transient absorption spectroscopy (TA), we determined the donor-acceptor distance distribution in the reduced and oxidized states of CYPOR. Unmatched time resolution of TA enabled the quantitative assessment of the donor-acceptor FRET indicating that CYPOR assumes a closed conformation in both reduced and oxidized states in the absence of the redox partner...
October 14, 2016: Biochemistry
Mona A Alqazzaz, Kerry L Price, Sarah C R Lummis
Cys-loop receptors play important roles in signal transduction in multicellular organisms, but similar proteins exist in prokaryotes, the best studied of which is the Gloeobacter ligand-gated ion channel (GLIC). GLIC is activated by protons with 50% activation (pH50) at pH 5.5, and while a histidine residue in its pore-forming α-helix (M2) is known to be involved in gating, there is also evidence of a proton-sensitive region in the extracellular domain. However, this proton-sensitive region does not appear to be located in the region of GLIC equivalent to the agonist binding site in related proteins...
October 14, 2016: Biochemistry
Marat R Talipov, Jaladhi Nayak, Michael Lepley, Robert D Bongard, Daniel S Sem, Ramani Ramchandran, Rajendra Rathore
DUSP5 is an inducible nuclear dual-specificity phosphatase that specifically interacts with and deactivates extracellular signal-regulated kinases ERK1 and ERK2, which are responsible for cell proliferation, differentiation, and survival. The phosphatase domain (PD) of DUSP5 has unique structural features absent in other nuclear DUSPs, such as presence of a secondary anion-binding site in the proximity to the reaction center and a glutamic acid E264 positioned next to the catalytic cysteine C263, as well as a remote intra-molecular disulfide linkage...
October 14, 2016: Biochemistry
M Moazzem Hossain, Guangyi Zhao, Moon-Sook Woo, James H-C Wang, Jian-Ping Jin
Cell traction force (CTF) plays a critical role in controlling cell shape, enabling cell motility, and maintaining cellular homeostasis in many biological processes such as angiogenesis, development, wound healing, and cancer metastasis. Calponin is an actin filament-associated cytoskeletal protein in smooth muscles and multiple types of non-muscle cells. An established biochemical function of calponin is the inhibition of myosin ATPase in smooth muscle cells. Vertebrates have three calponin isoforms. Among them, calponin 2 is expressed in epithelial cells, endothelial cells, macrophages, myoblasts and fibroblasts, and plays a role in regulating cytoskeleton activities such as cell adhesion, migration and cytokinesis...
October 13, 2016: Biochemistry
Federico M Issoglio, Nicolas Campolo, Ari Zeida, Tilman Grune, Rafael Radi, Dario A Estrin, Silvina Bartesaghi
Glutamine synthetase is an important enzyme that catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. In mammals, it plays a key role in preventing excitotoxicity in the brain and detoxifying ammonia in the liver. In plants and bacteria, it is fundamental for nitrogen metabolism, being critical for the survival of the organism. In this work, we show how the use of classical molecular dynamics simulations and multiscale quantum mechanics/molecular mechanics simulations allowed us to examine the structural properties and dynamics of human glutamine synthetase (HsGS), as well as the reaction mechanisms involved in the catalytic process with atomic level detail...
October 13, 2016: Biochemistry
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