Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions.


:Urea lesions are formed in DNA because of free radical damage of the thymine base, and their occurrence in DNA blocks DNA polymerases, which has deleterious consequences. Recently, it has been shown that urea is capable of forming hydrogen bonding and stacking interactions with nucleobases, which are responsible for the unfolding of RNA in aqueous urea. Base pairing and stacking are inherent properties of nucleobases; because urea is able to form both, this study attempts to investigate if urea can mimic nucleobases in the context of nucleic acid structures by examining the effect of introducing urea lesions complementary to the four different nucleobases on the overall helical integrity of B-DNA duplexes and their thermodynamic stabilities using molecular dynamics (MD) simulations. The MD simulations resulted in stable duplexes without significant changes in the global B-DNA conformation. The urea lesions occupy intrahelical positions by forming hydrogen bonds with nitrogenous nucleobases, in agreement with experimental results. Furthermore, these urea lesions form hydrogen bonding and stacking interactions with other nucleobases of the same and partner strands, analogous to nucleobases in typical B-DNA duplexes. Direct hydrogen bond interactions are observed for the urea-purine pairs within DNA duplexes, whereas two different modes of pairing, namely, direct hydrogen bonds and water-mediated hydrogen bonds, are observed for the urea-pyrimidine pairs. The latter explains the complexities involved in interpreting the experimental nuclear magnetic resonance data reported previously. Binding free energy calculations were further performed to confirm the thermodynamic stability of the urea-incorporated DNA duplexes with respect to pure duplexes. This study suggests that urea mimics nucleobases by pairing opposite all four nucleobases and maintains the overall structure of the B-DNA duplexes.






Suresh G,Padhi S,Patil I,Priyakumar UD




Has Abstract


2016-10-11 00:00:00












  • In vitro interaction between ceruloplasmin and human serum transferrin.

    abstract::The thermodynamics of the interactions of serum apotransferrin (T) and holotransferrin (TFe(2)) with ceruloplasmin (Cp), as well as those of human lactoferrin (Lf), were assessed by fluorescence emission spectroscopy. Cp interacts with two Lf molecules. The first interaction depends on pH and μ, whereas the second doe...


    pub_type: 杂志文章


    authors: Ha-Duong NT,Eid C,Hémadi M,El Hage Chahine JM

    更新日期:2010-12-07 00:00:00

  • Dimerization specificity of adult and neonatal chicken skeletal muscle myosin heavy chain rods.

    abstract::The dimerization specificity of the recombinantly expressed and purified rod domain of adult and neonatal chicken myosin heavy chain was analyzed using metal chelation chromatography. Our results indicate that full-length adult and neonatal rods preferentially formed homodimers when renatured from an equimolar mixture...


    pub_type: 杂志文章


    authors: Singh S,Bandman E

    更新日期:2006-04-18 00:00:00

  • Progressive Rod-Cone Degeneration (PRCD) Protein Requires N-Terminal S-Acylation and Rhodopsin Binding for Photoreceptor Outer Segment Localization and Maintaining Intracellular Stability.

    abstract::The light-sensing outer segments of photoreceptor cells harbor hundreds of flattened membranous discs containing the visual pigment, rhodopsin, and all the proteins necessary for visual signal transduction. PRCD (progressive rod-cone degeneration) protein is one of a few proteins residing specifically in photoreceptor...


    pub_type: 杂志文章


    authors: Spencer WJ,Pearring JN,Salinas RY,Loiselle DR,Skiba NP,Arshavsky VY

    更新日期:2016-09-13 00:00:00

  • A deuterium surface coil NMR study of the metabolism of D-methionine in the liver of the anesthetized rat.

    abstract::The hepatic metabolism of deuteriated D-methionine has been studied in the intact, anesthetized rat using 2H NMR spectroscopy. The rate of formation of the principal labeled metabolite, [methyl-2H3]sarcosine, from the D-[methyl-2H3]methionine precursor was found to be as rapid as the rate observed previously in NMR st...


    pub_type: 杂志文章


    authors: London RE,Gabel SA

    更新日期:1988-10-04 00:00:00

  • Phospholipase Cβ3 Membrane Adsorption and Activation Are Regulated by Its C-Terminal Domains and Phosphatidylinositol 4,5-Bisphosphate.

    abstract::Phospholipase Cβ (PLCβ) enzymes hydrolyze phosphatidylinositol 4,5-bisphosphate to produce second messengers that regulate intracellular Ca2+, cell proliferation, and survival. Their activity is dependent upon interfacial activation that occurs upon localization to cell membranes. However, the molecular basis for how ...


    pub_type: 杂志文章


    authors: Hudson BN,Hyun SH,Thompson DH,Lyon AM

    更新日期:2017-10-17 00:00:00

  • Recognition by the thyroid hormone receptor of canonical DNA response elements.

    abstract::To shed more light on the molecular requirements for recognition of thyroid response elements (TREs) by thyroid receptors (TRs), we compared the specific aspects of DNA TRE recognition by different TR constructs. Using fluorescence anisotropy, we performed a detailed and hierarchical study of TR-TRE binding. This was ...


    pub_type: 杂志文章


    authors: Figueira AC,Lima LM,Lima LH,Ranzani AT,Mule Gdos S,Polikarpov I

    更新日期:2010-02-09 00:00:00

  • Specific interaction between ribosomal protein S4 and the alpha operon messenger RNA.

    abstract::The Escherichia coli ribosomal protein S4 is known to repress translation of its own gene and several other ribosomal protein (r-protein) genes in the alpha operon as part of a general mechanism coordinating the levels of rRNA and r-protein synthesis. Using a filter binding assay and RNA transcripts prepared in vitro,...


    pub_type: 杂志文章


    authors: Deckman IC,Draper DE

    更新日期:1985-12-31 00:00:00

  • Sites of covalent attachment of CYP4 enzymes to heme: evidence for microheterogeneity of P450 heme orientation.

    abstract::Typical cytochrome P450s secure the heme prosthetic group with a cysteine thiolate ligand bound to the iron, electrostatic interactions with the heme propionate carboxylates, and hydrophobic interactions with the heme periphery. In addition to these interactions, CYP4B1 covalently binds heme through a monoester link f...


    pub_type: 杂志文章


    authors: Baer BR,Schuman JT,Campbell AP,Cheesman MJ,Nakano M,Moguilevsky N,Kunze KL,Rettie AE

    更新日期:2005-10-25 00:00:00

  • Catalytic function and local proton structure at the type 2 copper of nitrite reductase: the correlation of enzymatic pH dependence, conserved residues, and proton hyperfine structure.

    abstract::Electron nuclear double resonance (ENDOR) of protons at Type 2 and Type 1 cupric active sites correlates with the enzymatic pH dependence, the mutation of nearby conserved, nonligating residues, and electron transfer in heterologously expressed Rhodobacter sphaeroides nitrite reductase. Wild-type enzyme showed a pH 6 ...


    pub_type: 杂志文章


    authors: Zhao Y,Lukoyanov DA,Toropov YV,Wu K,Shapleigh JP,Scholes CP

    更新日期:2002-06-11 00:00:00

  • Limited proteolysis as a probe of the conformation and nucleic acid binding regions of nucleolin.

    abstract::Nucleolin, also called protein C23, is a RNA-associated protein implicated in the early stages of ribosome assembly. To study the general conformation and map the nucleic acid binding regions, rat nucleolin was subjected to limited proteolysis using trypsin and chymotrypsin in the presence or absence of poly(G). The c...


    pub_type: 杂志文章


    authors: Olson MO,Kirstein MN,Wallace MO

    更新日期:1990-06-19 00:00:00

  • Rate constants in two dimensions of electron transfer between pyruvate oxidase, a membrane enzyme, and ubiquinone (coenzyme Q8), its water-insoluble electron carrier.

    abstract::The functionality of the membrane-bound, ubiquinone-dependent pyruvate oxidase from the respiratory chain of Escherichia coli was reconstituted with a supported lipidic structure. The artificial structure was especially designed to allow the electrochemical control of the quinone pool through the lateral mobility of t...


    pub_type: 杂志文章


    authors: Marchal D,Pantigny J,Laval JM,Moiroux J,Bourdillon C

    更新日期:2001-02-06 00:00:00

  • Purification, characterization, and inhibition of peptide deformylase from Escherichia coli.

    abstract::Peptide deformylase (EC catalyzes the removal of a formyl group from the N-termini of nascent ribosome-synthesized polypeptides, an obligatory step during protein maturation in eubacteria. Since its discovery in crude Escherichia coli extracts 3 decades ago, the deformylase has resisted all attempts of purif...


    pub_type: 杂志文章


    authors: Rajagopalan PT,Datta A,Pei D

    更新日期:1997-11-11 00:00:00

  • Properties of Paracoccus denitrificans amicyanin.

    abstract::Paracoccus denitrificans synthesizes an inducible, periplasmic, blue copper protein [Husain, M., & Davidson, V.L. (1985) J. Biol. Chem. 260, 14626-14629] that can be classified as an amicyanin on the basis of its ability to accept electrons from methylamine dehydrogenase. The amino acid composition and sequence of the...


    pub_type: 杂志文章


    authors: Husain M,Davidson VL,Smith AJ

    更新日期:1986-05-06 00:00:00

  • The subcellular distribution of adenylate and guanylate cyclases in murine lymphoid cells.

    abstract::Membrane vesicles can be prepared from murine lymphoid cells by nitrogen cavitation and fractionated by sedimentation through nonlinear sucrose density gradients. Two subpopulations of membrane vesicles, PMI and PMII, can be distinguished on the basis of sedimentation rate. The subcellular distribution of adenylate an...


    pub_type: 杂志文章


    authors: Watson J,Nilsen-Hamilton M,Hamilton RT

    更新日期:1976-04-06 00:00:00

  • Another role for CO with nitrogenase? CO stimulates hydrogen evolution catalyzed by variant Azotobacter vinelandii Mo-nitrogenases.

    abstract::A likely entry/exit path for nitrogenase substrates, products, and/or protons involves residues α277(Arg), α192(Ser), and α356(Gly), all of which are highly conserved among MoFe proteins from different organisms. The α192(Ser) and α277(Arg) residues form part of a hydrogen-bonded network that also involves α195(His), ...


    pub_type: 杂志文章


    authors: Fisher K,Hare ND,Newton WE

    更新日期:2014-10-07 00:00:00

  • Kinetics of the subtransition of asymmetrically substituted phosphatidylcholines.

    abstract::The thermodynamics and kinetics of the subtransition L epsilon----P beta of sonicated unilamellar vesicles of 1-myristoyl-2-stearoylphosphatidylcholine (1M-2S-PC) and of 1-stearoyl-2-myristoylphosphatidylcholine (1S-2M-PC) were studied by equilibrium cooling curves and temperature-jump relaxation spectrometry with an ...


    pub_type: 杂志文章


    authors: Tümmler B,Herrmann U,Maass G,Eibl H

    更新日期:1984-08-28 00:00:00

  • Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,).

    abstract::In globular proteins, there are intermolecular hydrogen bonds between protein and water molecules, and between water molecules, which are bound with the proteins, in addition to intramolecular hydrogen bonds. To estimate the contribution of these hydrogen bonds to the conformational stability of a protein, the thermod...


    pub_type: 杂志文章


    authors: Takano K,Yamagata Y,Funahashi J,Hioki Y,Kuramitsu S,Yutani K

    更新日期:1999-09-28 00:00:00

  • The nitrite anion binds to human hemoglobin via the uncommon O-nitrito mode.

    abstract::The nitrite anion is known to oxidize and degrade hemoglobin (Hb). Recent literature reports suggest a nitrite reductase activity for Hb, converting nitrite into nitric oxide. Surprisingly, no structural information about Hb-nitrite interactions has been reported. We have determined the crystal structure of the ferric...


    pub_type: 杂志文章


    authors: Yi J,Safo MK,Richter-Addo GB

    更新日期:2008-08-12 00:00:00

  • Dissection of porphyrin-induced conformational dynamics in the heme biosynthesis enzyme ferrochelatase.

    abstract::Human ferrochelatase (EC catalyzes the insertion ferrous iron into protoporphyrin IX as the last step in heme biosynthesis, an essential process to most organisms given the vast intracellular functions of heme. Even with multiple ferrochelatase structures available, the exact mechanism for iron insertion int...


    pub_type: 杂志文章


    authors: Asuru AP,An M,Busenlehner LS

    更新日期:2012-09-11 00:00:00

  • Cyclic peptides incorporating 4-carboxyphenylalanine and phosphotyrosine are potent inhibitors of pp60(c-)(src).

    abstract::The protein tyrosine kinase, pp60(c-)(src), is involved in cellular signaling and is activated during mitosis and in various tumors. We have been employing cyclic decapeptides to identify the determinants for substrate binding and phosphorylation to develop inhibitors competitive with protein substrates of Src. A stru...


    pub_type: 杂志文章


    authors: Wang W,Ramdas L,Sun G,Ke S,Obeyesekere NU,Budde RJ,McMurray JS

    更新日期:2000-05-02 00:00:00

  • Nematode Sgt1-homologue D1054.3 binds open and closed conformations of Hsp90 via distinct binding sites.

    abstract::Heat shock protein 90 (Hsp90) is a highly conserved ATP-driven machine involved in client protein maturation, folding, and activation. The chaperone is supported by a set of cochaperones that confer client specificities. One of those proteins is the suppressor of G2 allele of skp1 (Sgt1), which participates together w...


    pub_type: 杂志文章


    authors: Eckl JM,Drazic A,Rutz DA,Richter K

    更新日期:2014-04-22 00:00:00

  • Identification of the catalytic nucleophile of tRNA (m5U54)methyltransferase.

    abstract::A covalent complex between tRNA (m5U54)methyltransferase, 5-fluorouridine tRNA(Phe), and S-adenosyl-L-[methyl-3H]methionine was formed in vitro and purified. Previously, it was shown that in this complex the 6-position of fluorouridine-54 is covalently linked to a catalytic nucleophile and the 5-position is bound to t...


    pub_type: 杂志文章


    authors: Kealey JT,Santi DV

    更新日期:1991-10-08 00:00:00

  • Distribution of cytokinin-active nucleosides in isoaccepting transfer ribonucleic acids from Agrobacterium tumefaciens.

    abstract::The cytokinin-active isoprenoid nucleosides of Agrobacterium tumefaciens transfer ribonucleic acid were identified by high-pressure liquid chromatography, permethylation, and mass spectroscopy. Besides the expected 6-[(3-methylbut-2-enyl)amino]-9-(beta-D-ribofuranosyl)purine (i6A) and its 2-methylthio derivative (ms2i...


    pub_type: 杂志文章


    authors: Morris RO,Regier DA,Olson RM Jr,Struxness LA,Armstrong DJ

    更新日期:1981-10-13 00:00:00

  • Solution structure of oxidized cytochrome c6 from the green alga Monoraphidium braunii.

    abstract::Cytochrome c6 from Monoraphidium braunii, an 89-amino acid electron transfer protein, has been investigated by NMR in solution, in its oxidized form, at pH 7 and 300 K. By using a combination of COSY, TOCSY, and NOESY experiments, 84% of the proton resonances have been assigned. A total of 1668 experimental NOE constr...


    pub_type: 杂志文章


    authors: Banci L,Bertini I,De la Rosa MA,Koulougliotis D,Navarro JA,Walter O

    更新日期:1998-04-07 00:00:00

  • Thiophilic adsorption: a comparison of model protein behavior.

    abstract::A newly recognized type of protein-ligand interaction phenomenon has resulted in the preparation of simple, nonionic, and highly specific gel derivatives for selective adsorption chromatography. The essential structure of the immobilized ligand can be represented as agarose-CH2CH2SO2CH2CH2SCH2CH2OH, which was prepared...


    pub_type: 杂志文章


    authors: Hutchens TW,Porath J

    更新日期:1987-11-03 00:00:00

  • Unexpected findings from target analysis of immunoglobulin E and its receptor.

    abstract::The membrane receptor for immunoglobulin E (IgE) and its ligand, IgE, were irradiated with high-energy electrons. Loss of binding activity was measured for each, and the size of the functional targets was assessed. In both cases, the target size was substantially smaller than the covalent structure of the molecule. Th...


    pub_type: 杂志文章


    authors: Fewtrell C,Kempner E,Poy G,Metzger H

    更新日期:1981-11-10 00:00:00

  • Implication of His68 in the substrate site of Bacillus subtilis adenylosuccinate lyase by mutagenesis and affinity labeling with 2-[(4-bromo-2,3-dioxobutyl)thio]adenosine 5'-monophosphate.

    abstract::Adenylosuccinate lyase of Bacillus subtilis is inactivated by 2-[(4-bromo-2,3-dioxobutyl)thio]adenosine 5'-monophosphate (2-BDB-TAMP) at pH 7.0. As the reagent concentration is increased, a maximum rate constant is approached, indicative of reversible enzyme-reagent complex formation (KR = 68 +/- 9 microM) prior to ir...


    pub_type: 杂志文章


    authors: Lee TT,Worby C,Bao ZQ,Dixon JE,Colman RF

    更新日期:1998-06-09 00:00:00

  • Structural consequences of cysteinylation of Cu/Zn-superoxide dismutase.

    abstract::The metalloenzyme Cu/Zn-superoxide dismutase (SOD1) catalyzes the reduction of superoxide anions into molecular oxygen and hydrogen peroxide. Hydrogen peroxide can oxidize SOD1, resulting in aberrant protein conformational changes, disruption of SOD1 function, and DNA damage. Cells may have evolved mechanisms of regul...


    pub_type: 杂志文章


    authors: Auclair JR,Brodkin HR,D'Aquino JA,Petsko GA,Ringe D,Agar JN

    更新日期:2013-09-10 00:00:00

  • Temperature dependence of the structure of the substrate and active site of the Thermus thermophilus chorismate mutase E x S complex.

    abstract::Molecular dynamics (MD) simulations of Thermus thermophilus chorismate mutase substrate complex (TtCM x S) have been carried out at 298 K, 333 K, and the temperature of optimum activity: 343 K. The enzyme exists as trimeric subunits with active sites shared between two neighboring subunits. Two features distinguish in...


    pub_type: 杂志文章


    authors: Zhang X,Bruice TC

    更新日期:2006-07-18 00:00:00

  • Calcium-modulated guanylate cyclase transduction machinery in the photoreceptor--bipolar synaptic region.

    abstract::Rod outer segment membrane guanylate cyclase (ROS-GC) transduction system is a central component of the Ca(2+)-sensitive phototransduction machinery. The system is composed of two parts: Ca(2+) sensor guanylate cyclase activating protein (GCAP) and ROS-GC. GCAP senses Ca(2+) impulses and inhibits the cyclase. This ope...


    pub_type: 杂志文章


    authors: Venkataraman V,Duda T,Vardi N,Koch KW,Sharma RK

    更新日期:2003-05-20 00:00:00