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Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics

J. Norberg, L. Nilsson
1994 Biophysical Journal  
ABSIRACT Mocuar dynamic simaton were caied out on tw conformatdions of th dinudeoside guany1yl-3',5'-uridline (GpU) in aqueous soluion with one sockwn counterion.  ...  One staked conf in and one with the C3'-3'-P-0' trsion angle twisted 180°to crate an unstacked confoma We observed a relatively stable behavior of the smacked cnformato, whch retaied Sed throughout the  ...  Guschlbaer for discussion of earUier work on the dinucleotide GpU and Dr. T. Kulinsi and Pro£ R Rigler for experimental results.  ... 
doi:10.1016/s0006-3495(94)80541-7 pmid:7948694 pmcid:PMC1225424 fatcat:ud7l4zcoindr3n2jhmdgbqccfq

The orientation of eosin-5-maleimide on human erythrocyte band 3 measured by fluorescence polarization microscopy

S.M. Blackman, C.E. Cobb, A.H. Beth, D.W. Piston
1996 Biophysical Journal  
We have employed polarized fluorescence confocal microscopy to measure the orientation of eosin-5-maleimide covalently reacted with Lys-430 of human erythrocyte band 3.  ...  Delayed fluorescence and phosphorescence anisotropy decays of control and trypsin-treated band 3 in ghosts, analyzed as multiple uniaxially rotating populations using the amplitudes predicted by confocal  ...  DWP is a Beckman Young Investigator of the Arnold and Mabel Beckman Foundation. SMB is supported by National Institutes of Health training grant T32 GM07347.  ... 
doi:10.1016/s0006-3495(96)79216-0 pmid:8804603 pmcid:PMC1233471 fatcat:kainfqpky5b55egfsjzakokqry

Potent Inhibition of Mammalian Ribonucleases by 3′,5′-Pyrophosphate-linked Nucleotides

Nello Russo, Robert Shapiro
1999 Journal of Biological Chemistry  
The most potent of them, 5-phospho-2-deoxyuridine 3-pyrophosphate, P 3 5-ester with adenosine 3-phosphate (pdUp-pAp), binds to RNase A with K i values of 27 and 220 nM at pH 5.9 and 7, respectively.  ...  Molecular modeling based on the crystal structure of the complex of bovine pancreatic RNase A with the inhibitor 5-diphosphoadenosine 3-phosphate (ppAp) (Leonidas, D. D., Shapiro, R., Irons, L.  ...  James for providing the atomic coordinates of human RNase-2.  ... 
doi:10.1074/jbc.274.21.14902 pmid:10329690 fatcat:46abghyoc5gzzcf2i3csibafha

Synthesis and Properties of Energetic Hydrazinium 5-Nitro-3-dinitromethyl-2H-pyrazole by Unexpected Isomerization of N-Nitropyrazole

Yiying Zhang, Yanan Li, Tao Yu, Yingzhe Liu, Sanping Chen, Zhongxue Ge, Chenghui Sun, Siping Pang
2019 ACS Omega  
A new energetic salt, hydrazinium 5-nitro-3-dinitromethyl-2H-pyrazole, was synthesized using 1-nitro-3-trinitromethylpyrazole and hydrazine as raw materials and fully characterized by IR and NMR spectroscopy  ...  The salt has good density, high positive enthalpy of formation superior to those of the RDX and HMX, and good detonation properties comparable to those of RDX.  ...  ■ ACKNOWLEDGMENTS The authors acknowledge financial support from the National Natural Science Foundation of China (21576026, U153062, and 21805222).  ... 
doi:10.1021/acsomega.9b01910 pmid:31763523 pmcid:PMC6868590 fatcat:sowb46uwbba7rervpmc74xfcle

Preparation, Spectrochemical, and Computational Analysis of L-Carnosine (2-[(3-Aminopropanoyl)amino]-3-(1H-imidazol-5-yl)propanoic Acid) and Its Ruthenium (II) Coordination Complexes in Aqueous Solution

Michael Lee Branham, Parvesh Singh, Krishna Bisetty, Myalo Sabela, Thirumala Govender
2011 Molecules  
This study reports the synthesis and characterization of novel ruthenium (II) complexes with the polydentate dipeptide, L-carnosine (2-[(3-aminopropanoyl)amino]-3-(1H-imidazol-5-yl)propanoic acid).  ...  with equimolar amounts of ruthenium chloride (black-alpha form) at 60 °C for 36 h.  ...  Acknowledgements The authors are grateful to the South African National Research Foundation (NRF), University of KwaZulu-Natal, and Durban University of Technology for financial support.  ... 
doi:10.3390/molecules161210269 pmid:22158629 pmcid:PMC6264669 fatcat:lwnhb5jkkbgeflobrbkfvfzguu

A Weak Fano Threefold Arising as a Blowup of a Curve of Genus 5 and Degree 8 on P^3 [article]

Joseph W. Cutrone, Michael A. Limarzi, Nicholas A. Marshburn
2018 arXiv   pre-print
This article constructs a smooth weak Fano threefold of Picard number two with small anti-canonical morphism that arises as a blowup of a smooth curve of genus 5 and degree 8 in P^3.  ...  and constructs the link in the style of ACM17.  ...  In addition, we would like to thank all the organizers of the Workshop in Algebraic Geometry held on December 18-22, 2016, in Hanga Roa, Chile.  ... 
arXiv:1712.05295v2 fatcat:yycs2nlibbdencfetrbxgl4ope

Inhibition of cell movement and proliferation by cell–cell contact-induced interaction of Necl-5 with nectin-3

Tsutomu Fujito, Wataru Ikeda, Shigeki Kakunaga, Yukiko Minami, Mihoko Kajita, Yasuhisa Sakamoto, Morito Monden, Yoshimi Takai
2005 Journal of Cell Biology  
In addition, Necl-5 heterophilically trans-interacts with nectin-3, a cell-cell adhesion molecule known to form adherens junctions in cooperation with cadherin.  ...  We show here that Necl-5 was downregulated from cell surface upon cell-cell contacts in I NIH3T3 cells.  ...  In the absence of this mAb-i, the amount of cell surface Necl-5 and the degree of DNA synthesis of NIH3T3 cells cultured at the higher density decreased in a roughly parallel manner (Fig. 5, A [b] and  ... 
doi:10.1083/jcb.200501090 pmid:16216929 pmcid:PMC2171219 fatcat:nrgmh7egzvbfnfy7r5nzloxh3i

Recognition of 5′-YpG-3′ Sequences by Coupled Stacking/Hydrogen Bonding Interactions with Amino Acid Residues

Jason S. Lamoureux, Jason T. Maynes, J.N. Mark Glover
2004 Journal of Molecular Biology  
The 3 0 -base is recognized by canonical direct readout, while the 5 0 -base is recognized through a variation of indirect readout, whereby the conformational flexibility of the particular dinucleotide  ...  step, namely a 5 0 -pyrimidinepurine-3 0 step, facilitates its recognition by the amino acid via cation-p interactions.  ...  In contrast, only about 10% of 5 0 -YpG-3 0 steps in the free DNA structure database display this kind of unstacking, indicating that arginine-induced 5 0 -YpG-3 0 unstacking may be a common but not universal  ... 
doi:10.1016/j.jmb.2003.10.071 pmid:14672650 fatcat:a6endyiqsrdttp4pfznhgfvlbe

Cationic 5,10,15,20-Tetrakis(N-methylpyridinium-4-yl)porphyrin Fully Intercalates at 5'-CG-3' Steps of Duplex DNA in Solution†

Anton B. Guliaev, Neocles B. Leontis
1999 Biochemistry  
Intra-and intermolecular NOEs observed in the complex showed that the porphyrin intercalates at the central 5′-CG-3′ step of the DNA duplex without disrupting the flanking base pairs.  ...  T4MPyP 4+ binding to [d(GCACGTGC)] 2 produced a single set of (mostly) upfield-shifted DNA resonances in slow exchange with the resonances of the free DNA.  ...  Stephen Neidle (U.K.) for the crystallographic coordinates of T4MPyP 4+ , Dr. D. Y. Chen for assistance with NMR spectroscopy, and Pascal Auffinger for critical reading of the manuscript.  ... 
doi:10.1021/bi9913808 pmid:10569925 fatcat:ozlen55hgfe43og772e267yw4u

Pathological Society of Great Britain and Ireland 140th meeting; 3-5 January 1980, at the University of Oxford

1980 Journal of Pathology  
The relationship of cellular changes in the human breast to the phases of the Samples obtained from breast biopsies of menstrual cycle is poorly defined.  ...  Intrahepatocytic copper granules were found in 13 cases (29.5 per cent.) of cirrhosis, irrespective of the degree of activity of the process, but in none of the non-cirrhosis forms.  ...  All rabbits were initially immunised by 3 mg TG in Freund's complete adjuvant intramuscularly, followed after 14 days by 5 mg TG intravenously.  ... 
doi:10.1002/path.1711310307 fatcat:km2sjs5atnds5gxgdgyx6gkkye

Synthesis and reactivity of an unexpected highly sensitive 1-carboxymethyl-3-diazonio-5-nitrimino-1,2,4-triazole

Thomas M. Klapötke, Andreas Nordheider, Jörg Stierstorfer
2012 New Journal of Chemistry  
The thermal behavior of 2 and 3 was investigated using a Linseis PT10 differential scanning calorimeter with a heating View Article Online rate of 5 degrees per minute. 28 Unfortunately, 2 and 3 have  ...  After recrystalli zation from water yellow crystals suitable for X ray analysis were formed. Yield: 85%. Mp: 125 1C (dec., DSC, 5 K min À1 ); 1 Fig. 3 3 Molecular unit of 2.  ...  After release of dinitrogen 1 carboxymethyl 3 azido 5 nitrimino 1,2,4 triazole (3) was formed which shows lower sensitivity values, but also in the range of primary explosives.  ... 
doi:10.1039/c2nj40044h fatcat:pcwbesnaozckvng3buhsved74a

Structural Basis for the High-Affinity Inhibition of Mammalian Membranous Adenylyl Cyclase by 2',3'-O-(N-Methylanthraniloyl)-Inosine 5'-Triphosphate

M. Hubner, A. Dixit, T.-C. Mou, G. H. Lushington, C. Pinto, A. Gille, J. Geduhn, B. Konig, S. R. Sprang, R. Seifert
2011 Molecular Pharmacology  
2Ј,3Ј-O-(N-Methylanthraniloyl)-ITP (MANT-ITP) is the most potent inhibitor of mammalian membranous adenylyl cyclase (mAC) 5 (AC5, K i , 1 nM) yet discovered and surpasses the potency of MANT-GTP by 55-  ...  AC5 inhibitors may be valuable drugs for treatment of heart failure. The aim of this study was to elucidate the structural basis for the high-affinity inhibition of mAC by MANT-ITP.  ...  Wrote or contributed to the writing of the manuscript: Hü bner, Dixit, Mou, Lushington, Pinto, Gille, Geduhn, König, Sprang, and Seifert.  ... 
doi:10.1124/mol.111.071894 pmid:21498658 pmcid:PMC3127541 fatcat:mx4tuxxnpzb23n4uklrnxkeqmu

Beneficial Metabolic Effects of 2′,3′,5′-tri-acetyl-N6- (3-Hydroxylaniline) Adenosine in the Liver and Plasma of Hyperlipidemic Hamsters

Yang Sun, Zeqin Lian, Chunying Jiang, Yinghong Wang, Haibo Zhu, Akos Vertes
2012 PLoS ONE  
Methodology/Principal Findings: As a new way, we performed 1 H NMR-based metabonomics to evaluate the beneficial effects of 29,39,59-tri-acetyl-N 6 -(3-hydroxylaniline) adenosine (WS070117) on plasma and  ...  As a result, metabonomics-based findings such as the PCA and OPLS-DA plotting of metabolic state and analysis of potential biomarkers in plasma and liver correlated well to the assessment of biochemical  ...  Juan Lv of Bruker Corporation in Germany. Author Contributions  ... 
doi:10.1371/journal.pone.0032115 pmid:22470419 pmcid:PMC3314636 fatcat:3zbpspwxtffqpbkdgq7r3sofmy

Mapping of the epitope/paratope interactions of a monoclonal antibody directed against adenosine 3′,5′-monophosphate

N Nass, C Colling, M Cramer, H G Genieser, E Butt, E Winkler, L Jaenicke, B Jastorff
1992 Biochemical Journal  
A series of systematically modified cyclic AMP (cAMP) analogues, including newly synthesized benzimidazole riboturanosyl 3',5'-monophosphates was used to map the essential molecular interactions between  ...  The ribose phosphate moiety is recognized by a combination of charge interactions and H-bonds to the exocyclic and the 5'-oxygen atoms and a hydrophobic interaction at the 2'-position.  ...  Klein for critical discussion of the manuscript.  ... 
doi:10.1042/bj2850129 pmid:1379038 pmcid:PMC1132755 fatcat:3ijfzssjyzcfnetuicyfxkt37a

Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia coli MenD (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase)

Alice Dawson, Paul K. Fyfe, William N. Hunter
2008 Journal of Molecular Biology  
The thiamine diphosphate (ThDP) and metal-ion-dependent enzyme 2-succinyl-5-enolpyruvyl-6hydroxy-3-cyclohexadiene-1-carboxylate synthase, or MenD, catalyze the Stetter-like conjugate addition of α-ketoglutarate  ...  These features, formed by highly conserved amino acids, match well to the chemical properties of the substrates.  ...  It consists of a narrow cavity having a width and length of approximately 8 and 15 Å, respectively, and the distance from the surface of the protein to ThDP C2 is nearly 20 Å (Fig. 7) .  ... 
doi:10.1016/j.jmb.2008.10.048 pmid:18983854 pmcid:PMC3656419 fatcat:naz4ieo74rhczgbb3gdsvkq4w4
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