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Sugar Ring (sugar + ring)
Selected AbstractsAn ab initio theoretical study of electronic structure and properties of 2,-deoxyguanosine in gas phase and aqueous mediaJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2002S. K. Mishra Abstract Molecular geometries of two structural forms of 2,-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2,-endo and C3,-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2,-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2,-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water,air interface. Though the normal Watson,Crick-type base pairing would not be possible with the keto-N7R form of 2,-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti -conformation of 2,-deoxyguanosine including the dihedral angle ,CN agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2,-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H+ and OH, fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH, group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2,-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 530,540, 2002; DOI 10.1002/jcc.10046 [source] Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformationJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 6 2005S. Mezzache Abstract A ladder of relative proton affinities (PA) for a series of modified uridines (e.g. araU, ddU, 5BrU, 5BrdU and 5IU) was established from competitive dissociations of proton-bound heterodimers using Cooks and co-workers' kinetic method. The studied heterodimers are constituted of a modified nucleoside and either an amino acid or a nucleoside with known PA value. These non-covalent heterodimers were prepared under electrospray conditions to be selected and dissociated into the ion-trap analyzer. These results allowed our PA ladder of uridine and deoxyuridine analogs substituted at the C-5 position in the uracil ring to be extended. From this scale, it was showed that the substitution of hydrogen atom at the C-2, position in the sugar ring by a hydroxyl group involves a decrease of about 7 kJ mol,1. The experimental values for U, 5MeU, dU, 5MedU, ddU and araU are consistent with those obtained by DFT calculations (B3P86/6,31+G*//B3LYP/6,31G*). Several neutral and protonated conformations of these compounds were considered, in particular the ring conformation of furanose and the orientation of the base with respect to the sugar ring. These calculated results showed the influence of sugar substituent on the conformation of the neutral form of theses nucleosides. However, the most stable protonated structure is the same for all the studied nucleosides except for araU, where the position of the anti 2,-OH group imposes a specific conformation. Copyright © 2005 John Wiley & Sons, Ltd. [source] Isolation of inulin-type oligosaccharides from Chinese traditional medicine: Morinda officinalis How and their characterization using ESI-MS/MSJOURNAL OF SEPARATION SCIENCE, JSS, Issue 1 2010Zhenmin Yang Abstract Inulin-type oligosaccharides with different DP were prepared by size-exclusion chromatography and purity of each oligosaccharide was determined by HPLC equipped with cyclodextrin-bond column. The purities of obtained inulin-type oligosaccharides with different DP were more than 98% by one-step process. The DP and molecular weight were obtained through ESI-MS in negative mode. The characterization of the inulin-type oligosaccharides with different DP was studied by MS/MS spectra obtained by collision-induced dissociation of molecular ions ([M,H],). When the DP was lower, the fragment ions were formed through cross-ring cleavages of two bonds within the sugar ring and glycosidic cleavages. However, with the increase of DP, the ions resulting from glycosidic cleavages between two sugar residues were predominant. [source] Crystallization and preliminary X-ray analysis of heparinase II from Pedobacter heparinusACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004David Shaya Heparinase II from Pedobacter heparinus (formerly Flavobacterium heparinum), which acts on both heparin and heparan sulfate, is one of several glycosaminoglycan-degrading enzymes produced by this organism. This enzyme, with a molecular weight of 84,kDa, utilizes a lytic mechanism to cleave the ,(1,4) glycosidic bond between hexosamine (d -glucosamine) and l -iduronic or d -glucuronic acid, resulting in a product with an unsaturated sugar ring at the non-reducing end. The enzyme was crystallized by the hanging-drop vapour-diffusion method. The crystals belong to orthorhombic space group P212121 and diffract to 2,Å resolution. There are two molecules in the asymmetric unit, consistent with the finding that recombinant heparinase II functions as a dimer in solution. [source] Comparison between the orthorhombic and tetragonal forms of the heptamer sequence d[GCG(xT)GCG]/d(CGCACGC)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010Koen Robeyns Cyclohexene nucleic acid (CeNA) building blocks can be introduced into natural DNA sequences without a large conformational influence because of the ability of the six-membered sugar ring to mimic both the C2,- endo and C3,- endo conformations of the naturally occurring ribofuranose sugar ring. The non-self-complementary DNA sequence d[GCG(xT)GCG]/d(CGCACGC) with one incorporated CeNA (xT) moiety crystallizes in two forms: orthorhombic and tetragonal. The tetragonal form, which diffracts to 3,Å resolution, is a kinetically stable polymorph of the orthorhombic form [Robeyns et al. (2010), Artificial DNA, 1, 1,7], which diffracts to 1.17,Å resolution and is the thermodynamically stable form of the CeNA-incorporated duplex. Here, the two structures are compared, with special emphasis on the differences in crystal packing and the irreversible conversion of the kinetic form into the high-resolution diffracting thermodynamic form. [source] Structure of a family 3b, carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum: structural diversity and implications for carbohydrate bindingACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010Svetlana Petkun Family 3 carbohydrate-binding modules (CBM3s) are associated with both cellulosomal scaffoldins and family 9 glycoside hydrolases (GH9s), which are multi-modular enzymes that act on cellulosic substrates. CBM3s bind cellulose. X-ray crystal structures of these modules have established an accepted cellulose-binding mechanism based on stacking interactions between the sugar rings of cellulose and a planar array of aromatic residues located on the CBM3 surface. These planar-strip residues are generally highly conserved, although some CBM3 sequences lack one or more of these residues. In particular, CBM3b, from Clostridium thermocellum Cel9V exhibits such sequence changes and fails to bind cellulosic substrates. A crystallographic investigation of CBM3b, has been initiated in order to understand the structural reason(s) for this inability. CBM3b, crystallized in space group C2221 (diffraction was obtained to 2.0,Å resolution in-house) with three independent molecules in the asymmetric unit and in space group P41212 (diffraction was obtained to 1.79,Å resolution in-house and to 1.30,Å resolution at a synchrotron) with one molecule in the asymmetric unit. The molecular structure of Cel9V CBM3b, revealed that in addition to the loss of several cellulose-binding residues in the planar strip, changes in the backbone create a surface `hump' which could interfere with the formation of cellulose,protein surface interactions and thus prevent binding to crystalline cellulose. [source] Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinementACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Xiaorui Chen The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0,Å resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42,Å resolution and of a membrane protein at 3.2,Å resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B -factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures. [source] | ||||||||||