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Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues.
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL
(2012) Biochemistry 51: 9234-44
MeSH Terms: Carbohydrate Conformation, Catalytic Domain, Crystallography, X-Ray, DNA, Archaeal, DNA-Directed DNA Polymerase, Deoxyadenine Nucleotides, Deoxyribonucleotides, Nucleic Acid Conformation, Substrate Specificity, Sulfolobus solfataricus
Show Abstract · Added May 27, 2014
DNA polymerases select for the incorporation of deoxyribonucleotide triphosphates (dNTPs) using amino acid side-chains that act as a "steric-gate" to bar improper incorporation of rNTPs. An additional factor in the selection of nucleotide substrates resides in the preferred geometry for the furanose moiety of the incoming nucleotide triphosphate. We have probed the role of sugar geometry during nucleotide selection by model DNA polymerases from Sulfolobus solfataricus using fixed conformation nucleotide analogues. North-methanocarba-dATP (N-MC-dATP) locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker, and South-methanocarba-dATP (S-MC-dATP) locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker. Dpo4 preferentially inserts N-MC-dATP and in the crystal structure of Dpo4 in complex with N-MC-dAMP, the nucleotide analogue superimposes almost perfectly with Dpo4 bound to unmodified dATP. Biochemical assays indicate that the S. solfataricus B-family DNA polymerase Dpo1 can insert and extend from both N-MC-dATP and S-MC-dATP. In this respect, Dpo1 is unexpectedly more tolerant of substrate conformation than Dpo4. The crystal structure of Dpo4 bound to S-MC-dADP shows that poor incorporation of the Southern pucker by the Y-family polymerase results from a hydrogen bond between the 3'-OH group of the nucleotide analogue and the OH group of the steric gate residue, Tyr12, shifting the S-MC-dADP molecule away from the dNTP binding pocket and distorting the base pair at the primer-template junction. These results provide insights into substrate specificity of DNA polymerases, as well as molecular mechanisms that act as a barrier against insertion of rNTPs.
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10 MeSH Terms
Size and conformation of Ficoll as determined by size-exclusion chromatography followed by multiangle light scattering.
Fissell WH, Hofmann CL, Smith R, Chen MH
(2010) Am J Physiol Renal Physiol 298: F205-8
MeSH Terms: Carbohydrate Conformation, Chromatography, Gel, Ficoll, Light, Models, Chemical, Particle Size, Scattering, Radiation, Viscosity
Show Abstract · Added August 21, 2013
The characteristics of the glomerular filtration barrier (GFB) are challenging to measure, as macromolecular solutes in blood may be metabolized or transported by various cells in the kidney. Urinary solute concentrations generally reflect the cumulative influence of multiple transport processes rather than the intrinsic behavior of the GFB alone. Synthetic tracer molecules which are not secreted, absorbed, or modified by the kidney are useful tools. Ficoll, a globular polymer of epichlorohydrin and sucrose, is round, physiologically inert, and easily labeled, making it a nearly ideal glomerular probe. Fissell et al. reported filtration data suggesting that Ficoll was not as spherical as had been previously suggested (Fissell WH, Manley S, Dubnisheva A, Glass J, Magistrelli J, Eldridge AN, Fleischman AJ, Zydney AL, Roy S. Am J Physiol Renal Physiol 293: F1209-F1213, 2007). More recently, two investigators published comparisons of neutral and anionic Ficoll clearance that suggest Ficoll may undergo conformational changes when chemically derivatized (Asgeirsson D, Venturoli D, Rippe B, Rippe C. Am J Physiol Renal Physiol 291: F1083-F1089, 2006; Guimaraes MAM, Nikolovski J, Pratt LM, Greive K, Comper WD. Am J Physiol Renal Physiol 285: F1118-F1124, 2003). To investigate Ficoll's characteristics further, we examined two commercial preparations, Ficoll 70 and Ficoll 400, by size-exclusion chromatography using a differential refractive index detector combined with light-scattering and viscosity detectors. A slope of 0.45 was obtained from the plot of the logarithm of molecular mass against the logarithm of root-mean square radius. The Mark-Houwink exponent values of 0.34 and 0.36 were calculated for Ficoll 70 and Ficoll 400, respectively. These results suggest Ficoll's conformation in physiological saline solution is likely intermediate between a solid sphere and a well-solvated linear random coil. The measurements help explain our previous observations and guide interpretation of in vivo experiments.
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Interconversion of the cis-5R,6S- and trans-5R,6R-thymine glycol lesions in duplex DNA.
Brown KL, Adams T, Jasti VP, Basu AK, Stone MP
(2008) J Am Chem Soc 130: 11701-10
MeSH Terms: Carbohydrate Conformation, DNA, Deoxyribose, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Conformation, Oligonucleotides, Thermodynamics, Thymine
Show Abstract · Added May 29, 2014
Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, is formed in DNA by the reaction of thymine with reactive oxygen species. The 5R Tg lesion was incorporated site-specifically into 5'-d(G(1)T(2)G(3)C(4)G(5)Tg(6)G(7)T(8)T(9)T(10)G(11)T(12))-3'; Tg = 5R Tg. The Tg-modified oligodeoxynucleotide was annealed with either 5'-d(A(13)C(14)A(15)A(16)A(17)C(18)A(19)C(20)G(21)C(22)A(23)C(24))-3', forming the Tg(6) x A(19) base pair, corresponding to the oxidative damage of thymine in DNA, or 5'-d(A(13)C(14)A(15)A(16)A(17)C(18)G(19)C(20)G(21)C(22)A(23)C(24))-3', forming the mismatched Tg(6) x G(19) base pair, corresponding to the formation of Tg following oxidative damage and deamination of 5-methylcytosine in DNA. At 30 degrees C, the equilibrium ratio of cis-5R,6S:trans-5R,6R epimers was 7:3 for the duplex containing the Tg(6) x A (19) base pair. In contrast, for the duplex containing the Tg(6) x G(19) base pair, the cis-5R,6S:trans-5R,6R equilibrium favored the cis-5R,6S epimer; the level of the trans-5R,6R epimer remained below the level of detection by NMR. The data suggested that Tg disrupted hydrogen bonding interactions, either when placed opposite to A(19) or G(19). Thermodynamic measurements indicated a 13 degrees C reduction of T(m) regardless of whether Tg was placed opposite dG or dA in the complementary strand. Although both pairings increased the free energy of melting by 3 kcal/mol, the melting of the Tg x G pair was more enthalpically favored than was the melting of the Tg x A pair. The observation that the position of the equilibrium between the cis-5R,6S and trans-5R,6R thymine glycol epimers in duplex DNA was affected by the identity of the complementary base extends upon observations that this equilibrium modulates the base excision repair of Tg [Ocampo-Hafalla, M. T.; Altamirano, A.; Basu, A. K.; Chan, M. K.; Ocampo, J. E.; Cummings, A., Jr.; Boorstein, R. J.; Cunningham, R. P.; Teebor, G. W. DNA Repair (Amst) 2006, 5, 444-454].
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8 MeSH Terms
Characterization of glycosylation sites of the epidermal growth factor receptor.
Zhen Y, Caprioli RM, Staros JV
(2003) Biochemistry 42: 5478-92
MeSH Terms: Amino Acid Sequence, Animals, Binding Sites, CHO Cells, Carbohydrate Conformation, Carbohydrate Sequence, Cells, Cultured, Chromatography, High Pressure Liquid, Cricetinae, ErbB Receptors, Gas Chromatography-Mass Spectrometry, Glycosylation, Humans, Lung Neoplasms, Molecular Sequence Data, Peptide Fragments, Peptide Mapping, Protein Binding, Recombinant Proteins, Trypsin
Show Abstract · Added March 5, 2014
The epidermal growth factor receptor is a transmembrane glycoprotein that mediates the cellular responses to epidermal growth factor (EGF) and transforming growth factor-alpha (TGF-alpha). In this study of the human EGF receptor naturally expressed in A431 cells, the glycosylation sites of the full-length, membrane-bound receptor and of a secreted form of the receptor were characterized by mass spectrometry. Our data show that the naturally expressed human EGF receptor is fully glycosylated on eight of the 11 canonical sites; two of the sites are not glycosylated, and one is partially glycosylated, a pattern of site-usage similar but not identical to those reported for the recombinant human EGF receptor heterologously expressed in Chinese hamster ovary cells. We also confirm the partial glycosylation of an atypical NNC site first identified in the receptor expressed in Chinese hamster ovary cells. We show that an additional canonical site in the secreted form of the receptor is fully glycosylated. While the pattern of glycosylation is the same for the sites shared by the full-length and the secreted forms of the receptor, the oligosaccharides of the full-length receptor are more extensively processed. Finally, we provide evidence that in addition to the known secreted form of the receptor, a proteolytic cleavage product of the receptor corresponding to the full extracytoplasmic, ligand-binding domain is present in the conditioned medium.
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20 MeSH Terms
Crystal structure of a B-form DNA duplex containing (L)-alpha-threofuranosyl (3'-->2') nucleosides: a four-carbon sugar is easily accommodated into the backbone of DNA.
Wilds CJ, Wawrzak Z, Krishnamurthy R, Eschenmoser A, Egli M
(2002) J Am Chem Soc 124: 13716-21
MeSH Terms: Carbohydrate Conformation, Circular Dichroism, Crystallography, X-Ray, DNA, Models, Molecular, Nucleic Acid Conformation, Nucleosides, Oligonucleotides, Tetroses
Show Abstract · Added March 5, 2014
(L)-alpha-Threofuranosyl-(3'-->2')-oligonucleotides (TNA) containing vicinally connected phosphodiester linkages undergo informational base pairing in an antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. TNA is derived from a sugar containing only four carbon atoms and is one of the simplest potentially natural nucleic acid alternatives investigated thus far in the context of a chemical etiology of nucleic acid structure. Compared to DNA and RNA that contain six covalent bonds per repeating nucleotide unit, TNA contains only five. We have determined the atomic-resolution crystal structure of the B-form DNA duplex [d(CGCGAA)Td(TCGCG)](2) containing a single (L)-alpha-threofuranosyl thymine (T) per strand. In the modified duplex base stacking interactions are practically unchanged relative to the reference DNA structure. The orientations of the backbone at the TNA incorporation sites are slightly altered in order to accommodate fewer atoms and covalent bonds. The conformation of the threose is C4'-exo with the 2'- and 3'-substituents assuming quasi-diaxial orientation.
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9 MeSH Terms
Heteronuclear NMR studies of 13C-labeled yeast cell wall beta-glucan oligosaccharides.
Yu L, Goldman R, Sullivan P, Walker GF, Fesik SW
(1993) J Biomol NMR 3: 429-41
MeSH Terms: Candida albicans, Carbohydrate Conformation, Carbohydrate Sequence, Cell Wall, Glucans, Glucosyltransferases, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Molecular Structure, Oligosaccharides
Show Abstract · Added March 5, 2014
The structures of uniformly 13C-labeled beta-glucan octa- and undeca-oligosaccharides enzymatically prepared by the yeast cell wall glucanosyl transferase of Candida albicans were characterized by using a combination of HCCH-COSY, HCCH-TOCSY, and HMBC experiments. The oligosaccharide structures indicate that the cell wall glucanosyl transferase cleaves two glucosyl units from the reducing end of the initial linear beta(1-->3) penta-oligosaccharide and subsequently transfers the remainder to another oligosaccharide at the nonreducing end via a beta(1-->6) linkage. These results indicate that the combined action of cell wall glucanase and glucanosyl transferase activities could not only introduce intrachain beta(1-->6) linkages within a single glucan strand, but also result in cross-linking of two initially separate glucan strands with concurrent introduction of intrachain beta(1-->6) linkages. Since isolated fungal membranes only synthesize linear beta(1-->3) glucan strands, wall-associated enzymes probably participate in the assembly of the final wall glucan structure during cell growth and division.
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10 MeSH Terms
The structure of the asparagine-linked carbohydrate unit of rat alpha-lactalbumin.
Prasad R, Hudson BG, Strickland DK, Ebner KE
(1980) J Biol Chem 255: 1248-51
MeSH Terms: Animals, Asparagine, Carbohydrate Conformation, Carbohydrate Sequence, Female, Glycopeptides, Glycoside Hydrolases, Lactalbumin, Methylation, Pregnancy, Rats
Show Abstract · Added December 10, 2013
Rat alpha-lactalbumin is unique in contrast to alpha-lactalbumin isolated from other species in that it exists in three charge forms. Each form contains carbohydrate and is active in the lactose synthetase reaction. Form II comprises about 80% of the total alpha-lactalbumin and contains a single heteropolysaccharide unit which is attached to the polypeptide chain at Asn45. The detailed structure of this unit was ascertained using specific exoglycosidases, endoglycosidases, and methylation analysis. The following structure is proposed for the heteropolysaccharide unit: (formula: see text).
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Structure and metal-binding properties of lipopolysaccharides from heptoseless mutants of Escherichia coli studied by 13C and 31P nuclear magnetic resonance.
Strain SM, Fesik SW, Armitage IM
(1983) J Biol Chem 258: 13466-77
MeSH Terms: Cadmium, Calcium, Carbohydrate Conformation, Carbohydrate Sequence, Escherichia coli, Heptoses, Lipopolysaccharides, Magnetic Resonance Spectroscopy, Metals, Metals, Rare Earth, Mutation
Show Abstract · Added March 5, 2014
The structure and metal-binding properties of lipopolysaccharides (LPS) from heptoseless mutants of Escherichia coli were studied by 13C and 31P NMR techniques. Carbon-13 NMR spectra were used to determine the linkages and configurations of the saccharide backbone and the types and locations of fatty acyl groups in E. coli LPS. Resonance assignments for native LPS were made by chemical shift correlation with model compounds, deacylated LPS, lipid A, deacylated lipid A, and fatty acids released from LPS by mild alkaline hydrolysis. The 3-deoxy-D-manno-octulosonate (KDO) disaccharide was tentatively assigned the structure KDO alpha 2 leads to 5KDO alpha 2 leads to. The presence of amide- and ester-linked 3-hydroxy and 3-acyloxy fatty acids in native LPS was confirmed directly from the 13C spectrum and evidence is presented for a labile acyl ester at C-3' (GlcNII) of the lipid A moiety. A significant finding was that the KDO disaccharide is linked to the C-6' position of the lipid A moiety, rather than C-3', as previously reported. The effects of binding Ca2+, Cd2+, Yb3+, Gd3+, and La3+ on the 31P NMR spectrum of LPS indicated that the glycosidic diphosphate moiety participates in a high affinity metal-binding site.
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11 MeSH Terms
Heteronuclear three-dimensional NMR spectroscopy of isotopically labelled biological macromolecules.
Fesik SW, Zuiderweg ER
(1990) Q Rev Biophys 23: 97-131
MeSH Terms: Animals, Carbohydrate Conformation, Humans, Isotope Labeling, Macromolecular Substances, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Conformation, Software
Added March 5, 2014
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9 MeSH Terms
Bovine glomerular basement membrane. Location and structure of the asparagine-linked oligosaccharide units and their potential role in the assembly of the 7 S collagen IV tetramer.
Langeveld JP, Noelken ME, Hård K, Todd P, Vliegenthart JF, Rouse J, Hudson BG
(1991) J Biol Chem 266: 2622-31
MeSH Terms: Amino Acid Sequence, Amino Acids, Animals, Asparagine, Basement Membrane, Carbohydrate Conformation, Carbohydrate Sequence, Cattle, Chromatography, High Pressure Liquid, Collagen, Glycopeptides, Glycosylation, Kidney Glomerulus, Magnetic Resonance Spectroscopy, Mannose, Models, Molecular, Molecular Sequence Data, Oligosaccharides, Sequence Homology, Nucleic Acid
Show Abstract · Added December 10, 2013
Collagen IV contains an amino-terminal tetramerization domain (7 S) that is involved in aggregation and cross-linking as part of the process of self-assembly of the collagen IV matrix of basement membranes. We determined the structure and location of the Asn-linked oligosaccharides of the 7 S tetramer. Two glycopeptides, GP-1 and GP-2, were isolated from tryptic digests of the 7 S tetramer and were characterized. GP-1 and GP-2 are derived from the alpha 1(IV) chain and the alpha 2(IV) chain, respectively. Each glycopeptide contained one sequence, -Asn-Xaa-Thr-, which was shown to be N-glycosylated at Asn, corresponding to position 126 of the alpha 1 chains and 138 of the alpha 2 chain. 1H NMR spectroscopic analysis of the oligosaccharide is a biantennary N-acetyllactosamine type of N-linked oligosaccharide with a broad heterogeneity in the presence of the sugar residues at their nonreducing termini as indicated. [formula: see text] The location of the Asn-linked oligosaccharide units and Hyl-linked disaccharide units and their orientation with respect to the surface of the triple helix were calculated using two models. We conclude that both units are important determinants in the assembly of the 7 S tetramer.
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19 MeSH Terms