Conformational Analysis of the Deoxyribofuranose Ring in DNA by means of Sums of Proton-proton Coupling Constants: A Graphical Method

Abstract

A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-pro ton couplings. The coupling data required for this analysis consist of sums of couplings, which are referred to as Σ1′ (= J1′2′ + J1′2″), Σ2′ (= J1′2′ + J2′3′+J2′2″), Σ2″ (= J1′2″ + J 2″3′ + J2′2″) and Σ3′ (= J2′3′ + J2″3′ + J3′4′). These sums of couplings correspond to the distance between the outer peaks of the H1′, H2′, H2″ and H3′ {³¹P} resonances, respectively, (except for Σ2′ and Σ2″ in the case of a small chemical shift difference between the H2′ and H2″ resonances) and can often be obtained from ¹H-NMR spectra via first-order measurement, obviating the necessity of a computer-assisted simulation of the fine structure of these resonances. Two different types of graphs for the interpretation of the coupling data are discussed: the first type of graph serves to probe as to whether or not the sugar ring occurs as a single conformer, and if so to analyze the coupling data in terms of the geometry of this sugar ring. In cases where the sugar ring does not occur as a single conformer, but as a blend of N-and S-type sugar puckers, the second type of graph is used to analyze the coupling data in terms of the geometry and population of the most abundant form.

It is shown that the latter type of analysis can be carried out on the basis of experimental values for merely Σ1′, Σ2′ and Σ2″, without any assumptions or restrictions concerning a relation between the geometry of the N- and S-type conformer. In addition, the question is discussed as to how insight can be gained into the conformational purity of the sugar ring from the observed fine structure of the H1′ resonance. Finally, a comparison is made between experimental coupling data reported for single-stranded and duplex DNA fragments and covalent RNA-DNA hybrids on the one hand and the predicted couplings and sums of couplings presented in this paper on the other hand.     

May the Force Be with You: Metabolism of Arginine and Pyrimidines

<正>"Why do arginine and pyrimidines have to be considered together?"This was the question I asked when I was invited by Barbara Zimmermann to attend the 23rd International Conference on Arginine and Pyrimidines(ICAP)three years ago.The meeting was held in the summer of 2012 at Bogota,Columbia,known as the"the Athens of South America".I am not alone in wanting to know more about the relationship between arginine and pyrimidines.Last summer,when I was organising the next ICAP meeting at Oxford(Aughey et al.,2014),one of my colleagues asked me,"Why such a weird name for a conference?"I am not sure if I had given her a satisfying answer and I was enthused to find out what the reasons may be.     

Synthesis of Acycloalkenyl Derivatives of Pyrimidines and Purines

Abstract

Conjugate addition of an anionic nucleophile (nucleobase) to an active triple bond (α, β unsaturated carboxylate or phosphonate) was used for preparing α-ethenyl carboxylate or phosphonate derivatives of purines and pyrimidines.     

Excessive Clustering of Third Codon Position Pyrimidines in Prokaryotes

Abstract

The third codon positions are generally thought to be largely neutral, allowing for synonymous mutations. To see how much the third positions are loaded in general we analyzed the sequences of the nucleotides in the third positions. Simple word count analysis revealed excessive clustering of pyrimidines in the third position sequences of prokaryotic mRNA. The clusters have a clear tendency to follow one after another at characteristic distance of 25–30 triplets. Thus, the third codon positions do carry a rather strong message. Possible connection with loop-fold structure of proteins and (cotranslational) protein folding is discussed.     

Metabolism of Pyrimidines and Pyrimidine Nucleosides by Salmonella typhimurium

The pathways by which uracil, cytosine, uridine, cytidine, deoxyuridine, and deoxycytidine are metabolized by Salmonella typhimurium are established. The various 5-fluoropyrimidine analogues are shown to exert their toxic effects only after having been converted to the nucleotide level, and these conversions are shown to be catalyzed by the same enzymes which similarly convert the natural substrates. Methods for isolating mutant strains blocked in various steps of metabolism of pyrimidine bases and nucleosides are described.     

Macrophage-Released Pyrimidines Inhibit Gemcitabine Therapy in Pancreatic Cancer

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超氧阴离子自由基与嘧啶反应产物的量子化学研究

超氧阴离子自由基与嘧啶反应产物的量子化学研究班福强,戴柏青（哈尔滨师范大学,１５００８０）关键词超氧阴离子自由基;嘧啶;ＵＨＦ从头算超氧阴离子自由基（简称超氧自由基,）是一种重要的活性氧,与其他活性氧［如羟自由基（·ＯＨ）和过氧化氢（Ｈ２Ｏ２）等］一...     

Pyrimidines and the X-ray response of Tribolium confusum Duval

Radiosensitizing effects of incorporation into DNA of the halogenated pyrimidines 5-bromouracil or 5-iodouracil, or their nucleosides (BUdR and IUdR), have been demonstrated in a variety of cell types. The results indicate that these antimetabolites influence lethality in x-irradiated adult Tribolium. At relatively low concentrations in the medium, BUdR and IUdR exhibit toxicity 3 to 5 weeks after transfer of beetles to analog-containing medium. Toxicity of IUdR on nonirradiated adults is less pronounced than that of BUdR and is slower to develop. Analog-treated Tribolium exposed to 7 kR, which is sublethal for adults in normal medium, die much earlier than those treated with analog alone or with lethal doses of x-rays alone. Transfer of beetles to normal medium after 3 weeks or less in the presence of analog virtually eliminates lethality attributable to the analog. X-irradiation at the time of transfer, however, leads to high mortality, and the amount of mortality appears to be a function of the duration of analog treatment. Insects grown in medium containing uracil or thymine exhibit the same survival as those reared in unsupplemented medium. Two weeks after 7 kR of irradiation a sharp decline in survival is seen in both uracil- and thymine-treated groups.     

Conformational changes associated with protein-protein interactions

Motions related to protein-protein binding events can be surveyed from the perspective of the Database of Macromolecular Movements. There are a number of alternative conceptual models that describe these events, particularly induced fit and pre-existing equilibrium. There is evidence for both alternatives from recent studies of conformational change. However, there is increasing support for the pre-existing equilibrium model, whereby proteins are found to simultaneously exist in populations of diverse conformations.     

Synthesis and Biological Activities of Unsaturated Ketohexopyranosyl Nucleosides of Pyrimidines

Abstract

Synthesis of unsaturated ketohexopyranosyl nucleosides of a few pyrimidines is described. The results of their bioevaluation for anticancer and antiviral activity are also discussed.     

Chemical evolution XXIX. Pyrimidines from hydrogen cyanide.

Dilute (0.1 M) solutions of HCN condense to oligomers at pH 8-9. Hydrolysis of these oligomers at pH 8.5 or with 6 N HCl yields 4,5-dihydroxypyrimidine, as the most abundant pyrimidine product along with orotic acid and 5-hydroxyuracil. These results, together with the earlier data, demonstrate that the three major nitrogen-containing classes of biomolecules could have originated from HCN on the primitive earth. The observation of the formation of orotic acid and 4-aminoimidazole-5-carboxamide by the hydrolysis of the HCN oligomers suggests that once the initially formed pyrimidines and purines were consumed, those life forms persisted which evolved enzymes for conversion of these intermediates to the pyrimidines and purines present in contemporary RNA.     

Long Range Effect of Mutations on Specific Conformational Changes in the Extracellular Loop 2 of Angiotensin II Type 1 Receptor

The topology of the second extracellular loop (ECL2) and its interaction with ligands is unique in each G protein-coupled receptor. When the orthosteric ligand pocket located in the transmembrane (TM) domain is occupied, ligand-specific conformational changes occur in the ECL2. In more than 90% of G protein-coupled receptors, ECL2 is tethered to the third TM helix via a disulfide bond. Therefore, understanding the extent to which the TM domain and ECL2 conformations are coupled is useful. To investigate this, we examined conformational changes in ECL2 of the angiotensin II type 1 receptor (AT1R) by introducing mutations in distant sites that alter the activation state equilibrium of the AT1R. Differential accessibility of reporter cysteines introduced at four conformation-sensitive sites in ECL2 of these mutants was measured. Binding of the agonist angiotensin II (AngII) and inverse agonist losartan in wild-type AT1R changed the accessibility of reporter cysteines, and the pattern was consistent with ligand-specific “lid” conformations of ECL2. Without agonist stimulation, the ECL2 in the gain of function mutant N111G assumed a lid conformation similar to AngII-bound wild-type AT1R. In the presence of inverse agonists, the conformation of ECL2 in the N111G mutant was similar to the inactive state of wild-type AT1R. In contrast, AngII did not induce a lid conformation in ECL2 in the loss of function D281A mutant, which is consistent with the reduced AngII binding affinity in this mutant. However, a lid conformation was induced by [Sar¹,Gln²,Ile⁸] AngII, a specific analog that binds to the D281A mutant with better affinity than AngII. These results provide evidence for the emerging paradigm of domain coupling facilitated by long range interactions at distant sites on the same receptor.     

Metabolism of Pyrimidines in Protoplasts from Cultured Catharanthus roseus Cells

The metabolism of [2-¹⁴C]thymine, [2-¹⁴C]thymidine, [2-¹⁴C]uraciland [¹⁴C]uridine was investigated in protoplasts obtained fromsuspension cultures of Catharanthus roseus. Most of the exogenouslysupplied thymine, thymidine and uracil was degraded, and salvageof these pyrimidines accounted for 5–36 per cent of thetotal amount of ¹⁴C-labelled precursors which was metabolized.However, more than 80 per cent of the labelled uridine was utilizedfor the biosynthesis of nucleotides and nucleic acids, and therest was degraded. In contrast to the results from protoplastsof sugar cane cells in suspension culture, the data indicatethat protoplasts possess a pathway for the degradation of pyrimidines,and that the overall metabolism of these pyrimidines in protoplastsis very similar to the metabolism in the intact cells. Catharanthus roseus, madagascar periwinkle, protoplasts, pyrimidine metabolism     

Conformational analysis of stiff chiral polymers with end-constraints

We present a Lie-group-theoretic method for the kinematic and dynamic analysis of stiff chiral polymers with end constraints. The first is to determine the minimum energy conformations of stiff polymers with end constraints and the second is to perform normal mode analysis based on the determined minimum energy conformations. In this paper, we use concepts from the theory of Lie groups and principles of variational calculus to model such polymers as inextensible or extensible chiral elastic rods with coupling between stiffnesses. This method is general enough to include any stiffness and chirality parameters in the context of elastic filament models with the quadratic elastic potential energy function. As an application of this formulation, the analysis of DNA conformations is discussed. We demonstrate our method with examples of DNA conformations in which topological properties such as writhe, twist and linking number are calculated from the results of the proposed method. Given these minimum energy conformations, we describe how to perform the normal mode analysis. The results presented here build both on recent experimental work in which DNA mechanical properties have been measured and theoretical work in which the mechanics of non-chiral elastic rods has been studied.     

Antifungal Activity of Ring Poly-Chlorinated Pyrimidines: Structure Activity Relationships

A total of 48 ring chlorinated pyrimidines was screened against strains of five fungi by the disc-plate method, in liquid culture, and for activity of the vapors of the compounds. Correlations of the results obtained by the three methods were made, and structure to activity relationships were discussed. The outstanding members of this series were found to be 2,4,5-trichloropyrimidine, 4,5,6-trichloropyrimidine, and 2-chloromethyl-4,5,6-trichloropyrimidine, in this screening system.     

Conformational studies of proteins with aromatic side-chain effects

We present here a brief analysis of ultraviolet isotropic absorption and related circular dichroism of the n–π* and π–π* transitions for the peptide (amide) chromophore in the 185–240 mμ region. Investigations by ultraviolet absorption and circular dichroism techniques on natural amino acids with aromatic chromophores in their side chains are also reported. By taking into account both the peptide and aromatic transitions we discuss the conformational studies of proteins with aromatic side-chain effects. Our attention is largely focused on the optical rotatory dispersion and circular dichroism spectra of these proteins in the near ultraviolet region, where characteristic aromatic side-chain bands occur. The 185–240 mμ region is also discussed when evidence exists of overlapping Cotton effects of aromatic and peptide groups.     

Conformational stability of ribonuclease A complexes with specific inhibitors

Isotermic unfolding of ribonuclease A, phosphopyridoxyl-8Lys41-RNAase A and complexes of the enzyme with cytidine, 2'-CMP, 3'-CMP, 3'-AMP and with the phosphoric ester of 1-(omega-oxypropyl)-cytosine in presence of urea has been studied. The stabilization of the protein structure resulting from the complex formation was shown to be determined by the ligand nucleobase binding. The comparison of the results obtained with those known from the literature suggests, that binding and catalytic zones of the enzyme active site form an integrated network system which is substained by multipoint contacts between the constituents. The change in the state of any part within the enzyme active state affects the energetics of the whole protein globule.     

Conformational change in poly-L-lysine on reaction with polyacids

When solutions of poly-L -lysine and poly(acrylic acid) in salt solutions at neutral pH are mixed, complexes are formed. Optical rotatory dispersion studies of these complexes away from the equivalence point reveals the formation of α-helices. The α-helix content of the polylysine never rises above about 50%. On addition of 25% by volume of dioxane, the turbidity of the complex solutions disappears, and there is some enhancement of the α-helix content. Poly(phosphoric acid) behaves essentially in the same way as poly(acrylic acid). Poly(uridylic acid) forms complexes with polylysine but with no detectable formation of α-helix. The same is true of ribosomal RNA and native and denatured DNA. A number of other polyacid polybase systems involving basic proteins have been examined, but again no α-helix formation is induced. The results are related to the case of biological nucleoproitein complexes, and the conformational specificity of these systems is discussed. The effect of scattering on measured optical rotation has been investigated and is shown to be unimportant up to quite high levels.     

Conformational Dynamics of Titin PEVK Explored with FRET Spectroscopy

The proline-, glutamate-, valine-, and lysine-rich (PEVK) domain of the giant muscle protein titin is thought to be an intrinsically unstructured random-coil segment. Various observations suggest, however, that the domain may not be completely devoid of internal interactions and structural features. To test the validity of random polymer models for PEVK, we determined the mean end-to-end distances of an 11- and a 21-residue synthetic PEVK peptide, calculated from the efficiency of the fluorescence resonance energy transfer (FRET) between an N-terminal intrinsic tryptophan donor and a synthetically added C-terminal IAEDANS acceptor obtained in steady-state and time-resolved experiments. We find that the contour-length scaling of mean end-to-end distance deviates from predictions of a purely statistical polymer chain. Furthermore, the addition of guanidine hydrochloride decreased, whereas the addition of salt increased the FRET efficiency, pointing at the disruption of structure-stabilizing interactions. Increasing temperature between 10 and 50°C increased the normalized FRET efficiency in both peptides but with different trajectories, indicating that their elasticity and conformational stability are different. Simulations suggest that whereas the short PEVK peptide displays an overall random structure, the long PEVK peptide retains residual, loose helical configurations. Transitions in the local structure and dynamics of the PEVK domain may play a role in the modulation of passive muscle mechanics.