Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil

The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.     

DNA base stacking: The stacked uracil/uracil and thymine/thymine minima

The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)‐corrected M06‐2X/6‐31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4‐dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center‐of‐mass, whereas the other monomer remained still. Both face‐to‐back (one molecule exactly on top of the other) and face‐to‐face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas‐phase M06‐2X/6‐31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies. © 2012 Wiley Periodicals, Inc.     

Influence of the nucleobase and anchimeric assistance of the carboxyl acid groups in the hydrolysis of amino acid nucleoside phosphoramidates

Nucleoside phosphoramidates (NPs) are a class of nucleotide analogues that has been developed as potential antiviral/antitumor prodrugs. Recently, we have shown that some amino acid nucleoside phosphoramidates (aaNPs) can act as substrates for viral polymerases like HIV‐1 RT. Herein, we report the synthesis and hydrolysis of a series of new aaNPs, containing either natural or modified nucleobases to define the basis for their differential reactivity. Aqueous stability, kinetics, and hydrolysis pathways were studied by NMR spectroscopy at different solution pD values (5–7) and temperatures. It was observed that the kinetics and mechanism (P? N and/or P? O bond cleavage) of the hydrolysis reaction largely depend on the nature of the nucleobase and amino acid moieties. Aspartyl NPs were found to be more reactive than Gly or β‐Ala NPs. For aspartyl NPs, the order of reactivity of the nucleobase was 1‐deazaadenine>7‐deazaadenine>adenine>thymine≥3‐deazaadenine. Notably, neutral aqueous solutions of Asp‐1‐deaza‐dAMP degraded spontaneously even at 4 °C through exclusive P? O bond hydrolysis (a 50‐fold reactivity difference for Asp‐1‐deaza‐dAMP vs. Asp‐3‐deaza‐dAMP at pD 5 and 70 °C). Conformational studies by NMR spectroscopy and molecular modeling suggest the involvement of the protonated N3 atom in adenine and 1‐ and 7‐deazaadenine in the intramolecular catalysis of the hydrolysis reaction through the rare syn conformation.     

Multifunctional, biocompatible supramolecular hydrogelators consist only of nucleobase, amino acid, and glycoside

The integration of nucleobase, amino acid, and glycoside into a single molecule results in a novel class of supramolecular hydrogelators, which not only exhibit biocompatibility and biostability but also facilitate the entry of nucleic acids into cytosol and nuclei of cells. This work illustrates a simple way to generate an unprecedented molecular architecture from the basic biological building blocks for the development of sophisticated soft nanomaterials, including supramolecular hydrogels.     

Interaction between monomethylolurea and sodium bicarbonate in water

Processes occurring in the ternary water-salt system containing monomethylolurea and sodium bicarbonate are studied using physicochemical (visual polythermal and isothermal) methods. The germinability and the energy of germination of cotton plant seeds in saline soils is shown to increase due to chemical binding of sodium bicarbonate with monomethylolurea.     

Proton nuclear magnetic resonance study on the aromatic amino acid-guanine nucleotide system: effect of base methylation on the stacking interaction with tyrosine and phenylalanine

The stacking interactions of tyrosine methylester (TyrOMe)-guanosine-5'-monophosphate (GMP), TyrOMe-7-methylguanosine-5'-monophosphate (m7GMP), phenylalanine methylester (PheOMe)-GMP and PheOMe-m7GMP pairs in neutral buffer solution have been studied by proton nuclear magnetic resonance (1H-NMR). The H8 proton signal of GMP showed no noticeable temperature dependence, while the signals of other protons showed usual dependences arising from the ring stacking interaction with aromatic amino acids. The results can be interpreted in terms of the intramolecular C-H ... O hydrogen bonding and ring stacking. Complex formations in 1:1 molar ratio were deduced for all pairs from their Job plots. The association constant for each pair was obtained by analysis of the Scatchard plot. Further, the van't Hoff plot provided thermodynamic parameters of the complex structure. The analyses of these data suggested that albeit the N-quaternization of GMP strengthens the stacking interaction with aromatic amino acid, the bulky methyl group in m7GMP facilitates the dissociation from the amino acid with small environmental change. The possible conformations of GMP and m7GMP in the interaction states are discussed on the basis of the coupling constants.     

Interaction between casein and sodium dodecyl sulfate

The interaction of the anionic surfactant sodium dodecyl sulfate (SDS) with 2.0 mg/ml casein was first investigated using isothermal titration calorimetry (ITC), dynamic light scattering (DLS), and fluorescence spectra. ITC results show that individual SDS molecules first bind to casein micelles by the hydrophobic interaction. The micelle-like SDS aggregate is formed on the casein chains when SDS concentration reaches the critical aggregation concentration (c1), which is far below the critical micellar concentration (cmc) of SDS in the absence of casein. With the further increase of SDS concentration to the saturate binding concentration c2, SDS molecules no longer bind to the casein chains, and free SDS micelles coexist with casein micelles bound with SDS aggregates in the system. DLS results show that the addition of SDS leads to an increase in the hydrodynamic radius of casein micelles with bound surfactant at SDS concentration higher than 4 mM, and also an increase in the casein monomer molecule (or submicelles) at SDS concentration higher than 10 mM. Fluorometric results suggest the addition of SDS leads to some changes in the binding process of hydrophobic probes to casein micelles.     

Interaction between polyacrylamide and sodium dodecyl sulfate

Summary Some preliminar results about the interaction between -SDS and polyacrylamide reveal that without added salts, the two compounds mixt by keeping their own properties while, in salt presence, there is probably complex formation.

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Resumé Quelques résultats préliminaires de l'étude des interactions entre SDS et polyacrylamide montrent un comportement diffèrent en presence et en absence de sels; dans ce dernier cas seulement on peut s'attendre à la formation de complexes.

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With 3 figures     

Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.     

Cell-selective labeling of bacterial proteomes with an orthogonal phenylalanine amino acid reporter

Orthogonal amino acid reporters allow the selective labeling of different cell types in heterogeneous populations through the expression of engineered aminoacyl tRNA synthetases. Here, we demonstrate that para-ethynylphenylalanine (PEP) can be used as an orthogonal amino acid reporter for efficient selective labeling of an intracellular bacterial pathogen during infection.     

Experimental and theoretical studies of sodium cation interactions with the acidic amino acids and their amide derivatives

The binding of Na+ to aspartic acid (Asp), glutamic acid (Glu), asparagine (Asn), and glutamine (Gln) is examined in detail by studying the collision-induced dissociation (CID) of the four sodiated amino acid complexes with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Analysis of the energy-dependent CID cross sections provides 0 K sodium cation affinities for the complexes after accounting for unimolecular decay rates, internal energy of the reactant ions, and multiple ion-molecule collisions. Quantum chemical calculations for a number of geometric conformations of each Na+(L) complex are determined at the B3LYP/6-311+G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated examination of both experimental work and quantum chemical calculations allows the energetic contributions of individual functionalities as well as steric influences of relative chain lengths to be thoroughly explored. Na+ binding affinities for the amide complexes are systematically stronger than those for the acid complexes by 14 +/- 1 kJ/mol, which is attributed to an inductive effect of the OH group in the carboxylic acid side chain. Additionally, the Na+ binding affinity for the longer-chain amino acids (Glx) is enhanced by 4 +/- 1 kJ/mol compared to the shorter-chain Asx because steric effects are reduced.     

Hydrogen exchange between tert-butyl cation and sulfuric acid

The D/H exchange between tert-butyl-d₉ cation and H₂SO₄ was investigated. The cation participating in the exchange was recovered in the form of p-di-tert-butylbenzene. The mass spectroscopic measurements show a continuous distribution, from zero to nine, of the deuterium atoms in the tert-butyl group originating from the cation.

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D/H --d, H₂SO₄. , , ---. — — - .

     

Interaction energies between tetrahydrobiopterin analogues and aromatic residues in tyrosine hydroxylase and phenylalanine hydroxylase

The phenylalanine residues 300 and 309 in the enzyme tyrosine hydroxylase are known to aid in the positioning and binding of tetrahydrobiopterin (BH4) to the enzyme active site. The residues phenylalanine 254 and tyrosine 325 similarly aid in binding BH4 in phenylalanine hydroxylase. BH4 is a cofactor necessary for enzyme function, and mutations in these residues have been shown to cause a decrease in enzyme function. We examine the pairwise interactions between each aromatic residue and BH4 using second-order Moller Plesset theory and density functional theory to determine the amount of binding due to these aromatic residues. Further, we perform in silico point mutations of these residues to determine if several likely mutations can cause a decrease in protein function. Our results show that dispersion dominates these interactions, and electrostatics alone is not enough to bind the BH4.     

叶酸与氨基酸相互作用的荧光光谱

在模拟动物生理条件下,利用荧光光谱法在分子水平上研究了叶酸同色氨酸、酪氨酸、苯丙氨酸的相互作用;根据双对数方程求出了不同温度下两者反应的结合常数和结合位点数.结果表明:叶酸能导致氨基酸的荧光猝灭,三种氨基酸的猝灭机制均为静态猝灭;从相应的热力学参数可知,色氨酸和酪氨酸与叶酸之间的主要作用力为疏水作用力,而苯丙氨酸与叶酸之间的主要作用力为氢键和范德华力.     

4‐Vinyl­benzyl analogs of adenine and uracil: reactive monomers for nucleobase polymeric resins

The crystal structures of 9‐(4‐vinyl­benzyl)­adenine, C₁₄H₁₃N₅, and 1‐(4‐vinyl­benzyl)­uracil, C₁₃H₁₂N₂O₂, are composed of zigzag ribbon‐like structures that are stabilized by conventional (N—H?N‐type) hydrogen bonds for the former and conventional (N—H?O‐type) and non‐conventional (C—H?O‐type) hydrogen bonds for the latter; the hydrogen‐bonding patterns are represented by graph‐sets R(9) and R(8), respectively. The adenine and uracil moieties in these alkyl­ated derivatives are planar and are inclined at angles of 84.44 (4) and 79.07 (7)°, respectively, with respect to the phenyl rings.     

芘荧光探针法研究海藻酸钠与SDS的作用

采用芘荧光法研究了海藻酸钠(NaAlg)与十二烷基硫酸钠(SDS)在不同pH水溶液中的相互作用.以芘单体的荧光光谱第一峰与第三峰的荧光强度之比(I1/I3)及激基缔合物与单体荧光强度之比(IE/IM)来探测芘分子所处环境的极性.结果表明:NaAlg水溶液随pH值降低,出现了聚合物的疏水微区;pH从7降到5,NaAlg类似简单盐,对SDS的临界胶束浓度(CMC)有明显的影响;在pH 3时,海藻酸主链上有足够的疏水片段,使得SDS与海藻酸通过疏水性作用而聚集.NaCl对NaAlg /SDS体系的影响亦较明显.