Acid dissociation constants of uridine-5′-diphosphate compounds determined by phosphorus nuclear magnetic resonance spectroscopy and internal pH referencing

The acid dissociation constant (pK_a) of small, biological molecules is an important physical property used for investigating enzyme mechanisms and inhibitor design. For phosphorus-containing molecules, the ³¹P nuclear magnetic resonance (NMR) chemical shift is sensitive to the local chemical environment, particularly to changes in the electronic state of the molecule. Taking advantage of this property, we present a ³¹P NMR approach that uses inorganic phosphate buffer as an internal pH reference to determine the pK_a values of the imide and second diphosphate of uridine-5′-diphosphate compounds, including the first reported values for UDP-GlcNAc and UDP-S-GlcNAc. New methods for using inorganic phosphate buffer as an internal pH reference, involving mathematical correction factors and careful control of the chemical shift reference sample, are illustrated. A comparison of the newly determined imide and diphosphate pK_a values of UDP, UDP-GlcNAc, and UDP-S-GlcNAc with other nucleotide phosphate and thio-analogs reveals the significance of the monosaccharide and sulfur position on the pK_a values.     

Investigating the Broad Matrix-Gate Network in the Mitochondrial ADP/ATP Carrier through Molecular Dynamics Simulations

The mitochondrial ADP/ATP carrier (AAC) exports ATP and imports ADP through alternating between cytosol-open (c-) and matrix-open (m-) states. The salt bridge networks near the matrix side (m-gate) and cytosol side (c-gate) are thought to be crucial for state transitions, yet our knowledge on these networks is still limited. In the current work, we focus on more conserved m-gate network in the c-state AAC. All-atom molecular dynamics (MD) simulations on a variety of mutants and the CATR-AAC complex have revealed that: (1) without involvement of other positive residues, the charged residues from the three Px[DE]xx[KR] motifs only are prone to form symmetrical inter-helical network; (2) R235 plays a determinant role for the asymmetry in m-gate network of AAC; (3) R235 significantly strengthens the interactions between H3 and H5; (4) R79 exhibits more significant impact on m-gate than R279; (5) CATR promotes symmetry in m-gate mainly through separating R234 from D231 and fixing R79; (6) vulnerability of the H2-H3 interface near matrix side could be functionally important. Our results provide new insights into the highly conserved yet variable m-gate network in the big mitochondrial carrier family.     

Synthesis of Well‐Defined Adenosine Diphosphate Ribose Oligomers

The post‐translational modification of proteins that is known as adenosine diphosphate ribosylation (ADPr) regulates a wide variety of important biological processes, such as DNA‐damage repair and cellular metabolism. This modification is also involved in carcinogenesis and the process of aging. Therefore, a better understanding of the function of ADP‐ribosylation is crucial for the development of novel therapeutics. To facilitate the elucidation of the biology of ADPr, the availability of well‐defined fragments of poly(ADP‐ribose) is essential. Herein we report a solid‐phase synthetic approach for the preparation of ADP‐ribose oligomers of exactly defined length. The methodology is exemplified by the first reported synthesis of an ADP‐ribose dimer and trimer.     

Fragmentation behavior of Amadori‐peptides obtained by non‐enzymatic glycosylation of lysine residues with ADP‐ribose in tandem mass spectrometry

Mono‐ and poly‐adenosine diphosphate (ADP)‐ribosylation are common post‐translational modifications incorporated by sequence‐specific enzymes at, predominantly, arginine, asparagine, glutamic acid or aspartic acid residues, whereas non‐enzymatic ADP‐ribosylation (glycation) modifies lysine and cysteine residues. These glycated proteins and peptides (Amadori‐compounds) are commonly found in organisms, but have so far not been investigated to any great degree. In this study, we have analyzed their fragmentation characteristics using different mass spectrometry (MS) techniques. In matrix‐assisted laser desorption/ionization (MALDI)‐MS, the ADP‐ribosyl group was cleaved, almost completely, at the pyrophosphate bond by in‐source decay. In contrast, this cleavage was very weak in electrospray ionization (ESI)‐MS. The same fragmentation site also dominated the MALDI‐PSD (post‐source decay) and ESI‐CID (collision‐induced dissociation) mass spectra. The remaining phospho‐ribosyl group (formed by the loss of adenosine monophosphate) was stable, providing a direct and reliable identification of the modification site via the b‐ and y‐ion series. Cleavage of the ADP‐ribose pyrophosphate bond under CID conditions gives access to both neutral loss (347.10 u) and precursor‐ion scans (m/z 348.08), and thereby permits the identification of ADP‐ribosylated peptides in complex mixtures with high sensitivity and specificity. With electron transfer dissociation (ETD), the ADP‐ribosyl group was stable, providing ADP‐ribosylated c‐ and z‐ions, and thus allowing reliable sequence analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

Effect of low and high concentrations of KCl dopant on ADP crystal properties

The experimental results of the influence of low (1 M%) and high (10 M%) concentrations of potassium chloride (KCl) dopant on ADP crystals are presented. The dopant results in an increase in the metastable zone width leading to an enhanced crystal growth rate, at its low concentrations. In the presence of high concentrations of the dopant in the medium, the growth rate decreases appreciably. Further, low concentrations of dopant improve the crystalline quality with better transparency. The diffraction patterns reveal that there is no change in basic structure except for variation in intensity by doping. Slight broadening is observed in FTIR of ADP in the 3500–3000 cm⁻¹ range in the presence of high [KCl]. It appears that the dopant has not altered much the optical transparency of the crystal. SEM studies of pure and doped samples reveal that structure defect centers are formed in ADP crystals by the dopant. Second harmonic generation (SHG) efficiency measurements indicate that nonlinear optical (NLO) property is enhanced appreciably by [KCl] dopant and the SHG is more pronounced at high concentrations. It seems that the molecular alignment of the crystal facilitates non-linearity in the presence of the dopant.     

Electroanalytical Characterization of Adenosine Mono-, Di- and Triphosphate Oxidation on Carbon Electrode

Abstract

Electrochemical oxidation of adenosine mononucleotides was characterized using a pencil graphite carbon electrode for the first time. All three adenosine mononucleotides, adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP), showed irreversible electro-activity at the carbon electrode, yielding a well-defined oxidation current response. The peak potential was highly dependent on pH. The lowest mononucleotide concentration detected was 1 µM. The electro-analytical data presented here for the oxidation of adenosine mononucleotides provides the basis for further bioanalytical investigations related to DNA-drug interactions.     

MicroITIES Detection of Adenosine Phosphates

The complexation between a triamide ligand derived from tris‐2‐(aminoethyl)amine: N‐{2‐[bis‐(2‐(4‐tert‐butylbenzoyl)‐aminoethyl)‐amino]‐ethyl}4‐tert‐butylbenzamide, L , and the three adenosine‐containing nucleotides, ATP, ADP, and AMP, was investigated by facilitated ion transfer processes through a microhole array film. Differential pulse voltammetry (DPV) was used to measure the transfer currents for the respective nucleotides. The three nucleotides were found to have different transfer potentials with transfer currents proportional to their aqueous concentrations. Based on the differences of the transfer potentials, it is concluded that the host ligand, L, interacts with the phosphate moiety and the Gibbs transfer energy is dominated by the charge generated by the phosphate groups. The linear relationship between the current response and nucleotide concentration forms the basis of an anion sensor with a dynamic range from 0.1 mM to 5 mM .     

Elastic coiled-coils act as energy buffers in the ATP synthase

In the ATP synthase, transmission of energy from the membrane-embedded F0 sector to the catalytic F1 sector is accomplished by two stalks composed of coiled-coils. The great efficiency of the enzyme, despite the presence of a symmetry mismatch between the F1 and F0 sectors, suggests the involvement of elastic elements that store energy during the catalytic cycle. Here, the stalk subunits γ and b are investigated as the source of this elastic compliance using a continuum mechanical model of coiled-coils and energy arguments. The analysis shows that the compliance of both subunits is required for efficient energy transmission between F0 and F1. In addition, the predicted mechanical properties of coiled-coils in the ATP synthase suggest mechanisms whereby regulatory subunits influence the enzyme activity.     

Surface chemical analysis and chromatographic characterization of polyethylenimine-coated hydroxyapatite with various amount of polyethylenimine

Polyethylenimine (PEI) has been widely used as a coating material to produce stationary phase for ion-exchange chromatography of biomolecules. However, a precise study of the PEI coating fraction has been lacking, despite such quantification being very important for fundamental research as well as identifying further industrial applications.In this study, we produced four types of PEI-coated hydroxyapatite (PEI-HAp) with various fractions of PEI (0.16%, 0.5%, 1.0%, 1.5%) using a spray-drying system to evaluate correlations between coating fractions and the thermochemical or chromatographic behaviors of theses products. The thermal analyses of these matrices showed two exothermic peaks when the PEI coating fraction exceeded 1.0%. The one peak indicated a PEI decomposition peak and the other would indicate bond dissociation of PEI layers formed over the HAp surface as the PEI concentration increased. Furthermore, the chromatographic analysis for the surface chemical characteristics showed the correlation between coating fraction and the retention time of protein or nucleotide. Acidic or phosphorylated proteins were more strongly adsorbed as the PEI coating fraction increased when the initial coating fraction was low, but at fraction exceeding 0.5%, constant retention was observed. The retention time of nucleotides increased in proportion to the fraction of PEI added. The good selectivity of PEI-HAp may be attributable to multifunctional interactions of electrostatic and bare Ca sites on HAp, not just the amino sites of PEI. These precise studies of PEI coating fraction are our original novel contributions, which could be achieved by quantitative consideration using thermal analysis and chromatography.