Electrostatic Interaction Sites Research Articles

Molecular Dynamics Simulations of Quinoline in the Liquid Phase

Molecular dynamics simulations of liquid quinoline have been performed at experimental densities corresponding to the temperature range 276-320 K. The intermolecular potential is a simple effective two-body potential between rigid molecules having 17 atomic Lennard-Jones and electrostatic Coulomb interaction sites. The vaporization enthalpy is overestimated by 8-9% with respect to the experimental value. The translational diffusion coefficient exhibits a small non-Arrhenius behavior with a change in temperatures near 290 and 303 K. The rotational diffusion tensor is rotated around the z axis perpendicular to the molecular plane by an angle of 4-6° with respect to the frame of reference defined by the principal axes of inertia. The rotational diffusion tensor presents a significant anisotropy with D(rot,y)/D(rot,x) ≃ 0.6-0.5 and D(rot,z)/D(rot,x) ≃ 1.6-1.3 between 276 and 320 K when the x axis is defined as the long molecular axis and the y axis is situated nearly along the central C-C bond. The rotational diffusion coefficients, the reorientational correlation times of the C-H vectors, and the T1(13)C NMR relaxation times present a non-Arrhenius break around 288-290 K in agreement with several experimental results. In addition, a non-Arrhenius break can also be observed at 303 K for these properties. It has been found that the structure evolves smoothly in the studied temperature range. Center of mass-center of mass and atom-atom radial distribution functions show a monotonous evolution with temperature. Various types of first-neighbor dimers have been defined, and their population analysis has revealed a continuous monotonous evolution with temperature. Thus, the non-Arrhenius behavior observed for translational and rotational diffusion is correlated with the monotonous evolution of the population of first-neighbor dimers at a microscopic level and not with a sharp structural transition.

Recrystallization of Water in Non-Water-Soluble (Meth)Acrylate Polymers Is Not Rare and Is Not Devitrification

Change in the state of water sorbed into four kinds of non-water-soluble poly(meth)acrylates with low water content by temperature (T) perturbation was examined on the basis of T variable mid-infrared (MIR) spectroscopy. Many studies using differential scanning calorimetry suggested that there was no change in the state. T dependence of their MIR spectra, however, clearly demonstrated various changes in the state. Furthermore, recrystallization, which was crystallization during heating, was observed in all four polymers. The recrystallization observed in this study was not devitrification, which is the change in the state from glassy water to crystalline water, but vapor deposition during heating (vapor re-deposition). There were only two reports about recrystallization of water in a non-water-soluble polymer before this report; therefore, it might be considered to be a rare phenomenon. However, as demonstrated in this study, it is not a rare phenomenon. Recrystallization (vapor re-deposition) of water in the polymer matrices is related to a balance between flexibility and strength of the electrostatic interaction sites of polymer matrices but might not be related to the biocompatibility of polymers.

Design, optimization and evaluation of specific affinity adsorbent for oligopeptides

A major challenge in the development of affinity adsorbents is the design of specific adsorbents for target molecules. In this paper, a two-step strategy was used to design a specific adsorbent for oligopeptides. Based on the structural characteristics of target peptide DFLAE (DE5), the affinity ligand CDenHis bearing hydrophobic inclusion and electrostatic interaction sites was prepared by grafting histidine onto β-cyclodextrin (CD) using ethylenediamine; ligands with single hydrophobic inclusion or electrostatic interaction sites (CDen and HisOMe) were used as reference ligands. Results indicated that the binding affinity ( K a) of CDenHis with DE5 was 6.23 × 10 4 M −1, 23- and 61-fold higher than that of CDen and HisOMe, respectively. Computer simulations were used to further optimize the steric configuration of CDenHis. It was found that the optimized ligand CDdnHis exhibited a much improved binding affinity for DE5 ( K a = 1.02 × 10 5 M −1). Moreover, the corresponding adsorbent A-CDdnHis not only showed much better adsorption ability compared with A-CDenHis, but also excellent adsorption specificity for DE5-containing peptides. Kinetic analysis and adsorption mechanism studies suggested that the configuration matching of CDdnHis with DE5 and the cooperation of multiple interactions led to the fast and selective adsorption of DE5-containing peptides to A-CDdnHis.

Preparation and characterization of mixed-mode monolithic silica column for capillary electrochromatography

A silica-based monolithic stationary phase with mixed-mode of reversed phase (RP) and weak anion-exchange (WAX) for capillary electrochromatography (CEC) has been prepared. The mixed-mode monolithic silica column was prepared using the sol-gel technique and followed by a post-modification with hexadecyltrimethoxysilane (HDTMS) and aminopropyltrimethoxysilane (APTMS). The amino groups on the surface of the stationary phase were used to generate a substantial anodic EOF as well as to provide electrostatic interaction sites for charged compounds at low pH. A cathodic EOF was observed at pH above 7.3 due to the full ionization of residual silanol groups and the suppression in the ionization of amino groups. A variety of analytes were used to evaluate the electrochromatographic characterization and column performance. The monolithic stationary phase exhibited RP chromatographic behavior toward neutral solutes. The model anionic solutes were separated by the mixed-mode mechanism, which comprised RP interaction, WAX, and electrophoresis. Symmetrical peaks can be obtained for basic solutes because positively charged amino groups can effectively minimize the adsorption of positively charged analytes to the stationary phase.

Molecular Basis for Cation Selectivity in Claudin-2–based Paracellular Pores: Identification of an Electrostatic Interaction Site

Yu et al. 2009. J. Gen. Physiol. doi:10.1085/jgp.200810154 [OpenUrl][1][Abstract/FREE Full Text][2] [1]: {openurl}?query=rft_id%253Dinfo%253Adoi%252F10.1085%252Fjgp.200810154%26rft_id%253Dinfo%253Apmid%252F19114638%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%

Molecular Basis for Cation Selectivity in Claudin-2–based Paracellular Pores: Identification of an Electrostatic Interaction Site

Paracellular ion transport in epithelia is mediated by pores formed by members of the claudin family. The degree of selectivity and the molecular mechanism of ion permeation through claudin pores are poorly understood. By expressing a high-conductance claudin isoform, claudin-2, in high-resistance Madin-Darby canine kidney cells under the control of an inducible promoter, we were able to quantitate claudin pore permeability. Claudin-2 pores were found to be narrow, fluid filled, and cation selective. Charge selectivity was mediated by the electrostatic interaction of partially dehydrated permeating cations with a negatively charged site within the pore that is formed by the side chain carboxyl group of aspartate-65. Thus, paracellular pores use intrapore electrostatic binding sites to achieve a high conductance with a high degree of charge selectivity.

The Use of ECD/ETD to Identify the Site of Electrostatic Interaction in Noncovalent Complexes

Electrostatic interactions play an important role in the formation of noncovalent complexes. Our previous work has highlighted the role of certain amino acid residues, such as arginine, glutamate, aspartate, and phosphorylated/sulfated residues, in the formation of salt bridges resulting in noncovalent complexes between peptides. Tandem mass spectrometry (MS) studies of these complexes using collision-induced dissociation (CID) have provided information on their relative stability. However, product-ion spectra produced by CID have been unable to assign specifically the site of interaction for the complex. In this work, tandem MS experiments were conducted on noncovalent complexes using both electron capture dissociation (ECD) and electron-transfer dissociation (ETD). The resulting spectra were dominated by intramolecular fragments of the complex with the electrostatic interaction site intact. Based upon these data, we were able to assign the binding site for the peptides forming the noncovalent complex.

Pressurized CEC of neutral and charged solutes using silica monolithic stationary phases functionalized with 3‐(2‐aminoethylamino)propyl ligands

A novel silica monolithic stationary phase functionalized with 3-(2-aminoethylamino)propyl ligands for pressurized CEC has been presented. The monolithic capillary columns were prepared by a sol-gel process in 75 microm id fused-silica capillaries and followed by a chemical modification. The diamino groups on the surface of the stationary phase are meant to generate the chromatographic surface and a substantial anodic EOF as well as to provide electrostatic interaction sites for charged solutes. The electrochromatographic characterization and column performance were evaluated by a variety of neutral and charged solutes. It was observed that the anodic EOF for the diamine-bonded monolith was greatly affected by the reaction time with 3-(2-aminoethylamino)propyltrimethoxysilane and the PEG amount in the sol-gel reaction mixture in addition to the mobile phase conditions. The monolithic stationary phase exhibited hydrophilic interaction chromatographic behavior toward neutral solutes. Good separations of various solutes including phenols, nucleic acid bases, nucleosides and nucleotides were achieved under different experimental conditions. Fast and efficient separations were obtained with high plate counts reaching more than 130,000 plates/m.

Novel non-peptide GPIIb/IIIa antagonists: synthesis and biological activities of 2-[4-[2-(4-amidinobenzoylamino)-2-(substituted)acetyl]-3-(2-methoxy-2-oxoethyl)-2-oxopiperazinyl] acetic acids.

To improve the in vitro and in vivo potency of our first low molecular weight GPIIb/IIIa antagonist 1 (TAK-029), a series of 2-[4-[2-(4-amidinobenzoylamino)-2-(substituted)acetyl]-3-(2-methoxy-2-oxoethyl)-2-oxopiper-azinyllacetic acids were synthesized through modification of the glycine moiety of 1 and evaluated for their ability to inhibit in vitro adenosine 5'-diphosphate (ADP)-induced platelet aggregation of guinea pig platelet rich plasma (PRP). Among the compounds examined, the (3S,2S)-4-methoxyphenylalanine derivative 4h showed the most potent antagonistic activity with an IC50 value of 13 nM. Dose-dependent inhibition of ex vivo platelet aggregation was achieved with oral administration of 4h (0.3-1.0 mg/kg) to guinea pigs. Complete inhibition was observed for up to 8 h, and 43% inhibition could still be observed 24 h after oral administration of 1.0 mg/kg. The long-lasting antiplatelet effect of 4h suggests that 4h would be suitable for once-a-day dosing. Structure-activity relationships (SAR) were examined in the series of the phenylalanine derivatives. An increase in the electron density around the 4-position of the phenyl ring of the phenylalanine moiety led to an increase in the antiplatelet activity, suggesting the existence of a hydrophobic and electrostatic interaction site in addition to the ionic binding sites in the GPIIb/IIIa.

Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands.

Different classes of Peripheral-type Benzodiazepine Receptor (PBR) ligands were examined and common structural elements were detected and used to develop a rational binding model based on energetically allowed ligand conformations. Two lipophilic regions and one electrostatic interaction site are essential features for high affinity ligand binding, while a further lipophilic region plays an important modulator role. A comparative molecular field analysis, performed over 130 PBR ligands by means of the GRID/GOLPE methodology, led to a PLS model with both high fitting and predictive values (r2 = 0.898, Q2 = 0.761). The outcome from the 3D QSAR model and the GRID interaction fields computed on the putative endogenous PBR ligands DBI (Diazepam Binding Inhibitor) and TTN (Tetracontatetraneuropeptide) was used to identify the amino acids most probably involved in PBR binding. Three amino acids, bearing lipophilic side chains, were detected in DBI (Phe49, Leu47 and Met46) and in TTN (Phe33, Leu31 and Met30) as likely residues underlying receptor binding. Moreover, a qualitative comparison of the molecular electrostatic potentials of DBI, TTN and selected synthetic ligands indicated also similar electronic properties. Convergent results from the modeling studies of synthetic and endogenous ligands suggest a common binding mode to PBRs. This may help the rational design of new high affinity PBR ligands.

Complementary DNA cloning and characterization of ferredoxin localized in bundle-sheath cells of maize leaves.

In maize (Zea mays L.) two leaf-specific ferredoxin (Fd) isoproteins, Fd I and Fd II, are distributed differentially in mesophyll and bundle-sheath cells. A novel cDNA encoding the precursor of Fd II (pFD2) was isolated by heterologous hybridization using a cDNA for Fd I (pFD1) as a probe. The assignment of the cDNAs to the Fds was verified by capillary liquid-chromatography/electrospray ionization-mass spectrometry. RNA-blot analysis demonstrated that transcripts for Fd I and Fd II accumulated specifically in mesophyll and bundle-sheath cells, respectively. The mature regions of pFD1 and pFD2 were expressed in Escherichia coli as functional Fds. Fd I and Fd II had similar redox potentials of -423 and -406 mV, respectively, but the Km value of Fd-NADP+ reductase for Fd II was about 3-fold larger than that for Fd I. Asparagine at position 65 of Fd II is a unique residue compared with Fd I and other Fds from various plants, which have aspartic acid or glutamic acid at the corresponding position as an electrostatic interaction site with Fd-NADP+ reductase. Substitution of asparagine-65 with aspartic acid increased the affinity of Fd II with Fd-NADP+ reductase to a level comparable to that of Fd I. These structural and functional differences of Fd I and Fd II may be related to their cell-specific expression in the leaves of a C4 plant.

Identification of electrostatic interaction sites between the regulatory and catalytic subunits of cyclic AMP-dependent protein kinase.

Two classes of molecules inhibit the catalytic subunit (C) of the cyclic AMP-dependent protein kinase (cAPK), the heat-stable protein kinase inhibitors (PKIs) and the regulatory (R) subunits. Basic sites on C, previously identified as important for R/C interaction in yeast TPK1 and corresponding to Lys213, Lys217, and Lys189 in murine C alpha, were replaced with either Ala or Thr and characterized for their kinetic properties and ability to interact with RI and PKI. rC(K213A) and rC(K217A) were both defective in forming holoenzyme with RI but were inhibited readily with PKI. This contrasts with rC(R133A), which is defective in binding PKI but not RI (Wen & Taylor, 1994). Thus, the C-subunit employs two distinct electrostatic surfaces to achieve high-affinity binding with these two types of inhibitory molecules even though all inhibitors share a common consensus site that occupies the active site cleft. Unlike TPK1, mutation of Lys189 had no effect. The mutant C subunits that were defective in binding RI, rC(K213A) and rC(K217A), were then paired with three RI mutants, rRI(D140A), rRI(E143A), and rRI(D258A), shown previously to be defective in recognition of C. Although the mutations at Asp140 and Asp258 in RI were additive with respect to the C mutations. rC(K213A) and rRI(E143A) were compensatory, thus identifying a specific electrostatic interaction site between RI and C. The results are discussed in terms of the RI and C crystal structures and the sequence homology between the yeast and mammalian enzymes.

Structural investigation of protein kinase C inhibitors

The phospholipid and Ca 2+ dependent protein kinase (PKC) plays an essential role in a variety of cellular events. Inhibition of PKC was shown to arrest growth in tumor cell cultures making it a target for possible antitumor therapy. Calphostins are potent inhibitors of PKC with high affinity for the enzyme regulatory site. Structural characteristics of calphostins, which confer the inhibitory activity, are investigated by comparing their optimized structures with the existing models for PKC activation. The resulting model of inhibitory activity assumes interaction with two out of the three electrostatic interaction sites postulated for activators. The model shows two sites of hydrophobic interaction and enables the inhibitory activity of gossypol to be accounted for.