Specific Hydrogen Bonds Research Articles

One short cysteine-rich sequence pattern - two different disulfide-bonded structures - a molecular dynamics simulation study.

The nematocyst walls of Hydra are formed by proteins containing small cysteine-rich domains (CRDs) of ~25 amino acids. The first CRD of nematocyst outer all antigen (NW1) and the C-terminal CRD of minicollagen-1 (Mcol1C) contain six cysteines at identical sequence positions, however adopt different disulfide bonded structures. NW1 shows the disulfide connectivities C2-C14/C6-C19/C10-C18 and Mcol1C C2-C18/C6-C14/C10-C19. To analyze if both show structural preferences in the open, non-disulfide bonded form, which explain the formation of either disulfide connectivity pattern, molecular dynamics (MD) simulations at different temperatures were performed. NW1 maintained in the 100-ns MD simulations at 283 K a rather compact fold that is stabilized by specific hydrogen bonds. The Mcol1C structure fluctuated overall more, however stayed most of the time also rather compact. The analysis of the backbone Φ/ψ angles indicated different turn propensities for NW1 and Mcol1C, which mostly can be explained based on published data about the influence of different amino acid side chains on the local backbone conformation. Whereas a folded precursor mechanism may be considered for NW1, Mcol1C may fold according to the quasi-stochastic folding model involving disulfide bond reshuffling and conformational changes, locking the native disulfide conformations. The study further demonstrates the power of MD simulations to detect local structural preferences in rather dynamic systems such as the open, non-disulfide bonded forms of NW1 and Mcol1C, which complement published information from NMR backbone residual dipolar couplings. Because the backbone structural preferences encoded by the amino acid sequence embedding the cysteines influence which disulfide connectivities are formed, the data are generally interesting for a better understanding of oxidative folding and the design of disulfide stabilized therapeutics.

Reflections on the 20th anniversary of RNA.

Reflections on the 20th anniversary of RNA.

Plasmid DNA mono-ion complex stabilized by hydrogen bond for in vivo diffusive gene delivery.

Our original concept of the mono-ion complex (MIC) between plasmid DNA (pDNA) and a monocationic biocompatible polymer has been stabilized by hydrogen bond formation. To form the hydrogen bond with pDNA, ω-amide-pentylimidazolium end-modified poly(ethylene glycol), that is, APe-Im-PEG, has been synthesized. Agarose gel retardation assay and circular dichroism measurement have revealed that the MIC between pDNA and APe-Im-PEG has been stabilized by the hydrogen bond between pDNA and the ω-amide group and that the stable MIC has surprisingly further migrated into gel, as compared with naked pDNA. The rise of melting temperature suggests that the specific hydrogen bond forms between an adenine-thymine base pair and the ω-amide group. The resulting pDNA MIC with APe-Im-PEG has enhanced gene expression by intramuscular administration in mice, as compared with a poly(ethylenimine) polyion complex (PIC). These results suggest that the pDNA MIC is diffusive in vivo administration site, as compared with pDNA PICs. Our methodology for MIC stabilization by a ω-amide group is expected to offer superior supramolecular systems to those by ubiquitous PICs for in vivo diffusive gene delivery.

Effects of protonation on foaming properties of dodecyldimethylamine oxide solutions: a pH-study.

The critical micelle concentration (cmc), the surface excess (Γ), as well as the micelle aggregation number (m) of the surfactant dodecyldimethylamine oxide (C12DMAO) have been reported to strongly depend on the pH-value of the aqueous surfactant solution. At high ionic strength, the cmc displays a minimum, while both Γ and m have a maximum at a pH-value close to the pKa of the surfactant. These experimental observations have been explained as being due to specific hydrogen bonds between the head groups, which are formed once the surfactant is partly or fully protonated. This investigation addresses the question of whether the pH also affects the foaming properties of C12DMAO solutions. To answer this question we measured the foamability and the foam stability of C12DMAO solutions at a fixed C12DMAO concentration of 5 cmc for five different pH-values, namely pH = 2, 3, 5, 8, and 10. We found that the foamability is hardly affected by the pH-value, while the foam stability strongly depends on the pH. As is the case for the above mentioned properties, the foam stability also displays an extremum in the studied pH-range, namely a maximum at pH = 5. We discuss our results in terms of the hydrogen bond hypothesis and show that this hypothesis indeed is in line with the observed trend for the foam stability. Moreover, we discuss that hydrogen bond formation may rationalize how the molecular structure of a surfactant affects foam stability.

Crystal Engineering and Charge Density Study of Pharmaceutical Nonlinear Optical Material: Melamine-Barbital Co-Crystal

This paper presents topological analysis of charge density from multipolar refinement and ab initio calculations for both melamine-barbital co-crystal and isolated molecules. The comparison of electron density properties for the isolated molecules and for the co-crystal allowed one to unravel the factors contributing to the formation of specific hydrogen bond patterns in the co-crystal structure. The inspection of charge density properties revealed that N1A of barbital and N3B of melamine compete for H1A atom in hydrogen bond formation. The hydrogen bond shows an intermediate character between closed and shared shell interaction. The tendency of barbital to adopt tautomeric forms in solution which can be correlated with the shift of electron density (mesomeric effect) was emphasized. Charge density studies confirmed the existence of the mesomeric form B of barbital in the studied co-crystal. The form B was also reported in polar co-crystals comprised of barbital and barbituric acid.

The Amyloid Precursor Protein Shows a pH-Dependent Conformational Switch in Its E1 Domain

The amyloid precursor protein (APP) and its proteolytic cleavage product Aβ are widely believed to be central to the etiology of Alzheimer's disease (AD). APP and its family members are also essential for proper neuronal development and homeostasis. APP is located at the cell surface and within intracellular compartments, cellular regions that exhibit different pH values. The AD-associated amyloidogenic processing of APP is initiated predominantly in intracellular acidic compartments, whereas its non-amyloidogenic cleavage is initiated at the cell surface at slightly basic pH. We analyzed the influence of pH on the APP-E1 domain and found that its two constituting subdomains, GFLD and CuBD, interact with each other in a pH-dependent manner. Dynamic light scattering showed that APP-E1 represents a more open conformation at neutral pH and a more closed conformation at acidic pH. Analyzing a 1.4 Å, high-resolution X-ray structure of E1 derived from merohedrally twinned crystals resulted in the identification of individual residues that are responsible for these pH-dependent interactions. Mutational studies and dynamic light scattering measurements further proved that specific hydrogen bonds between the two carboxylates of D177 and E87, as well as between N89 and H147, are major determinants of this pH-driven conformational switch in APP-E1. These findings show how APP can adopt different conformations depending on pH and suggest that the protein fulfils different functions at distinct localizations within the cell. Additionally, our data suggest a novel strategy for treating AD based on regulating the amyloidogenic processing of APP by the specific interruption of the interaction between the APP-E1 subdomains.

Tea catechins-cross-linked methylcellulose active films for inhibition of light irradiation and lipid peroxidation induced β-carotene degradation

Methylcellulose is a water soluble cellulose with excellent film-forming properties. However, the utility of methylcellulose in food packaging is limited because it disintegrates readily upon contact with moisture. In this study, an active methylcellulose film was developed using a dry/wet casting method. Tea catechins could permeate into methylcellulose films and physically cross-linked methylcellulose via formation of specific hydrophobic interactions and hydrogen bonds. Cross-linking converted the readily water-soluble methylcellulose film into insoluble methylcellulose–tea catechins (TC–MC) films with high tea catechins-binding capabilities (231.6–391.2 gallic acid equivalent mg/g). The chemical structures and compositions of the complex films were characterized by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX). Cross-linking of methylcellulose with tea catechins reduced the water vapor permeability (WVP), swelling ratio and solubility of the films but increased their tensile strengths. The tea catechins binding to MC–TC films provided the films with superior light and water vapor barrier properties. The active films could release unbound tea catechins to scavenge free radicals and inhibit bacterial growth. Degradations of β-carotene caused by ultraviolet-visible light and lipid peroxidation were effectively inhibited by the active films.

Development of a cyclometalated iridium complex with specific intramolecular hydrogen-bonding that acts as a fluorescent marker for the endoplasmic reticulum and causes photoinduced cell death.

Cyclometalated iridium complexes have important applications as phosphorescent probes for cellular imaging due to their photophysical properties. Moreover, these properties also make them potential candidates as photosensitizers for photodynamic therapy (PDT) of tumors and skin diseases. Treatment of MCF7 breast carcinoma cells with a heteroleptic phosphorescent cyclometalated iridium(III) complex C2 followed by confocal imaging indicates that the complex selectively localizes and exhibits high fluorescence in the endoplasmic reticulum. In an unprecedented approach, systematic alteration of functional groups or the metal core in C2 to synthesize a series of iridium(III) complexes (C1–C10) and an organometallic rhenium complex C11 with an imidazolyl modified phenanthroline ligand has indicated the functional groups and their interactions that are responsible for this selective localization. Remarkably, the exposure of the cells treated with C2 to irradiation at 405 nm for one hour led to membrane blebbing and cell death, demonstrating a photosensitizing property of the compound.

Dynamics of the Plasma Membrane Proton Pump.

Proton transfer over distances longer than that of a hydrogen bond often requires water molecules and protein motions. Following transfer of the proton from the donor to the acceptor, the change in the charge distribution may alter the dynamics of protein and water. To begin to understand how protonation dynamics couple to protein and water dynamics, here we explore how changes in the protonation state affect water and protein dynamics in the AHA2 proton pump. We find that the protonation state of the proton donor and acceptor groups largely affects the dynamics of internal waters and of specific hydrogen bonds, and the orientation of transmembrane helical segments that couple remote regions of the protein. The primary proton donor/acceptor group D684, can interact with water molecules from the cytoplasmic bulk and/or other protein groups.

Molecular docking, isolation and biological evaluation of Rhizophora mucronata flavonoids as anti-nociceptive agents

The anti-nociceptive effect of Rhizophora mucronata was evaluated on chemically and thermally induced nociception in mice. Albino mice received a dose of 10, 15, 20, or 25mg/kg of alkaline chloroform fraction (Alk-CF) of R. mucronata by oral administration. Compared with controls, Alk-CF decreased the writhing numbers (P<0.01) in a dose-dependent manner. Further, we determined that Alk-CF contained, a potent compared to control, also potent anti-nociceptive agent that acted via opioid receptors and using HPLC, identified this compound as luteolin. Docking simulation demonstrated that luteolin interacted strongly with cyclooxygenase, forming a number of specific hydrogen bonds. This study identified peripheral and central anti-nociceptive activities of R. mucronata that involve opioid receptor, and in which the active compound is luteolin as a source of new anti-nociceptive agent.

Local microphase separation of a binary liquid under nanoscale confinement.

The structural and diffusive properties of an ethanol-water mixture under hydrophilic nanoscale confinement are investigated by means of molecular dynamics simulations based on the CHARMM force field. The resulting density profiles illustrate that demixing of solvents occurs at the pore wall region, which is composed of silanol molecules in our case. Ethanol molecules are more likely to attach to the wall via hydrogen bonds than water molecules. A noticeable O-H bond orientation is observed for the ethanol molecules in this region, which can be explained by the formation of two specific hydrogen bonds between ethanol and silanol. Water, in contrast, resides mostly outside the interfacial region and is in favor of forming small hydrogen bonded strings and clusters with other water molecules. This phenomenon is corroborated by both the orientation of ethanol hydroxyl groups and the radial distribution functions of the solvent oxygen atom to the silanol hydrogen atom. Ethanol selectively attaches to the wall and forms a layer close to the wall. The hydrophobic headgroups of these ethanol molecules lead to an internal hydrophobic interface layer, which in turn yields cluster structures in the adjacent water. The self-diffusion of water in the confined ethanol-water mixture at the center of the pore is faster than that of water in the bulk ethanol-water mixture; ethanol, on the other hand, diffuses slower when it is confined.

The influence of Ser-154, Cys-113, and the phosphorylated threonine residue on the catalytic reaction mechanism of Pin1.

Pin1 is an enzyme that specifically catalyzes the cis-trans isomerization of proline amide bonds in peptides that contain a phosphorylated threonine or serine residue in the position preceding proline. In the cell, the isomerization reaction is associated with cellular signaling and has been related to diseases such as Alzheimer and cancer. The catalytic mechanism by which Pin1 accelerates the isomerization reaction, however, is still unknown. In this study, we use molecular dynamics simulation in combination with the QM/MM methodology to disclose the influence of the residues Ser-154 and Cys-113 in the enzyme and the phosphorylated threonine residue in the peptide on the reaction mechanism. To account for the correct electrostatic interaction between the three residues and the reactive center, we derive atomic charges that account for the varying electrostatic field in the catalytic cavity. Different methods based on reproducing the molecular electrostatic potential or an atoms in molecules approach were investigated. Finally, the reaction mechanism is analyzed with the mean reaction force and the influence of the three residues is disclosed. Our results show that Pin1 specifically catalyzes the isomerization of the trans conformer in a jump-rope type of motion, as suggested by us and confirmed experimentally by others. This is accomplished by anchoring the threonine phosphate residue on one end of the peptide through electrostatic interactions with the basic triad of the enzyme and at the other end through specific enzyme-peptide hydrogen bonds. Cys-113 reduces the structural contribution to the activation free energy through the stabilization of the cis conformer, and Ser-154 in combination with Gln-131 assist in the isomerization reaction of the trans isomer.

Density Functional Theory Study on Raman Spectra of Rhodamine Molecules in Different Forms

Rhodamine molecules are one of the most used dyes for applications related to Raman spectroscopy. We have systematically studied Raman spectra of Rhodamine 6G, Rhodamine 123, and Rhodamine B (RhB) molecules using density functional theory. It is found that with BP86 functional the calculated Raman spectra of cationic Rhodamine molecules are in good agreement with corresponding experimental spectra in aqueous solution. It is shown that the involvement of the counter ion, chlorine, and the specific hydrogen bonds has noticeable effects on the Raman spectra of RhB that can partially explain the observed difference between Raman spectra of RhB in solution and on gold surfaces. It also indicates that an accurate description of surface enhanced Raman scattering for Rhodamine molecules on metal surface still requires to take into account the changes induced by the interfacial interactions.

Optical nonlinearity and electric conductivity origin study on sucrose crystal by using IR, Raman, INS, NMR, and EPR spectroscopies

The supposed importance of hydrogen bonds toward the origin of second harmonic generation (SHG) and electric conductivity in crystalline sucrose was investigated by IR (4000–10cm−1), INS (2000–10cm−1, at 35K), polarized Raman (3600–50cm−1) spectra, and 1H NMR second moment line records in the temperature range 450–80K. The temperature dependence of NIR (7000–5500cm−1) polarized spectra gave information about –CH2 motions complementary to NMR results concerning –CH2OH group rearrangements. The EPR spectra were applied to study the generation of radical ions by exposure to NIR radiation. Density functional theory quantum chemical calculations were performed to reproduce the vibrational spectra in order to complete as far as possible the assignments of bands observed by us and in the literature in sucrose crystals, and to throw more light on the possible reasons of sucrose electric conductivity and optical nonlinearity by the knowledge of theoretical values of dipole moments, polarizabilities, first order hyperpolarizabilities of sucrose molecule and clusters as well as ionization energy and electron affinity. The proton transfer in one specific hydrogen bond parallel to the helical axis b is proposed to be the most important in SHG and conductivity origin.

Crystal Structures of β-Primeverosidase in Complex with Disaccharide Amidine Inhibitors

β-Primeverosidase (PD) is a disaccharide-specific β-glycosidase in tea leaves. This enzyme is involved in aroma formation during the manufacturing process of oolong tea and black tea. PD hydrolyzes β-primeveroside (6-O-β-d-xylopyranosyl-β-d-glucopyranoside) at the β-glycosidic bond of primeverose to aglycone, and releases aromatic alcoholic volatiles of aglycones. PD only accepts primeverose as the glycone substrate, but broadly accepts various aglycones, including 2-phenylethanol, benzyl alcohol, linalool, and geraniol. We determined the crystal structure of PD complexes using highly specific disaccharide amidine inhibitors, N-β-primeverosylamidines, and revealed the architecture of the active site responsible for substrate specificity. We identified three subsites in the active site: subsite -2 specific for 6-O-β-d-xylopyranosyl, subsite -1 well conserved among β-glucosidases and specific for β-d-glucopyranosyl, and wide subsite +1 for hydrophobic aglycone. Glu-470, Ser-473, and Gln-477 act as the specific hydrogen bond donors for 6-O-β-d-xylopyranosyl in subsite -2. On the other hand, subsite +1 was a large hydrophobic cavity that accommodates various aromatic aglycones. Compared with aglycone-specific β-glucosidases of the glycoside hydrolase family 1, PD lacks the Trp crucial for aglycone recognition, and the resultant large cavity accepts aglycone and 6-O-β-d-xylopyranosyl together. PD recognizes the β-primeverosides in subsites -1 and -2 by hydrogen bonds, whereas the large subsite +1 loosely accommodates various aglycones. The glycone-specific activity of PD for broad aglycone substrates results in selective and multiple release of temporally stored alcoholic volatile aglycones of β-primeveroside.

A Mutant of Uracil DNA Glycosylase That Distinguishes between Cytosine and 5-Methylcytosine

We demonstrate that a mutant of uracil DNA glycosylase (N123D:L191A) distinguishes between cytosine and methylcytosine. Uracil DNA glycosylase (UDG) efficiently removes uracil from DNA in a reaction in which the base is flipped into the enzyme’s active site. Uracil is selected over cytosine by a pattern of specific hydrogen bonds, and thymine is excluded by steric clash of its 5-methyl group with Y66. The N123D mutation generates an enzyme that excises cytosine. This N123D:L191A mutant excises C when it is mispaired with A or opposite an abasic site, but not when it is paired with G. In contrast no cleavage is observed with any substrates that contain 5-methylcytosine. This enzyme may offer a new approach for discriminating between cytosine and 5-methylcytosine.

Study on the interaction of catalase with pesticides by flow injection chemiluminescence and molecular docking

The interaction mechanisms of catalase (CAT) with pesticides (including organophosphates: disulfoton, isofenphos-methyl, malathion, isocarbophos, dimethoate, dipterex, methamidophos and acephate; carbamates: carbaryl and methomyl; pyrethroids: fenvalerate and deltamethrin) were first investigated by flow injection (FI) chemiluminescence (CL) analysis and molecular docking. By homemade FI–CL model of lg[(I0−I)/I]=lgK+nlg[D], it was found that the binding processes of pesticides to CAT were spontaneous with the apparent binding constants K of 103–105Lmol−1 and the numbers of binding sites about 1.0. The binding abilities of pesticides to CAT followed the order: fenvalerate>deltamethrin>disulfoton>isofenphos-methyl>carbaryl>malathion>isocarbophos>dimethoate>dipterex>acephate>methomyl>methamidophos, which was generally similar to the order of determination sensitivity of pesticides. The thermodynamic parameters revealed that CAT bound with hydrophobic pesticides by hydrophobic interaction force, and with hydrophilic pesticides by hydrogen bond and van der Waals force. The pesticides to CAT molecular docking study showed that pesticides could enter into the cavity locating among the four subdomains of CAT, giving the specific amino acid residues and hydrogen bonds involved in CAT–pesticides interaction. It was also found that the lgK values of pesticides to CAT increased regularly with increasing lgP, Mr, MR and MV, suggesting that the hydrophobicity and steric property of pesticide played essential roles in its binding to CAT.

Crystal structure of NTPDase2 in complex with the sulfoanthraquinone inhibitor PSB-071

In many vertebrate tissues CD39-like ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) act in concert with ecto-5'-nucleotidase (e5NT, CD73) to convert extracellular ATP to adenosine. Extracellular ATP is a cytotoxic, pro-inflammatory signalling molecule whereas its product adenosine constitutes a universal and potent immune suppressor. Interference with these ectonucleotidases by use of small molecule inhibitors or inhibitory antibodies appears to be an effective strategy to enhance anti-tumour immunity and suppress neoangiogenesis. Here we present the first crystal structures of an NTPDase catalytic ectodomain in complex with the Reactive Blue 2 (RB2)-derived inhibitor PSB-071. In both of the two crystal forms presented the inhibitor binds as a sandwich of two molecules at the nucleoside binding site. One of the molecules is well defined in its orientation. Specific hydrogen bonds are formed between the sulfonyl group and the nucleoside binding loop. The methylphenyl side chain functionality that improved NTPDase2-specificity is sandwiched between R245 and R394, the latter of which is exclusively found in NTPDase2. The second molecule exhibits great in-plane rotational freedom and could not be modelled in a specific orientation. In addition to this structural insight into NTPDase inhibition, the observation of the putative membrane interaction loop (MIL) in two different conformations related by a 10° rotation identifies the MIL as a dynamic section of NTPDases that is potentially involved in regulation of catalysis.

The Open State of Human VDAC Isoforms Compared through MD Simulations

Voltage dependent anion channel (VDAC) is the pore-forming protein of outer mitochondrial membrane. In mammals three isoforms exist: VDAC1, VDAC2, VDAC3 (1). The VDAC1 is the most abundant (2) and studied isoform, the only one whose 3D structure was solved at high resolution. All-atom MD simulations (∼1 μs each) were used to compare the open-state of the three human isoforms, obtaining a structural characterization particularly focused on the localization and mobility of N-termini (3) and its interaction with the β-barrel. In addition, each isoform was simulated in presence of KCl 0.5 M to investigate ions diffusion events, either in absence and presence of a 10 mV external electric field, in order to compare the selectivity, permeability ratio and ion currents.The specific hydrophobic interactions and hydrogen bonds between N-terminal fragments and the barrel were found to be related to the intrinsic breathing motions of the latter. The overall shape of channels can be described as an ellipse, whose axes fluctuations are markedly anticorrelated in hVDAC1 and hVDAC3 while, essentially, no correlation was observed in hVDAC2.Free-energy profiles of chloride and potassium ions reflect the anion selectivity of the isoforms with no significant differences in the average translocation time in both directions. However, a comprehensive explanation of differences between chloride and potassium was obtained with the cluster analysis that showed a preferential localization of the former in the middle of the pore while the latter 'segregated' at the periphery. The relative number of clusters in the three human isoforms of VDAC agrees with their relative selectivity. The position of the clusters matches with the charged residues distribution around the lumen.1. Messina A. (2012) BBA 181:1466.2. De Pinto V. (2010) BBA 1797:1268.3. Reina S. (2010) FEBS Lett. 584:2837.

Proton-Coupled Water and Hydrogen-Bond Dynamics in Channelrhodopsin

Channelrhodopsin is a light-gated cation channel whose reaction cycle involves proton-transfer reactions. Understanding how channelrhodopsin works is important, as it may assist in designing channelrhodopsin variants with specific properties for optogenetics applications.To dissect structural elements that may act as gates and to explore how protein and water dynamics respond to changes in the protonation state, we combined extensive bioinformatics analyses with molecular dynamics simulations of channelrhodopsin and of bacteriorhodopsin mutants that model specific channelrhodopsin interactions, or have altered proton-transfer kinetics. In some of these mutants, we find that perturbation of specific hydrogen bonds is coupled to the rapid formation of water bridges that could assist proton transfer. In simulations on channelrhodopsin embedded in hydrated lipid membranes, the dynamics of water wires and hydrogen bonds inter-connecting remote regions of the protein are tightly coupled to the protonation state.This work has been supported by the Marie Curie International Reintegration Award FP7-PEOPLE-2010-RG 276920 and by the SFB 1078 ‘Protonation Dynamics in Protein Function'.