DDM Molecules Research Articles

Electronic Interaction of Epoxy Resin with Copper at the Adhered Interface.

A better understanding of the aggregation states of adhesive molecules in the interfacial region with an adherend is crucial for controlling the adhesion strength and is of great inherent academic interest. The adhesion mechanism has been described through four theories: adsorption, mechanical, diffusion, and electronic. While interfacial characterization techniques have been developed to validate the aforementioned theories, that related to the electronic theory has not yet been thoroughly studied. We here directly detected the electronic interaction between a commonly used thermosetting adhesive, cured epoxy of diglycidyl ether of bisphenol A (DGEBA) and 4,4'-diaminodiphenylmethane (DDM), and copper (Cu). This study used a combination of density functional theory (DFT) calculations and femtosecond transient absorption spectroscopic (TAS) measurements as this epoxy adhesive-Cu pairing is extensively used in electronic device packaging. The DFT calculations predicted that π electrons in a DDM molecule adsorbed onto the Cu surface flowed out onto the Cu surface, resulting in a positive charge on the DDM. TAS measurements for the Cu/epoxy multilayer film, a model sample containing many metal/adhesive interfaces, revealed that the electronic states of excited DDM moieties at the Cu interface were different from those in the bulk region. These results were in good accordance with the prediction by DFT calculations. Thus, it can be concluded that TAS is applicable to characterize the electronic interaction of adhesives with metal adherends in a nondestructive manner.

Mechanism of Inhibition of Cytochrome c Oxidase by Triton X-100.

It is known that Triton X-100 (TX) reversibly inhibits activity of cytochrome c oxidase (CcO). The mechanism of inhibition is analyzed in this work. The action of TX is not directed to the reaction of CcO with cytochrome c, does not cause transition of the enzyme to the "slow" form, and is not associated with monomerization of the enzyme complex. TX completely suppresses oxygen reduction by CcO, but inhibition is prevented and partially reversed by dodecyl-β-D-maltoside (DDM), a detergent used to maintain CcO in solution. A 1/1 stoichiometry competition is shown between DDM and TX for binding to CcO, with Ki = 0.3 mM and affinity of DDM for the enzyme of 1.2 mM. TX interaction with the oxidized enzyme induces spectral response with maximum at 421 nm and [TX]1/2 = 0.28 mM, presumably associated with heme a3. When CcO interacts with excess of H2O2 TX affects equilibrium of the oxygen intermediates of the catalytic center accelerating the FI-607 → FII-580 transition, inhibits generation of O2·- by the enzyme, and, to a lesser extent, suppresses the catalase partial activity. The observed effects can be explained by inhibition of the conversion of the intermediate FII-580 to the free oxidized state during the catalytic cycle. TX suppresses intraprotein electron transfer between hemes a and a3 during enzyme turnover. Partial peroxidase activity of CcO remains relatively resistant to TX under conditions that block oxidase reaction effectively. These features indicate an impairment of the K proton channel conductivity. We suggest that TX interacts with CcO at the Bile Acid Binding Site (BABS) that is located on the subunit I at the K-channel mouth and contacts with amphipathic regulators of CcO [Buhrow et al. (2013) Biochemistry, 52, 6995-7006]. Apparently, TX mimics the physiological ligand of BABS, whereas the DDM molecule mimics an endogenous phospholipid bound at the edge of BABS that controls effective affinity for the ligand.

Glucose-modified carbosilane dendrimers: Interaction with model membranes and human serum albumin.

Glycodendrimers are a novel group of dendrimers (DDMs) characterized by surface modifications with various types of glycosides. It has been shown previously that such modifications significantly decrease the cytotoxicity of DDMs. Here, we present an investigation of glucose-modified carbosilane DDMs (first-third-generation, DDM1-3Glu) interactions with two models of biological structures: lipid membranes (liposomes) and serum protein (human serum albumin, HSA). The changes in lipid membrane fluidity with increasing concentration of DDMs was monitored by spectrofluorimetry and calorimetry methods. The influence of glycodendrimers on serum protein was investigated by monitoring changes in protein fluorescence intensity (fluorescence quenching) and as protein secondary structure alterations by circular dichroism spectrometry. Generally, all generations of DDMGlu induced a decrease of membrane fluidity and interacted weakly with HSA. Interestingly, in contrast to other dendritic type polymers, the extent of the DDM interaction with both biological models was not related to DDM generation. The most significant interaction with protein was shown in the case of DDM2Glu, whereas DDM1Glu induced the highest number of changes in membrane fluidity. In conclusion, our results suggest that the flexibility of a DDM molecule, as well as its typical structure (hydrophobic interior and hydrophilic surface) along with the formation of larger aggregates of DDM2-3Glu, significantly affect the type and extent of interaction with biological structures.

The mutual promotion of photolysis and laccase-catalysis on removal of dichlorophen from water under simulated sunlight irradiation

The combined removal of dichlorophen (DDM) by photolysis and laccase-catalysis in aqueous solution under simulated sunlight irradiation was investigated. It was found that DDM could be effectively degraded under simulated sunlight irradiation, which was triggered primarily by singlet/triplet state (1DDM∗/3DDM∗). The photolysis process of DDM is highly pH-dependent, mainly because of the change in electronic density distribution on the aromatic ring of DDM in its varied ionic speciation under different pH. The significant role of singlet oxygen (1O2) and 3DDM∗ in DDM photolysis was verified by experimental measurements and density functional theory (DFT) calculation. The combination of photolysis and laccase-catalysis processes can promote the removal of DDM synergistically. Product identification revealed that photolysis and laccase-catalysis attacked DDM molecule at different moieties. Single aromatic ring products were formed via photo-oxidation of DDM by 1O2. Meanwhile, photolysis can efficiently remove the oxidative coupling products of DDM formed in laccase-catalysis process, which are considered to be potentially high toxic products. In addition, this study also provided first evidence of the laccase inactivation mechanisms induced by simulated sunlight, namely, the destruction of copper catalytic centers and secondary structure.

Structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry and molecular dynamics simulations.

The structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry (IMS) and vacuum molecular dynamics (MD) simulations is reported. Direct evidence is provided for the ability of the surfactant dodecyl-β-D-maltoside (DDM) to prevent charge-induced unfolding of the membrane protein (PagP) in the gas-phase. Restraints obtained by IMS are used to map the surfactant positions onto the protein surface. Surfactants occupying more exposed positions at the apexes of the β-barrel structure are most in-line with the experimental observations. MD simulations provide additional evidence for this assembly organization through surfactant inversion and migration on the protein structure in the absence of solvent. Surfactant migration entails a net shift from apolar membrane spanning regions to more polar regions of the protein structure with the DDM molecule remaining attached to the protein via headgroup interactions. These data provide evidence for the role of protein-DDM headgroup interactions in stabilizing membrane protein structure from gas-phase unfolding.

All-atom molecular dynamics simulation of a photosystem i/detergent complex.

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

The Membrane Protein LeuT in Micellar Systems: Aggregation Dynamics and Detergent Binding to the S2 Site

Structural and functional properties of integral membrane proteins are often studied in detergent micellar environments (proteomicelles), but how such proteomicelles form and organize is not well understood. This makes it difficult to evaluate the relationship between the properties of the proteins measured in such a detergent-solubilized form and under native conditions. To obtain mechanistic information about this relationship for the leucine transporter (LeuT), a prokaryotic homologue of the mammalian neurotransmitter/sodium symporters (NSSs), we studied the properties of proteomicelles formed by n-dodecyl-β,d-maltopyranoside (DDM) detergent. Extensive atomistic molecular dynamics simulations of different protein/detergent/water number ratios revealed the formation of a proteomicelle characterized by a constant-sized shell of detergents surrounding LeuT protecting its transmembrane segments from unfavorable hydrophobic/hydrophilic exposure. Regardless of the DDM content in the simulated system, this shell consisted of a constant number of DDM molecules (∼120 measured at a 4 Å cutoff distance from LeuT). In contrast, the overall number of DDMs in the proteomicelle (aggregation number) was found to depend on the detergent concentration, reaching a saturation value of 226±17 DDMs in the highest concentration regime simulated. Remarkably, we found that at high detergent-to-protein ratios we observed two independent ways of DDM penetration into LeuT, both leading to a positioning of the DDM molecule in the second substrate (S2) binding site of LeuT. Consonant with several recent experimental studies demonstrating changes in functional properties of membrane proteins due to detergent, our findings highlight how the environment in which the membrane proteins are examined may affect the outcome and interpretation of their mechanistic features.

Like Fish Out of Water: Membrane Proteins in Detergent Micelles

Biophysical studies of structure-function relations of membrane proteins are often done in detergent micelles. However, the scarce molecular understanding of the way in which such micelles form and organize around guest proteins makes it difficult to evaluate the relation between the experimental models and the properties of the membrane proteins in their native environment. Because experimental conditions were shown to have a major effect on structure-function relations of the leucine transporter (LeuT), a prokaryotic homolog of the mammalian neurotransmitter:sodium symporter proteins and a prototype for their study, we investigated LeuT in dodecyl-β-maltoside (DDM) detergent micelles. Atomistic molecular dynamics (MD) simulations revealed the formation of a constant-sized “detergent core” within 4A of LeuT consisting of ∼120 DDM molecules regardless of the DDM-to-protein number ratio. However, we found that the aggregation number of the protein-detergent complex (i.e., the number of DDMs associated with the micelle surrounding the protein) depends on detergent concentration. Notably, this aggregation number appears to determine the extent of detergent penetration into the LeuT extracellular vestibule. Thus, we observed DDM penetration into LeuT via two pathways, but the penetration was detected only in the constructs with high detergent content. In constructs with low DDM concentration, any detergent penetration was at most transient. Entering from the “side” of LeuT, a DDM molecule passes between the extracellular segments of transmembrane helix 6 (TMH6) and TMH10, and interacts with TMH1 residues Arg30 and Gln34 in the secondary substrate-binding site (S2) of LeuT. When insertion is “from the top”, the DDM passes by extracellular loop 4 (ECL4) before it penetrates the S2 site at the level of Phe320 (in ECL4) and Leu400 (in TMH10). These findings are discussed in light of experiments that established a modulatory effect of DDM concentration on LeuT activity.

Zn[Htma][ddm]: An Interesting Three-Dimensional Chiral Nonlinear Optical-Active Zinc-Trimesate Framework

The three-dimensional (3D) chiral helical framework of the new polymeric solid, Zn[Htma][ddm] (1) (tma = trimesate, ddm = p,p′-diamino-diphenyl-methane), has been prepared by the hydrothermal reaction of zinc acetate dihydrate, H3tma, and ddm. X-ray single-crystal structural analysis reveals that 1 (C22H18N2O6Zn) crystallizes in the orthorhombic P212121 space group, Z = 4 (a = 5.4533(3) Å, b = 17.593(1) Å, c = 20.542(1) Å, V = 1970.8(2) Å3). Tetrahedrally coordinated zinc centers in 1 bridged by the rigid trigonal tectonic tma ligands with Δ-configuration plus the flexible ddm molecules give rise to an interesting 3D chiral helical diamondoid network single enantiomer that has been confirmed by solid-state circular dichroism spectra. 1 is stable up to about 297 °C in the ambient environment and exhibits an intense fluorescent emission band at 420 nm upon excitation at 326 nm and the band gap semiconducing character. The theoretical calculations reveal that 1 is a potential nonlinear optical-active material.

Halorhodopsin from Natronomonas pharaonis Forms a Trimer Even in the Presence of a Detergent, Dodecyl‐β‐d‐maltoside

Halorhodopsin (HR) is a transmembrane seven-helix retinal protein, and acts as an inward light-driven Cl(-) pump. HR from Natronomonas pharaonis (NpHR) can be expressed in Escherichia coli inner membrane in large quantities. Here, we showed that NpHR forms the trimer structure even in the presence of 0.1% (2 mm) to 1% (20 mm) dodecyl-beta-d-maltoside (DDM), whose concentrations are much higher than the critical micelle concentration (0.17 mm). This conclusion was drawn from the following observations. (1) NpHR in the DDM solution showed an exciton-coupling circular dichroism (CD) spectrum. (2) From the elution volume of gel filtration, the molecular mass of the NpHR-DDM complex was estimated. After evaluation of the mass of the bound DDM molecules, the mass of NpHR calculated was approximately equal to that of the trimer. (3) The cross-linked NpHR by glutaraldehyde gave the SDS-PAGE corresponding to the trimer. Mass spectra of these samples also support the notion of the trimer. Using the membrane fractions expressing NpHR (Escherichia coli and Halobacterium salinarum), CD spectra showed exciton-coupling, which suggests strongly the trimer structure in the cell membrane.

Supramolecular pseudometallacycles in a nickel compound with 4,4-diaminodiphenylmethane: Synthesis and structure of {Ni[(CH2(C6H4NH2)2]2(NO3)2(H2O)2}

The [Ni(DDM)2(NO3)2(H2O)2] complex (DDM is 4,4-diaminodiphenylmethane [CH2(C6H4NH2)2]) is synthesized, and its structure is determined. The crystals are triclinic, space group P\( \bar 1 \), a = 5.846(1) A, b = 9.450(2) A, c = 13.390(3) A, α = 105.63(3)°, β = 98.13(3)°, γ = 105.84(3)°, V = 666.6(2) A3, ρcalcd = 1.553 g/cm3, Z = 2. The Ni(II) ion (in the inversion center) is bound to a distorted octahedral array formed by the nitrogen atoms of the primary amino groups of the DDM molecules and the oxygen atoms of the monodentate nitrato groups and water molecules (Ni(1)-N(3) 2.119(2) A, Ni(1)-O(1) 2.122(2) A, Ni(1)-O(w) 2.047(2) A, angles at the Ni atoms vary in the 85.08(9)°–94.92(9)° interval). The structure contains supramolecular metallacycles formed by the O(w)-H…N(2) hydrogen bonds between the coordinated H2O molecules and the terminal amino groups of DDM. The metallacycles are joined by the Ni2+ ions into infinite chains running in the [111] direction.

Crystal structure of a self-assembling lipopeptide detergent at 1.20 Å

Lipopeptide detergents (LPDs) are a new class of amphiphile designed specifically for the structural study of integral membrane proteins. The LPD monomer consists of a 25-residue peptide with fatty acyl chains linked to side chains located at positions 2 and 24 of the peptide. LPDs are designed to form alpha-helices that self-assemble into cylindrical micelles, providing a more natural interior acyl chain packing environment relative to traditional detergents. We have determined the crystal structure of LPD-12, an LPD coupled to two dodecanoic acids, to a resolution of 1.20 A. The LPD-12 monomers adopt the target conformation and associate into cylindrical octamers as expected. Pairs of helices are strongly associated as Alacoil-type antiparallel dimers, and four of these dimers interact through much looser contacts into assemblies with approximate D(2) symmetry. The aligned helices form a cylindrical shell with a hydrophilic exterior that protects an interior hydrophobic cavity containing the 16 LPD acyl chains. Over 90% of the methylene/methyl groups from the acylated side chains are visible in the micelle interiors, and approximately 90% of these adopt trans dihedral angle conformations. Dodecylmaltoside (DDM) was required for the crystallization of LPD-12, and we find 10-24 ordered DDM molecules associated with each LPD assembly, resulting in an overall micelle molecular weight of approximately 30 kDa. The structures confirm the major design objectives of the LPD framework, and reveal unexpected features that will be helpful in the engineering additional versions of lipopeptide amphiphiles.

Purification and Mutagenesis of LpxL, the Lauroyltransferase of Escherichia coli Lipid A Biosynthesis

Escherichia coli lipid A is a hexaacylated disaccharide of glucosamine with secondary laurate and myristate chains on the distal unit. Hexaacylated lipid A is a potent agonist of human Toll-like receptor 4, whereas its tetra- and pentaacylated precursors are antagonists. The inner membrane enzyme LpxL transfers laurate from lauroyl-acyl carrier protein to the 2'- R-3-hydroxymyristate moiety of the tetraacylated lipid A precursor Kdo 2-lipid IV A. LpxL has now been overexpressed, solubilized with n-dodecyl beta- d-maltopyranoside (DDM), and purified to homogeneity. LpxL migration on a gel filtration column is consistent with a molecular mass of 80 kDa, suggestive of an LpxL monomer (36 kDa) embedded in a DDM micelle. Mass spectrometry showed that deformylated LpxL was the predominant species, noncovalently bound to as many as 12 DDM molecules. Purified LpxL catalyzed not only the formation in vitro of Kdo 2-(lauroyl)-lipid IV A but also a slow second acylation, generating Kdo 2-(dilauroyl)-lipid IV A. Consistent with the Kdo dependence of crude LpxL in membranes, Kdo 2-lipid IV A is preferred 6000-fold over lipid IV A by the pure enzyme. Sequence comparisons suggest that LpxL shares distant homology with the glycerol-3-phosphate acyltransferase (GPAT) family, including a putative catalytic dyad located in a conserved H(X) 4D/E motif. Mutation of H132 or E137 to alanine reduces specific activity by over 3 orders of magnitude. Like many GPATs, LpxL can also utilize acyl-CoA as an alternative acyl donor, albeit at a slower rate. Our results show that the acyltransferases that generate the secondary acyl chains of lipid A are members of the GPAT family and set the stage for structural studies.

Layered structure of the silver coordination polymer with nonrigid aromatic diamine {Ag[CH2(C6H4NH2)2]2(CH3C6H4NH2)}NO3

The complex [Ag(DDM)2(CH3C6H4NH2)]NO3, where DDM is 4,4-diaminodiphenylmethane [CH2(C6H4NH2)2], was synthesized and its structure was determined. The crystals are monoclinic, space group P21/n, a = 9.543(2) A, b = 18.056(4) A, c = 1.901(2) A, β = 106.94(3)°, V = 1796.8(6) A3, ρcalcd = 1.443 g/cm3, Z = 4. The Ag atom (at the inversion center) is coordinated at the vertices of an almost undistorted octahedron by six nitrogen atoms of the primary amino groups from four bridging DDM molecules and two terminal p-toluidine molecules (Ag-N, 2.546(3) A; NAgN, 89.7–90.3°). Wavelike layers composed of conjugate multiunit metal rings, each containing four Ag+ ions and four bridging DDM ligands, are formed in the structure in the [101] direction (a 2D polymer). Uncoordinated NO 3 − anions are arranged in the cavities between the layers and link them by N-H⋯O hydrogen bonds.

Identification and Characterization of the Slowly Exchanging pH-dependent Conformational Rearrangement in KcsA

Gating of ion channels is strictly regulated by physiological conditions as well as intra/extracellular ligands. To understand the underlying structures mediating ion channel gating, we investigated the pH-dependent gating of the K(+) channel KcsA under near-physiological conditions, using solution-state NMR. In a series of (1)H(15)N-TROSY HSQC (transverse relaxation optimized spectroscopy-heteronuclear single quantum coherence) spectra measured at various pH values, significant chemical shift changes were detected between pH 3.9 and 5.2, reflecting a conformational rearrangement associated with the gating. The pH-dependent chemical shift changes were mainly observed for the resonances from the residues near the intracellular helix bundle, which has been considered to form the primary gate in the K(+) channel, as well as the intracellular extension of the inner helix. The substitution of His-25 by Ala abolished this pH-dependent conformational rearrangement, indicating that the residue serves as a "pH-sensor" for the channel. Although the electrophysiological open probability of KcsA is less than 10%, the conformations of the intracellular helix bundle between the acidic and neutral conditions seem to be remarkably different. This supports the recently proposed "dual gating" properties of the K(+) channel, in which the activation-coupled inactivation at the selectivity filter determines the channel open probability of the channel. Indeed, a pH-dependent chemical shift change was also observed for the signal from the Trp-67 indole, which is involved in a hydrogen bond network related to the activation-coupled inactivation. The slow kinetic parameter obtained for the intracellular bundle seems to fit better into the time scale for burst duration than very fast fluctuations within a burst period, indicating the existence of another gating element with faster kinetic properties.

Electrochemical, Spectroscopic, and Mass Spectrometric Studies of the Interaction of Silver Species with Polyamidoamine Dendrimers

Electrochemical, spectroscopic, and mass spectrometric (MS) methods were used to probe the interaction (complexation) of silver ions and zerovalent silver species with polyamidoamine generation 1 amine-terminated (PAMAMG1NH2) and generation 2 hydroxy-terminated (PAMAMG2OH) dendrimers (DDMs). Stability constants (Kq+) and stoichiometries (q) (i.e., the number of silver ions complexed per DDM molecule) were determined from the voltammetric data, that is, shifts in potential and changes in peak or limiting current with addition of DDM. When the mole ratio of DDM to Ag+ is > or = 1, Ag+ binds with PAMAMG2OH to form a dominant 1:1 complex with a value of 1.1 x 10(7) M(-1). Under similar conditions, Ag+ binds with PAMAMG1NH2, yielding a 1:1 complex with = 4 x 10(9) M(-1), which is consistent with the finding of the MS experiments. When the mole ratio is < 1, q > or = 2. The E0' of the Ag-PAMAMG1NH2(+/0) couple shifted to a more negative value than that of the Ag(+/0) couple. The negative shift in the halfwave potential also suggests that DDM binds more strongly with Ag+ than with zerovalent silver species. Spectroscopic results suggest that hydroxyl-terminated PAMAMG2OH favors the formation of small zerovalent silver clusters after reduction while amine-terminated PAMAMG1NH2 allows for simultaneous formation of both clusters and larger nanoparticles at similar conditions. Other quantities, such as diffusion coefficients of the complexes and molar absorptivity of the Ag+ DDMs, are also reported.

Drug Binding Revealed by Tandem Mass Spectrometry of a Protein−Micelle Complex

The protein-micelle complex formed between the protein EmrE and the lipid dodecylmaltoside has been examined by mass spectrometry. The results show that despite the unfavorable hydrophobic environment in the mass spectrometer it is possible to preserve protein submicelle complexes in the gas phase. The peaks assigned to the submicelle complexes are broad in nature and consistent with a heterogeneous distribution of lipid molecules attached to the protein complex. As such, the spectrum cannot be interpreted. To simplify this complexity we used a tandem mass spectrometry procedure in which discrete m/z values are isolated from the peak and subjected to collision-induced dissociation. These spectra reveal clusters of DDM molecules as well as sequential release of TPP+ and EmrE from the complex as the collision cell voltage is raised. Taken together, the results provide direct evidence for drug binding within a relevant gas-phase protein-micelle complex.