Hydrophobic Channel Research Articles

Analyzing Structural Properties of Heterogeneous Cardiolipin-Bound Cytochrome C and Their Regulation by Surface-Enhanced Infrared Absorption Spectroscopy.

Apoptotic mechanisms are not fully understood due to limitations in present analytical methods. Such understanding may be advanced by unravelling the structural properties of heterogeneous cardiolipin (CL)-bound cytochrome c (cyt c) and the factors or events that regulate them. In this study, surface-enhanced infrared absorption spectroscopy (SEIRAS) was employed to probe the adsorption of cyt c on CL membranes in biomimetic conditions. The results clearly show that pure electrostatic interactions result in the unfolding of partial α-helices, while the synergy between hydrogen bonding and electrostatic interactions governs orientation homogeneity of adsorbed protein, and conformational transition between α-helices and β-sheet. Hydrogen bonding plays a dual role; along with hydrophobic interactions, it may disturb the microenvironment of some secondary structures such as the β-turn type III, while it also triggers structural changes in lipid molecules likely resulting from the extension of CL acyl chains to the hydrophobic channels of cyt c. These findings provide the details of protein transitions in early apoptosis at the molecular level.

Fabrication of user-defined copper conductive patterns onto paper substrate for flexible electronics by combining wax patterning with electroless plating

In this paper, user-defined copper conductive patterns were successfully fabricated via electroless deposition onto paper substrate by using a four-step treatment process. The pristine paper samples are first dipped in 3-aminopropyltrimethoxysilane (APTMS) solution to form a uniform layer for the subsequent absorption of gold nanoparticles. Then the paper samples were wax patterned and immersed in gold nanoparticles solution in preparation for the next step electroless deposition. Herein, wax pattern was achieved via a stylus printer to print desired stencil dot matrix, which acted as hydrophobic channels, onto the paper substrate. FT-IR measurement, ultrasonic washing test and Scotch®-tape test were utilized to investigate the interaction mechanism between APTMS molecules and paper substrate. Contact angle measurement demonstrated that the hydrophobic surface of wax patterned paper. SEM images showed that the thickness of copper conductive patterns was estimated to be 2.44 μm, which was corresponding well with Surface Profiler measurement. X-ray diffraction analysis showed that the copper films deposited on paper substrate has a structure with Cu (1 1 1) preferred orientation and the resistivity of Cu patterns measured by a digital four-point probe was 6.8 µΩ cm, which was 4.2 times of the bulk Cu. Notably, only one cycle of printing wax on paper substrate could successfully regulate the deposition area of Cu films. Those above advantages make this method a promising candidate for applications in constructing functional flexible electronic devices.

Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex.

The endoplasmic reticulum-mitochondria encounter structure (ERMES) is a protein complex that plays a tethering role in physically connecting ER and mitochondria membranes. The ERMES complex is composed of Mdm12, Mmm1, and Mdm34, which have a SMP domain in common, and Mdm10. Here, we report the crystal structure of S. cerevisiae Mdm12. The Mdm12 forms a dimeric SMP structure through domain swapping of the β1-strand comprising residues 1-7. Biochemical experiments reveal a phospholipid-binding site located along a hydrophobic channel of the Mdm12 structure and that Mdm12 might have a binding preference for glycerophospholipids harboring a positively charged head group. Strikingly, both full-length Mdm12 and Mdm12 truncated to exclude the disordered region (residues 74-114) display the same organization in the asymmetric unit, although they crystallize as a tetramer and hexamer, respectively. Taken together, these studies provide a novel understanding of the overall organization of SMP domains in the ERMES complex, indicating that Mdm12 interacts with Mdm34 through head-to-head contact, and with Mmm1 through tail-to-tail contact of SMP domains.

Water populations in restricted environments of lipid membrane interphases.

We employ molecular dynamics simulations to study the hydration properties of Dipalmitoylphosphatidylcholine (DPPC) bilayers, both in the gel and the liquid crystalline states. We show that while the tight hydration centers (PO and CO moieties) are significantly hydrated in both phases, the gel-fluid transition involves significant changes at the second hydration shell, particularly at the buried region between the hydrocarbon tails. Thus, while almost no buried water population exists in the gel state below the carbonyls, this hydrophobic region becomes partially water accesible in the liquid crystalline state. We shall also show that such water molecules present a lower H-bond coordination as compared to the molecules at the primary hydration shell. This means that, while the latter are arranged in relatively compact nanoclusters (as already proposed), the buried water molecules tend to organize themselves in less compact structures, typically strings or branched strings, with a scarce population of isolated molecules. This behavior is similar to that observed in other hydration contexts, like water penetrating carbon nanotubes or model hydrophobic channels or pores, and reflects the reluctance of water to sacrifice HB coordination.

Distorted cone conformation and unique packing structure of p-sulfonatocalix[5]arene via complexation of N-methyl-N′-(naphthalen-2-ylmethyl)-4,4′-bipyridinium

The inclusion complex of p-sulfonatocalix[5]arene (SC5A) with N-methyl-N′-(naphthalen-2-ylmethyl)-4,4′-bipyridinium (MVNp2+) guest was successfully prepared in single-crystal form. The obtained structure shows that SC5A is significantly distorted from the common ‘cone’ conformation induced by the complexation of MVNp2+. Moreover, the crystal packing of MVNp2+⊂SC5A reveals that the SC5A hosts do not assemble into a typical bilayer array, but arrange themselves into an unseen face-to-back bis-chain. As a result, hydrophobic molecular channels are fabricated rarely by SC5A hosts. A host–guest solution study was further performed by using NMR spectroscopy and microcalorimetry, the results of which are in accordance with the above crystallographic results. The molecular binding behaviors of SC5A with N-methyl-N′-adamantane carbomethyl-4,4′-bipyridinium (MVAd2+) guest that is structurally similar to MVNp2+ but with a different side group were also studied by using NMR spectroscopy and microcalorimetry in solution, the results of which are similar to those of SC5A with MVNp2+ guest as well.

Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme.

Many heme-containing proteins with a histidine in the distal E7 (HisE7) position can form sulfheme in the presence of hydrogen sulfide (H2S) and a reactive oxygen species such as hydrogen peroxide. For reasons unknown, sulfheme derivatives are formed specifically on solvent-excluded heme pyrrole B. Sulfhemes severely decrease the oxygen-binding affinity in hemoglobin (Hb) and myoglobin (Mb). Here, use of hybrid quantum mechanical/molecular mechanical methods has permitted characterization of the entire process of sulfheme formation in the HisE7 mutant of hemoglobin I (HbI) from Lucina pectinata. This process includes a mechanism for H2S to enter the solvent-excluded active site through a hydrophobic channel to ultimately form a hydrogen bond with H2O2 bound to Fe(III). Proton transfer from H2O2 to His64 to form compound (Cpd) 0, followed by hydrogen transfer from H2S to the Fe(III)-H2O2 complex, results in homolytic cleavage of the O-O and S-H bonds to form a reactive thiyl radical (HS(•)), ferryl heme Cpd II, and a water molecule. Subsequently, the addition of HS(•) to Cpd II, followed by three proton transfer reactions, results in the formation of a three-membered ring ferric sulfheme that avoids migration of the radical to the protein matrix, in contrast to that in other peroxidative reactions. The transformation of this three-membered episulfide ring structure to the five-membered thiochlorin ring structure occurs through a significant potential energy barrier, although both structures are nearly isoenergetic. Both three- and five-membered ring structures reveal longer NB-Fe(III) bonds compared with other pyrrole nitrogen-Fe(III) bonds, which would lead to decreased oxygen binding. Overall, these results are in agreement with a wide range of experimental data and provide fertile ground for further investigations of sulfheme formation in other heme proteins and additional effects of H2S on cell signaling and reactivity.

Structure of the sirtuin-linked macrodomain SAV0325 from Staphylococcus aureus.

Cells use the post‐translational modification ADP‐ribosylation to control a host of biological activities. In some pathogenic bacteria, an operon‐encoded mono‐ADP‐ribosylation cycle mediates response to host‐induced oxidative stress. In this system, reversible mono ADP‐ribosylation of a lipoylated target protein represses oxidative stress response. An NAD+‐dependent sirtuin catalyzes the single ADP‐ribose (ADPr) addition, while a linked macrodomain‐containing protein removes the ADPr. Here we report the crystal structure of the sitruin‐linked macrodomain protein from Staphylococcus aureus, SauMacro (also known as SAV0325) to 1.75‐Å resolution. The monomeric SauMacro bears a previously unidentified Zn2+‐binding site that putatively aids in substrate recognition and catalysis. An amino‐terminal three‐helix bundle motif unique to this class of macrodomain proteins provides a structural scaffold for the Zn2+ site. Structural features of the enzyme further indicate a cleft proximal to the Zn2+ binding site appears well suited for ADPr binding, while a deep hydrophobic channel in the protein core is suitable for binding the lipoate of the lipoylated protein target.

Electro-osmotic flow of power-law fluid and heat transfer in a micro-channel with effects of Joule heating and thermal radiation

A mathematical model has been developed for studying the electro-osmotic flow and heat transfer of bio-fluids in a micro-channel in the presence of Joule heating effects. The flow of bio-fluid is governed by the non-Newtonian power-law fluid model. The effects of thermal radiation and velocity slip condition have been examined in the case of hydrophobic channel. The Poisson–Boltzmann equation governing the electrical double layer field and a body force generated by the applied electric potential field are taken into consideration. The results presented here pertain to the case where the height of the channel is much greater than the thickness of electrical double layer comprising the Stern and diffuse layers. The expressions for flow characteristics such as velocity, temperature, shear stress and Nusselt number have been derived analytically under the purview of the present model. The results estimated on the basis of the data available in the existing scientific literatures are presented graphically. The effects of thermal radiation have an important bearing on the therapeutic procedure of hyperthermia, particularly in understanding the heat transfer in micro-channel in the presence of electric potential. The dimensionless Joule heating parameter has a reducing impact on Nusselt number for both pseudo-plastic and dilatant fluids, nevertheless its impact on Nusselt number is more pronounced for dilatant fluid. Furthermore, the effect of viscous dissipation has a significant role in controlling heat transfer and should not be neglected.

Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.

The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.

Azobenzene-bridged bile acid dimers: an interesting class of conjugates with conformation-controlled bioactivity

The synergetic combination of the distinct properties of azobenzene and bile acid could afford stable tweezer-like conformation with tunable hydrophilic and hydrophobic channels, thus increasing their antimicrobial activity toward both Gram-positive and Gram-negative bacteria, which can be conveniently switched off when the conformation turn back to the extended state.

ZIF-8 incorporated polyether block amide membrane for phenol permselective pervaporation with high efficiency

Abstract In recent years, zeolitic imidazolate framework-8 (ZIF-8) has received tremendous attention due to its hydrophobic inner channels and good compatibility with the polymer as an inorganic filler for preparation of the mixed matrix membrane (MMM). In this study, ZIF-8 particles were synthesized and incorporated into Ploy (ether block amide) matrix (PEBA-2533) to fabricate a MMM for the enhancement of phenol permselective pervaporation. The structure and morphology of ZIF-8 particle and the obtained MMMs were characterized by XRD, SEM, FTIR, contact angle and BET. It is found that the hydrophobicity of the membrane was enhanced by the incorporation of hydrophobic ZIF-8, and the obtained MMM withstand the extreme operation conditions of pervaporation. The effects of particle loading amount, feed concentration and temperature on the separation performance of ZIF-8 incorporated MMMs were investigated in details. Compared with the pure PEBA-2533 membrane, the permeate flux of ZIF-8 incorporated PEBA-2533 MMM with a 10 wt% loading amount was significantly increased from 846 g m−2 h−1 to 1310 g m−2 h−1, while the separation factor increased from 39 to 53 at 70 °C with 8000 ppm feed phenol concentration. The enhancement of the pervaporation performance could be mainly attributed to the preferential highly permeable regions of the bimodal membrane structure for phenol molecules, which was consisted of ZIF-8 particles. Finally, both of the excellent overall membrane pervaporation performance and the long-term revealed that such a ZIF-8 incorporated MMM has a great potential in separation and recovery of phenol from its aqueous solution for a practical process.

Electrochemical sensing platform amplified with a nanobiocomposite of L-phenylalanine ammonia-lyase enzyme for the detection of capsaicin

The present study involves the development of a sensitive electrochemical biosensor for the determination of capsaicin extracted from chilli fruits, based on a novel signal amplification strategy using enzyme technology. For the first time, platinum electrode modified with multiwalled carbon nanotubes where phenylalanine ammonia-lyase enzyme was immobilized using nafion was characterized by attenuated total reflectance infrared spectroscopy, transmittance electron microscopy and thermo-gravimetric analysis supported by computational methods. Cyclic and differential pulse voltammetry measurements were performed to better understand the redox mechanism of capsaicin. The performance of the developed electrochemical biosensor was tested using spiked samples with recoveries ranging from 98.9 to 99.6%. The comparison of the results obtained from bare and modified platinum electrodes revealed the sensitivity of the developed biosensor, having a detection limit (S/N=3) of 0.1863µgmL−1 and electron transfer rate constant (ks) of 3.02s−1. Furthermore, adsorption and ligand-enzyme docking studies were carried out to better understand the redox mechanisms supported by density functional theory calculations. These results revealed that capsaicin forms hydrogen bonds with GLU355, GLU541, GLU586, ARG and other amino acids of the hydrophobic channel of the binding sites thereby facilitating the redox reaction for the detection of capsaicin.

Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies

COX-2 is a well-known drug target in inflammatory disorders. COX-1/COX-2 selectivity of NSAIDs is crucial in assessing the gastrointestinal side effects associated with COX-1 inhibition. Celecoxib, rofecoxib, and valdecoxib are well-known specific COX-2 inhibiting drugs. Recently, polmacoxib, a COX-2/CA-II dual inhibitor has been approved by the Korean FDA. These COXIBs have similar structure with diverse activity range. Present study focuses on unraveling the mechanism behind the 10-fold difference in the activities of these sulfonamide-containing COXIBs. In order to obtain insights into their binding with COX-2 at molecular level, molecular dynamics simulations studies, and MM-PBSA approaches were employed. Further, per-residue decomposition of these energies led to the identification of crucial amino acids and interactions contributing to the differential binding of COXIBs. The results clearly indicated that Leu338, Ser339, Arg499, Ile503, Phe504, Val509, and Ser516 (Leu352, Ser353, Arg513, Ile517, Phe518, Val523, and Ser530 in PGHS-1 numbering) were imperative in determining the activity of these COXIBs. The binding energies and energy contribution of various residues were similar in all the three simulations. The results suggest that hydrogen bond interaction between the hydroxyl group of Ser516 and five-membered ring of diarylheterocycles augments the affinity in COXIBs. The SAR of the inhibitors studied and the per-residue energy decomposition values suggested the importance of Ser516. Additionally, the positive binding energy obtained with Arg106 explains the binding of COXIBs in hydrophobic channel deep in the COX-2 active site. The findings of the present work would aid in the development of potent COX-2 inhibitors.

Effect of PTFE nanoparticles in catalyst layer with high Pt loading on PEM fuel cell performance

In this study, Polytetrafluoroethylene (PTFE) was added to catalyst layer structure. This modification was aimed at facilitating excess water removal from the cathode catalyst layer with high Pt loading (1.2 mg/cm2). The weight percentage of PTFE in the catalyst inks varied from zero to 30. Membrane electrode assemblies were prepared with a commercial catalyst containing 70 wt % Pt on carbon, by ultrasonic spray coating technique. PEM fuel cell performance testing was carried out with two different membrane electrode assembly configuration in order to identify the effect of PTFE in anode and cathode catalyst layer structures on water transport mechanism and cell performance. In the first configuration (MEA1), PTFE nanoparticles were added to anode and cathode catalyst layers. In the second configuration (MEA2), PTFE nanoparticles were added only on cathode catalyst layer. PEM fuel cell tests were carried out at both H2/O2 and H2/Air gas-feeding modes. Electrochemical characterization with impedance spectroscopy was carried out to investigate the influence of PTFE nanoparticles on reaction kinetics and mass transport. PTFE nanoparticles in catalyst layers of 5PTFE_AC provided meso-macro hydrophobic channeling, providing enhanced water management compared to conventional catalyst layers. Higher hydrophobicity in cathode catalyst layer coupled with high airflow rate promotes increased back diffusion rate of water, diminishing flooding at cathode GDL.

Structural Basis of Lipid Targeting and Destruction by the Type V Secretion System of Pseudomonas aeruginosa

The type V secretion system is a macromolecular machine employed by a number of bacteria to secrete virulence factors into the environment. The human pathogen Pseudomonas aeruginosa employs the newly described type Vd secretion system to secrete a soluble variant of PlpD, a lipase of the patatin-like family synthesized as a single macromolecule that also carries a polypeptide transport-associated domain and a 16-stranded β-barrel. Here we report the crystal structure of the secreted form of PlpD in its biologically active state. PlpD displays a classical lipase α/β hydrolase fold with a catalytic site located within a highly hydrophobic channel that entraps a lipidic molecule. The active site is covered by a flexible lid, as in other lipases, indicating that this region in PlpD must modify its conformation in order for catalysis at the water–lipid interface to occur. PlpD displays phospholipase A1 activity and is able to recognize a number of phosphatidylinositols and other phosphatidyl analogs. PlpD is the first example of an active phospholipase secreted through the type V secretion system, for which there are more than 200 homologs, revealing details of the lipid destruction arsenal expressed by P. aeruginosa in order to establish infection.

Miconidin Acetate and Primin as Potent 5-Lipoxygenase Inhibitors from Brazilian Eugenia hiemalis (Myrtaceae)

This paper describes the isolation and identification of primin and miconidin acetate as metabolites from the flower bud extract of Eugenia hiemalis as well as the anti-inflammatory activity of miconidin acetate by inhibition of 5-lipoxygenase. Miconidin acetate inhibited leukotriene B4 formation catalyzed by the human recombinant enzyme (IC50 = 0.3 ± 0.17 µM) more than primin (IC50 = 1.4 ± 0.6 µM) and zileuton (IC50 = 1.1 ± 0.7 µM). Miconidin acetate (20 µM) inhibited LTB4 formation to an extent of 59 ± 12 % in vitro using a cell-based assay, comparable to the positive control zileuton (69 ± 12 % inhibition at a concentration of 10 µM). The binding modes of miconidin acetate were further evaluated in silico by molecular docking to the human 5-lipoxygenase crystal structure. The hydroxyl group was predicted to form a hydrogen bond with the terminal Ile676, while the pentyl moiety occupied the hydrophobic substrate channel. The obtained results show that flower buds of E. hiemalis are an interesting source of anti-inflammatory compounds, mainly of miconidin acetate.

The Uptake and Assembly of Alkanes within a Porous Nanocapsule in Water: New Information about Hydrophobic Confinement.

In Nature, enzymes provide hydrophobic cavities and channels for sequestering small alkanes or long-chain alkyl groups from water. Similarly, the porous metal oxide capsule [{Mo(VI) 6 O21 (H2 O)6 }12 {(Mo(V) 2 O4 )30 (L)29 (H2 O)2 }](41-) (L=propionate ligand) features distinct domains for sequestering differently sized alkanes (as in Nature) as well as internal dimensions suitable for multi-alkane clustering. The ethyl tails of the 29 endohedrally coordinated ligands, L, form a spherical, hydrophobic "shell", while their methyl end groups generate a hydrophobic cavity with a diameter of 11 Å at the center of the capsule. As such, C7 to C3 straight-chain alkanes are tightly intercalated between the ethyl tails, giving assemblies containing 90 to 110 methyl and methylene units, whereas two or three ethane molecules reside in the central cavity of the capsule, where they are free to rotate rapidly, a phenomenon never before observed for the uptake of alkanes from water by molecular cages or containers.

The Uptake and Assembly of Alkanes within a Porous Nanocapsule in Water: New Information about Hydrophobic Confinement

AbstractIn Nature, enzymes provide hydrophobic cavities and channels for sequestering small alkanes or long‐chain alkyl groups from water. Similarly, the porous metal oxide capsule [{MoVI6O21(H2O)6}12{(MoV2O4)30(L)29(H2O)2}]41− (L=propionate ligand) features distinct domains for sequestering differently sized alkanes (as in Nature) as well as internal dimensions suitable for multi‐alkane clustering. The ethyl tails of the 29 endohedrally coordinated ligands, L, form a spherical, hydrophobic “shell”, while their methyl end groups generate a hydrophobic cavity with a diameter of 11 Å at the center of the capsule. As such, C7 to C3 straight‐chain alkanes are tightly intercalated between the ethyl tails, giving assemblies containing 90 to 110 methyl and methylene units, whereas two or three ethane molecules reside in the central cavity of the capsule, where they are free to rotate rapidly, a phenomenon never before observed for the uptake of alkanes from water by molecular cages or containers.

On the Yih–Marangoni instability of a two-phase plane Poiseuille flow in a hydrophobic channel

The linear stability analysis of a plane Poiseuille flow of two immiscible, incompressible fluids of different viscosities and densities in a hydrophobic channel, in the presence of an insoluble surfactant at the interface is examined, within the framework of Orr–Sommerfeld system. The walls of the channel are modeled as walls with velocity slip/no-slip. The equations governing the flow system are solved numerically by a Chebyshev collocation method for a wide range of dimensionless parameters describing the flow system. The effects of slip on the neutral stability boundaries for the interface modes in the presence/absence of an insoluble surfactant at the interface are examined for different thickness ratios of the two layers, with density and/or viscosity stratification. Slip conditions at the wall show a promise for control of the Yih–Marangoni instability of the corresponding flow system in a rigid channel. The influence of the parameters on the critical Reynolds number for the shear mode is assessed. The study reveals that it is possible to control instabilities in interface dominated rigid channel flows by designing the walls of the channel as hydrophobic/rough/porous or undulated surfaces as these can be modeled as one with slip at the substrates.

Receptor-Mediated HDL-Lipid Uptake is Regulated by Elastic Properties of the Plasma Membrane

Proper supply of mammalian cells with cholesterol is crucial for membrane function and cellular survival and is regulated by several mechanisms, including cellular uptake, synthesis, storage and export. Transport of excess cholesterol from the periphery back to the liver for excretion into the bile is achieved by high-density lipoproteins (HDL). HDL particles are captured from the blood stream by the scavenger receptor class B type I (SR-BI), the so-called HDL receptor. The subsequent lipid transfer process, however, is highly speculative: it has been proposed to occur after HDL endocytosis or directly at the cell surface across an unstirred water layer or via a hydrophobic channel in the receptor. Here we show via direct imaging techniques that, upon contact with the membrane, HDL is incorporated into the hydrophobic core of the lipid bilayer and amphiphilic cargo is immediately released to the plasma membrane. Particle incorporation and cargo transfer is abolished at increased membrane cholesterol concentrations, as a consequence of the reduced membrane elasticity. Our observations reveal a mechanism for regulation of lipid uptake, which is based on sensing plasma membrane cholesterol levels: HDL-receptors tether particles close to the plasma membrane; once in proximity, elastic membrane properties regulate the particles’ fusion with the bilayer and subsequent cargo transfer. The data indicate that the plasma membrane itself signals a cell's cholesterol demand: high cholesterol levels act repulsive, low cholesterol levels fusogenic.