Antibiotic Action and Peptidoglycan Formation on Tethered Lipid Bilayer Membranes

Label-Free Probing of Electron Transfer Kinetics of Single Microbial Cells on a Single-Layer Graphene via Structural Color Microscopy

Studies of electron transfer at the population level veil the nature of the cell itself; however, in situ probing of the electron transfer dynamics of individual cells is still challenging. Here we propose label-free structural color microscopy for this aim. We demonstrate that Shewanella oneidensis MR-1 cells show unique structural color scattering, changing with the redox state of cytochrome complexes in the outer membrane. It enables quantitatively and noninvasive studies of electron transfer in single microbial cells during bioelectrochemical activities, such as extracellular electron transfer (EET) on a transparent single-layer graphene electrode. Increasing the applied potential leads to the associated EET current, accompanied by more oxidized cytochromes. The high spatiotemporal resolution of the proposed method not only demonstrates the large diversity in EET activity among microbial cells but also reveals the subcellular asymmetric distribution of active cytochromes in a single cell. We anticipate that it provides a potential platform for further exploring the electron transfer mechanism of subcellular structure.

Spinning and Fully Integrated Microdevice for Rapid Screening of Vancomycin-Resistant Enterococcus

This study introduces a spinning and fully integrated paper-based microdevice that can perform multiple functions, including DNA extraction, amplification, and colorimetric detection, for monitoring two major vancomycin-resistant Enterococci (VREs), which carry the vanA and vanB genes. The spinning microdevice is composed of a stationary part and a spinning part. The square-shaped stationary part has two zones: the lysis and reaction zones. The spinning part, which has a spin wheel-like shape, was inserted perpendicularly into the stationary part so that its two semicircles remained on the upper and lower parts. Sodium hydroxide-treated glass microfiber filter discs, inserted in the upper semicircle, were soaked in the lysis chambers by folding them toward the lysis zone to capture DNA in the lysis chambers. The captured DNA was transferred to the reaction chambers by folding the discs toward the reaction chambers. Water was added to the sodium hydroxide-treated glass microfiber filter discs to elute purified DNA into the reaction chambers. The upper semicircle was then unfolded, and the reaction chambers were sealed for subsequent loop-mediated isothermal amplification (LAMP) for 45 min. After the reaction, the spinning part was spun in the lysis zone direction to bring the lower semicircle, inserted with phenolphthalein-treated glass microfiber filter discs, toward the upper part of the stationary part. By folding it toward the reaction chambers, the lower semicircle came into contact with them and the phenolphthalein-treated glass microfiber filter discs were soaked in the reaction chambers and expressed color after 30 s. Based on the pH change during the LAMP reaction, the phenolphthalein-treated discs remained pink in the absence of target DNA, while those in contact with the positive samples turned colorless. A sensitive detection with a VRE limit of detection of 10² CFU/mL for tap water spiked with VRE carrying the vanA gene was achieved using this microdevice. Both VREs, carrying vanA and vanB genes, were successfully identified from tap water and contaminated equipment surfaces within 75 min. The introduced microdevice demonstrated a rapid, accurate, and sensitive performance for the environmental assessment of VRE contamination in resource-limited regions.

Why Do Tethered-Bilayer Lipid Membranes Suit for Functional Membrane Protein Reincorporation?

Membrane proteins (MPs) are essential for cellular functions. Understanding the functions of MPs is crucial as they constitute an important class of drug targets. However, MPs are a challenging class of biomolecules to analyze because they cannot be studied outside their native environment. Their structure, function and activity are highly dependent on the local lipid environment, and these properties are compromised when the protein does not reside in the cell membrane. Mammalian cell membranes are complex and composed of different lipid species. Model membranes have been developed to provide an adequate environment to envisage MP reconstitution. Among them, tethered-Bilayer Lipid Membranes (tBLMs) appear as the best model because they allow the lipid bilayer to be decoupled from the support. Thus, they provide a sufficient aqueous space to envisage the proper accommodation of large extra-membranous domains of MPs, extending outside. Additionally, as the bilayer remains attached to tethers covalently fixed to the solid support, they can be investigated by a wide variety of surface-sensitive analytical techniques. This review provides an overview of the different approaches developed over the last two decades to achieve sophisticated tBLMs, with a more and more complex lipid composition and adapted for functional MP reconstitution.

The Use of Tethered Bilayer Lipid Membranes to Identify the Mechanisms of Antimicrobial Peptide Interactions with Lipid Bilayers

This review identifies the ways in which tethered bilayer lipid membranes (tBLMs) can be used for the identification of the actions of antimicrobials against lipid bilayers. Much of the new research in this area has originated, or included researchers from, the southern hemisphere, Australia and New Zealand in particular. More and more, tBLMs are replacing liposome release assays, black lipid membranes and patch-clamp electrophysiological techniques because they use fewer reagents, are able to obtain results far more quickly and can provide a uniformity of responses with fewer artefacts. In this work, we describe how tBLM technology can and has been used to identify the actions of numerous antimicrobial agents.

Engineering lipid bilayer membranes for protein studies

Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques.

Tethered bilayer lipid membranes on mixed self-assembled monolayers of a novel anchoring thiol: impact of the anchoring thiol density on bilayer formation

Tethered bilayer lipid membranes (tBLMs) are designed on mixed self-assembled monolayers (SAMs) of a novel synthetic anchoring thiol, 2,3-di-o-palmitoylglycerol-1-tetraethylene glycol mercaptopropanoic acid ester (TEG-DP), and a new short dilution thiol molecule, tetraethylene glycol mercaptopropanoic acid ester (TEG). tBLM formation was accomplished by self-directed fusion of small unilamellar vesicles of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. The influence of the dilution of the anchoring thiol molecule in the SAM on the vesicle fusion process and on the properties of the resulting tBLMs is studied. It is observed by quartz crystal microbalance that vesicle fusion is a one-step process for a pure TEG-DP SAM as well as for mixed SAMs containing a high concentration of the anchoring thiol. However, upon dilution of the anchoring thiol to moderate concentrations, this process is decelerated and possibly follows a pathway different from that observed on a pure TEG-DP SAM. Electrochemical impedance spectroscopy is used to qualitatively correlate the composition of the SAM to the electrical properties of the tBLM. In this paper we also delineate the necessity of a critical concentration of this anchoring TEG-DP thiol as a requisite for inducing the fusion of vesicles to form a tBLM.

Structure, Stability, and Cluster-Cage Interactions in Nitride Clusterfullerenes M3N@C2n (M = Sc, Y; 2n = 68−98): a Density Functional Theory Study

Extensive semiempirical calculations of the hexaanions of IPR (isolated pentagon rule) and non-IPR isomers of C(68)-C(88) and IPR isomers of C(90)-C(98) followed by DFT calculations of the lowest energy structures were performed to find the carbon cages that can provide the most stable isomers of M(3)N@C(2n) clusterfullerenes (M = Sc, Y) with Y as a model for rare earth ions. DFT calculations of isomers of M(3)N@C(2n) (M = Sc, Y; 2n = 68-98) based on the most stable C(2n)(6-) cages were also performed. The lowest energy isomers found by this methodology for Sc(3)N@C(68), Sc(3)N@C(78), Sc(3)N@C(80), Y(3)N@C(78), Y(3)N@C(80), Y(3)N@C(84), Y(3)N@C(86), and Y(3)N@C(88) are those that have been shown to exist by single-crystal X-ray studies as Sc(3)N@C(2n) (2n = 68, 78, 80), Dy(3)N@C(80), and Tb(3)N@C(2n) (2n = 80, 84, 86, 88) clusterfullerenes. Reassignment of the carbon cage of Sc(2)@C(76) to the non-IPR Cs: 17490 isomer is also proposed. The stability of nitride clusterfullerenes was found to correlate well with the stability of the empty 6-fold charged cages. However, the dimensions of the cage in terms of its ability to encapsulate M(3)N clusters were also found to be an important factor, especially for the medium size cages and the large Y(3)N cluster. In some cases the most stable structures are based on the different cage isomers for Sc(3)N and Y(3)N clusters. Up to the cage size of C(84), non-IPR isomers of C(2n)(6-) and M(3)N@C(2n) were found to compete with or to be even more stable than IPR isomers. However, the number of adjacent pentagon pairs in the most stable non-IPR isomers decreases as cage size increases: the most stable M(3)N@C(2n) isomers have three such pairs for 2n = 68-72, two pairs for n = 74-80, and only one pair for n = 82, 84. For C(86) and C(88) the lowest energy IPR isomers are much more stable than any non-IPR isomer. The trends in the stability of the fullerene isomers and the cluster-cage binding energies are discussed, and general rules for stability of clusterfullerenes are established. Finally, the high yield of M(3)N@C(80) (Ih) clusterfullerenes for any metal is explained by the exceptional stability of the C(80)(6-) (Ih: 31924) cage, rationalized by the optimum distribution of the pentagons leading to the minimization of the steric strain, and structural similarities of C(80) (Ih: 31924) with the lowest energy non-IPR isomers of C(760(6-), C(78)(6-), C(82)(6-), and C(84)(6-) pointed out.

Protein-directed assembly of binary monolayers at the interface and surface patterns of protein on the monolayers

Ferritin-directed assembly of binary monolayers of zwitterionic dipalmitoylphosphatidylcholine and cationic dioctadecyldimethylammonium bromide (DOMA) at the interface and surface patterns of ferritin on the monolayers have been investigated using a combination of infrared reflection absorption spectroscopy, surface plasmon resonance, and atomic force microscopy. Ferritin binding to the binary monolayers at the air-water interface at the surface pressure 30 mN/m, primarily driven by the electrostatic interaction, gives rise to a change in tilt angle of hydrocarbon chains from 15 degrees +/- 1 degrees to 10 degrees +/- 1 degrees with respect to the normal of the monolayer at the mole fraction of DOMA (XDOMA) of 0.1. The chains at XDOMA = 0.3 are oriented vertical to the water surface before and after protein binding. A new mechanism for protein binding to the binary monolayers is proposed. The secondary structures of the adsorbed ferritin are prevented from changing to some extent due to the existence of the monolayers. The amounts of the bound protein on the monolayers at the air-water interface are increased in comparison with those on the pre-immobilized monolayers at low XDOMA. The increased amounts and different patterns of the adsorbed protein at the monolayers are mostly attributed to the formation of multiple binding sites available for ferritin, which is due to the lateral reorganization of the lipid components in the monolayers induced by the protein in the subphase. The created multiple binding sites on the monolayer surfaces through the protein-directed assembly can be preserved for subsequent protein binding.

Antibacterial natural products in medicinal chemistry--exodus or revival?

To create a drug, nature's blueprints often have to be improved through semisynthesis or total synthesis (chemical postevolution). Selected contributions from industrial and academic groups highlight the arduous but rewarding path from natural products to drugs. Principle modification types for natural products are discussed herein, such as decoration, substitution, and degradation. The biological, chemical, and socioeconomic environments of antibacterial research are dealt with in context. Natural products, many from soil organisms, have provided the majority of lead structures for marketed anti-infectives. Surprisingly, numerous "old" classes of antibacterial natural products have never been intensively explored by medicinal chemists. Nevertheless, research on antibacterial natural products is flagging. Apparently, the "old fashioned" natural products no longer fit into modern drug discovery. The handling of natural products is cumbersome, requiring nonstandardized workflows and extended timelines. Revisiting natural products with modern chemistry and target-finding tools from biology (reversed genomics) is one option for their revival.

Biological Soft Materials

With one or two exceptions, biological materials are "soft", meaning that they combine viscous and elastic elements. This mechanical behavior results from self-assembled supramolecular structures that are stabilized by noncovalent interactions. It is an ongoing and profound challenge to understand the self-organization of biological materials. In many cases, concepts can be imported from soft-matter physics and chemistry, which have traditionally focused on materials such as colloids, polymers, surfactants, and liquid crystals. Using these ideas, it is possible to gain a new perspective on phenomena as diverse as DNA condensation, protein and peptide fibrillization, lipid partitioning in rafts, vesicle fusion and budding, and others, as discussed in this selective review of recent highlights from the literature.

Approaches to Open Fullerenes: Synthesis and Kinetic Stability of Diels−Alder Adducts of Substituted Isobenzofurans and C60

We have examined the reactions of 1,3-disubstituted isobenzofurans with the fullerene C60 in the context of an approach to open a large orifice on the fullerene framework. A variety of substituted isobenzofurans (6a-h), generated from the reaction of 1,4-substituted 1,4-epoxynaphthalenes 3a-h with 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine (4a) or 1,2,4,5-tetrazine (4b), were added to C60 to afford the Diels-Alder adducts 7a-h. The thermal stability of these adducts toward retro-Diels-Alder fragmentation differs greatly in solution from that in the solid state. In solution, the relatively facile retro-Diels-Alder fragmentation of monoadducts 7a and 7c, to give C60 and the free isobenzofurans 6a and 6c, have rate constants (and activation barriers) of k=9.29x10(-5) s-1 at 70 degrees C (Ea=32.6 kcal mol-1) and k=1.36x10(-4) s-1 at 40 degrees C (Ea=33.7 kcal mol-1), respectively, indicating that the addition of isobenzofurans to C60 is readily reversible at those temperatures. In the solid state, thermogravimetric analysis of adduct 7a indicates that its decomposition occurs only within the temperature range of 220-300 degrees C. As a result, these compounds can be stored at room temperature in the solid state for several weeks without significant decomposition but have to be handled within several hours in solution.

C78 Cage Isomerism Defined by Trimetallic Nitride Cluster Size: A Computational and Vibrational Spectroscopic Study

Molecular structures of Dy(3)N@C(78) and Tm(3)N@C(78) clusterfullerenes are addressed by the IR and Raman vibrational spectroscopic studies and density functional theory (DFT) computations. First, extensive semiempirical calculations of 2927 isomers of C(78) hexaanions followed by DFT optimization were applied to establish their relative stability. Then, DFT calculations of a series of M(3)N@C(78) (M = Sc, Y, Lu, La) isomers were performed which have shown that the stability order of the isomers depends on the cluster size. While the Sc(3)N cluster is planar in the earlier reported Sc(3)N@C(78) (D(3)h: 24,109) clusterfullerenes, relatively large Y(3)N and Lu(3)N clusters would be forced to be pyramidal inside this cage, which would result in their destabilization. Instead, these clusters remain planar in the nonisolated pentagon rule (non-IPR) C(2): 22,010 isomer making Y(3)N@C(78) and Lu(3)N@C(78) clusterfullerenes with this cage structure the most stable ones. Finally, on the basis of a detailed analysis of their IR and Raman spectra supplemented with DFT vibrational calculations, the recently isolated Tm(3)N@C(78) and the major isomer of Dy(3)N@C(78) are assigned to the non-IPR C(2): 22,010 cage structure. A detailed assignment of their experimental and computed IR and Raman spectra is provided to support this conclusion and to exclude other cage isomers.

Directed Assembly of Binary Monolayers with a High Protein Affinity: Infrared Reflection Absorption Spectroscopy (IRRAS) and Surface Plasmon Resonance (SPR)

Infrared reflection absorption spectroscopy (IRRAS) and surface plasmon resonance (SPR) techniques have been employed to investigate human serum albumin (HSA) binding to binary monolayers of zwitterionic dipalmitoylphosphatidylcholine (DPPC) and cationic dioctadecyldimethylammonium bromide (DOMA). At the air-water interface, the favorable electrostatic interaction between DPPC and DOMA leads to a dense chain packing. The tilt angle of the hydrocarbon chains decreases with increasing mole fraction of DOMA (X(DOMA)) in the monolayers at the surface pressure 30 mN/m: DPPC ( approximately 30 degrees ), X(DOMA) = 0.1 ( approximately 15 degrees ), and X(DOMA) = 0.3 ( approximately 0 degrees ). Negligible protein binding to the DPPC monolayer is observed in contrast to a significant binding to the binary monolayers. After HSA binding, the hydrocarbon chains at X(DOMA) = 0.1 undergo an increase in tilt angle from 15 degrees to 25 approximately 30 degrees , and the chains at X(DOMA) = 0.3 remain almost unchanged. The two components in the monolayers deliver through lateral reorganization, induced by the protein in the subphase, to form multiple interaction sites favorable for protein binding. The surfaces with a high protein affinity are created through the directed assembly of binary monolayers for use in biosensing.

A novel method to fabricate patterned bilayer lipid membranes

We introduce a new method for forming tethered bilayer lipid membranes on surfaces patterned using a photocleavable self-assembled monolayer (SAM). A SAM terminated with a hydrophobic fluorocarbon residue was bound to a gold surface through a link containing a photocleavable ortho-nitrobenzyl moiety. Hydrophilic regions were produced by irradiation with soft UV (365 nm) through a photomask. The patterned surface was characterized by scanning electron microscopy and electrochemical impedance spectroscopy. Tethered bilayer lipid membranes with well-defined bilayer and monolayer regions were then formed by exposure to egg PC vesicles. The membranes had resistance and capacitance values of 0.52 MOmega.cm2 and 0.83 microF.cm-2, respectively.

Fluorescent reagents for in vitro studies of lipid-linked steps of bacterial peptidoglycan biosynthesis: derivatives of UDPMurNAc-pentapeptide containing d-cysteine at position 4 or 5

UDPMurNAc-L-Ala-gamma-D-Glu-X-D-Ala-DAla (X = L-Lys or m-DAP) is the cytoplasmic precursor for the lipid-linked cycle of bacterial peptidoglycan biosynthesis, consisting of at least four enzymatic reactions, which are targets for antibacterial agents. Fluorescent derivatives of the UDPMurNAc-pentapeptide labelled at the 3rd, 4th, and 5th position of the peptide chain were prepared chemoenzymatically, in order to study the reactions catalysed by enzymes in this cycle. Derivatives labelled on the epsilon-amino group of the 3rd amino acid (N-dansyl, N-fluorescamine and N-phthalaldehyde) were prepared by chemical modification. Two methods were developed for preparation of analogues of UDPMurNAc-pentapeptide containing D-cysteine at position 4 or 5: either by MurF-catalysed ligation of the UDPMurNAc-tripeptide to synthetic D-Ala-D-Cys or D-Cys-D-Ala dipeptides; or by enzymatic synthesis of D-Ala-D-Cys by ligase VanD. D-Cys-containing UDPMurNAc-pentapeptides were labelled with pyrene maleimide, to give 4-pyrene and 5-pyrene labelled derivatives. The fluorescent UDPMurNAc-pentapeptides were processed as substrates by Escherichia coli MraY or E. coli membranes, giving 1.5-150-fold changes in fluorescence upon transformation to lipid intermediate I. Subsequent processing to lipid intermediate II gave rise only to small changes in fluorescence. Pyrene-labelled lipid intermediates I and II can be generated using Micrococcus flavus membranes, enabling the study of the later lipid-linked steps.

Tb3N@C84: An Improbable, Egg-Shaped Endohedral Fullerene that Violates the Isolated Pentagon Rule

The structure of isomer 2 of Tb3N@C84 has been determined through single-crystal X-ray diffraction on Tb3N@C84.NiII(OEP).2(C6H6). The carbon cage has a distinct egg shape due to the presence of a single pair of fused pentagons at one apex of the molecule. Thus, although 24 IPR structures are available to the C84 cage, Nature utilizes one of the 51 568 isomeric structures that do not conform to the IPR for this unusual molecule. The Tb3N portion of isomer 2 of Tb3N@C84 is strictly planar. One Tb atom is nestled within the fold of the fused pentagons, while the other Tb atoms are disordered over four pairs of sites.

The C60 Formation Puzzle “Solved”: QM/MD Simulations Reveal the Shrinking Hot Giant Road of the Dynamic Fullerene Self-Assembly Mechanism

The dynamic self-assembly mechanism of fullerene molecules is an irreversible process emerging naturally under the nonequilibrium conditions of hot carbon vapor and is a consequence of the interplay between the dynamics and chemistry of polyyne chains, pi-conjugation and corresponding stabilization, and the dynamics of hot giant fullerene cages. In this feature article we briefly present an overview of experimental findings and past attempts to explain fullerene formation and show in detail how our recent quantum chemical molecular dynamics simulations of the dynamics of carbon vapor far from thermodynamic equilibrium have assisted in the discovery of the combined size-up/size-down "shrinking hot giant" road that leads to the formation of buckminsterfullerene C60, C70, and larger fullerenes. This formation mechanism is the first reported case of order created out of chaos where a distinct covalent bond network of an entire molecule is spontaneously self-assembled to a highly symmetric structure and fully explains the fullerene formation process consistently with all available experimental observations a priori. Experimental evidence suggests that it applies universally to all fullerene formation processes irrespective of the carbon source.