A biochemical analysis into the co-translational folding of a G protein-coupled receptor; GPR35

The folding and targeting of membrane proteins poses a major challenge to the cell, as they must remain insertion competent while their highly hydrophobic transmembrane (TM) domains are transferred from the ribosome, through the aqueous cytosol and into the lipid bilayer. The biogenesis of a mature membrane protein takes place through the insertion and integration into the lipid bilayer. A number of TM proteins have been shown to gain some degree of secondary structure within the ribosome tunnel and to retain this conformation throughout maturation. Although studies into the folding and targeting of a number of membrane proteins have been carried out to date, there is little information on one of the largest class of eukaryotic membrane proteins; the G-protein-coupled receptors (GPCRs). This project studies the early folding events of the human ortholog of GPR35. To analyse the structure of the 1st TM domain, intermediates were generated and assessed by the biochemical method of pegylation (PEG-MAL). A structurally-similar microbial opsin (Bacterioopsin) was also used to investigate the differences in the early protein folding within eukaryotic and prokaryotic translation systems. Results showed that neither the 1st TM domain of GPR35 nor Bacterioopsin were capable of compacting in the ribosome tunnel before their N-terminus reached the ribosome exit point. The results for this assay remained consistent whether the proteins were translated in a eukaryotic or prokaryotic translation system. To examine the communication mechanism between the ribosome, the nascent chain and the protein targeting pathway, crosslinking experiments were carried out using the homobifunctional lysine cross-linker BS3. Specifically, the data generated here show that the nascent chain of GPR35 reaches the ribosomal protein uL23 in an extended conformation and interacts with the SRP protein as it exits the ribosome tunnel. This confirms the role of SRP in the co-translational targeting of GPR35. Using these methods insights into the early folding of GPCRs has been obtained. Further experiments using site-directed mutagenesis to reduce hydrophobicity in the 1st TM domain of GPR35, highlighted the mechanisms by which GPCRs are targeted to the endoplasmic reticulum. Confirming that hydrophobicity within the signal anchor sequence is essential of SRP-dependent targeting. Following the successful interaction of the nascent GPR35 and SRP, GPR35 is successfully targeted to ER membranes, shown here as dog pancreas microsomes (DPMs). Glycosylation of the GPR35 N-terminus was used to determine nascent chain structure as it is inserted into the ER membrane. These glycosylation experiments confirm that TM1 has obtained its compacted state whilst residing in the translocon. Finally, a site-specific cross-linking approach using the homobifunctional cysteine cross-linker, BMH, was used to study the lateral integration of GPR35 into the ER. Cross-linking of GPR35 TM1 and TM2 could be detected adjacent to a protein of ~45kDa, believed to be Sec61α. The loss of this adduct, as the nascent chain extends, showed the lateral movement of GPR35 TM1 from the translocon was dependent on the subsequent synthesis of TM2.

Solid-liquid interactions in microscale structures and devices

Liquid-solid interactions become important as dimensions approach mciro/nano-scale. This dissertation focuses on liquid-solid interactions in two distinct applications: capillary driven self-assembly of thin foils into 3D structures, and droplet wetting of hydrophobic micropatterned surfaces. The phenomenon of self-assembly of complex structures is common in biological systems. Examples include self-assembly of proteins into macromolecular structures and self-assembly of lipid bilayer membranes. The principles governing this phenomenon have been applied to induce self-assembly of millimeter scale Si thin films into spherical and other 3D structures, which are then integrated into light-trapping photovoltaic (PV) devices. Motivated by this application, we present a generalized analytical study of the self-folding of thin plates into deterministic 3D shapes, through fluid-solid interactions, to be used as PV devices. This study consists of developing a model using beam theory, which incorporates the two competing components — a capillary force that promotes folding and the bending rigidity of the foil that resists folding into a 3D structure. Through an equivalence argument of thin foils of different geometry, an effective folding parameter, which uniquely characterizes the driving force for folding, has been identified. A criterion for spontaneous folding of an arbitrarily shaped 2D foil, based on the effective folding parameter, is thus established. Measurements from experiments using different materials and predictions from the model match well, validating the assumptions used in the analysis. As an alternative to the mechanics model approach, the minimization of the total free energy is employed to investigate the interactions between a fluid droplet and a flexible thin film. A 2D energy functional is proposed, comprising the surface energy of the fluid, bending energy of the thin film and gravitational energy of the fluid. Through simulations with Surface Evolver, the shapes of the droplet and the thin film at equilibrium are obtained. A critical thin film length necessary for complete enclosure of the fluid droplet, and hence successful self-assembly into a PV device, is determined and compared with the experimental results and mechanics model predictions. The results from the modeling and energy approaches and the experiments are all consistent. Superhydrophobic surfaces, which have unique properties including self-cleaning and water repelling are desired in many applications. One excellent example in nature is the lotus leaf. To fabricate these surfaces, well designed micro/nano- surface structures are often employed. In this research, we fabricate superhydrophobic micropatterned Polydimethylsiloxane (PDMS) surfaces composed of micropillars of various sizes and arrangements by means of soft lithography. Both anisotropic surfaces, consisting of parallel grooves and cylindrical pillars in rectangular lattices, and isotropic surfaces, consisting of cylindrical pillars in square and hexagonal lattices, are considered. A novel technique is proposed to image the contact line (CL) of the droplet on the hydrophobic surface. This technique provides a new approach to distinguish between partial and complete wetting. The contact area between droplet and microtextured surface is then measured for a droplet in the Cassie state, which is a state of partial wetting. The results show that although the droplet is in the Cassie state, the contact area does not necessarily follow Cassie model predictions. Moreover, the CL is not circular, and is affected by the micropatterns, in both isotropic and anisotropic cases. Thus, it is suggested that along with the contact angle — the typical parameter reported in literature quantifying wetting, the size and shape of the contact area should also be presented. This technique is employed to investigate the evolution of the CL on a hydrophobic micropatterned surface in the cases of: a single droplet impacting the micropatterned surface, two droplets coalescing on micropillars, and a receding droplet resting on the micropatterned surface. Another parameter which quantifies hydrophobicity is the contact angle hysteresis (CAH), which indicates the resistance of the surface to the sliding of a droplet with a given volume. The conventional methods of using advancing and receding angles or tilting stage to measure the resistance of the micropatterned surface are indirect, without mentioning the inaccuracy due to the discrete and stepwise motion of the CL on micropillars. A micronewton force sensor is utilized to directly measure the resisting force by dragging a droplet on a microtextured surface. Together with the proposed imaging technique, the evolution of the CL during sliding is also explored. It is found that, at the onset of sliding, the CL behaves as a linear elastic solid with a constant stiffness. Afterwards, the force first increases and then decreases and reaches a steady state, accompanied with periodic oscillations due to regular pinning and depinning of the CL. Both the maximum and steady state forces are primarily dependent on area fractions of the micropatterned surfaces in our experiment. The resisting force is found to be proportional to the number of pillars which pin the CL at the trailing edge, validating the assumption that the resistance mainly arises from the CL pinning at the trailing edge. In each pinning-and-depinning cycle during the steady state, the CL also shows linear elastic behavior but with a lower stiffness. The force variation and energy dissipation involved can also be determined. This novel method of measuring the resistance of the micropatterned surface elucidates the dependence on CL pinning and provides more insight into the mechanisms of CAH.

Release currents of IP₃ receptor channel clusters and concentration profiles

We simulate currents and concentration profiles generated by Ca2+ release from the endoplasmic reticulum (ER) to the cytosol through IP3 receptor channel clusters. Clusters are described as conducting pores in the lumenal membrane with a diameter from 6 nm to 36 nm. The endoplasmic reticulum is modeled as a disc with a radius of 1–12 mm and an inner height of 28 nm. We adapt the dependence of the currents on the trans Ca2+ concentration (intralumenal) measured in lipid bilayer experiments to the cellular geometry. Simulated currents are compared with signal mass measurements in Xenopus oocytes. We find that release currents depend linearly on the concentration of free Ca2+ in the lumen. The release current is approximately proportional to the square root of the number of open channels in a cluster. Cytosolic concentrations at the location of the cluster range from 25 μM to 170 μM. Concentration increase due to puffs in a distance of a few micrometers from the puff site is found to be in the nanomolar range. Release currents decay biexponentially with timescales of < 1 s and a few seconds. Concentration profiles decay with timescales of 0.125–0.250 s upon termination of release.

A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.

Manufacturing methods for liposome adjuvants

A wide range of studies have shown that liposomes can act as suitable adjuvants for a range of vaccine antigens. Properties such as their amphiphilic character and biphasic nature allow them to incorporate antigens within the lipid bilayer, on the surface, or encapsulated within the inner core. However, appropriate methods for the manufacture of liposomes are limited and this has resulted in issues with cost, supply, and wider scale application of these systems. Within this chapter we explore manufacturing processes that can be used for the production of liposomal adjuvants, and we outline new manufacturing methods can that offer fast, scalable, and cost-effective production of liposomal adjuvants.

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy andmicroscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in thesemembranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3–4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using themasmembrane reporters.

Electrochemical surface plasmon resonance detection of enzymatic reaction in bilayer lipid

In this paper, electrochemical surface plasmon resonance (SPR) method was first used to detect enzymatic reaction in bilayer lipid membrane (BLM) based on immobilizing horseradish peroxidase (HRP) in the BLMs supported by the redox polyaniline (PAn) film. By SPR kinetic curve in situ monitoring the redox transformation of PAn film resulted from the reaction between HRP and PAn, the enzymatic reaction of HRP with H2O2, was successfully analyzed by electrochemical SPR spectroscopy.

Concentration and time dependant behavior of chlorpromazine interaction with supported bilayer lipid membrane

The interaction of chlorpromazine (CPZ) with supported bilaver lipid (dipalmitoyphosphatidylcholine) membrane (s-BLM) on the glassy carbon electrode (GCE) was investigated using cyclic voltammetry and ac impedance spectroscopy. The experimental data, based on the voltammetric response of Ru(NH3)(6)(3+) associated with the oxidation of CPZ on the electrode, indicated that the interaction of CPZ with s-BLM was concentration and time dependant. The interaction between them could be divided into three stages by the concentration of CPZ: low, middle and high concentration. At the first stage, s-BLM was not affected by CPZ and the interaction was only a penetration of a small quantity of CPZ molecule into s-BLM. At the second stage, the defects formed in s-BLM due to the penetration of more CPZ molecule into s-BLM. At the last stage, a high CPZ:lipid ratio reached in s-BLM, resulting in the solubilization of s-BLM. The interaction time had different effect at three stages.

A study on the interaction between ibuprofen and bilayer lipid membrane

Ibuprofen is a well-known nonsteroidal anti-inflammatory drug, which can interact with lipid membranes. In this paper, the interaction of ibuprofen with bilayer lipid membrane was studied by UV-vis spectroscopy, cyclic voltammetry and AC impedance spectroscopy. UV-vis spectroscopy data indicated directly that ibuprofen could interact with lipid vesicles. In electrochemical experiments, ibuprofen displayed a biphasic behavior on bilayer lipid membrane supported on a glassy carbon electrode. It could stabilize the lipid membrane in low concentration, while it induced defects formation, even removed off bilayer lipid membrane from the surface of the electrode with increasing concentration. The mechanism about the interaction between ibuprofen and supported bilayer lipid membrane was discussed.

Growth of cationic lipid toward bilayer, lipid membrane by solution spreading: scanning probe microscopy study

The growth of cationic lipid dioctadecyldimethylammonium bromide (DODAB) toward bilayer lipid membrane (BLM) by solution spreading on cleaved mica surface was studied by atomic force microscopy (AFM). Bilayer of DODAB was formed by exposing mica to a solution of DODAB in chloroform and subsequently immersing into potassium chloride solution for film developing. AFM studies showed that at the initial stage of the growth, the adsorbed molecules exhibited the small fractal-like aggregates. These aggregates grew up and expanded laterally into larger patches with time and experienced from monolayer to bilayer, finally a close-packed bilayer film (5.4 +/- 0.2 nm) was approached. AFM results of the film growth process indicated a growth mechanism of nucleation, growth and coalescence of dense submonolayer, it revealed the direct information about the film morphology and confirmed that solution spreading was an effective technique to prepare a cationic bilayer in a short time.

Defect formation induced by PAMAM dendrimers on Pt-supported bilayer lipid membranes investigated by electrochemistry

The interaction of polyamidoamine (PAMAM) dendrimers (generations 1-7) with supported bilayer lipid membranes was studied by cyclic votammetry and ac impedance. It is shown that the dendrimers (generations 4-6) can induce defects in the Pt-electrode-supported bilayer lipid membrane. The ability of dendrimers to induce defects was dependent on their shapes and surface charge. The results are consistent with a change in the morphology of the dendrimers from an open, branched structure for generations 1-4 to a closed, increasingly compact surface for generations 5-7.

Concentration-dependent behavior of nisin interaction with supported bilayer lipid membrane

Nisin is a positively charged antibacterial peptide that binds to the negatively charged membranes of gram-positive bacteria. The initial interaction of the peptide with the model membrane of negatively charged DPPG (dipalmitoylphosphatidylglycerol) was studied by cyclic voltammetry and a.c. impedance spectroscopy. Nisin could induce pores the supported bilayer lipid membrane, thus, it led to the marker ions Fe(CN)(6)(3-/4-) crossing the lipid membrane and giving the redox reaction on the glassy carbon electrode (GCE). Experimental results suggested that the pore formation on supported bilayer lipid membrane was dependent on the concentration of nisin and it included three main concentration stages: low, middling, high concentration.

Characterization and property of DNA incorporated bilayer lipid membranes

Calf-thymus DNA-incorporated bilayer lipid membranes supported on a glassy carbon (GC) electrode was prepared by making layers of phosphatidylcholine dimyristoyl (DMPC) on GC electrode. DNA in the BLM was characterized by cyclic voltammetry, IR and AFM, and lipid layers formed on the GC electrode were demonstrated to be a bilayer lipid membrane by electrochemical impedance experiment. In IR and AFM experiments the findings indicated that DNA was incorporated into BLM. The ion channel of bilayer lipid membranes incorporated was studied. The result showed that the ion channel was opened in the presence of the stimulus quinacrine. In the absence of quinacrine the channel was switched. The process can repeat itself many times. The impedance spectroscopy measurements demonstrate that the stimulus quinacrine opens the channel for permeation of marker ion. The mechanism of forming an ion channel was investigated.

Interaction of K7Fe3+P2W17O62H2 with supported bilayer lipid membranes on platinum electrode

The influence of K7Fe3+P2W17O62H2 on l-alpha-phosphatidylcholine/cholesterol bilayer lipid membrane on Pt electrode was studied by voltammetry and AC impedance spectroscopy. The interaction of the polyoxometalates with the BLM can promote the access of Ru(NH3)(6)(3+) and [Fe(CN)(6)](3-/4-) to the electrode surface. It was found that some kind of pores had been formed on the BLM by AFM. The phenomenon is attributed to the interaction of K7Fe3+P2W17O62H2 with phosphatidylcholine phosphate groups located in its outer leaflet. Experimental results are helpful to understand the biological activity of the polyoxometalates in vivo.

Study of the ion channel behavior of didodecyldimethylammonium bromide formed bilayer lipid membrane stimulated by PF6-

Bilayer lipid membranes ( BLM) formed from didode-cyldimethylammonium bromide were made on the freshly exposed surface of a glassy carbon (GC) and were demonstrated by the ac impedance spectroscopy. The ion channels of membrane properties induced by PF6- were studied by the cyclic voltammetric methods. Experimental results indicated that the ion channel of BLM was open in the presence of the PF6- due to the interaction of PF6- with the BLM, while it was switched off in the absence of PF6-. Because the ion channel behavior was affected by the concentration of PF6-, a sensor for PF6- can be developed.