Membrane lipid organization and nicotinic acetylcholine receptor function: A two-way physiological relationship.

Nicotinic acetylcholine receptors (nAChRs) are involved in a great range of physiological and pathological conditions. Since they are transmembrane proteins, they interact strongly with the lipids surrounding them. Thus, the plasma membrane composition and heterogeneity play an essential role for the correct nAChR function, on the one hand, and the nAChR influences its immediate lipid environment, on the other hand. The aim of this work was to investigate in more detail the role of the biophysical properties of the membrane in nAChR function and vice versa, focusing on the relationship between Chol and nAChRs. To this end, we worked with different model systems which were treated either with (i) more Chol, (ii) cholesteryl hemisuccinate, or (iii) the enzyme cholesterol oxidase to generate different membrane sterol conditions and in the absence and presence of γTM4 peptide as a representative model of the nAChR. Fluorescence measurements with crystal violet and patch-clamp recordings were used to study nAChR conformation and function, respectively. Using confocal microscopy of giant unilamellar vesicles we probed the membrane phase state/order and organization (coexistence of lipid domains) and lipid-nAChR interaction. Our results show a feedback relationship between membrane organization and nAChR function, i.e. whereas the presence of a model of nAChRs conditions membrane organization, changing its lipid microenvironment, membrane organization and composition perturb nAChRs function. We postulate that nAChRs have a gain of function in disordered membrane environments but a loss of function in ordered ones, and that Chol molecules at the outer leaflet in annular sites and at the inner leaflet in non-annular sites are related to nAChR gating and desensitization, respectively. Thus, depending on the membrane composition, organization, and/or order, the nAChR adopts different conformations and locates in distinct lipid domains and this has a direct effect on its function.

SERS in PAH-Os and gold nanoparticle self-assembled multilayers.

We present a detailed structural and surface-enhanced Raman scattering (SERS) study of poly(allylamine) modified with Os(byp)2ClPyCHO (PAH-Os) and gold nanoparticles self-assembled multilayers [PAH-Os+(Au-nanoparticlesPAH-Os)n, n=1 and 5]. Atomic force microscopy and variable-angle spectroscopic ellipsometry measurements indicate that the first nanoparticle layer grows homogenously by partially covering the substrate without clustering. Analyzing the sample thickness and roughness we infer that the growth process advances thereafter by filling with nanoparticles the interstitial spaces between the previously adsorbed nanoparticles. After five immersion steps the multilayers reach a more compact structure. The interaction between plasmons of near-gold nanoparticles provides a new optical absorption around 650 nm which, in addition, allows a more effective SERS process in that spectral region than at the single-plasmon resonance (approximately 530 nm). We compare the electronic resonance Raman and SERS amplification mechanisms in these self-assembled multilayers analyzing Raman resonance scans and Raman intensity micromaps. As a function of nanoparticle coverage we observe large changes in the Raman intensity scans, with maxima that shift from the electronic transitions, to the plasmon resonance, and finally to the coupled-plasmon absorption. The Raman micromaps, on the other hand, evidence huge intensity inhomogeneities which we relate to "hot spots." Numerical discrete dipole approximation calculations including the interaction between gold nanoparticles are presented, providing a qualitative model for the coupled-plasmon absorption and redshifted Raman hot spots in these samples.

Layer-by-layer self-assembly of glucose oxidase and Os(Bpy)2CIPyCH2NH-poly(allylamine) bioelectrode.

The uptake of glucose oxidase (GOx) onto a polycationic redox polymer (PAA-Os)-modified surface, by adsorption from dilute aqueous GOx solutions, was followed by the quartz crystal microbalance (QCM) and shows double exponential kinetics. The electrochemistry of the layer-by-layer-deposited redox-active polymer was followed by cyclic voltammetry in glucose-free solutions, and the enzyme catalysis mediated by the redox polymer was studied in beta-D-glucose-containing solutions. AFM studies of the different layers showed the existence of large two dimension enzyme aggregates on the osmium polymer for 1 microM GOx and less aggregation for 50 nM GOx solutions. When the short alkanethiol, 2,2'-diaminoethyldisulfide was preadsorbed onto gold, a monoexponential adsorption law was observed, and single GOx enzyme molecules could be seen on the surface where the enzyme was adsorbed from 50 nM GOx in water.

Probing biopolymers with the atomic force microscope: a review.

This short review presents an overview of atomic force microscopy (AFM) of biopolymers and specific examples of some of the biopolymers that have been analyzed by AFM. These specific examples include extracellular polymeric substances on the surfaces of bacterial biofilms, condensed DNA, DNA constructs, and DNA-protein interactions. In addition, two examples are presented for AFM analyses of proteins: laminin flexing its arms in solution and neurofilaments entropically brushing away the space around themselves.

Probing protein-protein interactions in real time.

We have used a prototype small cantilever atomic force microscope to observe, in real time, the interactions between individual protein molecules. In particular, we have observed individual molecules of the chaperonin protein GroES binding to and then dissociating from individual GroEL proteins, which were immobilized on a mica support. This work suggests that the small cantilever atomic force microscope is a useful tool for studying protein dynamics at the single molecule level.

A novel approach for analyzing the structure of DNA modified by Benzo[a]pyrene diol epoxide at single-molecule resolution.

Benzo[a]pyrene diol epoxide (BPDE) has been shown to bind specifically to the exocyclic amino group of deoxyguanosine in duplex DNA. Interestingly, this metabolite exhibits stereoselectivity in its tumorigenic and mutagenic effects. It is thought that local DNA conformation is altered at the site of the adduct, resulting in aberrant biological processes, and that in certain sequence contexts BPDE-DNA adducts induce bends in the DNA. In the work presented here, we compared DNA structural alterations of BPDE-modified DNA and unmodified DNA via tapping mode atomic force microscopy (AFM). DNA fragments 366 base pairs (bp) in length were generated by PCR from the duplicated multiple-cloning site of pBEND2 inserted into pGEM-3Zf(-), and either mock-modified or treated with BPDE to give modification levels between 1 and 5% of the nucleotides. Control or BPDE-modified DNA was adsorbed to mica and visualized in air by AFM. The contour lengths and end-to-end lengths of individual molecules were measured. The ratio of end-to-end distance to contour length was significantly smaller for modified DNA molecules than for the unmodified DNA preparation, although the frequency distributions of the contour lengths were similar for the two preparations. This suggests BPDE-DNA adducts cause significant bending of DNA molecules, confirming previous conclusions based on more indirect measurements. The average induced bend angle for BPDE-DNA adducts is estimated to be at least 30 degrees.

Recent highlights from atomic force microscopy of DNA.

Abstract Seven recent highlights are presented from atomic force microscopy (AFM) of DNA in this lab. The first two involve advances in the observation of enzymatic reactions in near-physiological solutions. E. coli RNA polymerase was observed to process along its DNA template in a series of time-lapse images [S. Kasas, et al., Biochemistry 36, 461 (1997)], and a new small-cantilever atomic force microscope (AFM) imaged DNA degradation by DNase I at rates as fast as two seconds per image. The next five highlights involve structural observations of DNA and DNA-protein complexes, including DNA condensed for gene delivery, sequence-dependent DNA condensation, an AFM assay for RNA polymerase, and AFM evidence for a yeast kinetochore complex that may be involved in holding together sister chromatids during cell division.

DNA toroids: stages in condensation.

The effects of polylysine (PLL) and PLL-asialoorosomucoid (AsOR) on DNA condensation have been analyzed by AFM. Different types of condensed DNA structures were observed, which show a sequence of conformational changes as circular plasmid DNA molecules condense progressively. The structures range from circular molecules with the length of the plasmid DNA to small toroids and short rods with approximately 1/6 to 1/8 the contour length of the uncondensed circular DNA. Single plasmid molecules of 6800 base pairs (bp) condense into single toroids of approximately 110 nm diameter, measured center-to-center. The results are consistent with a model for DNA condensation in which circular DNA molecules fold several times into progressively shorter rods. Structures intermediate between toroids and rods suggest that at least some toroids may form by the opening up of rods as proposed by Dunlap et al. [(1997) Nucleic Acids Res. 25, 3095]. Toroids and rods formed at lysine:nucleotide ratios of 5:1 and 6:1. This high lysine:nucleotide ratio is discussed in relation to entropic considerations and the overcharging of macroions. PLL-AsOR is much more effective than PLL alone for condensing DNA, because several PLL molecules are attached to a single AsOR molecule, resulting in an increased cation density.

Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)-binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy.

Yeast centromeric DNA (CEN DNA) binding factor 3 (CBF3) is a multisubunit protein complex that binds to the essential CDEIII element in CEN DNA. The four CBF3 proteins are required for accurate chromosome segregation and are considered to be core components of the yeast kinetochore. We have examined the structure of the CBF3-CEN DNA complex by atomic force microscopy. Assembly of CBF3-CEN DNA complexes was performed by combining purified CBF3 proteins with a DNA fragment that includes the CEN region from yeast chromosome III. Atomic force microscopy images showed DNA molecules with attached globular bodies. The contour length of the DNA containing the complex is approximately 9% shorter than the DNA alone, suggesting some winding of DNA within the complex. The measured location of the single binding site indicates that the complex is located asymmetrically to the right of CDEIII extending away from CDEI and CDEII, which is consistent with previous data. The CEN DNA is bent approximately 55 degrees at the site of complex formation. A significant fraction of the complexes are linked in pairs, showing three to four DNA arms, with molecular volumes approximately three times the mean volumes of two-armed complexes. These multi-armed complexes indicate that CBF3 can bind two DNA molecules together in vitro and, thus, may be involved in holding together chromatid pairs during mitosis.

Atomic force microscopy and other scanning probe microscopies.

The highlight of the past year is the unfolding and refolding of the muscle protein titin in the atomic force microscope. A related highlight in the intersection between experiment and theory is a recent review of the effects of molecular forces on biochemical kinetics. Other advances in scanning probe microscopy include entropic brushes, molecular sandwiches and applications of atomic force microscopy to gene therapy.

Preferential distribution of the fluorescent phospholipid probes NBD-phosphatidylcholine and rhodamine-phosphatidylethanolamine in the exofacial leaflet of acetylcholine receptor-rich membranes from Torpedo marmorata.

The distribution of the two fluorescent phospholipid analogs across acetylcholine receptor (AChR)-rich membranes from Torpedo marmorata has been studied by a combination of nonradiative fluorescence resonance energy transfer using fluorescent lipid probes and quenching of their fluorescence with Co2+ and 2,4,6-trinitrobenzenesulfonic acid. The fluorescent lipid analogs were supplied to the AChR-rich membrane or liposome suspension by simply injecting ethanol solutions of the probes into the medium. The efficiency of the fluorescence energy transfer between NBD-labeled phosphatidylcholine and rhodamine-labeled ethanolamine glycerophospholipids was measured in model membranes prepared in such a way that the probes could be targeted at the same or opposite halves of the bilayer, and the results were compared with those obtained for native AChR-rich membranes. It is shown that NBD-PC and Rho-PE can be efficiently (95%) incorporated into AChR-rich membranes and liposomes. On the basis of the comparison with model liposomes, the energy transfer experiments suggest a preferential exofacial location of the parental phospholipids in the native AChR-rich membrane. Fluorescence quenching with Co2+ and TNBS showed these two phospholipid analogs to be located predominantly in the outer leaflet of the bilayer in AChR-rich membranes. From the Co2+ quenching of the lipid analogs, it was also possible to calculate the surface potential of the outer leaflet of the membrane as being on the order of -15 mV.

Imaging subcellular structures of rat mammary carcinoma cells by scanning force microscopy.

Scanning force microscopy (SFM) was used for imaging subcellular structures of cultured rat mammary carcinoma cells dried in air. Identification of cellular substructures was achieved by immunofluorescence and specific fluorescence probes. Cells grown attached to a glass support exhibited submicrometer thickness in the dried state. Inside the nuclear domain the nucleoli appeared as prominent conical protrusions. Membrane extensions, microspikes and microvilli were well preserved at the cell periphery after fixation in glutaraldehyde vapor and air-drying and were distinguishable either as isolated elements or intercellular communications. The plasma membrane and soluble proteins were selectively removed with nonionic detergent in a buffer system. The mitochondria were concentrated primarily in the perinuclear space and exhibited a well defined filamentous shape. Their identity was confirmed by specific fluorescence staining with rhodamine 123. In the membrane-free system achieved by dry-cleaving of the sample surface, the cytoskeletal network was resolved as a complex mesh of actin-containing fiber bundles interwoven with a filigree arrangement of thinner filaments. The smallest fibrous substructures revealed by SFM with the scanning tips used to date were approximately 8 to 10 nm in height and 80 nm in width.

Probing specific molecular conformations with the scanning force microscope. Complexes of plasmid DNA and anti-Z-DNA antibodies.

An anti-Z-DNA IgG antibody was used to probe for the left-handed Z-DNA conformation of a d(CG)11 insert in a negatively supercoiled plasmid DNA (pAN022). The complexes were spread on mica in the presence of a quaternary ammonium detergent benzyldimethylalkylammonium chloride and imaged with a scanning force microscope (SFM). The high affinity anti-Z-DNA antibody was retained even after restriction endonuclease cleavage of the DNA. The two arms in the product molecules had unequal lengths in conformity with the known location of the Z-DNA forming insert. Most complexes exhibited one IgG per DNA molecule. The bound antibodies were up to approximately 35 nm in diameter and extended approximately 2 nm from the mica surface. They were generally in a lateral orientation relative to the DNA, in accordance with prior chemical modification experimental data indicating a bipedal mode of binding for an anti-Z-DNA IgG. However, the SFM images also suggest that the DNA bends to accommodate the two Fab combining regions of the antibody. This study demonstrates the utility of the SFM for investigating conformation-dependent molecular recognition.

Scanning force microscopy of circular and linear plasmid DNA spread on mica with a quaternary ammonium salt.

Scanning force microscopy (SFM) offers the potential for subnanometer resolution in the investigation of nucleic acids, proteins, and their complexes. SFM is not bound by the requirement of classical transmission electron microscopy (TEM) for contrast enhancement through shadow casting or negative staining. A primary challenge, however, has been the reproducible fixation of samples on an atomically flat surface such as mica. We have developed a method for the routine imaging by SFM of supercoiled, relaxed, and linearized plasmid DNA, immobilized on freshly cleaved mica through the spreading action of benzyldimethylalkylammonium chloride (BAC) at micromolar concentrations. A reproducibly high yield of well-spread, dispersed molecules is obtained and background contamination is minimal. The contour lengths of the relaxed and linearized molecules imaged in air agree well with the helical rise (3.4 A/bp) of B-DNA in solution. We have also introduced the use of quantitative image analysis of SFM images to determine apparent molecular width and height over the entire molecular path.