AFM structural study of the molecular chaperone GroEL and its two-dimensional crystals: an ideal "living" calibration sample

Direct Visualization of the Binding of Transforming Growth Factor Beta 1 with Cartilage Oligomeric Matrix Protein via High-Resolution Atomic Force Microscopy

This work reports the first direct observations of binding and complex formation between transforming growth factor beta 1 (TGF-β1) and cartilage oligomeric matrix protein (COMP) using high-resolution atomic force microscopy (AFM). Each COMP molecule consists of pentamers whose five identical monomeric units bundle at N-termini. From this central point, the five monomers' flexible arms extend outward with C-terminal domains at the distal ends, forming a bouquet-like structure. In commonly used buffer solutions, TGF-β1 molecules typically form homodimers (majority), double dimers (minority), and aggregates (trace amount). Mixing TGF-β1 and COMP leads to rapid binding and complex formation. The TGF-β1/COMP complexes contain one to three COMP and multiple TGF-β1 molecules. For complexes with one COMP, the structure is more compact and less flexible than that of COMP alone. For complexes with two or more COMP molecules, the conformation varies to a large degree from one complex to another. This is attributed to the presence of double dimers or aggregates of TGF-β1 molecules, whose size and multiple binding sites enable binding to more than one COMP. The number and location of individual TGF-β1 dimers are also clearly visible in all complexes. This molecular-level information provides a new insight into the mechanism of chondrogenesis enhancement by TGF-β1/COMP complexes, i.e., simultaneous and multivalent presentation of growth factors. These presentations help explain the high efficacy in sustained activation of the signaling pathway to augment chondrogenesis.

Self-reporting Polymeric Materials with Mechanochromic Properties

The mechanical transduction of force onto molecules is an essential feature of many biological processes that results in the senses of touch and hearing, gives important cues for cellular interactions and can lead to optically detectable signals, such as a change in colour, fluorescence or chemoluminescence. Polymeric materials that are able to visually indicate deformation, stress, strain or the occurrence of microdamage draw inspiration from these biological events. The field of self-reporting (or self-assessing) materials is reviewed. First, mechanochromic events in nature are discussed, such as the formation of bruises on skin, the bleeding of a wound, or marine glow caused by dinoflagellates. Then, materials based on force-responsive mechanophores, such as spiropyrans, cyclobutanes, cyclooctanes, Diels–Alder adducts, diarylbibenzofuranone and bis(adamantyl)-1,2-dioxetane are reviewed, followed by mechanochromic blends, chromophores stabilised by hydrogen bonds, and pressure sensors based on ionic interactions between fluorescent dyes and polyelectrolyte brushes. Mechanobiochemistry is introduced as an important tool to create self-reporting hybrid materials that combine polymers with the force-responsive properties of fluorescent proteins, protein FRET pairs, and other biomacromolecules. Finally, dye-filled microcapsules, microvascular networks, and hollow fibres are demonstrated to be important technologies to create damage-indicating coatings, self-reporting fibre-reinforced composites and self-healing materials.

Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science

Protein cages have become essential tools in bionanotechnology due to their well-defined, monodisperse, capsule-like structure. Combining them with synthetic polymers greatly expands their application, giving rise to novel nanomaterials fore.g.drug-delivery, sensing, electronic devices and for uses as nanoreactors.

Atomic Force Microscope nanolithography on chromosomes to generate single-cell genetic probes

BACKGROUND

Chromosomal dissection provides a direct advance for isolating DNA from cytogenetically recognizable region to generate genetic probes for fluorescence in situ hybridization, a technique that became very common in cyto and molecular genetics research and diagnostics. Several reports describing microdissection methods (glass needle or a laser beam) to obtain specific probes from metaphase chromosomes are available. Several limitations are imposed by the traditional methods of dissection as the need for a large number of chromosomes for the production of a probe. In addition, the conventional methods are not suitable for single chromosome analysis, because of the relatively big size of the microneedles. Consequently new dissection techniques are essential for advanced research on chromosomes at the nanoscale level.

RESULTS

We report the use of Atomic Force Microscope (AFM) as a tool for nanomanipulation of single chromosomes to generate individual cell specific genetic probes. Besides new methods towards a better nanodissection, this work is focused on the combination of molecular and nanomanipulation techniques which enable both nanodissection and amplification of chromosomal and chromatidic DNA. Cross-sectional analysis of the dissected chromosomes reveals 20 nm and 40 nm deep cuts. Isolated single chromosomal regions can be directly amplified and labeled by the Degenerate Oligonucleotide-Primed Polymerase Chain Reaction (DOP-PCR) and subsequently hybridized to chromosomes and interphasic nuclei.

CONCLUSIONS

Atomic force microscope can be easily used to visualize and to manipulate biological material with high resolution and accuracy. The fluorescence in situ hybridization (FISH) performed with the DOP-PCR products as test probes has been tested succesfully in avian microchromosomes and interphasic nuclei. Chromosome nanolithography, with a resolution beyond the resolution limit of light microscopy, could be useful to the construction of chromosome band libraries and to the molecular cytogenetic mapping related to the investigation of genetic diseases.

AFM of biological complexes: what can we learn?

The term "biological complexes" broadly encompasses particles as diverse as multisubunit enzymes, viral capsids, transport cages, molecular nets, ribosomes, nucleosomes, biological membrane components and amyloids. The complexes represent a broad range of stability and composition. Atomic force microscopy offers a wealth of structural and functional data about such assemblies. For this review, we choose to comment on the significance of AFM to study various aspects of biology of selected nonmembrane protein assemblies. Such particles are large enough to reveal many structural details under the AFM probe. Importantly, the specific advantages of the method allow for gathering dynamic information about their formation, stability or allosteric structural changes critical for their function. Some of them have already found their way to nanomedical or nanotechnological applications. Here we present examples of studies where the AFM provided pioneering information about the biology of complexes, and examples of studies where the simplicity of the method is used toward the development of potential diagnostic applications.

Ultra-resolution imaging of a self-assembling biomolecular system using robust carbon nanotube AFM probes

Nanoscale structural features of a novel self-assembling DNA based nanostructure have been resolved. Image data is of sufficient resolution to allow molecular orientation and the effect of surface adsorption to be characterized. This has been achieved using AFM with probes employing carbon nanotubes attached via a thin film of plasma polymerized hexane. This presents the nanotube with a highly hydrophobic coating to which it can adsorb, increasing production success and probe robustness.

SPR and AFM study of engineered biomolecule immobilisation techniques

A comparative study into two novel and diverse schemes designed to improve immobilization of biomolecules for biosensing purposes is presented. In the first method a silicon rich matrix is created using PECVD. The second method involves creating nano-patterns on the sensor surface to create a large number of surface discontinuities to which the proteins will bind preferentially. The basic theory of SPR is provided to show the importance of the surface sensitive nature of this optical transduction technique. The present work suggests that both may prove both for SPR and other biosensing applications. Of the two schemes proposed, the results for nano-patterning seem to suggest that it is promoting better surface attachment of biomolecules. The results of SPR and AFM studies are presented that have shown that each of these schemes promotes improved binding of various proteins.

How to orient the functional GroEL-SR1 mutant for atomic force microscopy investigations

We present high-resolution atomic force microscopy (AFM) imaging of the single-ring mutant of the chaperonin GroEL (SR-EL) from Escherichia coli in buffer solution. The native GroEL is generally unsuitable for AFM scanning as it is easily being bisected by forces exerted by the AFM tip. The single-ring mutant of GroEL with its simplified composition, but unaltered capability of binding substrates and the co-chaperone GroES, is a more suited system for AFM studies. We worked out a scheme to systematically investigate both the apical and the equatorial faces of SR-EL, as it binds in a preferred orientation to hydrophilic mica and hydrophobic highly ordered pyrolytic graphite. High-resolution topographical imaging and the interaction of the co-chaperone GroES were used to assign the orientations of SR-EL in comparison with the physically bisected GroEL. The usage of SR-EL facilitates single molecule studies on the folding cycle of the GroE system using AFM.

Atomic force microscopy of histological sections using a chemical etching method

Physiology and pathology have a big deal on tissue morphology, and the intrinsic spatial resolution of an atomic force microscope (AFM) is able to observe ultrastructural details. In order to investigate cellular and subcellular structures in histological sections with the AFM, we used a new simple method for sample preparation, i.e. chemical etching of semithin sections from epoxy resin-embedded specimens: such treatment appears to melt the upper layers of the embedding resin; thus, removing the superficial roughness caused by the edge of the microtome knife and bringing into high relief the biological structures hidden in the bulk. Consecutive ultrathin sections embedded in epoxy resin were observed with a transmission electron microscope (TEM) to compare the different imaging properties on the same specimen sample. In this paper we report, as an example, our AFM and TEM images of two different tissue specimens, rat pancreas and skeletal muscle fibres, showing that most of the inner details are visible with the AFM. These results suggest that chemical etching of histological sections may be a simple, fast and cost-effective method for AFM imaging with ultrastructural resolution.

Characterization of oligomeric species in the fibrillization pathway of the yeast prion Ure2p

The [URE3] prion of Saccharomyces cerevisiae shares many features with mammalian prions and poly-glutamine related disorders and has become a model for studying amyloid diseases. The development of the [URE3] phenotype is thought to be caused by a structural switch in the Ure2p protein. In [URE3] cells, Ure2p is found predominantly in an aggregated state, while it is a soluble dimer in wild-type cells. In vitro, Ure2p forms fibrils with amyloid-like properties. Several studies suggest that the N-terminal domain of Ure2p is essential for prion formation. In this work, we investigated the fibril formation of Ure2p by isolating soluble oligomeric species, which are generated during fibrillization, and characterized them with respect to size and structure. Our data support the critical role of the N-terminal domain for fibril formation, as we observed fibrils in the presence of 5 M guanidinium chloride, conditions at which the C-terminal domain is completely unfolded. Based on fluorescence measurements, we conclude that the structure of the C-terminal domain is very similar in dimeric and fibrillar Ure2p. When studying the time course of fibrillization, we detected the formation of small, soluble oligomeric species during the early stages of the process. Their remarkable resistance against denaturants, their increased content of beta-structure, and their ability to 'seed' Ure2p fibrillization suggest that conversion to the amyloid-like conformation has already occurred. Thus, they likely represent critical intermediates in the fibrillization pathway of Ure2p.