Improved Photocatalytic Performance of TiO2-Nitrogen-Doped Graphene Quantum Dot Composites Mediated by Heterogeneous Interactions

Photocatalysis is typically monitored via analysis of phases in isolation and focuses on the removal of a target analyte from the solution phase. Here we analyze the photocatalytic action of a TiO2-nitrogen-doped graphene quantum dot (NGQD) composite on a target analyte, phenol, using comprehensive multiphase NMR (CMP-NMR) which observes signals in solid, solution, and gel phases in situ. Phenol preferentially interacts with the composite photocatalyst compared to pure TiO2, increasing its effective concentration near the catalyst surface and its degradation rate. The presence of NGQDs in the composite reduced the fouling of the catalyst surface and caused a reduction of photogenerated intermediates. Increased heterogeneous interactions, likely mediated by π-π interactions, are hypothesized to cause each of these improvements in the observed photocatalytic performance by TiO2-NGQDs. CMP-NMR allows the elucidation of how the photocatalytic mechanism is enhanced via material design and provides a foundation for the development of efficient photocatalysts.

TiO2-NGQD composite photocatalysts with switchable photocurrent response

A series of titanium dioxide-nitrogen doped graphene quantum dot (TiO₂-NGQD) composite photocatalysts were synthesized through a simple hydrothermal reaction with varied NGQD content. Through a proposed Z-Scheme heterojunction, the composites were able to achieve increased photocurrent generation and photocatalytic degradation of phenol under both full spectrum and visible only illumination. The prepared composites were able to switch from anodic to cathodic photocurrent by changing the light source from full spectrum to visible wavelengths. The photocatalytic capabilities of the composites were tested by degrading phenol and this was monitored via nuclear magnetic resonance. All composites outperformed the commercial standard P25 TiO₂ under both full spectrum and visible irradiation, with the 8 wt% NGQD composite showing a visible improvement of over 600% compared to P25. With the ability to manipulate the generation of majority charge carriers, TiO₂-NGQDs have significant potential not only in photocatalysis, but in far reaching applications such as energy harvesting and water splitting.

A new perspective on the photocatalytic action of titanium dioxide on phenol elucidated using comprehensive multiphase NMR

Comprehensive Multiphase NMR (CMP-NMR) is a recently developed technique capable of simultaneously observing different phases - solutions, gels, and solids - while providing the chemical specificity of traditional NMR. With this new tool, the heterogeneous photocatalysis of phenol by titanium dioxide (P25 TiO₂) is re-examined to gain information about the occurrence of reaction at different regions between the catalyst and the solution. It was found that the proportion of phenol in different phases changes over the course of the photodegradation period. The photocatalyst appears to preferentially degrade phenol molecules that are weakly associated with the surface, such that they have restricted mobility in a 'gel-like' state. Diffusion Ordered Spectroscopy (DOSY) corroborates the relative change in phenol signals between freely diffusing solution and diffusion restricted gels as measured using CMP-NMR. The surface of P25 TiO₂ was found to foul over the course of the 200-hour photodegradation period that was monitored using the solid-state capabilities of the CMP-NMR. Finally, CMP-NMR showed differences in the photodegradation of phenol by P25 TiO₂ to that of a TiO₂-nitrogen doped graphene quantum dot (NGQD) composite. With the latter composite, no fouling of the surface was seen over time. This application of CMP-NMR to the field of catalysis demonstrates its potential to better understand and study photocatalytic systems in general.

Ultra-stable Electrochemical Sensor for Detection of Caffeic Acid Based on Platinum and Nickel Jagged-Like Nanowires

Electrochemical sensors have the high sensitivity, fast response, and simple operation for applications in biological, medical, and chemical detection, but limited by the poor stability and high cost of the electrode materials. In this work, we used PtNi lagged-like nanowire for caffeic acid (CA) electrochemical detection. The removal of outer layer Ni during reaction process contributed to the rehabilitation of active Pt sites at the surface, leading to the excellent electrocatalytic behavior of CA sensing. Carbon-supported PtNi-modified glassy carbon electrode (PtNi/C electrode) showed a broad CA detecting range (from 0.75 to 591.783 μM), a low detection limit (0.5 μM), and excellent stability. The electrode preserved high electrocatalytic performance with 86.98% of the initial oxidation peak current retained after 4000 potential cycles in 0.5 mM caffeic acid solution. It also demonstrates excellent anti-interference capability and is ready for use in the real sample analysis.

Whole-field macro- and micro-deformation characteristic of unbound water-loss in dentin hard tissue

High-resolution deformation measurements in a functionally graded hard tissue such as human dentin are essential to understand the unbound water-loss mediated changes and their role in its mechanical integrity. Yet a whole-field, 3-dimensional (3D) measurement and characterization of fully hydrated dentin in both macro- and micro-scales remain to be a challenge. This study was conducted in 2 stages. In stage-1, a stereo-digital image correlation approach was utilized to determine the water-loss and load-induced 3D deformations of teeth in a sagittal section over consecutively acquired frames, from a fully hydrated state to nonhydrated conditions for a period up to 2 hours. The macroscale analysis revealed concentrated residual deformations at the dentin-enamel-junction and the apical regions of root in the direction perpendicular to the dentinal tubules. Significant difference in the localized deformation characteristics was observed between the inner and outer aspects of the root dentin. During quasi-static loadings, further increase in the residual deformation was observed in the dentin. In stage-2, dentin microstructural variations induced by dynamic water-loss were assessed with environmental scanning electron microscopy and atomic force microscopy (AFM), showing that the dynamic water-loss induced distention of dentinal tubules with concave tubular edges, and concurrent contraction of intertubular dentin with convex profile. The findings from the current macro- and micro-scale analysis provided insight on the free-water-loss induced regional deformations and ultrastructural changes in human dentin.

Universal aqueous synthesis of ultra-small polymer-templated nanoparticles: synthesis optimization methodology for counterion-collapsed poly(acrylic acid)

A long polyelectrolyte chain collapses into a nano-sized particle upon the addition of counterions under appropriate solution conditions. This phenomenon forms the basis for a simple universal method for aqueous synthesis of ultra-small (<10 nm) metal, metal oxide, and other types of nanoparticles in the following manner: the counterion-collapsed polyelectrolyte chains are made stable by crosslinking, effectively trapping the counterions, which are subsequently chemically modified, to form metal nanoparticles via reduction or metal oxides nanoparticles via oxidation, within the collapsed polymer nanoparticle. This highly versatile platform methodology can be applied to almost any polyelectrolyte–counterion pair, making possible the rapid development of syntheses of different nanoparticles within the same chemical environment. Using poly(acrylic acid) as a model system, a methodology for the optimization of conditions for the polyelectrolyte collapse by various mono- and multi-valent metal cations is developed. The optimal counterion concentration did not correlate with ionic strength and metal ion valency and was highly variable from system to system. By monitoring the polyelectrolyte conformation using viscosity and turbidity measurements, the appropriate metal ion concentration for each nanoparticle system was determined.

High Efficiency Photoelectrocatalytic Methanol Oxidation on CdS Quantum Dots Sensitized Pt Electrode

A cadmium sulfide quantum dots sensitized Pt (Pt-CdS) composite was synthesized using a solvothermal method and characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and UV-vis diffuse reflectance spectroscopy. The catalytic properties of the as-prepared electrode for methanol oxidation were evaluated by cyclic voltammetry (CV), chronoamperometry, electrochemical impedance spectrum (EIS) and photocurrent responses. The as-prepared Pt-CdS electrode displayed a significant enhancement in the electrocatalytic activity and stability for methanol oxidation in the presence of visible light irradiation. The synergistic effect of both the electro- and photocatalytic reaction contributes to this enhanced catalytic performance. Our result suggests a new paradigm to construct photoelectrocatalysts with high performance and good stability for direct methanol fuel cells with the assistance of visible-light illumination.

Angiopoietin-1 peptide QHREDGS promotes osteoblast differentiation, bone matrix deposition and mineralization on biomedical materials

Bone loss occurs as a consequence of a variety of diseases as well as from traumatic injuries, and often requires therapeutic intervention. Strategies for repairing and replacing damaged and/or lost bone tissue include the use of biomaterials and medical implant devices with and without osteoinductive coatings. The soluble growth factor angiopoietin-1 (Ang-1) has been found to promote cell adhesion and survival in a range of cell types including cardiac myocytes, endothelial cells and fibroblasts through an integrin-dependent mechanism. Furthermore, the short sequence QHREDGS has been identified as the integrin-binding sequence of Ang-1 and as a synthetic peptide has been found to possess similar integrin-dependent effects as Ang-1 in the aforementioned cell types. Integrins have been implicated in osteoblast differentiation and bone mineralization, processes critical to bone regeneration. By binding integrins on the osteoblast surface, QHREDGS could promote cell survival and adhesion, as well as conceivably osteoblast differentiation and bone mineralization. Here we immobilized QHREDGS onto polyacrylate (PA)-coated titanium (Ti) plates and polyethylene glycol (PEG) hydrogels. The osteoblast differentiation marker, alkaline phosphatase, peaked in activity 4-12 days earlier on the QHREDGS-immobilized PA-coated Ti plates than on the unimmobilized, DGQESHR (scrambled)- and RGDS-immobilized surfaces. Significantly more bone matrix was deposited on the QHREDGS-immobilized Ti surface than on the other surfaces as determined by atomic force microscopy. The QHREDGS-immobilized hydrogels also had a significantly higher mineral-to-matrix (M/M) ratio determined by Fourier transform infrared spectroscopy. Alizarin Red S and von Kossa staining and quantification, and environmental scanning electron microscopy showed that while both the QHREDGS- and RGDS-immobilized surfaces had extensive mineralization relative to the unimmobilized and DGQESHR-immobilized surfaces, the mineralization was more considerable on the QHREDGS-immobilized surface, both with and without the induction of osteoblast differentiation. Finally, treatment of cell monolayers with soluble QHREDGS was demonstrated to upregulate osteogenic gene expression. Taken together, these results demonstrate that the QHREDGS peptide is osteoinductive, inducing osteoblast differentiation, bone matrix deposition and mineralization.

Synthesis of water-soluble luminescent poly(acrylic acid)-encapsulated CdTe/CdS nanoparticles

Described is the synthesis in water under ambient conditions of water-soluble, luminescent poly(acrylic acid)-encapsulated CdTe/CdS nanoparticles. Counterion-collapsed poly(acrylic acid) is used as a nanotemplate for the formation of the quantum dot core. Gram quantities of nanoparticles are easily obtained. Simply varying the amount of thioacetamide used in the synthesis can shift the emission wavelengths of the resulting nanoparticles from green to yellow to red.

In vitro synthesis of native, fibrous long spacing and segmental long spacing collagen

Collagen fibrils are present in the extracellular matrix of animal tissue to provide structural scaffolding and mechanical strength. These native collagen fibrils have a characteristic banding periodicity of ~67 nm and are formed in vivo through the hierarchical assembly of Type I collagen monomers, which are 300 nm in length and 1.4 nm in diameter. In vitro, by varying the conditions to which the monomer building blocks are exposed, unique structures ranging in length scales up to 50 microns can be constructed, including not only native type fibrils, but also fibrous long spacing and segmental long spacing collagen. Herein, we present procedures for forming the three different collagen structures from a common commercially available collagen monomer. Using the protocols that we and others have published in the past to make these three types typically lead to mixtures of structures. In particular, unbanded fibrils were commonly found when making native collagen, and native fibrils were often present when making fibrous long spacing collagen. These new procedures have the advantage of producing the desired collagen fibril type almost exclusively. The formation of the desired structures is verified by imaging using an atomic force microscope.

Direct visualization of the formation of RecA/dsDNA complexes at the single-molecule level

The assembly of RecA on linear dsDNA with ATPγS in the reaction was elucidated using atomic force microscopy (AFM) on a single-molecule level. It was found that assembly generally (∼95%) proceeded from a single nucleation site that started from one end of the DNA strand. About 5% of the complexes were formed starting either from both ends or from the middle of dsDNA strand. In all these cases, the RecA coating was contiguous for each region suggesting the binding of RecA to DNA is cooperative. The AFM observation provides direct experimental evidence to show how RecA binds to linear dsDNA in the presence of ATPγS.

Note: A scanning electron microscope sample holder for bidirectional characterization of atomic force microscope probe tips

A novel sample holder that enables atomic force microscopy (AFM) tips to be mounted inside a scanning electron microscopy (SEM) for the purpose of characterizing the AFM tips is described. The holder provides quick and easy handling of tips by using a spring clip to hold them in place. The holder can accommodate two tips simultaneously in two perpendicular orientations, allowing both top and side view imaging of the tips by the SEM.

Direct evidence of the role of ATPγS in the binding of single-stranded binding protein (Escherichia coli) and RecA to single-stranded DNA

To gain insight into the influence of ATPγS on the competitive binding of RecA and single-stranded binding protein (SSB) on single-stranded DNA (ssDNA), AFM imaging was used to examine the three-dimensional structures of the different complexes formed by the binding of the two proteins on ssDNA in the presence and absence of ATPγS. In the presence of ATPγS, RecA attaches to ssDNA, displacing SSB, to form continuous binding regions that caused considerable elongation of the strand. When ATPγS is absent, RecA could not compete with SSB and only binds at a few sites that correspond to the vacancy in ssDNA left when SSB unbinds. These results provide direct evidence that, while SSB binding affinity to DNA is substantially higher than that of RecA, the presence of ATPγS is sufficient to alter the events and enable RecA coating of DNA.

Combinatorial polyelectrolyte multilayer film fabrication

A combinatorial strategy for the fabrication of a library of polyelectrolyte multilayer films is presented in this paper. This innovative approach involves the parallel formation of polyelectrolyte multilayer films in the individual wells of polystyrene microtitre plates under various deposition conditions. The progress of film formation was monitored via the intensity of the UV-vis absorbance of one of the depositing polyelectrolytes using a conventional microplate reader. We demonstrate the utility of this technique by building a library of 120 distinct polyelectrolyte multilayer films. Both the primer layer composition and salt content of the polyeletrolyte solutions were systematically varied in the preparation of films of nine bilayers. Film growth did not follow a linear adsorption regime for the first three bilayers regardless of the composition of the primer layer. We observed that increasing the sodium chloride concentration in the polyelectrolyte solutions resulted in increased polyelectrolyte absorption for all the conditions studied. The approach presented here is a convenient method of producing and characterizing multiple films rapidly and reproducibly, making it a valuable tool for optimizing film fabrication.

Potassium ion mediated collagen microfibril assembly on mica

Potassium ion can critically effect the interaction between collagen microfibrils and mica leading to different ordered structures that vary dramatically with changing ion concentration. AFM images of the structures formed at different ion concentrations appear to be intermediate stages in the progression from disordered to ordered film. At 200 mM potassium ion concentration, a nanometer-thick array of aligned and bundled microfibrils covering large areas can be created easily and reproducibly on mica.

Novel polymorphism of RecA fibrils revealed by atomic force microscopy

RecA fibrils in physiological conditions have been successfully imaged using Tapping Mode atomic force microscopy. This represents the first time images of recA have been obtained without drying, freezing and/or exposure to high vacuum conditions. While previously observed structures - the monomer, the hexamer, the short rod - were seen, a new type of fibril was also observed. This protofibril is narrower in diameter than the standard fibril, and occurs in three distinct morphologies: aperiodic, 100-nm periodic, and 150-nm periodic. In addition, much longer rods were observed, and appear curved and even circular.

Fibrous long spacing type collagen fibrils have a hierarchical internal structure

Nanodissection of single fibrous long spacing (FLS) type collagen fibrils by atomic force microscopy (AFM) reveals hierarchical internal structure: Fibrillar subcomponents with diameters of approximately 10 to 20 nm were observed to be running parallel to the long axis of the fibril in which they are found. The fibrillar subcomponent displayed protrusions with characteristic approximately 270 nm periodicity, such that protrusions on neighboring subfibrils were aligned in register. Hence, the banding pattern of mature FLS-type collagen fibrils arises from the in-register alignment of these fibrillar subcomponents. This hierarchical organization observed in FLS-type collagen fibrils is different from that previously reported for native-type collagen fibrils, displaying no supercoiling at the level of organization observed.

Direct and real-time visualization of the disassembly of a single RecA-DNA-ATPgammaS complex using AFM imaging in fluid

RecA disassembly from circular double-stranded DNA (dsDNA) was studied by atomic force microscopy (AFM) imaging in fluid on a single molecule scale. The RecA/DNA complex was formed in the presence of ATPgammaS, and the disassembly was then initiated by buffer exchange to rinse off ATPgammaS. Performing AFM imaging in fluid allowed direct and real-time visualization of the disassembly of RecA from dsDNA in solution. It was found that RecA disassembly commenced from multiple sites both in deionized water and in buffer; the areas where RecA dissociated showed the appearance of "gaps" in the filamentous structure. RecA further disassembled either through the already existing "gaps" or by generation of new gaps. The disassembly was slower in buffer than in deionized water, suggesting that ions also contribute to the stabilization of the complex. RecA hexamers and monomers were observed in deionized water and in buffer, respectively, during the disassembly process.

An enzyme-amplified diffraction-based immunoassay

We have previously shown that a gold-conjugated secondary label can be used to reduce the limit of detection in a diffraction-based assay by more than 40-fold. We now show that by using a combination of a peroxidase-conjugated secondary label and a precipitating substrate the limit of detection in a diffraction-based assay can be reduced by more than 1000-fold. The response to secondary enhancement was linear for concentrations from 50 to 2000 pg/mL of antidigoxin.

DNA base pair resolution by single molecule force spectroscopy

The forces that hold complementary strands of DNA together in a double helix, and the role of base mismatches in these, are examined by single molecule force spectroscopy using an atomic force microscope (AFM). These forces are important when considering the binding of proteins to DNA, since these proteins often mechanically stretch the DNA during their action. In AFM measurement of forces, there is an inherent instrumental limitation that makes it difficult to compare results from different experimental runs. This is circumvented by using an oligonucleotide microarray, which allowed a direct comparison of the forces between perfectly matched short oligonucleotides and those containing a single or double mismatch. Through this greatly increased sensitivity, the force contribution of a single AT base pair was derived. The results indicate that the contribution to forces from the stacking interactions is more important than that from hydrogen bonding.

Direct observation of the assembly of RecA/DNA complexes by atomic force microscopy

The formation of the RecA/DNA nucleofilament on nicked circular double stranded (ds) DNA in the presence of ATPgammaS was studied using the atomic force microscope (AFM) at nanometer resolution. The AFM allowed simultaneous observation of both dsDNA substrate and RecA protein-coated sections such that they are highly distinguishable. Using a time series of images, the complex formation was monitored. AFM imaging provided direct evidence that assembly of the nucleofilaments occurs via a nucleation and growth mechanism. The nucleation step is much slower than the growth phase, as demonstrated by the predominance of naked dsDNA at early and middle time points, followed by the rapid appearance of partially then fully formed complexes. Observation of the formation of nucleation sites without accompanying growth on unnicked dsDNA enabled an estimate of the nucleation rate, of 5 x 10(-5) RecA min(-1) bp(-1). The published model for the analysis of RecA assembly on dsDNA deduces a single kinetic parameter that prevents the separate determination of nucleation rate and growth rate. By directly measuring the nucleation rate with the AFM, this model is employed to determine a growth rate of 202 min(-1). These AFM results provide the first direct evidence of previous results on complex formation obtained only by indirect means.

An interactive triple-helical collagen builder

To facilitate the building of triple-helical polypeptide structures, we provide an interactive, platform-independent Tcl/Tk script. User specified amino acid sequences are parsed to obtain localized melting temperature estimates corresponding to helical propensity. These propensities may be graphically examined prior to their automated use in combination with two separate statistical parameter sets to build the complete polypeptide backbone and, if desired, predict side-chain terminal atom locations.

AVAILABILITY

The Tcl/Tk Triple Helical collagen Building Script (THe BuScr) and full documentation is freely available under the terms of the GNU General Public License at www.pence.ca/~jrainey/ or www.chem.utoronto.ca/staff/MCG/.

Statistically Based Reduced Representation of Amino Acid Side Chains

Preferred conformations of amino acid side chains have been well established through statistically obtained rotamer libraries. Typically, these provide bond torsion angles allowing a side chain to be traced atom by atom. In cases where it is desirable to reduce the complexity of a protein representation or prediction, fixing all side-chain atoms may prove unwieldy. Therefore, we introduce a general parametrization to allow positions of representative atoms (in the present study, these are terminal atoms) to be predicted directly given backbone atom coordinates. Using a large, culled data set of amino acid residues from high-resolution protein crystal structures, anywhere from 1 to 7 preferred conformations were observed for each terminal atom of the non-glycine residues. Side-chain length from the backbone C(alpha) is one of the parameters determined for each conformation, which should itself be useful. Prediction of terminal atoms was then carried out for a second, nonredundant set of protein structures to validate the data set. Using four simple probabilistic approaches, the Monte Carlo style prediction of terminal atom locations given only backbone coordinates produced an average root mean-square deviation (RMSD) of approximately 3 A from the experimentally determined terminal atom positions. With prediction using conditional probabilities based on the side-chain chi(1) rotamer, this average RMSD was improved to 1.74 A. The observed terminal atom conformations therefore provide reasonable and potentially highly accurate representations of side-chain conformation, offering a viable alternative to existing all-atom rotamers for any case where reduction in protein model complexity, or in the amount of data to be handled, is desired. One application of this representation with strong potential is the prediction of charge density in proteins. This would likely be especially valuable on protein surfaces, where side chains are much less likely to be fixed in single rotamers. Prediction of ensembles of structures provides a method to determine the probability density of charge and atom location; such a prediction is demonstrated graphically.

A quantitative diffraction-based sandwich immunoassay

It is shown that diffraction-based sensing can be enhanced for diagnostic purposes through the use of a secondary label. The limit of detection for anti-rabbit IgG was reduced more than 40-fold by using a gold-conjugated secondary antibody. The response to secondary antibody binding was linear for concentrations from 25 to 500 ng/ml of anti-rabbit IgG, suggesting that quantitative determinations can be readily done. Moreover, the binding of the secondary antibody was observed as soon as 1 min after its introduction to the surface-bound primary complex.

Hierarchical assembly and the onset of banding in fibrous long spacing collagen revealed by atomic force microscopy

The mechanism of formation of fibrillar collagen with a banding periodicity much greater than the 67 nm of native collagen, i.e. the so-called fibrous long spacing (FLS) collagen, has been speculated upon, but has not been previously studied experimentally from a detailed structural perspective. In vitro, such fibrils, with banding periodicity of approximately 270 nm, may be produced by dialysis of an acidic solution of type I collagen and alpha(1)-acid glycoprotein against deionized water. FLS collagen assembly was investigated by visualization of assembly intermediates that were formed during the course of dialysis using atomic force microscopy. Below pH 4, thin, curly nonbanded fibrils were formed. When the dialysis solution reached approximately pH 4, thin, filamentous structures that showed protrusions spaced at approximately 270 nm were seen. As the pH increased, these protofibrils appeared to associate loosely into larger fibrils with clear approximately 270 nm banding which increased in diameter and compactness, such that by approximately pH 4.6, mature FLS collagen fibrils begin to be observed with increasing frequency. These results suggest that there are aspects of a stepwise process in the formation of FLS collagen, and that the banding pattern arises quite early and very specifically in this process. It is proposed that typical 4D-period staggered microfibril subunits assemble laterally with minimal stagger between adjacent fibrils. alpha(1)-Acid glycoprotein presumably promotes this otherwise abnormal lateral assembly over native-type self-assembly. Cocoon-like fibrils, which are hundreds of nanometers in diameter and 10-20 microm in length, were found to coexist with mature FLS fibrils.

Investigating the ultrastructure of fibrous long spacing collagen by parallel atomic force and transmission electron microscopy

The ultrastructure of fibrous long spacing (FLS) collagen fibrils has been investigated by performing both atomic force microscopy (AFM) and transmission electron microscopy (TEM) on exactly the same area of FLS collagen fibril samples. These FLS collagen fibrils were formed in vitro from type I collagen and alpha1-acid glycoprotein (AAG) solutions. On the basis of the correlated AFM and TEM images obtained before and after negative staining, the periodic dark bands observed in TEM images along the longitudinal axis of the FLS collagen fibril correspond directly to periodic protrusions seen by AFM. This observation is in agreement with the original surmise made by Gross, Highberger, and Schmitt (Gross J, Highberger JH, Schmitt FO, Proc Natl Acad Sci USA 1954;40:679-688) that the major repeating dark bands of FLS collagen fibrils observed under TEM are thick relative to the interband region. Although these results do not refute the idea of negative stain penetration into gap regions proposed by Hodge and Petruska (Petruska JA, Hodge AJ. Aspects of protein structure. Ramachandran GN, editor. New York: Academic Press; 1963. p. 289-300), there is no need to invoke the presence of gap regions to explain the periodic dark bands observed in TEM images of FLS collagen fibrils.

A statistically derived parameterization for the collagen triple-helix

The triple-helix is a unique secondary structural motif found primarily within the collagens. In collagen, it is a homo- or hetero-tripeptide with a repeating primary sequence of (Gly-X-Y)(n), displaying characteristic peptide backbone dihedral angles. Studies of bulk collagen fibrils indicate that the triple-helix must be a highly repetitive secondary structure, with very specific constraints. Primary sequence analysis shows that most collagen molecules are primarily triple-helical; however, no high-resolution structure of any entire protein is yet available. Given the drastic morphological differences in self-assembled collagen structures with subtle changes in assembly conditions, a detailed knowledge of the relative locations of charged and sterically bulky residues in collagen is desirable. Its repetitive primary sequence and highly conserved secondary structure make collagen, and the triple-helix in general, an ideal candidate for a general parameterization for prediction of residue locations and for the use of a helical wheel in the prediction of residue orientation. Herein, a statistical analysis of the currently available high-resolution X-ray crystal structures of model triple-helical peptides is performed to produce an experimentally based parameter set for predicting peptide backbone and C(beta) atom locations for the triple-helix. Unlike existing homology models, this allows easy prediction of an entire triple-helix structure based on all existing high-resolution triple-helix structures, rather than only on a single structure or on idealized parameters. Furthermore, regional differences based on the helical propensity of residues may be readily incorporated. The parameter set is validated in terms of the predicted bond lengths, backbone dihedral angles, and interchain hydrogen bonding.

Diffraction-based assay for detecting multiple analytes

The principles of diffraction are utilized to enable the simultaneous detection of multiple analytes in solution, forming the basis of a multi-analyte sensor. Probe molecules are immobilized on a substrate such that each type of molecule defines a specific pattern within the same region of substrate. The binding of a target molecule to its complementary probe is heralded by a characteristic diffraction image. This principle is demonstrated using antibody conjugates.

A novel sample holder allowing atomic force microscopy on transmission electron microscopy specimen grids: repetitive, direct correlation between AFM and TEM images

A novel sample holder that allows atomic force microscopy (AFM) to be performed on transmission electron microscope (TEM) grids is described. Consequently, AFM and TEM images were repeatedly obtained on exactly the same sample area. For both techniques, a thin carbon film was used as the imaging substrate. Although these techniques have been previously used in conjunction, AFM and TEM images on exactly the same area have not been repeatedly obtained for any system. Correlation of AFM and TEM images is useful for work where the three-dimensional topographical information provided by the AFM could be used to better interpret the two-dimensional images provided by the TEM and vice versa. To demonstrate the applicability of such correlation, new results pertaining to a fibrillar collagen system are summarized.

A study of fibrous long spacing collagen ultrastructure and assembly by atomic force microscopy

Fibrous long spacing collagen (FLS) fibrils are collagen fibrils that display a banding with periodicity greater than the 67nm periodicity of native collagen. FLS fibrils can be formed in vitro by addition of alpha(1)-acid glycoprotein to an acidified solution of monomeric collagen, followed by dialysis of the resulting mixture. We have investigated the ultrastructure of FLS fibrils formed in vitro using the atomic force microscope (AFM). The majority of the fibrils imaged showed typical diameters of approximately 150nm and had a distinct banding pattern with a approximately 250nm periodicity. However, we have also observed an additional type of FLS fibril, which is characterized by a secondary banding pattern surrounding the primary bands. These results are compared with those obtained in past investigations of FLS ultrastructure carried out using the transmission electron microscope (TEM). The importance of the fibril's surface topography in TEM staining patterns is discussed. Images of FLS fibrils in various stages of assembly have also been collected, and the implications of these images in determining the mechanism of assembly and the formation of the characteristic banding pattern of the fibrils is discussed.

Ultrastructure and assembly of segmental long spacing collagen studied by atomic force microscopy

The in vitro formation of segmental long spacing (SLS) collagen as induced by the addition of ATP to acidified Type I collagen solutions has been examined with the atomic force microscope (AFM). AFM images obtained suggest that the assembly proceeds in a stepwise manner, through an intermediate stage of oligomers, which then associate laterally to form the so-called "SLS crystallites". Attempts to induce SLS formation by the addition of other polyanionic species to monomeric collagen solutions met with mixed success; ATP-gamma-S and GTP produced SLS crystallites, whereas inorganic phosphate and other polyanionic dyes did not. This indicates that the formation of SLS cannot simply be attributed to the negation of positive charges believed to be located on the end of the collagen monomer, but rather it is a complex function of the structure and charge of both the collagen monomer and polyanion.

Fibrous long spacing collagen ultrastructure elucidated by atomic force microscopy

Fibrous long spacing collagen (FLS) fibrils are collagen fibrils in which the periodicity is clearly greater than the 67-nm periodicity of native collagen. FLS fibrils were formed in vitro by the addition of alpha1-acid glycoprotein to an acidified solution of monomeric collagen and were imaged with atomic force microscopy. The fibrils formed were typically approximately 150 nm in diameter and had a distinct banding pattern with a 250-nm periodicity. At higher resolution, the mature FLS fibrils showed ultrastructure, both on the bands and in the interband region, which appears as protofibrils aligned along the main fibril axis. The alignment of protofibrils produced grooves along the main fibril, which were 2 nm deep and 20 nm in width. Examination of the tips of FLS fibrils suggests that they grow via the merging of protofibrils to the tip, followed by the entanglement and, ultimately, the tight packing of protofibrils. A comparison is made with native collagen in terms of structure and mechanism of assembly.

Paired helical filaments are twisted ribbons composed of two parallel and aligned components: image reconstruction and modeling of filament structure using atomic force microscopy

To study the structure of Alzheimer paired helical filaments (PHF) we examined isolated detergent-insoluble PHF using atomic force microscopy with image reconstruction. The reconstructed AFM images of Alzheimer PHF most closely resembled ribbon-like helices with thin edges. The presence of a conspicuous furrow in the PHF midline indicated that PHF were composed of two distinctive strands. Our present conception of the overall configuration of PHF is consistent with that proposed by Crowther and Wischik in 1985 but includes an essential component of the prevailing model: the presence of two strands. Thus, our new model of PHF structure, based on atomic force microscopy-derived data, indicates that the true structure of PHF is actually a hybrid of the prevailing PHF model and a thin helical ribbon.

Alzheimer paired helical filaments: a comparison with the twisted ribbon model

To investigate if Alzheimer paired helical filaments (PHF) closely resemble twisted ribbons, as indicated by recent high-resolution ultrastructural studies, we compared physical models of twisted ribbons with electron microscopic images of PHF. Uranyl-acetate-stained, isolated PHF with one or two helical turns were compared with scale models of twisted ribbons with one and two helical turns rotated at different angles. The various rotations of the twisted ribbon model corresponded well with the different orientations of randomly dispersed PHF. The electron-dense regions of individual PHF turns previously thought to represent a cross-over site of paired filaments corresponded to the edge of the twisted ribbon when the ribbon was oriented perpendicular to the filament axis. These data indicate that the overall configuration of PHF is a twisted ribbon but does not exclude possible configuration restrictions due to an ordered arrangement of subunits.

Sequential assembly of collagen revealed by atomic force microscopy

Most polymers which comprise biological filaments assemble by two mechanisms: nucleation and elongation or a sequential, stepwise process involving a hierarchy of intermediate species. We report the application of atomic force microscopy (AFM) to the study of the early events in the sequential or stepwise mode of assembly of a macromolecular filament. Collagen monomers were assembled in vitro and the early structural intermediates of the assembly process were examined by AFM and correlated with turbidimetric alterations in the assembly mixture. The assembly of collagen involved a sequence of distinctive filamentous species which increased in both diameter and length over the time course of assembly. The first discrete population of collagen oligomers were 1-2 nm in diameter (300-500 nm in length); at later time points, filaments approximately 2-6 nm in diameter (> 10 microns in length) many with a conspicuous approximately 67-nm axial period were observed. Occasional mature collagen fibrils with a approximately 67-nm axial repeat were found late in the course of assembly. Our results are consistent with initial end-to-end axial association of monomers to form oligomers followed by lateral association into higher-order filaments. On this basis, there appears to be at least two distinctive types of structural interactions (axial and lateral) which are operative at different levels in the assembly hierarchy of collagen.

Mallory body filaments become insoluble after normal assembly into intermediate filaments

The deposition of 8-to-10-nm filaments into inclusion bodies is a fundamental cellular change that occurs in several degenerative processes of many tissues. However, little is known about the pathological filaments including whether the filaments assemble by the same mechanisms that govern the assembly of normal intermediate filaments. We have addressed this issue by studying the in vitro reassembly of the cytokeratin filaments that are deposited into experimental murine Mallory bodies (MBs) but have not yet become covalently crosslinked components of the MB. The reassembly process of both normal hepatocellular and MB-derived cytokeratins (CKs) was similar and characterized by a hierarchy of protofilament and protofibrils with a prominent axial periodicity of approximately 21 nm (normal hepatocellular CK, 20.7 +/- 2 nm; MB-derived CK, 20.1 +/- 2 nm). Purified MB-derived CK and normal hepatocellular CK comigrated in polyacrylamide gel electrophoresis indicating composition by similar CK isoforms. These results indicate that intermediate filaments formed from MB-derived CK are indistinguishable from filaments assembled from normal CK. On this basis, we conclude that the intermediate filaments that form inclusion bodies are not aberrantly assembled but become aggregated and post-translationally modified after their initial formation.

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures.

Orientational Ordering of Polymers by Atomic Force Microscope Tip-Surface Interaction

Results of studies on the interaction between the tip of an atomic force microscope and polystyrene molecules in a film spread on a surface are reported. The tip produces a persistent deformation on the film; some of the polymer molecules are eventually pulled up by the tip. Nanometer-size structures are induced, resulting in a pattern that is periodic and is oriented perpendicular to the scan direction.