SURFNET: A program for visualizing molecular surfaces,cavities, and intermolecular interactions

The SURFNET program generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal cavities and surface grooves within a single molecule. The program is particularly useful in clearly delineating the regions of the active site of a protein. It can also generate 3D contour surfaces of the density distributions of any set of 3D data points. All output surfaces can be viewed interactively, along with the molecules or data points in question, using some of the best-known molecular modeling packages. In addition, PostScript output is available, and the generated surfaces can be rendered using various other graphics packages.     

Combing DNA on CTAB-coated surfaces

A fluorescence microscope (FM) coupled with an intensified charge-coupled device (ICCD) camera was used to investigate the combing of DNA on cetyltrimethyl ammonium bromide (CTAB)-coated glass surfaces. DNA molecules can be combed uniform and straight on CTAB-coated surfaces. Different combing characteristics at different pH values were found. At lower pH (ca. 5.5), DNA molecules were stretched 30% longer than the unextended and DNA extremities bound with CTAB-coated surfaces via hydrophobic interaction. At high pH values (e.g., 6.4 and 6.5), DNA molecules were extended about 10% longer and DNA extremities bound with CTAB-coated surfaces via electrostatic attraction. At pH 6.0, DNA molecules could be extended 30% longer on 0.2-mM CTAB-coated surfaces. CTAB cationic surfactant has both a hydrophobic motif and a positively charged group. So, CTAB-coated surfaces can bind DNA extremities via hydrophobic effect or electrostatic attraction at different pH values. It was also found that combing of DNA on CTAB-coated surfaces is reversible. The number of DNA base pairs binding to CTAB-coated surfaces was calculated.     

On the optimal sex-ratio: A stability analysis based on a characterization for one-locus multiallele viability models

Theoretical one-locus multiallele sex-determination models are found to admit even sex ratio equilibrium surfaces besides the equilibria for corresponding one-locus multiallele viability models. Both types of equilibria can be defined in terms of a single spectral radius function, the former corresponding to level surfaces and the latter to critical points. The stable equilibria in the corresponding viability models are associated with the local maxima, and the equilibrium structures for the sex-determination models can be fully described. Several optimality properties of the even-sex-ratio equilibrium surfaces can be deduced.Supported in part by NIH Grant 5R01 GM10452-20 and NSF Grant MCS79-24310     

Scanning tunneling microscopy with applications to biological surfaces

Each major advance in the field of microscopy has eventually been translated into major advances in the biological and medical sciences. The scanning tunneling microscope (STM) offers exciting new ways of imaging biological surfaces with resolution to the sub-molecular scale. Rigid, conductive surfaces can readily be imaged with the STM with atomic resolution. Unfortunately, few biological surfaces are sufficiently conductive or rigid enough to be examined directly with the STM. At present, non-conductive surfaces can be examined in two ways: 1) Sufficiently thin molecular layers attached to conductive substrates so that tunneling can occur through the molecules; or 2) coating or replicating non-conductive surfaces with metal layers so as to make them conductive, then imaging with the STM. We present images of biological and organic molecules obtained with these techniques that demonstrate the possibilities and limitations of each. Future advances leading to atomic resolution STM of biological surfaces depend on significant progress in the art and science of making biomaterials compatible with the restrictions of the instrument.     

A fast, precise and low-cost replication technique for nano- and high-aspect-ratio structures of biological and artificial surfaces

Biological surfaces are multifunctional interfaces between the organisms and their environment. Properties such as the wettability and adhesion of particles are linked to the micro- and nanostructures of their surfaces. In this study, we used plant and artificial surfaces covered with wax crystals to develop a low-cost replication technique with high resolution. The technique is applicable for fragile surface structures, as demonstrated for three-dimensional wax crystals, and is fast to prevent shrinking of the biological material by water loss during the molding process. Thermal evaporation of octacosan-1-ol has been used to create microstructured surfaces with small platelets as templates for molding. Epoxy resin as filling material provided the smallest deviations from the original surface structures and can be used for replication of nanostructures as small as 4.5 nm. Contact angle measurements of leaves and their replicas show that this technique can be used to develop biomimetic surfaces with similar wettability as in the plant surfaces.     

Droplets motion on chemically/topographically heterogeneous surfaces

We present a numerical study of droplets sliding across chemically heterogeneous surfaces formed by a periodic pattern of alternating hydrophobic and hydrophilic stripes, or topographically heterogeneous surfaces which are microgrooved. The numerical simulation performed by using a particle-based numerical method, Many-body Dissipative Particle Dynamics (MDPD), is adopted to observe the stick-slip motion of droplets driven by a constant body force. The fractions of two types of surfaces are varied from 0.3 to 0.7 to investigate their influence on stick-slip motion of droplets. The dynamic contact angles and the variation in distance D_fr between the front and the rear contact points are shown for different fractions. The jerky motion characterised by stick-slip motion can be found on chemically heterogeneous surfaces for all fractions we choose and the partial stick-slip motion can also be discovered on topographically heterogeneous surfaces except for fraction Φ_s = 0.3. The snapshots of droplet show that stick-slip motion is the consequence of the periodic deformation of droplet interface during crossing heterogeneous surfaces and can be controlled by fractions.     

Self-assembled monolayers on polymer surfaces

The method of forming self-assembled monolayers on polymer surfaces is reviewed. It is shown that the alkylsiloxane monolayers formed on polymer surfaces are structurally similar to the analogous monolayers formed on silicon wafers. These monolayers can be post-derivatized in order to introduce a number of hydrophobic, reactive and polar functionalities, some of which may be useful model systems for studying biological interactions at surfaces.     

Plasma equilibrium in 3D magnetic confinement systems and soliton theory

Single-valued conformal flux (magnetic) coordinates can always be introduced on arbitrary toroidal magnetic surfaces. It is shown how such coordinates can be obtained by transforming Boozer magnetic coordinates on the surfaces. The metrics is substantially simplified and the coordinate grid is orthogonalized at the expense of a more complicated representation of the magnetic field in conformal flux coordinates. This in turn makes it possible to introduce complex angular flux coordinates on any toroidal magnetic surface and to develop efficient methods for a complex analysis of the geometry of equilibrium magnetic surfaces. The complex analysis reveals how the plasma equilibrium problem is related to soliton theory. Magnetic surfaces of constant mean curvature are considered to exemplify this relationship.     

In search of the microbe/mineral interface: quantitative analysis of bacteria on metal surfaces using vertical scanning interferometry

To understand the development of biofilms on metal surfaces, analysis of initial bacterial attachment to surfaces is crucial. Here we present the results of a study, using Shewanella oneidensis MR-1 as a model organism, in which vertical scanning interferometry (VSI) was used to investigate the initial stages of cell attachment to glass, steel and aluminium surfaces. It was found that while VSI gave unambiguous results with opaque surfaces, when reflective surfaces were used, an artifact sometimes appeared, with the bacteria appearing as rod-shaped pits rather than as cells on the surface. When the bacteria were altered to increase opacity, this artifact disappeared, and upon further investigation, it was found that the observational artifact was the result of a conflict between light reflected from the bacteria and the light reflected from the bacteria–metal interface. These results suggest that not only can bacteria be measured on surfaces using VSI, but with some modifications to the analytical software, there may be a unique window for studying the bacterial/substrate interface that can be used for quantitative observations. Imaging and characterization of the bacteria–substrate interface in vivo (previously invisible) will provide new insights into the interactions that occur at this important juncture.     

Rapid probing of biological surfaces with a sparse-matrix peptide library

Finding unique peptides to target specific biological surfaces is crucial to basic research and technology development, though methods based on biological arrays or large libraries limit the speed and ease with which these necessary compounds can be found. We reasoned that because biological surfaces, such as cell surfaces, mineralized tissues, and various extracellular matrices have unique molecular compositions, they present unique physicochemical signatures to the surrounding medium which could be probed by peptides with appropriately corresponding physicochemical properties. To test this hypothesis, a naïve pilot library of 36 peptides, varying in their hydrophobicity and charge, was arranged in a two-dimensional matrix and screened against various biological surfaces. While the number of peptides in the matrix library was very small, we obtained “hits” against all biological surfaces probed. Sequence refinement of the “hits” led to peptides with markedly higher specificity and binding activity against screened biological surfaces. Genetic studies revealed that peptide binding to bacteria was mediated, at least in some cases, by specific cell-surface molecules, while examination of human tooth sections showed that this method can be used to derive peptides with highly specific binding to human tissue.     

Decreased solute adsorption onto cracked surfaces of mechanically injured articular cartilage: Towards the design of cartilage-specific functional contrast agents

Background

Currently available methods for contrast agent-based magnetic resonance imaging (MRI) and computed tomography (CT) of articular cartilage can only detect cartilage degradation after biochemical changes have occurred within the tissue volume. Differential adsorption of solutes to damaged and intact surfaces of cartilage may be used as a potential mechanism for detection of injuries before biochemical changes in the tissue volume occur.

Methods

Adsorption of four fluorescent macromolecules to surfaces of injured and sliced cartilage explants was studied. Solutes included native dextran, dextrans modified with aldehyde groups or a chondroitin sulfate (CS)-binding peptide and the peptide alone.

Results

Adsorption of solutes to fissures was significantly less than to intact surfaces of injured and sliced explants. Moreover, solute adsorption at intact surfaces of injured and sliced explants was less reversible than at surfaces of uninjured explants. Modification of dextrans with aldehyde or the peptide enhanced adsorption with the same level of differential adsorption to cracked and intact surfaces. However, aldehyde–dextran exhibited irreversible adsorption. Equilibration of explants in solutes did not decrease the viability of chondrocytes.

Conclusions and general significance

Studied solutes showed promising potential for detection of surface injuries based on differential interactions with cracked and intact surfaces. Additionally, altered adsorption properties at surfaces of damaged cartilage which visually look healthy can be used to detect micro-damage or biochemical changes in these regions. Studied solutes can be used in in vivo fluorescence imaging methods or conjugated with MRI or CT contrast agents to develop functional imaging agents.     

Using 96-well tissue culture polystyrene plates and a fluorescence plate reader as tools to study the survival and inactivation of viruses on surfaces

A method for studying the behavior of viruses on surfaces has been developed and is illustrated by determining the temperatures that inactivate adsorbed viral hemorrhagic septicemia virus (VHSV) and the concentration of 1-propanol that disinfected surfaces with adsorbed VHSV and chum salmon virus (CSV). VHSV is a rhabdovirus; CSV, a reovirus, and they were detected with two fish cell lines, EPC and CHSE-214, respectively. When polystyrene tissue culture surfaces were incubated with virus, rinsed, and left to dry, they still supported the attachment and spreading of cell lines and after 7 days these cells showed the characteristic CPE of the viruses. Thus cells appeared to be infected directly from surfaces on which viruses had been adsorbed. Applying this property to 96-well plates allowed duplicate surfaces to be examined for their infectiousness or support of CPE. For each treatment 80 replicate surfaces in a 96-well plate were tested at one time and the results expressed as the number of wells showing CPE. VHSV adsorbed to polystyrene was inactivated by drying in the dark at temperatures above 14 °C, but remained infectious for at least 15 days of drying at 4 °C. For chemical sterilization of polystyrene surfaces with adsorbed virus, disinfection was achieved with 1-propanol at 40% for VHSV and at 60% for CSV. As CPE can be conveniently monitored in 96-well plates with a fluorescence plate reader, this method can be used to rapidly evaluate a variety of treatments for their ability to inactivate surface-bound viruses.     

Amino acid architecture and the distribution of polar atoms on the surfaces of proteins

We propose that a necessary condition for a protein to be soluble is the absence of large hydrophobic patches on its solvent-accessible surface, which can cause aggregation to occur. We note that the polar nature of the backbone of all amino acids guarantees a minimum polar content and hence can interrupt such patches. As a result, a carefully conserved detailed atomic placement of residues on the protein surface is not necessary for solubility. In order to demonstrate this, we construct a measure based on the average hydrophobicity of a simply defined patch. We use this measurement to compare surfaces that exhibit a clear difference in their solubility properties, namely, a) the solvent accessible surfaces for a set of homo-dimers and the surfaces buried in their interfaces and b) for a set of monomers the surfaces of fragments of secondary structure which are solvent accessible/inaccessible. Having demonstrated a difference in the first set of distributions, we characterize the solvent accessible surfaces of monomeric proteins. To test if cooperative behavior occurs between the atoms for these surfaces, we construct a set of randomized surfaces, which obey a very simple stereochemical constraint. We find that the observed and randomized distributions are much more similar than the previous sets we examined. This implies that while surfaces of soluble proteins must have sufficient polar content, the relative placement of atoms of one amino acid with respect to the atoms of neighboring amino acid need not be finely tuned, which provides an innate robustness for protein design and folding.     

On the Electrostatic Interaction across a Salt Solution between Two Bodies Bearing Unequal Charges

We consider two parallel planar charged surfaces bearing unequal surface charge densities interacting across a region in ionic equilibrium with a neutral salt solution. Combining rules are derived appropriate for interactions across distances of separation greater than the characteristic Debye length. When ions are excluded from the regions behind the interacting surfaces there can be repulsion between charged surfaces of opposite sign; but surfaces bearing charges of the same sign never attract one another. Also, surfaces bearing electrostatic potential of like sign can attract.     

Innate non-specific cell substratum adhesion

Adhesion of motile cells to solid surfaces is necessary to transmit forces required for propulsion. Unlike mammalian cells, Dictyostelium cells do not make integrin mediated focal adhesions. Nevertheless, they can move rapidly on both hydrophobic and hydrophilic surfaces. We have found that adhesion to such surfaces can be inhibited by addition of sugars or amino acids to the buffer. Treating whole cells with αlpha-mannosidase to cleave surface oligosaccharides also reduces adhesion. The results indicate that adhesion of these cells is mediated by van der Waals attraction of their surface glycoproteins to the underlying substratum. Since glycoproteins are prevalent components of the surface of most cells, innate adhesion may be a common cellular property that has been overlooked.     

Plant–Microbe Interactions: Wetting of Ivy (Hedera helix L.) Leaf Surfaces in Relation to Colonization by Epiphytic Microorganisms

Abstract Leaf wettability, cuticular wax composition, and microbial colonization of upper and lower leaf surfaces of ivy (Hedera helix L.) was investigated for young and old leaves sampled in June and September. Contact angles of aqueous buffered solutions measured on young leaf surfaces ranged between 76° and 86° and were not dependent on the pH value of the applied droplets. Contact angles measured on old leaf surfaces were up to 32°, significantly lower than on young leaf surfaces. Furthermore, contact angles were significantly lower using aqueous solutions of pH 9.0 compared to pH 3.0, indicating the influence of ionizable functional groups on leaf surface wetting properties. Observed changes in leaf wetting properties did not correlate with different levels of alkanoic acids in cuticular waxes. However, microscopic examination of the leaf surfaces indicated the influence of epiphytic microorganisms on wetting properties of old leaves, since their surfaces were always colonized by epiphytic microorganisms (filamentous fungi, yeasts, and bacteria), whereas surfaces of young leaves were basically clean. In order to analyze the effect of epiphytic microorganisms on leaf surface wetting, surfaces of young and clean ivy leaves were artificially colonized with Pseudomonas fluorescens. This resulted in a significant increase and a pH dependence of leaf surface wetting in the same way as it was observed on old ivy leaf surfaces. From these results it can be deduced that the native wetting properties of leaf surfaces can be significantly masked by the presence of epiphytic microorganisms. The ecological implications of altered wetting properties for microorganisms using the leaf/atmosphere interface as habitat are discussed. Received: 20 March 1999; Accepted: 5 July 1999; Online Publication: 18 July 2000     

Enhanced cell attachment using a novel cell culture surface presenting functional domains from extracellular matrix proteins

Many factors contribute to the creation and maintenance of a realistic environment for cell growth in vitro, e.g. the consistency of the growth medium, the addition of supplements, and the surface on which the cells grow. The nature of the surface on which cells are cultured plays an important role in their ability to attach, proliferate, migrate and function. Components of the extracellular matrix (ECM) are often used to coat glass or plastic surfaces to enhance cell attachment in vitro. Fragments of ECM molecules can be immobilised on surfaces in order to mimic the effects seen by whole molecules. In this study we evaluate the application of a novel technology for the immobilisation of functional domains of known ECM proteins in a controlled manner on a surface. By examining the adherence of cultured PC12 cells to alternative growth surfaces, we show that surfaces coated with motifs from collagen I, collagen IV, fibronectin and laminin can mimic surfaces coated with the corresponding whole molecules. Furthermore, we show that the adherence of cells can be controlled by modifying the hydropathic properties of the surface to either enhance or inhibit cell attachment. Collectively, these data demonstrate the application of a new technology to enable optimisation of cell growth in the tissue culture laboratory.     

pH-dependent specific binding and combing of DNA.

Recent developments in the rapid sequencing, mapping, and analysis of DNA rely on the specific binding of DNA to specially treated surfaces. We show here that specific binding of DNA via its unmodified extremities can be achieved on a great variety of surfaces by a judicious choice of the pH. On hydrophobic surfaces the best binding efficiency is reached at a pH of approximately 5.5. At that pH a approximately 40-kbp DNA is 10 times more likely to bind by an extremity than by a midsegment. A model is proposed to account for the differential adsorption of the molecule extremities and midsection as a function of pH. The pH-dependent specific binding can be used to align anchored DNA molecules by a receding meniscus, a process called molecular combing. The resulting properties of the combed molecules will be discussed.     

Microexudates from Cells Grown in Tissue Culture

Cellular substrata of known molecular structure and measurable dimensions can be constructed as transferred films from Langmuir troughs or as adsorbed films. In addition, large molecules in culture media form measurable adsorbates. With the techniques of ellipsometry and surface chemistry it is possible to characterize and measure (within ± 3A) as a function of several parameters a microexudate of molecular dimensions deposited when tissue cultured cells contact certain substrata. The selective attraction of substratum and cell for microexudate has been determined, and the time course of deposition in Eagle's medium is characterized by a rapid initial accretion of material. During this period, microexudate can diffuse several cell diameters and cannot be detected in the culture medium. In Eagle's medium the cells cannot be detached from glass surfaces by versene or trypsin unless the surface of cell or substratum is coated with certain molecules. Trypsin becomes adsorbed to cell surfaces, continues to be enzymatically active on the surface, and digests protein components of microexudate and substratum. Microexudate appears to be a complex mosaic of molecules (including protein) synthesized within or on the surfaces of cells and secreted by cells or transferred from their surfaces to specific substrata. It is proposed that this mosaic plays, on the molecular level, a significant role in cell-to-cell interactions, cell locomotion and adhesion, and the selective application and spreading of cells on various surfaces.     

Microbial biogeography of public restroom surfaces

We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear linkages between communities on or in different body sites and those communities found on restroom surfaces. More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the efficacy of hygiene practices.