Study of the Chemical and Physical Influences upon in Vitro Peptide-Mediated Silica Formation

Herein, we report on the ability to create complex 2-D and 3-D silica networks in vitro via polycationic peptide-mediated biosilicification under experimentally altered chemical and physical influences. These structures differ from the sphere-like silica network of particles obtained in vitro under static conditions. Under chemical influences, overall morphologies were observed to shift from a characteristic network of sphere-like silica particles to a sheetlike structure in the presence of -OH groups from additives and to sharp-edged, platelike structures in the presence of larger polycationic peptide matrixes. Under physical influences, using externally applied force fields, overall silica morphologies were observed to transition from sphere-like to fiberlike and dendrite-like structures. These findings could lead to the future development of bio-inspired complex 2-D and 3-D silica micro- and nano-devices.

Enzyme immobilization in a biomimetic silica support

Robust immobilization techniques that preserve the activity of biomolecules have many potential applications. Silicates, primarily in the form of sol-gel composites or functionalized mesoporous silica, have been used to encapsulate a wide variety of biomolecules but the harsh conditions required for chemical synthesis limit their applicability. Silaffin polypeptides from diatoms catalyze the formation of silica in vitro at neutral pH and ambient temperature and pressure. Here we show that butyrylcholinesterase entrapped during the precipitation of silica nanospheres retained all of its activity. Ninety percent of the soluble enzyme was immobilized, and the immobilized enzyme was substantially more stable than the free enzyme. The mechanical properties of silica nanospheres facilitated application in a flow-through reactor. The use of biosilica for enzyme immobilization combines the excellent support properties of a silica matrix with a benign immobilization method that retains enzyme activity.

Identification of peptides that promote the rapid precipitation of germania nanoparticle networks via use of a peptide display libraryElectronic Supplementary Information (ESI) is available describing the biopanning, germania precipitation assay, and molybdenum blue assay procedures. See http://www.rsc.org/suppdata/cc/b4/b402480j/

Peptides that promote the rapid, room-temperature precipitation of amorphous germania nanoparticle networks from solution have been identified via use of a combinatorial peptide display library.

Entrapment of enzymes and nanoparticles using biomimetically synthesized silicaElectronic supplementary information (ESI) available: biosilicification reaction, enzyme assays, encapsulation of iron oxide. See http://www.rsc.org/suppdata/cc/b4/b404586f/This work was funded by the Air Force Office of Scientific Research

Entrapment of enzymes and nanoparticles using biosilicification reactions.

Biomolecular stress-sensitive gauges: surface-mediated immobilization of mechanosensitive membrane protein

We report the observation of structural reorganizations associated with unique, stress-assisted gating of mechanosensitive (MscL) membrane protein on a silicon surface modified with alkyl-terminated monolayers. We observed that the shape of MscL membrane proteins changed dramatically depending upon the packing density of alkyl tails and the surface tension of the supporting organic layer. High-resolution atomic force microscopy confirmed a transition from an elongated, prolate shape of MscL molecules within a monolayer with low surface tension to a flattened, oblate shape with a wide central opening within a monolayer with high surface tension. These observations are consistent with the conformation reorganizations associated with the two-stage, "iris"-like expansion proposed for the gating of the MscL molecules.

Immobilization of histidine-tagged proteins on nickel by electrochemical dip pen nanolithography

Dip-pen nanolithography (DPN) is becoming a popular technique to "write" molecules on a surface by using the tip of an atomic force microscope (AFM) coated with the desired molecular "ink". In this work, we demonstrate that poly-histidine-tagged peptides and proteins, and free-base porphyrins coated on AFM probes, can be chelated to ionized regions on a metallic nickel surface by applying an electric potential to the AFM tip in the DPN process. DPN has been accomplished in the Tapping Mode of AFM, which creates many possible applications of positioning and subsequently imaging biomolecules, especially on soft surfaces.

Controlled formation of biosilica structures in vitro

Herein we describe the controlled formation of biosilica structures by manipulation of the physical reaction environment; we were able to synthesize arched and elongated silica structures using a synthetic peptide; the results presented here are evidence that in vitro biocatalysis may be controlled in order to form desired silica structures.

Dip-pen nanolithography in tapping mode

Dip-pen nanolithography (DPN) is becoming a popular nano-patterning technique for depositing materials onto a substrate using the probe of an atomic force microscope (AFM). Here, we demonstrate the deposition of a short synthetic peptide by DPN using the Tapping Mode of AFM rather than the commonly used contact mode. DPN in Tapping Mode requires drive amplitude modifications for deposition, yet allows for gentle imaging of the deposited material and enables deposition on soft surfaces.

Biomimetic synthesis and patterning of silver nanoparticles

The creation of nanoscale materials for advanced structures has led to a growing interest in the area of biomineralization. Numerous microorganisms are capable of synthesizing inorganic-based structures. For example, diatoms use amorphous silica as a structural material, bacteria synthesize magnetite (Fe3O4) particles and form silver nanoparticles, and yeast cells synthesize cadmium sulphide nanoparticles. The process of biomineralization and assembly of nanostructured inorganic components into hierarchical structures has led to the development of a variety of approaches that mimic the recognition and nucleation capabilities found in biomolecules for inorganic material synthesis. In this report, we describe the in vitro biosynthesis of silver nanoparticles using silver-binding peptides identified from a combinatorial phage display peptide library.

Silica-precipitating peptides isolated from a combinatorial phage display peptide library

Many biological organisms contain specialized structures composed of inorganic materials. Cellular processes in vivo facilitate the organized assembly of mineral building blocks into complex structures. The structural hierarchy and complexity across a range of length scales are providing new ideas and concepts for materials chemistry. Proteins that direct biomineralization can be used to control the production of nanostructured materials and facilitate the fabrication of new structures. Here, we demonstrate that some of the silica-binding peptides isolated from a combinatorial phage peptide display library can be used in precipitating silica from a solution of silicic acid. The results described in this report demonstrate that peptides displayed by phages act as templates in inorganic material synthesis and provide a means of understanding how some of the biological systems may be carrying out materials chemistry in vivo.

Biological infrared imaging and sensing

A variety of thermoreceptors are present in animals and insects, which aid them in hunting, feeding and survival. Infrared (IR) imaging pit organs in Crotaline and Boid snakes enable them to detect, locate and apprehend their prey by detecting the IR radiation they emit. IR pit organs of common vampire bats (Desmodus rotundus) enable them to detect IR radiation emitted by blood-rich locations on homeothermic prey. The beetle Melanophila acuminata locates forest fires by IR-detecting pit organs in order to lay their eggs in freshly killed conifers. Thermoreceptors located in the wings and antennae of darkly pigmented butterflies (Pachliopta aristolochiae and Troides rhadamathus plateni) protect them from heat damage while sun basking. Blood-sucking bugs (Triatoma infestans) are speculated to possess thermoreceptors, which enable them to perceive the radiant heat emitted by homeothermic prey and estimate its temperature at a distance. This is a review of the diverse types of biological thermoreceptors, their structure and function, and how electron microscopy has been instrumental in determining their ultrastructure.

The thermostability of an alpha-helical coiled-coil protein and its potential use in sensor applications

Coiled-coil proteins are assemblies of two to four alpha-helices that pack together in a parallel or anti-parallel fashion. Coiled-coil structures can confer a variety of functional capabilities, which include enabling proteins, such as myosin, to function in the contractile apparatus of muscle and non-muscle cells. The TlpA protein encoded by the virulence plasmid of Salmonella is an alpha-helical protein that forms an elongated coiled-coil homodimer. A number of studies have clearly established the role of TlpA as a temperature-sensing gene regulator, however the potential use of a TlpA in a thermo-sensor application outside of the organism has not been exploited. In this paper, we demonstrate that TlpA has several characteristics that are common with alpha-helical coiled-coils and its thermal folding and unfolding is reversible and rapid. TlpA is extremely sensitive to changes in temperature. We have also compared the heat-stability of TlpA with other structurally similar proteins. Using a folding reporter, in which TlpA is expressed as a C-terminal fusion with green fluorescent protein (GFP), we were able to use fluorescence as an indicator of folding and unfolding of the fusion protein. Our results on the rapid conformational changes inherent in TlpA support the previous findings and we present here preliminary data on the use of a GFP-TlpA fusion protein as temperature sensor.

Ultrafast holographic nanopatterning of biocatalytically formed silica

Diatoms are of interest to the materials research community because of their ability to create highly complex and intricate silica structures under physiological conditions: what these single-cell organisms accomplish so elegantly in nature requires extreme laboratory conditions to duplicate-this is true for even the simplest of structures. Following the identification of polycationic peptides from the diatom Cylindrotheca fusiformis, simple silica nanospheres can now be synthesized in vitro from silanes at nearly neutral pH and at ambient temperatures and pressures. Here we describe a method for creating a hybrid organic/inorganic ordered nanostructure of silica spheres through the incorporation of a polycationic peptide (derived from the C. fusiformis silaffin-1 protein) into a polymer hologram created by two-photon-induced photopolymerization. When these peptide nanopatterned holographic structures are exposed to a silicic acid, an ordered array of silica nanospheres is deposited onto the clear polymer substrate. These structures exhibit a nearly fifty-fold increase in diffraction efficiency over a comparable polymer hologram without silica. This approach, combining the ease of processability of an organic polymer with the improved mechanical and optical properties of an inorganic material, could be of practical use for the fabrication of photonic devices.

Use of small fluorescent molecules to monitor channel activity

The Mechanosensitive channel of Large conductance (MscL) allows bacteria to rapidly adapt to changing environmental conditions such as osmolarity. The MscL channel opens in response to increases in membrane tension, which allows for the efflux of cytoplasmic constituents. Here we describe the cloning and expression of Salmonella typhimurium MscL (St-MscL). The amino acid sequence encoding for this MscL exhibits a high degree of similarity to Escherichia coli MscL (Eco-MscL). Using a fluorescence efflux assay, we demonstrate that efflux through the MscL channel during hypoosmotic shock can be monitored using endogenously produced fluorophores. These fluorophores are synthesized by a cotransformed gene, cobA. In addition, we observe that thermal stimulation, i.e., heat shock, can induce efflux through MscL.

The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor

The vacuolar hydrolase protease B in Saccharomyces cerevisiae is synthesized as an inactive precursor (Prb1p). The precursor undergoes post-translational modifications while transiting the secretory pathway. In addition to N- and O-linked glycosylations, four proteolytic cleavages occur during the maturation of Prb1p. Removal of the signal peptide by signal peptidase and the autocatalytic cleavage of the large amino-terminal propeptide occur in the endoplasmic reticulum (ER). Two carboxy-terminal cleavages of the post regions occur in the vacuole: the first cleavage is catalyzed by protease A and the second results from autocatalysis. We have isolated a mutant, pbn1-1, that exhibits a defect in the ER processing of Prb1p. The autocatalytic cleavage of the propeptide from Prb1p does not occur and Prb1p is rapidly degraded in the cytosol. PBN1 was cloned and is identical to YCL052c on chromosome III. PBN1 is an essential gene that encodes a novel protein. Pbn1p is predicted to contain a sub-C-terminal transmembrane domain but no signal sequence. A functional HA epitope-tagged Pbn1p fusion localizes to the ER. Pbn1p is N-glycosylated in its amino-terminal domain, indicating a lumenal orientation despite the lack of a signal sequence. Based on these results, we propose that one of the functions of Pbn1p is to aid in the autocatalytic processing of Prb1p.

Regulation of the proteinase B structural gene PRB1 in Saccharomyces cerevisiae

The expression of PRB1, the gene that encodes the precursor to the soluble vacuolar proteinase B (PrB) in Saccharomyces cerevisiae, is regulated by carbon and nitrogen sources and by growth phase. Little or no PRB1 mRNA is detectable during exponential growth on glucose as the carbon source; it begins to accumulate as cells exhaust the glucose. Previous work has shown that glucose repression of PRB1 transcription is not mediated by HXK2 or by the SNF1, SNF4, and SNF6 genes (C. M. Moehle and E. W. Jones, Genetics 124:39-55, 1990). We analyzed the effects of mutations in the MIG1, TUP1, and GRR1 genes on glucose repression of PRB1 and found that mutations in each partially alleviate glucose repression. tup1 and mig1 mutants fail to translocate all of the Prb1p into the lumen of the endoplasmic reticulum. A screen for new mutants revealed mutations in MIG1 and REG1, genes already known to regulate glucose repression, as well as in three new genes that we have named PBD1 to PBD3; all cause derepressed expression. Mutations that result in failure to completely derepress PRB1 were also identified in two new genes, named PND1 and PND2. Good nitrogen sources, like ammonia, repress PRB1 transcription; mutations in URE2 do not affect this response. Derepression upon transfer to a poor nitrogen source is dependent upon GLN3.