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Biomedical subjects

Rajesh R Naik

Publications and source records attributed to Rajesh R Naik.

At least 19 recordsLinked to original sources
PubMed2007

Computational study of the absorption spectra of green fluorescent protein mutants.

In this work, we present a theoretical study of the relationship between molecular structure and the red-shift in absorption spectra of S65G and S65T green fluorescent protein (GFP) mutants. To identify the effects of the protein environment, we combined results from molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics calculations to obtain structural properties, and applied time-dependent density functional theory to calculate the excitation energies. By using results from the MD simulations, we were able to provide a systematic analysis of the structural details that may effect the red-shift in the absorption spectra when taking into account temperature effects. Furthermore, a detailed study of hydrogen bonding during the MD simulations demonstrated differences between S65G and S65T, for example, regarding hydrogen bonding with Glu222. An analysis of the absorption spectra for different forms of the chromophore emphasized the dominance of the anionic forms in solution for the S65G and S65T GFP mutants.

Computer Simulation↗
PubMed2006

Direct measurements of interactions between polypeptides and carbon nanotubes.

The interactions of various polypeptides with individual carbon nanotubes (CNTs), both multiwall (MW) and single wall (SW), were investigated by atomic force microscopy (AFM). While adhesion forces arising from electrostatic attraction interactions between the protonated amine groups of polylysine and carboxylic groups on the acid-oxidized multi-wall carbon nanotubes (Ox-MWCNTs) dominate the interaction at a low pH, weaker adhesion forces via the hydrogen bonding between the neutral -NH2 groups of polylysine and -COO- groups of the Ox-MWCNTs were detected at a high pH. The adhesion force was further found to increase with the oxidation time for Ox-MWCNTs and to be negligible for oxidized single-wall carbon nanotubes (Ox-SWCNTs) because carboxylate groups were only attached onto the nanotube tips in the latter whereas onto both the nanotube tips and sidewall in the former. Furthermore, it was demonstrated that proteins containing aromatic moieties, such as polytryptophan, showed a stronger adhesion force with Ox-MWCNTs than that of polylysine because of the additional pi-pi stacking interaction between the polytryptophan chains and CNTs.

Amino Acid Sequence↗
PubMed2006

Novel nanocomposites from spider silk-silica fusion (chimeric) proteins.

Silica skeletal architectures in diatoms are characterized by remarkable morphological and nanostructural details. Silk proteins from spiders and silkworms form strong and intricate self-assembling fibrous biomaterials in nature. We combined the features of silk with biosilica through the design, synthesis, and characterization of a novel family of chimeric proteins for subsequent use in model materials forming reactions. The domains from the major ampullate spidroin 1 (MaSp1) protein of Nephila clavipes spider dragline silk provide control over structural and morphological details because it can be self-assembled through diverse processing methods including film casting and fiber electrospinning. Biosilica nanostructures in diatoms are formed in aqueous ambient conditions at neutral pH and low temperatures. The R5 peptide derived from the silaffin protein of Cylindrotheca fusiformis induces and regulates silica precipitation in the chimeric protein designs under similar ambient conditions. Whereas mineralization reactions performed in the presence of R5 peptide alone form silica particles with a size distribution of 0.5-10 microm in diameter, reactions performed in the presence of the new fusion proteins generate nanocomposite materials containing silica particles with a narrower size distribution of 0.5-2 microm in diameter. Furthermore, we demonstrate that composite morphology and structure could be regulated by controlling processing conditions to produce films and fibers. These results suggest that the chimeric protein provides new options for processing and control over silica particle sizes, important benefits for biomedical and specialty materials, particularly in light of the all aqueous processing and the nanocomposite features of these new materials.

Amino Acid Sequence↗
PubMed2005

Characterization of microbial contamination in United States Air Force aviation fuel tanks.

Bacteria and fungi, isolated from United States Air Force (USAF) aviation fuel samples, were identified by gas chromatograph fatty acid methyl ester (GC-FAME) profiling and 16S or 18S rRNA gene sequencing. Thirty-six samples from 11 geographically separated USAF bases were collected. At each base, an above-ground storage tank, a refueling truck, and an aircraft wing tank were sampled at the lowest sample point, or sump, to investigate microbial diversity and dispersion within the fuel distribution chain. Twelve genera, including four Bacillus species and two Staphylococcus species, were isolated and identified. Bacillus licheniformis, the most prevalent organism isolated, was found at seven of the 11 bases. Of the organisms identified, Bacillus sp., Micrococcus luteus, Sphinogmonas sp., Staphylococcus sp., and the fungus Aureobasidium pullulans have previously been isolated from aviation fuel samples. The bacteria Pantoea ananatis, Arthrobacter sp., Alcaligenes sp., Kocuria rhizophilia, Leucobacter komagatae, Dietza sp., and the fungus Discophaerina fagi have not been previously reported in USAF aviation fuel. Only at two bases were the same organisms isolated from all three sample points in the fuel supply distribution chain. Isolation of previously undocumented organisms suggests either, changes in aviation fuel microbial community in response to changes in aviation fuel composition, additives and biocide use, or simply, improvements in isolation and identification techniques.

Aircraft↗
PubMed2005

Polypeptide-templated synthesis of hexagonal silica platelets.

Several studies have demonstrated the use of biomimetic approaches in the synthesis of a variety of inorganic materials. Poly-L-lysine (PLL) promotes the precipitation of silica from a silicic acid solution within minutes. The molecular weight of PLL was found to affect the morphology of the resulting silica precipitate. Larger-molecular weight PLL produced hexagonal silica platelets, whereas spherical silica particles were obtained using low-molecular weight PLL. Here we report on the polypeptide secondary-structure transition that occurs during the silicification reaction. The formation of the hexagonal silica platelets is attributed to the PLL helical chains that are formed in the presence of monosilicic acid and phosphate ions. Hexagonal PLL crystals can also serve as templates in directing the growth of the silica in a manner that generates a largely mesoporous silica phase that is oriented with respect to the protein crystal template.

Microscopy, Electron, Scanning↗
PubMed2005

Constrained iron catalysts for single-walled carbon nanotube growth.

The diameter of single walled carbon nanotubes (SWNTs) determines the electronic properties of the nanotube. The diameter of carbon nanotubes is dictated by the diameter of the catalyst particle. Here we describe the use of iron nanoparticles synthesized within the Dps protein cage as catalysts for the growth of single-walled carbon nanotubes. The discrete iron particles synthesized within the Dps protein cages when used as catalyst particles gives rise to single-walled carbon nanotubes with a limited diameter distribution.

Journal Article↗
PubMed2005

Polypeptide-mediated silica growth on indium tin oxide surfaces.

Herein, we describe the formation of silica structures on indium tin oxide (ITO) surfaces using poly-L-lysine (PLL) to template the condensation of silicic acid. Precisely controlled electrostatic fields were used to preposition PLL onto ITO surfaces. Subsequent polypeptide-mediated silicification resulted in the formation of silica with concentration gradients that followed the pattern of the externally applied electrostatic field used in the deposition of the PLL. The resulting silica structures were securely attached to the ITO surface. The technique described here offers an inexpensive and rapid method for the deposition of polypeptides on surfaces.

Biomimetics↗
PubMed2004

Dissolution and regeneration of Bombyx mori silk fibroin using ionic liquids.

In this work, the suitability of imidazolium-based ionic liquid solvents is investigated for the dissolution and regeneration of silkworm (Bombyx mori) silk. Within an ionic liquid the anion plays a larger role in dictating the ultimate solubility of the silk. The dissolution of the silk in the ionic liquid is confirmed using wide-angle X-ray scattering. The dissolved silk is also processed into 100 mum-thick, two-dimensional films, and the structure of these films is examined. The rinse solvent, acetonitrile or methanol, has a profound impact on both the topography of the films and the secondary structure of the silk protein. The image depicts a silkworm cocoon dissolved in 1-butyl-3-methylimidazolium chloride and then regenerated as a film with birefringence.

Animals↗
PubMed2004

Engineered protein cages for nanomaterial synthesis.

Self-assembled particles of genetically engineered human L subunit ferritin expressing a silver-binding peptide were used as nanocontainers for the synthesis of silver nanoparticles. The inner cavity of the self-assembled protein cage displays a dodecapeptide that is capable of reducing silver ions to metallic silver. This chimeric protein cage when incubated in the presence of silver nitrate exhibits the growth of a silver nanocrystal within its cavity. Our studies indicate that it is possible to design chimeric cages, using specific peptide templates, for the growth of other inorganic nanoparticles.

Amino Acid Sequence↗
PubMed2004

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.

Adsorption↗
PubMed2003

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.

Bacterial Proteins↗
PubMed2003

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.

Electrochemistry↗