Self-Assembling Peptides: From Molecules to Nanobiomaterials

Abstract | Molecular self-assembly plays a vital role in the construction of various nanostructures using the ‘bottom-up’ approach. Peptides have been considered important bio-molecular building blocks for different nanoscale structures as they are biocompatible, biodegradable, generally non-toxic and can be attuned to environmental responses like pH, temperature, salt concentration and others. Peptide based nanostructures can offer various wonderful biological applications in tissue engineering, cell culture, regenerative medicine and drug delivery. In this review, the construction of short peptide-based different nanostructures including nanotubes, nanovesicles and nanofibers, short peptide-based nanoporous materials, short peptide-based nanofibrous hydrogels and nanovesicles for various biological applications has been discussed. Moreover, morphological transformations from one nanoscopic structure to an other type of nanostructure (e.g., nanotubes to nanovesicles) are also clearly discussed in this review.

Structure of DNA-functionalized dendrimer nanoparticles

Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated (corresponding to neutral pH) poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single strand DNAs (ssDNAs). The four ssDNA strands that are attached via an alkythiolate [-S(CH(2))(6)-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers are observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich (having more adenine and guanine) ssDNA strands than pyrimidine rich (thymine and cytosine) ssDNA strands. The degree of wrapping of ssDNA strands on the dendrimer molecule was found to be influenced by the charge ratio of DNA and the dendrimer. As the G4 dendrimer contains relatively more positive charge than G3 dendrimer, we observe extensive wrapping of ssDNAs on the G4 dendrimer than G3 dendrimer. This might indicate that DNA functionalized G3 dendrimer is more suitable to construct higher order nanostructures. The linker molecule was also found to undergo drastic conformational change during the simulation. During nanosecond long simulation some portion of the linker molecule was found to be lying nearly flat on the surface of the dendrimer molecule. The ssDNA strands along with the linkers are seen to penetrate the surface of the dendrimer molecule and approach closer to the center of the dendrimer indicating the soft sphere nature of the dendrimer molecule. The effective radius of DNA-functionalized dendrimer nanoparticles was found to be independent of base composition of ssDNAs and was observed to be around 19.5 angstrom and 22.4 angstrom when we used G3 and G4 PAMAM dendrimers as the core of the nanoparticle respectively. The observed effective radius of DNA-functionalized dendrimer molecules apparently indicates the significant shrinkage in the structure that has taken place in dendrimer, linker and DNA strands. As a whole our results describe the characteristic features of DNA-functionalized dendrimer nanoparticles and can be used as strong inputs to design effectively the DNA-dendrimer nanoparticle self-assembly for their active biological applications.

CNT loading into cationic cholesterol suspensions show improved DNA binding and serum stability and ability to internalize into cancer cells

Methods which disperse single-walled carbon nanotubes (SWNTs) in water as `debundled', while maintaining their unique physical properties are highly useful. We present here a family of cationic cholesterol compounds (Chol(+)) {Cholest-5en-3 beta-oxyethyl pyridinium bromide (Chol-PB+), Cholest-5en-3 beta-oxyethyl N-methyl pyrrolidinium bromide (Chol-MPB+), Cholest-5en-3 beta-oxyethyl N-methyl morpholinium bromide (Chol-MMB+) and Cholest-5en-3 beta-oxyethyl diazabicyclo octanium bromide (Chol-DOB+)}. Each of these could be easily dispersed in water. The resulting cationic cholesterol (Chol(+)) suspensions solubilized single-walled carbon nanotubes (SWCNTs) by the non-specific physical adsorption of Chol(+) to form stable, transparent, dark aqueous suspensions at room temperature. Electron microscopy reveals the existence of highly segregated CNTs in these samples. Zeta potential measurements showed an increase in potential of cationic cholesterol aggregates on addition of CNTs. The CNT-Chol(+) suspensions were capable of forming stable complexes with genes (DNA) efficiently. The release of double-helical DNA from such CNT-Chol(+) complexes could be induced upon the addition of anionic micellar solution of SDS. Furthermore, the CNT-based DNA complexes containing cationic cholesterol aggregates showed higher stability in fetal bovine serum media at physiological conditions. Confocal studies confirm that CNT-Chol(+) formulations adhere to HeLa cell surfaces and get internalized more efficiently than the cationic cholesterol suspensions alone (devoid of any CNTs). These cationic cholesterol-CNT suspensions therefore appear to be a promising system for further use in biological applications.

Size-mediated cytotoxicity of nanocrystalline titanium dioxide, pure and zinc-doped hydroxyapatite nanoparticles in human hepatoma cells

Nanoparticles are highly used in biological applications including nanomedicine. In this present study, the interaction of HepG2 hepatocellular carcinoma cells (HCC) with hydroxyapatite (HAp), zinc-doped hydroxyapatite, and titanium dioxide (TiO2) nanoparticles were investigated. Hydroxyapatite, zinc-doped hydroxyapatite and titanium dioxide nanoparticles were prepared by wet precipitation method. They were subjected to isochronal annealing at different temperatures. Particle morphology and size distribution were characterized by X-ray diffraction and transmission electron microscope. The nanoparticles were co-cultured with HepG2 cells. MTT assay was employed to evaluate the proliferation of tumor cells. The DNA damaging effect of HAp, Zn-doped HAp, and TiO2 nanoparticles in human hepatoma cells (HepG2) were evaluated using DNA fragmentation studies. The results showed that in HepG2 cells, the anti-tumor activity strongly depend on the size of nanoparticles in HCC cells. Cell cycle arrest analysis for HAp, zinc-doped HAp, and TiO2 nanoparticles revealed the influence of HAp, zinc-doped HAp, and titanium dioxide nanoparticles on the apoptosis of HepG2 cells. The results imply that the novel nano nature effect plays an important role in the biomedicinal application of nanoparticles.

Effect of equal channel angular extrusion on wear and corrosion behavior of the orthopedic Ti-13Nb-13Zr alloy in simulated body fluid

We report investigations on the texture, corrosion and wear behavior of ultra-fine grained (UFG) Ti-13Nb-Zr alloy, processed by equal channel angular extrusion (ECAE) technique, for biomedical applications. The microstructure obtained was characterized by X-ray line profile analysis, scanning electron microscope (SEM) and electron back scattered diffraction (EBSD). We focus on the corrosion resistance and the fretting behavior, the main considerations for such biomaterials, in simulated body fluid. To this end. potentiodynamic polarization tests were carried out to evaluate the corrosion behavior of the UFG alloy in Hanks solution at 37 degrees C. The fretting wear behavior was carried out against bearing steel in the same conditions. The roughness of the samples was also measured to examine the effect of topography on the wear behavior of the samples. Our results showed that the ECAE process increases noticeably the performance of the alloy as orthopedic implant. Although no significant difference was observed in the fretting wear behavior, the corrosion resistance of the UFG alloy was found to be higher than the non-treated material. (c) 2012 Elsevier B.V. All rights reserved.

Functionally graded hydroxyapatite-alumina-zirconia biocomposite: Synergy of toughness and biocompatibility

Functionally Gradient Materials (FGM) are considered as a novel concept to implement graded functionality that otherwise cannot be achieved by conventional homogeneous materials. For biomedical applications, an ideal combination of bioactivity on the material surface as well as good physical property (strength/toughness/hardness) of the bulk is required in a designed FGM structure. In this perspective, the present work aims at providing a smooth gradation of functionality (enhanced toughening of the bulk, and retained biocompatibility of the surface) in a spark plasma processed hydroxyapatite-alumina-zirconia (HAp-Al2O3-YSZ) FGM bio-composite. In the current work HAp (fracture toughness similar to 1.5 MPa.m(1/2)) and YSZ (fracture toughness similar to 62 MPa.m(1/2)) are coupled with a transition layer of Al2O3 allowing minimum gradient of mechanical properties (especially the fracture toughness similar to 3.5 MPa.m(1/2)).The in vitro cyto-compatibilty of HAp-Al2O3-YSZ FGM was evaluated using L929 fibroblast cells and Saos-2 Osteoblast cells for their adhesion and growth. From analysis of the cell viability data, it is evident that FGM supports good cell proliferation after 2, 3, 4 days culture. The measured variation in hardness, fracture toughness and cellular adhesion across the cross section confirmed the smooth transition achieved for the FGM (HAp-Al2O3-YSZ) nanocomposite, i.e. enhanced bulk toughness combined with unrestricted surface bioactivity. Therefore, such designed biomaterials can serve as potential bone implants. (C) 2012 Elsevier B.V. All rights reserved.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. (c) 2012 Wiley Periodicals, Inc.

Silver nanoparticles modified nanocapsules for ultrasonically activated drug delivery

Novel ultrasound-sensitive nanocapsules were designed via layer-by-layer assembly (LbL) of polyelectrolytes for remote activated release of biomolecules/drug. Nanocapsules embedded with silver nanoparticles in the walls were synthesized by alternate assembly of poly(allylamine hydrochloride) (PAH) and dextran sulfate (DS) on silica template followed by nanoparticle synthesis and subsequent template removal thus yielding nanocapsules. The silver NPs were synthesized in situ within the capsule walls under controlled conditions. The nanocapsules were found to be well dispersed and the silver NPs were evenly distributed within the shell. FITC-dextran permeated easily into the capsules containing silver NP's due to the pores generated during the formation of NP's. When the loaded nanocapsules were sonicated, the presence of the silver NPs in the shell structure led to rupturing of the shell into smaller fragments thus releasing the FITC-dextran. Such nanocapsules have the potential to be used as drug delivery vehicles and offer the scope for further development in the areas of modern medicine, material science, and biochemistry. (C) 2012 Elsevier B.V. All rights reserved.

Photocytotoxic lanthanide complexes

Lanthanide complexes have recently received considerable attention in the field of therapeutic and diagnostic medicines. Among many applications of lanthanides, gadolinium complexes are used as magnetic resonance imaging (MRI) contrast agents in clinical radiology and luminescent lanthanides for bioanalysis, imaging and sensing. The chemistry of photoactive lanthanide complexes showing biological applications is of recent origin. Photodynamic therapy (PDT) is a non-invasive treatment modality of cancer using a photosensitizer drug and light. This review primarily focuses on different aspects of the chemistry of lanthanide complexes showing photoactivated DNA cleavage activity and cytotoxicity in cancer cells. Macrocyclic texaphyrin-lanthanide complexes are known to show photocytotoxicity with the PDT effect in near-IR light. Very recently, non-macrocyclic lanthanide complexes are reported to show photocytotoxicity in cancer cells. Attempts have been made in this perspective article to review and highlight the photocytotoxic behaviour of various lanthanide complexes for their potential photochemotherapeutic applications.

Dynamics of Plasmon in Graphene Oxide

Dynamic effects of plasmon such as scattering with defect boundaries and oxygen impurities in the graphene oxide are investigated. Study of plasmon dynamics helps in understanding electronic, opto-electronic and biological applications of graphene based nanostructures. Tuning or control over such applications is made possible by graphene nanostructure engineering. We have modeled defects with increased smoothing of defect edge in graphene keeping area of the defect constant. Scattering of plasmons in graphene with defects is modeled using an electromagnetic field coupled inter-atomic potential approach with finite element discretization of the atomic vibrational and electromagnetic field degrees of freedom. Our calculations show pi + sigma plasmon red shifting under sharp defect edges whereas pi plasmon show high extinction efficiency. Strong localization of electric fields near the sharp defect edges is observed. Observations on plasmons and its dynamics draws attention in designing novel optoelectronic devices and binders for bio-molecules.

Stimuli-responsive weak polyelectrolyte multilayer films: A thin film platform for self triggered multi-drug delivery

Polyelectrolyte multilayer (PEM) thin film composed of weak polyelectrolytes was designed by layer-by-layer (LbL) assembly of poly(allylamine hydrochloride) (PAH) and poly(methacrylic acid) (PMA) for multi-drug delivery applications. Environmental stimuli such as pH and ionic strength showed significant influence in changing the film morphology from pore-free smooth structure to porous structure and favored triggered release of loaded molecules. The film was successfully loaded with bovine serum albumin (BSA) and ciprofloxacin hydrochloride (CH) by modulating the porous polymeric network of the film. Release studies showed that the amount of release could be easily controlled by changing the environmental conditions such as pH and ionic strength. Sustained release of loaded molecules was observed up to 8 h. The fabricated films were found to be biocompatible with epithelial cells during in-vitro cell culture studies. PEM film reported here not only has the potential to be used as self-responding thin film platform for transdermal drug delivery, but also has the potential for further development in antimicrobial or anti-inflammatory coatings on implants and drug-releasing coatings for stents. (C) 2015 Elsevier B.V. All rights reserved.

Peristaltic pump-based low range pressure sensor calibration system

Peristaltic pumps were normally used to pump liquids in several chemical and biological applications. In the present study, a peristaltic pump was used to pressurize the chamber (positive as well negative pressures) using atmospheric air. In the present paper, we discuss the development and performance study of an automatic pressurization system to calibrate low range (millibar) pressure sensors. The system includes a peristaltic pump, calibrated pressure sensor (master sensor), pressure chamber, and the control electronics. An in-house developed peristaltic pump was used to pressurize the chamber. A closed loop control system has been developed to detect and adjust the pressure leaks in the chamber. The complete system has been integrated into a portable product. The system performance has been studied for a step response and steady state errors. The system is portable, free from oil contaminants, and consumes less power compared to existing pressure calibration systems. The veracity of the system was verified by calibrating an unknown diaphragm based pressure sensor and the results obtained were satisfactory. (C) 2015 AIP Publishing LLC.

Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.