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Find video protocols related to scientific articles indexed in Pubmed.
Structure-Determining Step in the Hierarchical Assembly of Peptoid Nanosheets.
ACS Nano
PUBLISHED: 10-21-2014
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Organic two-dimensional nanomaterials are of growing importance, yet few general synthetic methods exist to produce them in high yields and to precisely functionalize them. We previously developed an efficient hierarchical supramolecular assembly route to peptoid bilayer nanosheets, where the organization of biomimetic polymer sequences is catalyzed by an air-water interface. Here we determine at which stages of assembly the nanoscale and atomic-scale order appear. We used X-ray scattering, grazing incidence X-ray scattering at the air-water interface, electron diffraction, and a recently developed computational coarse-grained peptoid model to probe the molecular ordering at various stages of assembly. We found that lateral packing and organization of the chains occurs during the formation of a peptoid monolayer, prior to its collapse into a bilayer. Identifying the structure-determining step enables strategies to influence nanosheet order, to predict and optimize production yields, and to further engineer this class of material. More generally, our results provide a guide for using fluid interfaces to catalytically assemble 2D nanomaterials.
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Morphology-conductivity relationship in crystalline and amorphous sequence-defined peptoid block copolymer electrolytes.
J. Am. Chem. Soc.
PUBLISHED: 10-09-2014
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Polymers that dissolve and conduct lithium ions are of great interest in the application of rechargeable lithium batteries. It is generally believed that the transport of ions in these systems is facilitated by rapid segmental motion typically found in rubbery, amorphous polymers. In this paper, we demonstrate that chemically identical ethyleneoxy-containing domains of a block copolymer exhibit comparable conductivities when in an amorphous or a crystalline state. An important feature of this study is the use of sequence-defined block copolypeptoids synthesized by submonomer solid-phase synthesis. Two structurally analogous ethyleneoxy-containing diblock copolypeptoids poly-N-(2-ethyl)hexylglycine-block-poly-N-2-(2-(2-methoxyethoxy)ethoxy)ethylglycine (pNeh-b-pNte) and poly-N-decylglycine-block-poly-N-2-(2-(2-methoxyethoxy)ethoxy)ethylglycine (pNdc-b-pNte) with 18 monomer units per block were synthesized. Both diblock copolypeptoids have the same conducting block, pNte, but different nonconducting blocks: pNeh, which is amorphous, and pNdc, which is crystalline. Both diblock copolypeptoids self-assemble into a lamellar morphology; however, pNte chains are amorphous in pNeh-b-pNte and crystalline in pNdc-b-pNte. This provides the platform for comparing lithium ion transport in amorphous and crystalline polymer domains that are otherwise similar.
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Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics.
Sci Rep
PUBLISHED: 09-05-2014
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In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic and hydrophobic interactions, with hydrophobic interactions playing the dominant role. While either strong electrostatic or hydrophobic interactions inhibit growth and reduces expression of the {104} faces, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate electrostatic interactions allow peptoids to weakly adsorb while moderate hydrophobic interactions cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of the {104} faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.
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Assembly and molecular order of two-dimensional peptoid nanosheets through the oil-water interface.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 09-02-2014
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Peptoid nanosheets are a recently discovered class of 2D nanomaterial that form from the self-assembly of a sequence-specific peptoid polymer at an air-water interface. Nanosheet formation occurs first through the assembly of a peptoid monolayer and subsequent compression into a bilayer structure. These bilayer materials span hundreds of micrometers in lateral dimensions and have the potential to be used in a variety of applications, such as in molecular sensors, artificial membranes, and as catalysts. This paper reports that the oil-water interface provides another opportunity for growth of these unique and highly ordered peptoid sheets. The monolayers formed at this interface are found through surface spectroscopic measurements to be highly ordered and electrostatic interactions between the charged moieties, namely carboxylate and ammonium residues, of the peptoid are essential in the ability of these peptoids to form ordered nanosheets at the oil-water interface. Expanding the mechanism of peptoid nanosheet formation to the oil-water interface and understanding the crucial role of electrostatic interactions between peptoid residues in nanosheet formation is essential for increasing the complexity and functionality of these nanomaterials.
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Crystallization in sequence-defined peptoid diblock copolymers induced by microphase separation.
J. Am. Chem. Soc.
PUBLISHED: 01-27-2014
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Atomic level synthetic control over a polymer's chemical structure can reveal new insights into the crystallization kinetics of block copolymers. Here, we explore the impact of side chain structure on crystallization behavior, by designing a series of sequence-defined, highly monodisperse peptoid diblock copolymers poly-N-decylglycine-block-poly-N-2-(2-(2-methoxyethoxy)ethoxy)ethylglycine (pNdc-b-pNte) with volume fraction of pNte (?Nte) values ranging from 0.29 to 0.71 and polydispersity indices ?1.00017. Both monomers have nearly identical molecular volumes, but the pNte block is amorphous while the pNdc block is crystalline. We demonstrate by X-ray scattering and calorimetry that all the block copolypeptoids self-assemble into lamellar microphases and that the self-assembly is driven by crystallization of the pNdc block. Interestingly, the microphase separated pNdc-b-pNte diblock copolymers form two distinct crystalline phases. Crystallization of the normally amorphous pNte chains is induced by the preorganization of the crystalline pNdc chains. We hypothesize that this is due to the similarity of chemical structure of the monomers (both monomers have linear side chains of similar lengths emanating from a polyglycine backbone). The pNte block remains amorphous when the pNdc block is replaced by another crystalline block, poly-N-isoamylglycine, suggesting that a close matching of the lattice spacings is required for induced crystallization. To our knowledge, there are no previous reports of crystallization of a polymer chain induced by microphase separation. These investigations show that polypeptoids provide a unique platform for examining the effect of intertwined roles of side chain organization on the thermodynamic properties of diblock copolymers.
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Nanometer-scale siRNA carriers incorporating peptidomimetic oligomers: physical characterization and biological activity.
Int J Nanomedicine
PUBLISHED: 01-01-2014
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Synthetic short interfering RNA (siRNA) oligonucleotides can trigger the RNA interference pathway and lead to selective gene silencing. Despite considerable enthusiasm and investment, formidable challenges remain that may deter translating this breakthrough discovery into clinical applications. In particular, the development of efficient, nontoxic, nonimmunogenic methods for delivering siRNA in vivo has proven to be exceptionally challenging. Thorough analysis of the relationship between the structure and function of siRNA carrier systems, both in isolation and in complex with RNA, will facilitate the design of efficient nonviral siRNA delivery vehicles. In this study, we explore the relationship between the physicochemical characteristics and the biological activity of "lipitoid" compounds as potent siRNA delivery vehicles. Lipitoids are cationic peptidomimetic oligomers incorporating a peptoid and a phospholipid moiety. Lipitoids can associate with siRNA oligonucleotides and self-assemble into spherical lipitoid-based nanoparticles (LNPs), with dimensions that are dependent upon the medium and the stoichiometric ratio between the cationic monomers of the lipitoid and anionic siRNA oligonucleotides. The morphology, gene silencing efficiency, and cytotoxicity of the siRNA-loaded LNPs are similarly sensitive to the stoichiometry of the complexes. The medium in which the LNPs are formed affects the assembled cargo particles' characteristics such as particle size, transfection efficiency, and stability. Formation of the LNPs in the biological, serum-free medium OptiMEM resulted in LNPs an order of magnitude larger than LNPs formed in water, and were twice as efficient in siRNA transfection compared to LNPs formed in water. Inhibitor studies were conducted to elucidate the efficiency of lysosomal escape and the uptake mechanism of the siRNA-loaded LNPs. Our results suggest that these lipitoid-based, siRNA-loaded spherical LNPs are internalized through a lipid raft-dependent and dynamin-mediated pathway, circumventing endosomal and lysosomal encapsulation. The lipitoid-siRNA nanospheres proved to be suitable platforms for investigating the critical parameters determining the efficiency of transfection agents, revealing the necessity for conducting characterization studies in biological media. The investigation of the LNP internalization pathway points to an alternative uptake route that bypasses the lysosome, explaining the surprisingly high efficiency of LNPs and suggesting that the uptake mechanism should be probed rather than assumed for the next generation of rationally designed transfection agents.
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Antibody-mimetic peptoid nanosheets for molecular recognition.
ACS Nano
PUBLISHED: 09-18-2013
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The ability of antibodies to bind a wide variety of analytes with high specificity and high affinity make them ideal candidates as molecular recognition elements for chemical and biological sensors. However, their widespread use in sensing devices has been hampered by their poor stability and high production cost. Here we report the design and synthesis of a new class of antibody-mimetic materials based on functionalized peptoid nanosheets. A high density of conformationally constrained peptide and peptoid loops are displayed on the surface of free-floating nanosheets to generate an extended, multivalent two-dimensional material that is chemically and biologically stable. The nanosheet serves as a robust, high-surface area scaffold upon which to display a wide variety of functional loop sequences. The functionalized nanosheets were characterized by atomic force microscopy, X-ray diffraction, and X-ray reflectivity measurements, and were shown to serve as substrates for enzymes (protease and casein kinase II), as well as templates for the growth of defined inorganic materials (gold metal).
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Nanoscale phase separation in sequence-defined peptoid diblock copolymers.
J. Am. Chem. Soc.
PUBLISHED: 09-16-2013
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Microphase-separated block copolymer materials have a wide array of potential applications ranging from nanoscale lithography to energy storage. Our understanding of the factors that govern the morphology of these systems is based on comparisons between theory and experiment. The theories generally assume that the chains are perfectly monodisperse; however, typical experimental copolymer preparations have polydispersity indices (PDIs) ranging from 1.01 to 1.10. In contrast, we present a systematic study of the relationship between chemical structure and morphology in the solid state using peptoid diblock copolymers with PDIs of ?1.00013. A series of comb-like peptoid block copolymers, poly(N-2-(2-(2-methoxyethoxy)ethoxy)ethylglycine)-block-poly(N-(2-ethylhexyl)glycine) (pNte-b-pNeh), were obtained by solid-phase synthesis. The number of monomers per chain was held fixed at 36, while the volume fraction of the Nte block (?Nte) was varied from 0.11 to 0.65. The experimentally determined order-disorder transition temperature exhibited a maximum at ?Nte = 0.24, not ?Nte = 0.5 as expected from theory. All of the ordered phases had a lamellar morphology, even in the case of ?Nte = 0.11. Our results are in qualitative disagreement with all known theories of microphase separation in block copolymers. This raises new questions about the intertwined roles of monomer architecture and polydispersity in the phase behavior of diblock copolymers.
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Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.
J Comput Chem
PUBLISHED: 08-16-2013
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Peptoids are positional isomers of peptides: peptoid sidechains are attached to backbone nitrogens rather than ?-carbons. Peptoids constitute a class of sequence-specific polymers resistant to biological degradation and potentially as diverse, structurally and functionally, as proteins. While molecular simulation of proteins is commonplace, relatively few tools are available for peptoid simulation. Here, we present a first-generation atomistic forcefield for peptoids. Our forcefield is based on the peptide forcefield CHARMM22, with key parameters tuned to match both experimental data and quantum mechanical calculations for two model peptoids (dimethylacetamide and a sarcosine dipeptoid). We used this forcefield to demonstrate that solvation of a dipeptoid substantially modifies the conformations it can access. We also simulated a crystal structure of a peptoid homotrimer, H-(N-2-phenylethyl glycine)3 -OH, and we show that experimentally observed structural and dynamical features of the crystal are accurately described by our forcefield. The forcefield presented here provides a starting point for future development of peptoid-specific simulation methods within CHARMM. © 2013 Wiley Periodicals, Inc.
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Coarse-grained, foldable, physical model of the polypeptide chain.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-29-2013
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Although nonflexible, scaled molecular models like Pauling-Coreys and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and ?-carbon units, connected by mechanical bonds (corresponding to ? and ?) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface.
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Peptoid polymers: a highly designable bioinspired material.
ACS Nano
PUBLISHED: 05-30-2013
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Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.
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Stabilization of nanoparticles under biological assembly conditions using peptoids.
Biopolymers
PUBLISHED: 12-20-2011
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Sequence-specific polymers are proving to be a powerful approach to assembly and manipulation of matter on the nanometer scale. This has been most impressive in the case of DNA, and progress has been made toward templating inorganic nanoparticles using DNA nanostructures. One obstacle to this progress is that inorganic nanomaterials are often incompatible with DNA assembly conditions, which involve aqueous solutions high in either or both monovalent and divalent salt. Synthetic oligopeptide ligands have been shown by others to improve nanoparticle stability in high concentrations of monovalent salt. Ligands that are peptoids, or sequence-specific N-functional glycine oligomers, allow precise and flexible control over the arrangement of binding groups, steric spacers, charge, and other functionality. We have synthesized short peptoids that can prevent the aggregation of gold nanoparticles in high-salt environments including divalent salt, and allow coadsorption of a single DNA molecule. This degree of precision and versatility is likely to prove essential in bottom-up assembly of nanostructures and in biomedical applications of nanomaterials.
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Folding of a single-chain, information-rich polypeptoid sequence into a highly ordered nanosheet.
Biopolymers
PUBLISHED: 12-20-2011
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The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A means to achieve this goal is to create synthetic polymers of defined sequence where all relevant folding information is incorporated into a single polymer strand. We present here the aqueous self-assembly of peptoid polymers (N-substituted glycines) into ultrathin, two-dimensional highly ordered nanosheets, where all folding information is encoded into a single chain. The sequence designs enforce a two-fold amphiphilic periodicity. Two sequences were considered: one with charged residues alternately positive and negative (alternating patterning), and one with charges segregated in positive and negative halves of the molecule (block patterning). Sheets form between pH 5 and 10 with the optimal conditions being pH 6 for the alternating sequence and pH 8 for the block sequence. Once assembled, the nanosheets remain stable between pH 6 and 10 with observed degradation beginning to occur below pH 6. The alternating charge nanosheets remain stable up to concentrations of 20% acetonitrile, whereas the block pattern displayed greater robustness remaining stable up to 30% acetonitrile. These observations are consistent with expectations based on considerations of the molecules electrostatic interactions. This study represents an important step in the construction of abiotic materials founded on biological informatic and folding principles.
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Solid-phase submonomer synthesis of peptoid polymers and their self-assembly into highly-ordered nanosheets.
J Vis Exp
PUBLISHED: 11-16-2011
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Peptoids are a novel class of biomimetic, non-natural, sequence-specific heteropolymers that resist proteolysis, exhibit potent biological activity, and fold into higher order nanostructures. Structurally similar to peptides, peptoids are poly N-substituted glycines, where the side chains are attached to the nitrogen rather than the alpha-carbon. Their ease of synthesis and structural diversity allows testing of basic design principles to drive de novo design and engineering of new biologically-active and nanostructured materials. Here, a simple manual peptoid synthesis protocol is presented that allows the synthesis of long chain polypeptoids (up to 50mers) in excellent yields. Only basic equipment, simple techniques (e.g. liquid transfer, filtration), and commercially available reagents are required, making peptoids an accessible addition to many researchers toolkits. The peptoid backbone is grown one monomer at a time via the submonomer method which consists of a two-step monomer addition cycle: acylation and displacement. First, bromoacetic acid activated in situ with N,N-diisopropylcarbodiimide acylates a resin-bound secondary amine. Second, nucleophilic displacement of the bromide by a primary amine follows to introduce the side chain. The two-step cycle is iterated until the desired chain length is reached. The coupling efficiency of this two-step cycle routinely exceeds 98% and enables the synthesis of peptoids as long as 50 residues. Highly tunable, precise and chemically diverse sequences are achievable with the submonomer method as hundreds of readily available primary amines can be directly incorporated. Peptoids are emerging as a versatile biomimetic material for nanobioscience research because of their synthetic flexibility, robustness, and ordering at the atomic level. The folding of a single-chain, amphiphilic, information-rich polypeptoid into a highly-ordered nanosheet was recently demonstrated. This peptoid is a 36-mer that consists of only three different commercially available monomers: hydrophobic, cationic and anionic. The hydrophobic phenylethyl side chains are buried in the nanosheet core whereas the ionic amine and carboxyl side chains align on the hydrophilic faces. The peptoid nanosheets serve as a potential platform for membrane mimetics, protein mimetics, device fabrication, and sensors. Methods for peptoid synthesis, sheet formation, and microscopy imaging are described and provide a simple method to enable future peptoid nanosheet designs.
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Protein side-chain translocation mutagenesis via incorporation of peptoid residues.
ACS Chem. Biol.
PUBLISHED: 10-13-2011
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For the last few decades, chemistry has played an important role in protein engineering by providing a variety of synthetic tools such as chemoselective side-chain modifications, chemical conjugation, incorporation of non-natural amino acids, and the development of protein-mimetic heteropolymers. Here we study protein backbone engineering in order to better understand the molecular mechanism of protein function and to introduce protease stable, non-natural residues into a protein structure. Using a combination of genetic engineering and chemical synthesis, we were able to introduce peptoid residues (N-substituted glycine residues) at defined positions into bovine pancreatic ribonuclease A. This results in a side-chain translocation from the C? carbon to the neighboring backbone nitrogen atom. To generate these peptoid substitutions, we removed the N-terminal S-peptide of the protein by proteolysis and chemically conjugated synthetic peptide-peptoid hybrids to the new N-terminus. A triple peptoid mutant containing a catalytic His12 peptoid mutation was active with a k(cat)/K(m) value of 1.0 × 10(4) M(-1) s(-1). This k(cat)/K(m) value is only 10-fold lower than the control wild-type conjugate and comparable in magnitude to many other natural enzymes. The peptoid mutations increased the chain flexibility at the site of peptoid substitution and at its C-terminal neighboring residue. Our ability to translocate side chains by one atom along the proten backbone advances a synthetic mutagenesis tool and opens up a new level of protein engineering.
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Shaken, not stirred: collapsing a peptoid monolayer to produce free-floating, stable nanosheets.
J. Am. Chem. Soc.
PUBLISHED: 10-12-2011
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Two-dimensional nanomaterials play a critical role in biology (e.g., lipid bilayers) and electronics (e.g., graphene) but are difficult to directly synthesize with a high level of precision. Peptoid nanosheet bilayers are a versatile synthetic platform for constructing multifunctional, precisely ordered two-dimensional nanostructures. Here we show that nanosheet formation occurs through an unusual monolayer intermediate at the air-water interface. Lateral compression of a self-assembled peptoid monolayer beyond a critical collapse pressure results in the irreversible production of nanosheets. An unusual thermodynamic cycle is employed on a preparative scale, where mechanical energy is used to buckle an intermediate monolayer into a more stable nanosheet. Detailed physical studies of the monolayer-compression mechanism revealed a simple preparative technique to produce nanosheets in 95% overall yield by cyclical monolayer compressions in a rotating closed vial. Compression of monolayers into stable, free-floating products may be a general and preparative approach to access 2D nanomaterials.
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Peptoid origins.
Biopolymers
PUBLISHED: 06-08-2011
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Peptoid oligomers were initially developed as part of a larger basic research effort to accelerate the drug-discovery process in the biotech/biopharma industry. Their ease of synthesis, stability, and structural similarity to polypeptides made them ideal candidates for the combinatorial discovery of novel peptidomimetic drug candidates. Diverse libraries of short peptoid oligomers provided one of the first demonstrations in the mid-1990s that high-affinity ligands to pharmaceutically relevant receptors could be discovered from combinatorial libraries of synthetic compounds. The solid-phase submonomer method of peptoid synthesis was so efficient and general that it soon became possible to explore the properties of longer polypeptoid chains in a variety of areas beyond drug discovery (e.g., diagnostics, drug delivery, and materials science). Exploration into protein-mimetic materials soon followed, with the fundamental goal of folding a non-natural sequence-specific heteropolymer into defined secondary or tertiary structures. This effort first yielded the peptoid helix and much later the peptoid sheet, both of which are secondary-structure mimetics that are close relatives to their natural counterparts. These crucial discoveries have brought us closer to building proteinlike structure and function from a non-natural polymer and have provided great insight into the rules governing polymer and protein folding. The accessibility of peptoid synthesis to chemists and nonchemists alike, along with a lack of information-rich non-natural polymers available to study, has led to a rapid growth in the field of peptoid science by many new investigators. This work provides an overview of the initial discovery and early developments in the peptoid field.
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A universal method for detection of amyloidogenic misfolded proteins.
Biochemistry
PUBLISHED: 05-03-2011
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Diseases associated with the misfolding of endogenous proteins, such as Alzheimers disease and type II diabetes, are becoming increasingly prevalent. The pathophysiology of these diseases is not totally understood, but mounting evidence suggests that the misfolded protein aggregates themselves may be toxic to cells and serve as key mediators of cell death. As such, an assay that can detect aggregates in a sensitive and selective fashion could provide the basis for early detection of disease, before cellular damage occurs. Here we report the evolution of a reagent that can selectively capture diverse misfolded proteins by interacting with a common supramolecular feature of protein aggregates. By coupling this enrichment tool with protein specific immunoassays, diverse misfolded proteins and sub-femtomole amounts of oligomeric aggregates can be detected in complex biological matrices. We anticipate that this near-universal approach for quantitative misfolded protein detection will become a useful research tool for better understanding amyloidogenic protein pathology as well as serve as the basis for early detection of misfolded protein diseases.
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Engineered biomimetic polymers as tunable agents for controlling CaCO3 mineralization.
J. Am. Chem. Soc.
PUBLISHED: 03-21-2011
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In nature, living organisms use peptides and proteins to precisely control the nucleation and growth of inorganic minerals and sequester CO(2)via mineralization of CaCO(3). Here we report the exploitation of a novel class of sequence-specific non-natural polymers called peptoids as tunable agents that dramatically control CaCO(3) mineralization. We show that amphiphilic peptoids composed of hydrophobic and anionic monomers exhibit both a high degree of control over calcite growth morphology and an unprecedented 23-fold acceleration of growth at a peptoid concentration of only 50 nM, while acidic peptides of similar molecular weight exhibited enhancement factors of only ?2 or less. We further show that both the morphology and rate controls depend on peptoid sequence, side-chain chemistry, chain length, and concentration. These findings provide guidelines for developing sequence-specific non-natural polymers that mimic the functions of natural peptides or proteins in their ability to direct mineralization of CaCO(3), with an eye toward their application to sequestration of CO(2) through mineral trapping.
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BMHP1-derived self-assembling peptides: hierarchically assembled structures with self-healing propensity and potential for tissue engineering applications.
ACS Nano
PUBLISHED: 02-11-2011
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Self-assembling peptides (SAPs) are rapidly gaining interest as bioinspired scaffolds for cell culture and regenerative medicine applications. Bone Marrow Homing Peptide 1 (BMHP1) functional motif (PFSSTKT) was previously demonstrated to stimulate neural stem cell (NSC) viability and differentiation when linked to SAPs. We here describe a novel ensemble of SAPs, developed from the BMHP1 (BMHP1-SAPs), that spontaneously assemble into tabular fibers, twisted ribbons, tubes and hierarchical self-assembled sheets: organized structures in the nano- and microscale. Thirty-two sequences were designed and evaluated, including biotinylated and unbiotinylated sequences, as well as a hybrid peptide-peptoid sequence. Via X-ray diffraction (XRD), CD, and FTIR experiments we demonstrated that all of the BMHP1-SAPs share similarly organized secondary structures, that is, ?-sheets and ?-turns, despite their heterogeneous nanostructure morphology, scaffold stiffness, and effect over NSC differentiation and survival. Notably, we demonstrated the self-healing propensity of most of the tested BMHP1-SAPs, enlarging the set of potential applications of these novel SAPs. In in vitro cell culture experiments, we showed that some of these 10-mer peptides foster adhesion, differentiation, and proliferation of human NSCs. RGD-functionalized and hybrid peptide-peptoid self-assembling sequences also opened the door to BMHP1-SAP functionalization with further bioactive motifs, essential to tailor new scaffolds for specific applications. In in vivo experiments we verified a negligible reaction of the host nervous tissue to the injected and assembled BMHP1-SAP. This work will pave the way to the development of novel SAP sequences that may be useful for material science and regenerative medicine applications.
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Hierarchical self-assembly of a biomimetic diblock copolypeptoid into homochiral superhelices.
J. Am. Chem. Soc.
PUBLISHED: 10-22-2010
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The aqueous self-assembly of a sequence-specific bioinspired peptoid diblock copolymer into monodisperse superhelices is demonstrated to be the result of a hierarchical process, strongly dependent on the charging level of the molecule. The partially charged amphiphilic diblock copolypeptoid 30-mer, [N-(2-phenethyl)glycine](15)-[N-(2-carboxyethyl)glycine](15), forms superhelices in high yields, with diameters of 624 ± 69 nm and lengths ranging from 2 to 20 ?m. Chemical analogs coupled with X-ray scattering and crystallography of a model compound have been used to develop a hierarchical model of self-assembly. Lamellar stacks roll up to form a supramolecular double helical structure with the internal ordering of the stacks being mediated by crystalline aromatic side chain-side chain interactions within the hydrophobic block. The role of electrostatic and hydrogen bonding interactions in the hydrophilic block is also investigated and found to be important in the self-assembly process.
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A?40 oligomers identified as a potential biomarker for the diagnosis of Alzheimers disease.
PLoS ONE
PUBLISHED: 08-02-2010
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Alzheimers Disease (AD) is the most prevalent form of dementia worldwide, yet the development of therapeutics has been hampered by the absence of suitable biomarkers to diagnose the disease in its early stages prior to the formation of amyloid plaques and the occurrence of irreversible neuronal damage. Since oligomeric A? species have been implicated in the pathophysiology of AD, we reasoned that they may correlate with the onset of disease. As such, we have developed a novel misfolded protein assay for the detection of soluble oligomers composed of A? x-40 and x-42 peptide (hereafter A?40 and A?42) from cerebrospinal fluid (CSF). Preliminary validation of this assay with 36 clinical samples demonstrated the presence of aggregated A?40 in the CSF of AD patients. Together with measurements of total A?42, diagnostic sensitivity and specificity greater than 95% and 90%, respectively, were achieved. Although larger sample populations will be needed to confirm this diagnostic sensitivity, our studies demonstrate a sensitive method of detecting circulating A?40 oligomers from AD CSF and suggest that these oligomers could be a powerful new biomarker for the early detection of AD.
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Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers.
Nat Mater
PUBLISHED: 03-08-2010
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The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A biomimetic approach is to explore the impact of monomer sequence on non-natural polymer structure and function. We present the aqueous self-assembly of two peptoid polymers into extremely thin two-dimensional (2D) crystalline sheets directed by periodic amphiphilicity, electrostatic recognition and aromatic interactions. Peptoids are sequence-specific, oligo-N-substituted glycine polymers designed to mimic the structure and functionality of proteins. Mixing a 1:1 ratio of two oppositely charged peptoid 36mers of a specific sequence in aqueous solution results in the formation of giant, free-floating sheets with only 2.7 nm thickness. Direct visualization of aligned individual peptoid chains in the sheet structure was achieved using aberration-corrected transmission electron microscopy. Specific binding of a protein to ligand-functionalized sheets was also demonstrated. The synthetic flexibility and biocompatibility of peptoids provide a flexible and robust platform for integrating functionality into defined 2D nanostructures.
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Gold nanoparticle self-similar chain structure organized by DNA origami.
J. Am. Chem. Soc.
PUBLISHED: 02-19-2010
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Here we demonstrate Au nanoparticle self-similar chain structure organized by triangle DNA origami with well-controlled orientation and <10 nm spacing. We show for the first time that a large DNA complex (origami) and multiple AuNP conjugates can be well-assembled and purified with reliable yields. The assembled structure could be used to generate high local-field enhancement. The same method can be used to precisely localize multiple components on a DNA template for potential applications in nanophotonic, nanomagnetic, and nanoelectronic devices.
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Templated display of biomolecules and inorganic nanoparticles by metal ion-induced peptide nanofibers.
Chem. Commun. (Camb.)
PUBLISHED: 02-03-2010
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We functionalized peptide nanofibers to provide a nano-scale template for the display of biomolecules and inorganic nanoparticles using metal ion coordination. Nanofibers assembled only in the presence of certain divalent metal ions, and could be readily dissolved by a metal-chelating reagent, EDTA.
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Novel peptoid building blocks: synthesis of functionalized aromatic helix-inducing submonomers.
Org. Lett.
PUBLISHED: 01-09-2010
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Peptoids, oligo-N-substituted glycines, can fold into well-defined helical secondary structures. The design and synthesis of new peptoid building blocks that are capable of both (a) inducing a helical secondary structure and (b) decorating the helices with chemical functionalities are reported. Peptoid heptamers containing carboxamide, carboxylic acid or thiol functionalities were synthesized, and the resulting peptoids were shown to form stable helices. A thiol-containing peptoid readily formed the homodisulfide, providing a convenient route to prepare peptoid helix homodimers.
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Close mimicry of lung surfactant protein B by "clicked" dimers of helical, cationic peptoids.
Biopolymers
PUBLISHED: 09-25-2009
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A family of peptoid dimers developed to mimic SP-B is presented, where two amphipathic, cationic helices are linked by an achiral octameric chain. SP-B is a vital therapeutic protein in lung surfactant replacement therapy, but its large-scale isolation or chemical synthesis is impractical. Enhanced biomimicry of SP-Bs disulfide-bonded structure has been previously attempted via disulfide-mediated dimerization of SP-B(1-25) and other peptide mimics, which improved surface activity relative to the monomers. Herein, the effects of disulfide- or "click"-mediated (1,3-dipolar cycloaddition) dimerization, as well as linker chemistry, on the lipid-associated surfactant activity of a peptoid monomer are described. Results revealed that the clicked peptoid dimer enhanced in vitro surface activity in a DPPC:POPG:PA lipid film relative to its disulfide-bonded and monomeric counterparts in both surface balance and pulsating bubble surfactometry studies. On the pulsating bubble surfactometer, the film containing the "clicked" peptoid dimer outperformed all presented peptoid monomers and dimers, and two SP-B derived peptides, attaining an adsorbed surface tension of 22 mN m(-1), and maximum and minimum cycling values of 42 mN m(-1) and near-zero, respectively.
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Peptoids as potential therapeutics.
Curr. Opin. Mol. Ther.
PUBLISHED: 05-30-2009
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Peptoids are oligomers of N-substituted glycine units. These molecules are almost perfectly suited for combinatorial approaches to drug discovery because large libraries can be synthesized easily from readily available primary amines. Moreover, major advances in screening methodology have allowed peptoid libraries of hundreds of thousands of compounds to be mined inexpensively and quickly for highly specific protein-binding molecules. These advances and the potential utility of peptoids as pharmacological agents are reviewed.
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High-throughput sequencing of peptoids and peptide-peptoid hybrids by partial edman degradation and mass spectrometry.
J Comb Chem
PUBLISHED: 01-22-2009
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A method for the rapid sequence determination of peptoids [oligo(N-substituted glycines)] and peptide-peptoid hybrids selected from one-bead-one-compound combinatorial libraries has been developed. In this method, beads carrying unique peptoid (or peptide-peptoid) sequences were subjected to multiple cycles of partial Edman degradation (PED) by treatment with a 1:3 (mol/mol) mixture of phenyl isothiocyanate (PITC) and 9-fluorenylmethyl chloroformate (Fmoc-Cl) to generate a series of N-terminal truncation products for each resin-bound peptoid. After PED, the Fmoc group was removed from the N-terminus and any reacted side chains via piperidine treatment. The resulting mixture of the full-length peptoid and its truncation products was analyzed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry, to reveal the sequence of the full-length peptoid. With a slight modification, the method was also effective in the sequence determination of peptide-peptoid hybrids. This rapid, high-throughput, sensitive, and inexpensive sequencing method should greatly expand the utility of combinatorial peptoid libraries in biomedical and materials research.
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Synthesis and characterization of designed BMHP1-derived self-assembling peptides for tissue engineering applications.
Nanoscale
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The importance of self-assembling peptides (SAPs) in regenerative medicine is becoming increasingly recognized. The propensity of SAPs to form nanostructured fibers is governed by multiple forces including hydrogen bonds, hydrophobic interactions and ?-? aromatic interactions among side chains of the amino acids. Single residue modifications in SAP sequences can significantly affect these forces. BMHP1-derived SAPs is a class of biotinylated oligopeptides, which self-assemble in ?-structured fibers to form a self-healing hydrogel. In the current study, selected modifications in previously described BMHP1-derived SAPs were designed in order to investigate the influence of modified residues on self-assembly kinetics and scaffold formation properties. The Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analysis demonstrated the secondary structure (?-sheet) formation in all modified SAP sequences, whereas atomic force microscopy (AFM) analysis further confirmed the presence of nanofibers. Furthermore, the fiber shape and dimension analysis by AFM showed flattened and twisted fiber morphology ranging from ?8 nm to ?70 nm. The mechanical properties of the pre-assembled and post assembled solution were investigated by rheometry. The shear-thinning behavior and rapid re-healing properties of the pre-assembled solutions make them a preferable choice for injectable scaffolds. The wide range of stiffnesses (G)--from ?1000 to ?27,000 Pa--exhibited by the post-assembled scaffolds demonstrated their potential for a variety of tissue engineering applications. The extra cellular matrix (ECM) mimicking (physically and chemically) properties of SAP scaffolds enhanced cell adhesion and proliferation. The capability of the scaffold to facilitate murine neural stem cell (mNSC) proliferation was evaluated in vitro: the increased mNSCs adhesion and proliferation demonstrated the potential of newly synthesized SAPs for regenerative medicine approaches.
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De novo structure prediction and experimental characterization of folded peptoid oligomers.
Proc. Natl. Acad. Sci. U.S.A.
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Peptoid molecules are biomimetic oligomers that can fold into unique three-dimensional structures. As part of an effort to advance computational design of folded oligomers, we present blind-structure predictions for three peptoid sequences using a combination of Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement. We correctly predicted the structure of a N-aryl peptoid trimer to within 0.2 ? rmsd-backbone and a cyclic peptoid nonamer to an accuracy of 1.0 ? rmsd-backbone. X-ray crystallographic structures are presented for a linear N-alkyl peptoid trimer and for the cyclic peptoid nonamer. The peptoid macrocycle structure features a combination of cis and trans backbone amides, significant nonplanarity of the amide bonds, and a unique "basket" arrangement of (S)-N(1-phenylethyl) side chains encompassing a bound ethanol molecule. REMD simulations of the peptoid trimers reveal that well folded peptoids can exhibit funnel-like conformational free energy landscapes similar to those for ordered polypeptides. These results indicate that physical modeling can successfully perform de novo structure prediction for small peptoid molecules.
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