Probing the conformational features of a phage display polypeptide sequence directed against single-walled carbon nanohorn surfaces

Binding Capabilities of Different Genetically Engineered pVIII Proteins of the Filamentous M13/Fd Virus and Single-Walled Carbon Nanotubes

Binding functional biomolecules to non-biological materials, such as single-walled carbon nanotubes (SWNTs), is a challenging task with relevance for different applications. However, no one has yet undertaken a comparison of the binding of SWNTs to different recombinant filamentous viruses (phages) bioengineered to contain different binding peptides fused to the virus coat proteins. This is important due to the range of possible binding efficiencies and scenarios that may arise when the protein’s amino acid sequence is modified, since the peptides may alter the virus’s biological properties or they may behave differently when they are in the context of being displayed on the virus coat protein; in addition, non-engineered viruses may non-specifically adsorb to SWNTs. To test these possibilities, we used four recombinant phage templates and the wild type. In the first circumstance, we observed different binding capabilities and biological functional alterations; e.g., some peptides, in the context of viral templates, did not bind to SWNTs, although it was proven that the bare peptide did. The second circumstance was excluded, as the wild-type virus was found to hardly bind to the SWNTs. These results may be relevant to the possible use of the virus as a “SWNT shuttle” in nano-scale self-assembly, particularly since the pIII proteins are free to act as binding-directing agents. Therefore, knowledge of the differences between and efficiencies of SWNT binding templates may help in choosing better binding phages or peptides for possible future applications and industrial mass production.

The first atomistic modelling-aided reproduction of morphologically defective single walled carbon nanohorns

A new modelling-aided approach for the atomistic model of single walled carbon nanohorn (SWNH) creation is presented, based on experimental evidence, on realistic potential of carbon-carbon interactions and on molecular simulations. A new model of SWNHs is next used to predict Ar adsorption properties and to check the molecular fundamentals of the adsorption mechanism. The influence of the apex angle value, nanohorn diameter and nanohorn length on the shapes of isotherms, enthalpy, high resolution α(s)-plots and adsorption potential distribution curves is checked. Finally the comparison with new experimental Ar adsorption results is shown and the conclusions on the porosity of real SWNH aggregates are given.

C-terminal amidation of an osteocalcin-derived peptide promotes hydroxyapatite crystallization

Genesis of natural biocomposite-based materials, such as bone, cartilage, and teeth, involves interactions between organic and inorganic systems. Natural biopolymers, such as peptide motif sequences, can be used as a template to direct the nucleation and crystallization of hydroxyapatite (HA). In this study, a natural motif sequence consisting of 13 amino acids present in the first helix of osteocalcin was selected based on its calcium binding ability and used as substrate for nucleation of HA crystals. The acidic (acidic osteocalcin-derived peptide (OSC)) and amidic (amidic osteocalcin-derived peptide (OSN)) forms of this sequence were synthesized to investigate the effects of different C termini on the process of biomineralization. Electron microscopy analyses show the formation of plate-like HA crystals with random size and shape in the presence of OSN. In contrast, spherical amorphous calcium phosphate is formed in the presence of OSC. Circular dichroism experiments indicate conformational changes of amidic peptide to an open and regular structure as a consequence of interaction with calcium and phosphate. There is no conformational change detectable in OSC. It is concluded that HA crystal formation, which only occurred in OSN, is attributable to C-terminal amidation of a natural peptide derived from osteocalcin. It is also proposed that natural peptides with the ability to promote biomineralization have the potential to be utilized in hard tissue regeneration.

Material binding peptides for nanotechnology

Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.

Effects of oligopeptide's conformational changes on its adsorption

We report the effects of peptide adsorption to cross-linked polymers (adsorbents) by its conformational changes. Two adsorbents, APhe and ALeu, were prepared and expected to show high affinity to the oligopeptide VW-8 (NH(2)-Val-Val-Arg-Gly-Cys-Thr-Trp-Trp-COOH) according to our previous studies. These absorbents bared the residues of phenylalanine and leucine, respectively, and carried both hydrophobic and electrical groups. The adsorbent AAsp, which carried only the electrostatic groups, was also prepared as a reference. Both APhe and ALeu were found to exhibit higher VW-8 capacity than AAsp, in which APhe showed the highest VW-8 capacity (13.6 mg/g). The VW-8 adsorption to ALeu and APhe was analyzed using a variety of techniques, including the surface plasmon resonance (SPR) technology, nuclear magnetic resonance (NMR) spectra and isothermal titration calorimetry (ITC). The comprehensive experimental data together indicated that APhe could induce a conformational change of VW-8 from a random-coil to a β-strand structure due to its ability to provide the strong ring stacking and electrostatic interactions, which is believed to be responsible for its highest adsorption affinity (K(a)=2.59×10(7) M(-1)). In contrast, the hydrophobic interactions provided by ALeu were not strong enough to induce a VW-8 conformational change to a regular structure, and therefore it exhibited a relatively lower affinity to VW-8 (K(a)=6.23×10(5) M(-1)). The results presented in this work showed that peptide adsorption can be influenced by its conformational changes induced by suitable adsorbents via strong non-covalent interactions.

The tooth enamel protein, porcine amelogenin, is an intrinsically disordered protein with an extended molecular configuration in the monomeric form

Amelogenins make up a class of proteins associated with the formation of mineralized enamel in vertebrates, possess highly conserved N- and C-terminal sequence regions, and represent an interesting model protein system for understanding biomineralization and protein assembly. Using bioinformatics, we report here the identification of molecular traits that classify 12 amelogenin proteins as members of the intrinsically disordered or unstructured protein family (IDPs), a group of proteins that normally exist as unfolded species but are capable of transformation to a folded state as part of their overall function. Using biophysical techniques (CD and NMR), we follow up on our bioinformatics studies and confirm that one of the amelogenins, recombinant porcine rP172, exists in an extended, unfolded state in the monomeric form. This protein exhibits evidence of conformational exchange between two states, and this exchange may be mediated by Pro residues in the sequence. Although the protein is globally unfolded, we detect the presence of local residual secondary structure [alpha-helix, extended beta-strand, turn/loop, and polyproline type II (PPII)] that may serve several functional roles within the enamel matrix. The extended, labile conformation of rP172 amelogenin is compatible with the known functions of amelogenin in enamel biomineralization, i.e., self-assembly, associations with other enamel matrix proteins and with calcium phosphate biominerals, and interaction with cell receptors. It is likely that the labile structure of this protein facilitates interactions of amelogenin with other macromolecules or with minerals for achievement of internal protein stabilization.

Identification and structural characterization of an unusual RING-like sequence within an extracellular biomineralization protein, AP7

The RING or Really Interesting New Gene represents a family of eukaryotic sequences that bind Zn (II) ions and participate in intracellular processes involving protein-protein interaction. Although found in over 400 different proteins, very little is known regarding the structure-function properties of these domains because of the aggregation problems associated with RING sequences. To augment this data set, we report an unusual 36 AA C-terminal sequence of an extracellular matrix mollusk shell protein, AP7, that exhibits partial homology to the RING family. This Cys, His-containing sequence, termed AP7C, binds Zn (II) and other multivalent ions, but does not utilize a tetracoordinate complexation scheme for binding such as that found in Zn (II) finger polypeptides. Moreover, unlike Zn (II) finger and RING domains, this 36 AA can fold into a relatively stable structure in the absence of Zn (II). This folded structure consists of three short helical segments (A, B, and C), with segments A and B separated by a 4 AA type I beta-turn region and segments B and C separated by a 7 AA loop-like region. Interestingly, the putative RING-like region, -RRPFHECALCYSI-, experiences slow conformational exchange between two structural states in solution, most likely in response to imido ring interconversion at P8 and P21. Poisson-Boltzmann solvation calculations reveal that the AP7C molecular surface possesses a cationic region near its N-terminus, which lies adjacent to the 30 AA mineral modification domain in the AP7 protein. Given that the AP7C sequence does not influence mineralization, it is probable that this cationic pseudo-RING region is utilized by the AP7 protein for other tasks such as protein-protein interaction within the mollusk shell matrix.

Conformational control of inorganic adhesion in a designer protein engineered for cuprous oxide binding

Combinatorial selection of peptides that bind technological materials has emerged as a valuable tool for room-temperature nucleation and assembly of complex nanostructured materials. At present, the parameters that control peptide-solid binding are poorly understood, but such knowledge is needed to build the next generation of hybrid materials. Here, we use a derivative of the DNA binding protein TraI engineered with a disulfide-bonded cuprous oxide binding sequence called CN225 to probe the influence of sequence composition and conformation on Cu2O binding affinity. We previously reported a statistically significant enrichment in paired arginines (RR) among a family of cuprous oxide binding peptides and hypothesized that this is a key motif for binding. However, systematic alanine (A) substitutions in the CN225 RR motif (creating RA, AR, and AA pairs) do not support the hypothesis that RR is critical for Cu2O binding by CN225. Instead, we find that the presentation of the peptide in a disulfide-constrained loop (i.e., the conformation present during combinatorial selection) is crucial for binding to the metal oxide. Our results suggest that caution should be exerted when extrapolating from statistical data and that, in some cases, conformation is more important than composition in determining peptide-inorganic adhesion.

Selection and analysis of solid-binding peptides

Nature has long used peptide- and protein-based manufacturing to create structures whose remarkable mechanical, transport, optical, and even magnetic properties are determined by a fine control of composition and architecture extending from the nanoscale to the macroscale. Although there is much to learn from the tools and strategies that have been evolutionary selected for building biomaterials, accessing compositions and architectures of engineering interest is crucial to the development of the next generation of hybrid functional materials. In recent years, portable amino acid sequences selected from combinatorial libraries and supporting the assembly, nucleation, and geometrical organization of solid phases have emerged as attractive tools for bionanofabrication. Here, we review how these polypeptides are selected and progress in the understanding of their interaction with inorganic and synthetic materials.

Conversion of a monodispersed globular protein into an amyloid-like filament by appending an artificial peptide at the N-terminal

The soluble, globular, alpha-helix-rich peptide SipA(446-684) is a domain of a bacterial protein that binds to mammalian filamentous-actin and re-arranges the host cell's cytoskeleton. We show that adding two copies of NHBP-1, a carbon nanomaterial binding peptide, to its N-terminal can induce SipA(446-684) to polymerize and assume a fibrillar structure under physiological conditions. The fibrils formed showed thioflavine T and Congo red staining profiles that are characteristic of and specific for amyloid-like structures. The alpha-helical structure of the globular protein was retained in the fibrils, suggesting the appended NHBP-1 sequence plays a key role in the formation of cross-beta spines within the fibrils. Consistent with that idea, we observed that a synthetic NHBP-1 peptide can form an amyloid-like structure under appropriate conditions. Thus, our findings add a new subtype of amyloid-like structure formation and suggest this method of assembly could be exploited in nano-biotechnology.