Modular, self-assembling peptide linkers for stable and regenerable carbon nanotube biosensor interfaces

In silico screening for oligopeptides useful as capture and reporting probes for interleukin-6 biosensing

IL-6 is an important interleukin associated with inflammation and several diseases such as cancer. Evaluation of its levels in human blood sera is a critical step for an accurate diagnosis of the diseases. Our goal is to design peptides that can selectively bind in different poses with good affinities to IL-6. For this purpose, we started from the crystal structures of different IL-6/protein complexes available in the Protein Data Bank (PDB) to select short peptides in the interaction zones, in which we intentionally introduced point mutations to increase their stability and affinity. To examine their usefulness as capture and reporting probes for the IL-6 biosensing, the five peptides and their interaction with IL-6 were studied in saline aqueous solution. Molecular docking, MD, and MM-PBSA were used to investigate the affinity and stability of these complexes. The conformational changes, the distance between the mass centers, the gyration radii, and the numbers of hydrogen bonds were analyzed to select the most suitable candidates. Three peptides, namely CTE17, CAY15 and CSE25, have the highest affinities presenting significant numbers of residues that have contact frequencies greater than 50% of simulation run time and are the most promising candidates. CTE17 and CSE25 showed they can form a stable sandwich with the target protein. For sake of comparison, we examined the previously known peptides (FND20, INL19 and CEK17) having affinity to IL-6 and the affinity of the lead i.e. CSE25 to two other interleukin family members (IL-4 and to IL-10).

Engineering soluble artificial epidermal growth factor receptor mimics capable of spontaneous in vitro dimerization

Epidermal growth factor receptor (EGFR) is a clinically validated target for a multitude of human cancers. The receptor is activated upon ligand binding through a critical dimerization step. Dimerization can be replicated in vitro by locally concentrating the receptor kinase domains on the surface of lipid-based vesicles. In this study we investigated the use of coiled coils to induce spontaneous receptor kinase domain dimerization in vitro to form non-membrane-bound artificial receptor mimics in solution. Two engineered forms of EGFR kinase domain fused to coiled coil complementary peptides were designed to self-associate upon mixing. Two fusion protein species (P3-EGFR and P4-EGFR) independently showed the same activity and polymerization profile known to exist with EGFR kinase domains. Upon mixing the two species, coiled coil heterodimers were formed that induced EGFR association to form dimers of the kinase domains. This was accompanied by 11.5-fold increase in the phosphorylation rate indicative of kinase domain activation equivalent to the levels achieved using vesicle localization and mimicking in vivo ligand-induced activation. This study presents a soluble tyrosine kinase receptor mimic capable of spontaneous in vitro activation that can facilitate functional and drug discovery studies for this clinically important receptor class.

Smart self-assembled hybrid hydrogel biomaterials

Hybrid biomaterials are systems created from components of at least two distinct classes of molecules, for example, synthetic macromolecules and proteins or peptide domains. The synergistic combination of two types of structures may produce new materials that possess unprecedented levels of structural organization and novel properties. This Review focuses on biorecognition-driven self-assembly of hybrid macromolecules into functional hydrogel biomaterials. First, basic rules that govern the secondary structure of peptides are discussed, and then approaches to the specific design of hybrid systems with tailor-made properties are evaluated, followed by a discussion on the similarity of design principles of biomaterials and macromolecular therapeutics. Finally, the future of the field is briefly outlined.

Self-assembly of coiled coils in synthetic biology: inspiration and progress

Biological self-assembly is very complex and results in highly functional materials. In effect, it takes a bottom-up approach using biomolecular building blocks of precisely defined shape, size, hydrophobicity, and spatial distribution of functionality. Inspired by, and drawing lessons from self-assembly processes in nature, scientists are learning how to control the balance of many small forces to increase the complexity and functionality of self-assembled nanomaterials. The coiled-coil motif, a multipurpose building block commonly found in nature, has great potential in synthetic biology. In this review we examine the roles that the coiled-coil peptide motif plays in self-assembly in nature, and then summarize the advances that this has inspired in the creation of functional units, assemblies, and systems.

Synthesis and electrochemical probing of water-soluble poly(sodium 4-styrenesulfonate-co-acrylic acid)-grafted multiwalled carbon nanotubes

Water-soluble poly(sodium 4-styrenesulfonate-co-acrylic acid)-grafted multiwalled carbon nanotubes (MWNT-g-P(SSS-co-AA)) with core-shell nanostructure were successfully synthesized by in situ free radical copolymerization of sodium 4-strenesulfonate (SSS) and acrylic acid (AA) in the presence of MWNTs terminated with vinyl groups; their structure was characterized by FTIR, (1)H NMR, Raman, TGA and TEM. The results showed that the thickness and content of the copolymer layer grafted onto the MWNT surface are about 7-12 nm and 82.3%, respectively. The P(SSS-co-AA) covalently grafted on MWNTs provides MWNT-g-P(SSS-co-AA) with good hydrophilicity and solubility in water. Then a novel MWNT-g-P(SSS-co-AA)-modified glassy carbon electrode was fabricated by coating; its electrochemical properties were evaluated by electrochemical probe of K(3)[Fe(CN)(6)], and its catalytic behaviors to the electrochemical oxidation processes of dopamine (DA) and serotonin (5-HT) were investigated. Since the MWNT-g-P(SSS-co-AA)-modified electrode possesses strong electron transfer capability, high electrochemical activity and catalytic ability, it can be used in sensitive, selective, rapid and simultaneous monitoring of biomolecules.

Conformational Selectivity of Peptides for Single-Walled Carbon Nanotubes

Carbon nanotubes show promising prospects for applications ranging from molecular electronics to ultrasensitive biosensors. An important aspect to understanding carbon nanotube properties is their interactions with biomolecules such as peptides and proteins, as these interactions are important in our understanding of nanotube interactions with the environment, their use in cellular systems, as well as their interface with biological materials for medical and diagnostic applications. Here we report the sequence and conformational requirements of peptides for high-affinity binding to single-walled carbon nanotubes (SWNTs). A new motif, X(1)THX(2)X(3)PWTX(4), where X(1) is G or H, X(2) is H or D or null, X(3) is null or R, and X4 is null or K, was identified from two classes of phage-displayed peptide libraries. The high affinity binding of the motif to SWNTs required constrained conformations which were achieved through either the extension of the amino acid sequence (e.g., LLADTTHHRPWT) or the addition of a constrained disulfide bond (e.g., CGHPWTKC). This motif shows specific high-affinity to the currently studied SWNTs, compared to previously reported peptides. The conformations of the identified peptides in complex with SWNTs were also characterized with a variety of biophysical methodologies including CD, fluorescence, NMR spectroscopy, and molecular modeling.