EKylation: Addition of an Alternating-Charge Peptide Stabilizes Proteins.

For nearly 40 years, therapeutic proteins have been stabilized by chemical conjugation of polyethylene glycol (PEG), but recently zwitterionic materials have proved to be a more effective substitute. In this work, we demonstrate that genetic fusion of alternating-charge extensions consisting of anionic glutamic acid (E) and cationic lysine (K) is an effective strategy for protein stabilization. This bioinspired "EKylation" method not only confers the stabilizing benefits of poly(zwitterions) but also allows for rapid biosynthesis of target constructs. Poly(EK) peptides of different predetermined lengths were appended to the C-terminus of a native ß-lactamase and its destabilized TEM-19 mutant. The EK-modified enzymes retained biological activity and exhibited increased stability to environmental stressors such as high temperature and high-salt solutions. This one-step strategy provides a broadly applicable alternative to synthetic polymer conjugation that is biocompatible and degradable.

Cellulose paper sensors modified with zwitterionic poly(carboxybetaine) for sensing and detection in complex media.

Poly(carboxybetaine) (PCB) functionalized cellulose paper was used as a paper-based microfluidic device. The results showed that the PCB modified paper sensor was able to achieve (a) more rapid and sensitive glucose detection from undiluted human serum compared to bare cellulose and (b) specific antigen detection via covalently immobilized antibodies.

Biologically inspired stealth peptide-capped gold nanoparticles.

Introduction into the human body makes most nanoparticle systems susceptible to aggregation via nonspecific protein binding. Here, we developed a peptide-capped gold nanoparticle platform that withstands aggregation in undiluted human serum at 37 °C for 24 h. This biocompatible and natural system is based on mimicking human proteins which are enriched in negatively charged glutamic acid and positively charged lysine residues on their surface. The multifunctional EKEKEKE-PPPPC-Am peptide sequence consists of a stealth glutamic acid/lysine portion combined with a surface anchoring linker containing four prolines and a cysteine. Particle stability was measured via optical spectroscopy and dynamic light scattering in single protein, high salt, and undiluted human serum solutions. In vitro cell experiments demonstrate EKEKEKE-PPPPC-Am capped gold nanoparticles effectively minimize nonspecific cell uptake by nonphagocytic bovine aortic endothelial cells and phagocytic murine macrophage RAW 264.7 cells. Cytotoxicity studies show that peptide-capped gold nanoparticles do not affect cell viability. Finally, the peptide EKEKEKE-PPPPC-Am was extended with cyclic RGD to demonstrate specific cell targeting and stealth without using poly(ethylene glycol). Adding the functional peptide via peptide sequence extension avoids complex conjugation chemistries that are used for connection to synthetic materials. Inductively coupled plasma mass spectroscopy results indicate high aortic bovine endothelial cell uptake of c[RGDfE(SGG-KEKEKE-PPPPC-Am)] capped gold nanoparticles and low uptake of the control scrambled sequence c[RDGfE(SGG-KEKEKE-PPPPC-Am)] capped gold nanoparticles.

Free energy of solvated salt bridges: a simulation and experimental study.

Charged amino acids are the most common on surfaces of proteins and understanding the interactions between these charged amino acids, salt bridging, is crucial for understanding protein-protein interactions. Previous simulations have been limited to implicit solvent or fixed binding geometry due to the sampling required for converged free energies. Using well-tempered metadynamics, we have calculated salt bridge free energy surfaces in water and confirmed the results with NMR experiments. The simulations give binding free energies, quantitative ranking of salt bridging strength, and insights into the hydration of the salt bridges. The arginine-aspartate salt bridge was found to be the weakest and arginine-glutamate the strongest, showing that arginine can discriminate between aspartate and glutamate, whereas the salt bridges with lysine are indistinguishable in their free energy. The salt bridging hydration is found to be complementary to salt bridge orientation with arginine having specific orientations.

Standardizing and simplifying analysis of peptide library data.

Peptide libraries allow researchers to quickly find hundreds of peptide sequences with a desired property. Currently, the large amount of data generated from peptide libraries is analyzed by hand, where researchers search for repeating patterns in the peptide sequences. Such patterns are called motifs. In this work, we describe a set of algorithms which allow quick, efficient, and standard analysis of peptide libraries. Four main techniques are described: (1) choice of the number of motifs present in a peptide library; (2) separation of the peptides into groups of similar sequences; (3) fitting of a model to the peptides to extract motifs; (4) analysis of the library using quantitative structure-property relationships if no clear motifs are present. The application of five previously published data sets shows these techniques can automatically repeat the work of experts quickly and allow much more flexibility in analysis. A new way of visually presenting peptide libraries is also described, which allows visual inspection of the grouping and spread of sequences. The algorithms have been implemented in an open-source plug-in called "peplib" and an online web application.

Screening nonspecific interactions of peptides without background interference.

The need to discover new peptide sequences to perform particular tasks has lead to a variety of peptide screening methods: phage display, yeast display, bacterial display and resin display. These are effective screening methods because the role of background binding is often insignificant. In the field of nonfouling materials, however, a premium is placed on chemistries that have extremely low levels of nonspecific binding. Due to the presence of background binding, it is not possible to use traditional peptide screening methods to select for nonfouling chemistries. Here, we developed a peptide screening method, as compared to traditional methods, that can successfully evaluate the effectiveness of nonfouling peptide sequences. We have tested the effect of different peptide lengths and chemistries on the adsorption of protein. The order of residues within a single sequence was also adjusted to determine the effect of charge segregation on protein adsorption.

Surface initiated atom transfer radical polymerization grafting of sodium styrene sulfonate from titanium and silicon substrates.

This study investigates the grafting of poly-sodium styrene sulfonate (pNaSS) from trichlorosilane/10-undecen-1-yl 2-bromo-2-methylpropionate functionalized Si and Ti substrates by atom transfer radical polymerization (ATRP). The composition, molecular structure, thickness, and topography of the grafted pNaSS films were characterized with x-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), variable angle spectroscopic ellipsometry (VASE), and atomic force microscopy (AFM), respectively. XPS and ToF-SIMS results were consistent with the successful grafting of a thick and uniform pNaSS film on both substrates. VASE and AFM scratch tests showed the films were between 25 and 49 nm thick on Si, and between 13 and 35 nm thick on Ti. AFM determined root-mean-square roughness values were ∼2 nm on both Si and Ti substrates. Therefore, ATRP grafting is capable of producing relatively smooth, thick, and chemically homogeneous pNaSS films on Si and Ti substrates. These films will be used in subsequent studies to test the hypothesis that pNaSS-grafted Ti implants preferentially adsorb certain plasma proteins in an orientation and conformation that modulates the foreign body response and promotes formation of new bone.

The effect of lightly crosslinked poly(carboxybetaine) hydrogel coating on the performance of sensors in whole blood.

Surface coatings of high packing densities have been routinely used to prevent nonspecific biomolecular and microorganism attachment. Hydrogels are another class of low fouling materials used to create three-dimensional matrixes for the free diffusion of small analytes or drugs and the high-loading of bio-recognition elements. However, biomolecules are subject to being entrapped within hydrogel matrixes or adhered onto hydrogel surfaces, making them questionable for use in whole blood. Here, we demonstrate the feasibility of a lightly crosslinked poly(carboxybetaine) hydrogel for use in whole blood, as opposite to the conventional wisdom of high packing density in surface coatings. Proteins are able to diffuse in and out of the matrix freely without being altered from their native conformations. In order to demonstrate its long-term performance in whole blood, this hydrogel was used as the surface coating of a glucose sensor. This work paves a new way for the development of surface coatings and sensors to achieve long-term stability and high performance in whole blood.

Simple and robust approach for passivating and functionalizing surfaces for use in complex media.

Pluronic is a popular triblock copolymer used as a surfactant to introduce hydrophilic coatings onto many different types of material surfaces, from engineering to biomedical applications. Unfortunately, this is limited in its ability to resist fouling from complex media (i.e., blood) and leaves the surface hard for further modification. Herein, we report a simple, yet robust approach for passivating and functionalizing surfaces based on zwitterionic poly(carboxybetaine) (PCB) based triblock copolymer, which can be directly applied to surfaces to prevent nonspecific protein adsorption from undiluted blood plasma, and to provide additional functionalities needed for the attachment of biomolecules. Several hydrophobic surfaces including polydimethylsiloxane, silanized silica, and self-assembled monolayers are tested to demonstrate its applicability to a wide range of systems. This approach provides a robust, convenient, and effective surface modification method for real-world applications from simple surface passivation to specific targeting in complex media.

Suppressing surface reconstruction of superhydrophobic PDMS using a superhydrophilic zwitterionic polymer.

Poly(dimethyl siloxane) (PDMS) is extensively used for biomedical applications due to its low cost, ease of fabrication, high durability and flexibility, oxygen permeability, and self-healing properties. PDMS, however, has some significant drawbacks. PDMS endures unacceptably high levels of nonspecific protein fouling when used with biological samples due to its superhydrophobic characteristics. Unfortunately, conventional surface modification methods do not work for PDMS due to its low glass transition temperature. This phenomenon has been well-known for years as "hydrophobic regeneration". For the same reason, it is also very difficult to bring functionalities onto PDMS surfaces. Herein, we demonstrate how a superhydrophilic zwitterionic material, poly(carboxybetaine methacrylate) (pCBMA), can provide a highly stable coating with long-term stabilty due to the sharp contrast in hydrophobicity between pCBMA and PDMS. This material is able to suppress nonspecific protein adsorption in complex media and functionalize desired biomolecules needed in applications, such as diagnostics, without sacrificing its nonfouling characteristics.

Sequence, structure, and function of peptide self-assembled monolayers.

Cysteine is commonly used to attach peptides onto gold surfaces. Here we show that the inclusion of an additional linker with a length of four residues (-PPPPC) and a rigid, hydrophobic nature is a better choice for forming peptide self-assembled monolayers (SAMs) with a well-ordered structure and high surface density. We compared the structure and function of the nonfouling peptide EKEKEKE-PPPPC-Am with EKEKEKE-C-Am. Circular dichroism, attenuated total internal reflection Fourier transform IR spectroscopy, and molecular dynamics results showed that EKEKEKE-PPPPC-Am forms a secondary structure while EKEKEKE-C-Am has a random structure. Surface plasmon resonance sensor results showed that protein adsorption on EKEKEKE-PPPPC-Am/gold is very low with small variation while protein adsorption on EKEKEKE-C-Am/gold is high with large variation. X-ray photoelectron spectroscopy results showed that both peptides have strong gold-thiol binding with the gold surface, indicating that their difference in protein adsorption is due to their assembled structures. Further experimental and simulation studies were performed to show that -PPPPC is a better linker than -PC, -PPC, and -PPPC. Finally, we extended EKEKEKE-PPPPC-Am with the cell-binding sequence RGD and demonstrated control over specific versus nonspecific cell adhesion without using poly(ethylene glycol). Adding a functional peptide to the nonfouling EK sequence avoids complex chemistries that are used for its connection to synthetic materials.

Poly(zwitterionic)protein conjugates offer increased stability without sacrificing binding affinity or bioactivity.

Treatment with therapeutic proteins is an attractive approach to targeting a number of challenging diseases. Unfortunately, the native proteins themselves are often unstable in physiological conditions, reducing bioavailability and therefore increasing the dose that is required. Conjugation with poly(ethylene glycol) (PEG) is often used to increase stability, but this has a detrimental effect on bioactivity. Here, we introduce conjugation with zwitterionic polymers such as poly(carboxybetaine). We show that poly(carboxybetaine) conjugation improves stability in a manner similar to PEGylation, but that the new conjugates retain or even improve the binding affinity as a result of enhanced protein-substrate hydrophobic interactions. This chemistry opens a new avenue for the development of protein therapeutics by avoiding the need to compromise between stability and affinity.