Rosetta-Enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins.

While loop motifs frequently play a major role in protein function, our understanding of how to rationally engineer proteins with novel loop domains remains limited. In the absence of rational approaches, the incorporation of loop domains often destabilizes proteins, thereby requiring massive screening and selection to identify sites that can accommodate loop insertion. We developed a computational strategy for rapidly scanning the entire structure of a scaffold protein to determine the impact of loop insertion at all possible amino acid positions. This approach is based on the Rosetta kinematic loop modeling protocol and was demonstrated by identifying sites in lipase that were permissive to insertion of the LAP peptide. Interestingly, the identification of permissive sites was dependent on the contribution of the residues in the near-loop environment on the Rosetta score and did not correlate with conventional structural features (e.g., B-factors). As evidence of this, several insertion sites (e.g., following residues 17, 47-49, and 108), which were predicted and confirmed to be permissive, interrupted helices, while others (e.g., following residues 43, 67, 116, 119, and 121), which are situated in loop regions, were nonpermissive. This approach was further shown to be predictive for ß-glucosidase and human phosphatase and tensin homologue (PTEN), and to facilitate the engineering of insertion sites through in silico mutagenesis. By enabling the design of loop-containing protein libraries with high probabilities of soluble expression, this approach has broad implications in many areas of protein engineering, including antibody design, improving enzyme activity, and protein modification.

Differential presentation of a single antimicrobial peptide is sufficient to identify LPS from distinct bacterial samples.

Rapid detection and identification of bacteria is important for human health, biodefense, and food safety. Small arrays of different antimicrobial peptides (AMPs) enable the identification of lipopolysaccharide (LPS) samples from a variety of bacterial species and strains. A model system for examining how peptide presentation affects LPS detection is the sheep myeloid antimicrobial peptide (SMAP-29), which contains a helix-turn-helix motif. Varying the cysteine attachment site on SMAP-29 controls the three-dimensional presentation of the peptide on the surface, altering the ability of the peptide to discriminate between LPS samples. A small array of only SMAP-29 variants-and no other peptides-is capable of discriminating among LPS samples from multiple bacterial species, as well as between different strains within the same species, with high accuracy.

A Multifunctional Surface That Simultaneously Balances Hydrophilic Enzyme Catalysis and Hydrophobic Water Repellency.

The compatibility of multiple functions at a single interface is difficult to achieve, but is even more challenging when the functions directly counteract one another. This study provides insight into the creation of a simultaneously multifunctional surface formed by balancing two orthogonal functions; water repellency and enzyme catalysis. A partially fluorinated thiol is used to impart bulk hydrophobicity on the surface, and an N-hydroxysuccinimide ester-terminated thiol provides a specific anchoring sites for the covalent enzyme attachment. Different ratios of the two thiols are mixed together to form amphiphilic self-assembled monolayers, which are characterized with polarization-modulation infrared reflection-absorption spectroscopy and contact angle goniometry. The enzyme activity is measured by a fluorescence assay. With the results collected here, specific surface compositions are identified at which the orthogonal functions of water repellency and enzyme catalysis are balanced and exist simultaneously. An understanding of how to effectively balance orthogonal functions at surfaces can be extended to a number of higher-scale applications.

Different interfacial behaviors of N- and C-terminus cysteine-modified cecropin P1 chemically immobilized onto polymer surface.

Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) were used to investigate the orientation of N-terminus cysteine-modified cecropin P1 (cCP1) at the polystyrene maleimide (PS-MA)/peptide phosphate buffer solution interface. The cCP1 cysteine group reacts with the maleimide group on the PS-MA surface to chemically immobilize cCP1. Previously, we found that the C-terminus cysteine-modified cecropin P1 (CP1c) molecules exhibit a multiple-orientation distribution at the PS-MA/peptide phosphate buffer solution interface, due to simultaneous physical adsorption and chemical immobilization of CP1c on the PS-MA surface. Differently, in this research, it was found that the interfacial orientation of cCP1 molecules varied from a horizontal orientation to the "tilting" orientation to the "standing up" orientation and then to the "multiple-orientation" distribution as the peptide concentration increased from 0.19 to 3.74 µM. This research shows the different interaction mechanisms between CP1c and PS-MA and between cCP1 and PS-MA.

Detection and classification of related lipopolysaccharides via a small array of immobilized antimicrobial peptides.

A small array of antimicrobial peptides comprising three cysteine-terminated natural sequences covalently immobilized to pendant surface maleimide groups are used to bind and successfully discriminate five types of lipopolysaccharide (LPS) molecules. Using surface plasmon resonance, LPSs isolated from four strains of Escherichia coli and one strain of Pseudomonas aeruginosa yield distinct binding profiles to the three immobilized peptides. Linear discriminant analysis generated 100% training set and 80% validation set classification success for the 40 samples evaluated. This work demonstrates the discriminatory binding capabilities of immobilized antimicrobial peptides toward LPS molecules and alludes to their use as probes in pathogen sensing devices potentially superior to the current state-of-the-art.

High-Throughput Multiobjective Optimization of Patterned Multifunctional Surfaces.

The realization and optimization of multifunctional materials is difficult, especially when the functionalities are directly incompatible. For example, it is challenging to make surfaces both enzymatically active and water repellent, as these two properties are directly competitive because of the hydrophilic nature of the enzyme-laden surfaces. Patterning discrete domains of distinct functionalities can represent a path to multifunctionality, but the innumerable possible domain permutations present a major barrier to optimizing performance. Here, we develop a high-throughput approach for exploring patterned multifunctional surfaces that is inspired by the microtiter plate architecture. As a model system, patterned surfaces are realized with horseradish peroxidase-decorated domains amidst a background of hydrophobic fluorinated self-assembled monolayers. In experiments exploring effects of pattern geometry, the measured enzyme activity is dependent only on the surface coverage. In contrast, roll-off behavior strongly depends on the parameters of the pattern geometry. Importantly, this finding enables the precise tailoring of distinct wetting behavior of the surfaces in a manner that is independent of their enzymatic activity. The high-throughput nature of the platform facilitates multiobjective optimization of surface functionalities in a general and flexible manner.

3D printed self-supporting elastomeric structures for multifunctional microfluidics.

Microfluidic devices fabricated via soft lithography have demonstrated compelling applications such as lab-on-a-chip diagnostics, DNA microarrays, and cell-based assays. These technologies could be further developed by directly integrating microfluidics with electronic sensors and curvilinear substrates as well as improved automation for higher throughput. Current additive manufacturing methods, such as stereolithography and multi-jet printing, tend to contaminate substrates with uncured resins or supporting materials during printing. Here, we present a printing methodology based on precisely extruding viscoelastic inks into self-supporting microchannels and chambers without requiring sacrificial materials. We demonstrate that, in the submillimeter regime, the yield strength of the as-extruded silicone ink is sufficient to prevent creep within a certain angular range. Printing toolpaths are specifically designed to realize leakage-free connections between channels and chambers, T-shaped intersections, and overlapping channels. The self-supporting microfluidic structures enable the automatable fabrication of multifunctional devices, including multimaterial mixers, microfluidic-integrated sensors, automation components, and 3D microfluidics.

Graphene Nanoplatelet-Polymer Chemiresistive Sensor Arrays for the Detection and Discrimination of Chemical Warfare Agent Simulants.

A cross-reactive array of semiselective chemiresistive sensors made of polymer-graphene nanoplatelet (GNP) composite coated electrodes was examined for detection and discrimination of chemical warfare agents (CWA). The arrays employ a set of chemically diverse polymers to generate a unique response signature for multiple CWA simulants and background interferents. The developed sensors' signal remains consistent after repeated exposures to multiple analytes for up to 5 days with a similar signal magnitude across different replicate sensors with the same polymer-GNP coating. An array of 12 sensors each coated with a different polymer-GNP mixture was exposed 100 times to a cycle of single analyte vapors consisting of 5 chemically similar CWA simulants and 8 common background interferents. The collected data was vector normalized to reduce concentration dependency, z-scored to account for baseline drift and signal-to-noise ratio, and Kalman filtered to reduce noise. The processed data was dimensionally reduced with principal component analysis and analyzed with four different machine learning algorithms to evaluate discrimination capabilities. For 5 similarly structured CWA simulants alone 100% classification accuracy was achieved. For all analytes tested 99% classification accuracy was achieved demonstrating the CWA discrimination capabilities of the developed system. The novel sensor fabrication methods and data processing techniques are attractive for development of sensor platforms for discrimination of CWA and other classes of chemical vapors.

The effects of solution structure on the surface conformation and orientation of a cysteine-terminated antimicrobial peptide cecropin P1.

The surface structure of an antimicrobial peptide, cecropin P1, immobilized to a gold surface via a terminal cysteine residue was investigated. Using reflection-absorption infrared spectroscopy, surface plasmon resonance, and X-ray photoelectron spectroscopy, the effects of pH, solution conformation, and concentration on the immobilized peptide conformation, average orientation, and surface density were determined. Under all conditions investigated, the immobilized peptides were alpha-helical in a predominately flat, random orientation. The addition of the reducing agent Tris(2-carboxyethyl) phosphine hydrochloride to the buffer resulted in a twofold increase in immobilized peptide surface density.