Quantifying the Extent of Hydration of a Surface-Bound Peptide Using Neutron Reflectometry.

Establishing how water, or the absence of water, affects the structure, dynamics, and function of proteins in contact with inorganic surfaces is critical to developing successful protein immobilization strategies. In the present article, the quantity of water hydrating a monolayer of helical peptides covalently attached to self-assembled monolayers (SAMs) of alkyl thiols on Au was measured using neutron reflectometry (NR). The peptide sequence was composed of repeating LLKK units in which the leucines were aligned to face the SAM. When immersed in water, NR measured 2.7 ± 0.9 water molecules per thiol in the SAM layer and between 75 ± 13 and 111 ± 13 waters around each peptide. The quantity of water in the SAM was nearly twice that measured prior to peptide functionalization, suggesting that the peptide disrupted the structure of the SAM. To identify the location of water molecules around the peptide, we compared our NR data to previously published molecular dynamics simulations of the same peptide on a hydrophobic SAM in water, revealing that 49 ± 5 of 95 ± 8 total nearby water molecules were directly hydrogen-bound to the peptide. Finally, we show that immersing the peptide in water compressed its structure into the SAM surface. Together, these results demonstrate that there is sufficient water to fully hydrate a surface-bound peptide even at hydrophobic interfaces. Given the critical role that water plays in biomolecular structure and function, these results are expected to be informative for a broad array of applications involving proteins at the bio/abio interface.

Direct Measurement of Water Permeation in Submerged Alkyl Thiol Self-Assembled Monolayers on Gold Surfaces Revealed by Neutron Reflectometry.

Self-assembled monolayers (SAMs) of alkyl thiols are frequently used to chemically functionalize gold surfaces for applications throughout materials chemistry, electrochemistry, and biotechnology. Despite this, a detailed understanding of the structure of the SAM-water interface generated from both formation and use of the SAM in an aqueous environment is elusive, and analytical measurements of the structure and chemistry of the SAM-water interface are an ongoing experimental challenge. To address this, we used neutron reflectometry (NR) to measure water association with both hydrophobic and hydrophilic SAMs under both wet and dry conditions. SAMs used for this study were made from hydrophobic decanethiol mixed with hydrophilic 11-azido-1-undecanethiol with compositions of 0-100% of the azide-terminated thiol. All SAMs were formed by conventional solution incubation of a Au substrate immersed in ethanol. Each SAM was characterized by grazing incidence angle reflection-absorption Fourier transfer infrared spectroscopy, contact angle goniometry, and electrochemical methods to confirm it was a completely formed monolayer with evidence of extensive crystalline-like domains. NR measured significant absorption of water into each SAM, ranging from 1.6 to 5.7 water molecules per alkyl thiol, when SAMs were immersed in water. Water infiltration was independent of SAM composition and terminal group hydrophilicity. These results demonstrate that water accesses defects, fluid regions, and heterogeneous domains inherent to even well-formed SAMs.

Apyrase suppression raises extracellular ATP levels and induces gene expression and cell wall changes characteristic of stress responses.

Plant cells release ATP into their extracellular matrix as they grow, and extracellular ATP (eATP) can modulate the rate of cell growth in diverse tissues. Two closely related apyrases (APYs) in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, function, in part, to control the concentration of eATP. The expression of APY1/APY2 can be inhibited by RNA interference, and this suppression leads to an increase in the concentration of eATP in the extracellular medium and severely reduces growth. To clarify how the suppression of APY1 and APY2 is linked to growth inhibition, the gene expression changes that occur in seedlings when apyrase expression is suppressed were assayed by microarray and quantitative real-time-PCR analyses. The most significant gene expression changes induced by APY suppression were in genes involved in biotic stress responses, which include those genes regulating wall composition and extensibility. These expression changes predicted specific chemical changes in the walls of mutant seedlings, and two of these changes, wall lignification and decreased methyl ester bonds, were verified by direct analyses. Taken together, the results are consistent with the hypothesis that APY1, APY2, and eATP play important roles in the signaling steps that link biotic stresses to plant defense responses and growth changes.

Preparation and Characterization of Biofunctionalized Inorganic Substrates.

Integrating the function of biological molecules into traditional inorganic materials and substrates couples biologically relevant function to synthetic devices and generates new materials and capabilities by combining biological and inorganic functions. At this so-called "bio/abio interface," basic biological functions such as ligand binding and catalysis can be co-opted to detect analytes with exceptional sensitivity or to generate useful molecules with chiral specificity under entirely benign reaction conditions. Proteins function in dynamic, complex, and crowded environments (the living cell) and are therefore appropriate for integrating into multistep, multiscale, multimaterial devices such as integrated circuits and heterogeneous catalysts. However, the goal of reproducing the highly specific activities of biomolecules in the perturbed chemical and electrostatic environment at an inorganic interface while maintaining their native conformations is challenging to achieve. Moreover, characterizing protein structure and function at a surface is often difficult, particularly if one wishes to compare the activity of the protein to that of the dilute, aqueous solution phase. Our laboratory has developed a general strategy to address this challenge by taking advantage of the structural and chemical properties of alkanethiol self-assembled monolayers (SAMs) on gold surfaces that are functionalized with covalently tethered peptides. These surface-bound peptides then act as the chemical recognition element for a target protein, generating a biomimetic surface in which protein orientation, structure, density, and function are controlled and variable. Herein we discuss current research and future directions related to generating a chemically tunable biofunctionalization strategy that has potential to successfully incorporate the highly specialized functions of proteins onto inorganic substrates.

Fibrillar structures formed by covalently bound, short, ß-stranded peptides on self-assembled monolayers.

The ability to maintain or reproduce biomolecular structures on inorganic substrates has the potential to impact diverse fields such as sensing and molecular electronics, as well as the study of biological self-assembly and structure-function relationships. Because the structure and self-assembly of biomolecules are exquisitely sensitive to their local chemical and electrostatic environment, the goal of reproducing or mimicking biological function in an abiological environment, including at a surface, is challenging. However, simple and well-characterized chemical modifications of prepared surfaces can be used to tune surface chemistry, structure, electrostatics, and reactivity of inorganic materials to facilitate biofunctionalization and function. Here, we describe the covalent attachment of 13-residue ß-stranded peptides containing alkyne groups to a flat gold surface functionalized with an azide-terminated self-assembled monolayer through a Huisgen cycloaddition, or "click", reaction. The chemical composition and structural morphology of these surfaces were characterized using X-ray photoelectron spectroscopy, grazing incidence angle reflection-absorption infrared spectroscopy, surface circular dichroism, and atomic force microscopy. The surface-bound ß-strands self-assemble into antiparallel ß-sheets to form fibrillar structures 24.9 ± 1.6 nm in diameter and 2.83 ± 0.74 nm in height on the reactive surface. The results herein provide a platform for studying and controlling the self-assembly process of biomolecules into larger supermolecular structures while allowing tunable control through chemical functionalization of the surface. Interest in the mechanisms of formation of fibrillar structures has most commonly been associated with neurodegenerative diseases, such as Alzheimer's and Parkinson's, but fibrils may actually represent the thermodynamic low-energy conformation of a much larger class of peptides and proteins. The protocol developed here is an important step toward uncovering not only the factors that dictate self-assembly but also the mechanisms by which this fibrillar class of superstructures forms.

Tuning Epoxy Thermomechanics via Thermal Isomerization: A Route to Negative Coefficient of Thermal Expansion Materials.

Fine control over the thermal expansion and contraction behavior of polymer materials is challenging. Most polymers have large coefficients of thermal expansion (CTEs), which preclude long performance lifetimes of composite materials. Herein, we report the design and synthesis of epoxy thermosets with low CTE values below their Tg and large contraction behavior above Tg by incorporating thermally contractile dibenzocyclooctane (DBCO) motifs within the thermoset network. This atypical thermomechanical behavior was rationalized in terms of a twist-boat to chair conformational equilibrium of the DBCO linkages. We anticipate these findings to be generally useful in the preparation of materials with designed CTE values.

Nanoscale Resolution of Electric-field Induced Motion in Ionic Diblock Copolymer Thin Films.

Understanding the responses of ionic block copolymers to applied electric fields is crucial when targeting applications in areas such as energy storage, microelectronics, and transducers. This work shows that the identity of counterions in ionic diblock copolymers substantially affects their responses to electric fields, demonstrating the importance of ionic species for materials design. In situ neutron reflectometry measurements revealed that thin films containing imidazolium based cationic diblock copolymers, tetrafluoroborate counteranions led to film contraction under applied electric fields, while bromide counteranions drove expansion under similar field strengths. Coarse-grained molecular dynamics simulations were used to develop a fundamental understanding of these responses, uncovering a nonmonotonic trend in thickness change as a function of field strength. This behavior was attributed to elastic responses of microphase separated diblock copolymer chains resulting from variations in interfacial tension of polymer-polymer interfaces due to the redistribution of counteranions in the presence of electric fields.

Review: recent advances and current challenges in scanning probe microscopy of biomolecular surfaces and interfaces.

The introduction of scanning probe microscopy (SPM) techniques revolutionized the field of condensed matter science by allowing researchers to probe the structure and composition of materials on an atomic scale. Although these methods have been used to make molecular- and atomic-scale measurements on biological systems with some success, the biophysical sciences remain on the cusp of a breakthrough with SPM technologies similar in magnitude to that experienced by fields related to solid-state surfaces and interfaces. Numerous challenges arise when attempting to connect biological molecules that are often delicate, dynamic, and complex with the experimental requirements of SPM techniques. However, there are a growing number of studies in which SPM has been successfully used to achieve subnanometer resolution measurements in biological systems where carefully designed and prepared samples have been paired with appropriate SPM techniques. We review significant recent innovations in applying SPM techniques to biological molecules, and highlight challenges that face researchers attempting to gain atomic- and molecular-level information of complex biomolecular structures.