Asymmetric -helicity loss within a peptide adsorbed onto charged colloidal substrates

Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity

Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.

Interactions between Oligoethylene Glycol-Capped AuNPs and Attached Peptides Control Peptide Structure

Peptide-functionalized nanoparticles (NPs) often rely on a well-defined peptide structure to function. Here, we report the attachment of model peptides to the ligand shell of AuNPs passivated with oligoethylene glycol (OEG). Specifically, peptides containing the repeating (LLKK)_n motif plus either one or two reactive functional groups were covalently linked to OEG-capped, ∼5 nm AuNPs via the Cu⁺-catalyzed azide-alkyne cycloaddition reaction. This work builds on a previous study from our group in which an (LLKK)_n peptide having two reactive functional groups was considered. Peptide attachment was confirmed by FTIR spectroscopy. Amino acid analysis was used to determine that 3-4 peptides were immobilized per AuNP. Circular dichroism spectroscopy revealed a structural change from random coil in solution to α-helical upon attachment to OEG-capped AuNPs. The key result of this study is that the nature of the capping layer on the AuNP surface influences peptide structure to a significant degree. Other important findings resulting from this work are that the AuNP-peptide conjugates reported here are water soluble and that the long axis of the helical peptides is oriented tangent to the AuNP surface. The latter point is important for applications involving biorecognition.

Conjugation of an α-Helical Peptide to the Surface of Gold Nanoparticles

We are interested in functionalizing gold nanoparticles (AuNPs) with proteins using a biomimetic approach in which an intermediate peptide "glue" directs the orientation of a protein relative to the AuNP surface. The first step toward this goal is described in the present article. Specifically, we show that ∼5 nm AuNPs can be functionalized with a mixed self-assembled monolayer (SAM) consisting of oligo(ethylene glycol) alkanethiols terminated with either hydroxyl or azide groups, and that the resulting materials are stable and soluble in water. The azide groups on the surface of the AuNPs can be subsequently linked to alkyne-functionalized peptides via a copper-catalyzed azide-alkyne cycloaddition (click) reaction. Analysis of the resulting material by Fourier transform infrared and circular dichroism spectroscopy demonstrates that the peptide is covalently linked to the SAM and that it exists in an α-helical conformation. In addition to our intended purpose of using these highly structured, biomimetic materials to orient proteins, they may also be useful for applications involving interactions between nanoparticles and cells.

Bilirubin Oxidase Adsorption onto Charged Self-Assembled Monolayers: Insights from Multiscale Simulations

The efficient immobilization and orientation of bilirubin oxidase (BOx) on different solid substrates are essential for its application in biotechnology. The T1 copper site within BOx is responsible for the electron transfer. In order to obtain quick direct electron transfer (DET), it is important to keep the distance between the T1 copper site and electrode surface small and to maintain the natural structure of BOx at the same time. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of BOx from Myrothecium verrucaria (MvBOx) adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH₂-SAM with different surface charge densities (±0.05 and ±0.19 C·m^-2). The results show that MvBOx adsorbs on negatively charged surfaces with a "back-on" orientation, whereas on positively charged surfaces, MvBOx binds with a "lying-on" orientation. The locations of the T1 copper site are closer to negatively charged surfaces. Furthermore, for negatively charged surfaces, the T1 copper site prefers to orient closer to the surface with lower surface charge density. Therefore, the negatively charged surface with low surface charge density is more suitable for the DET of MvBOx on electrodes. Besides, the structural changes primarily take place on the relatively flexible turns, coils, and α-helix. The native structure of MvBOx is well preserved when it adsorbs on both charged surfaces. This work sheds light on the controlling orientation and conformational information on MvBOx on charged surfaces at the atomistic level. This understanding would certainly promote our understanding of the mechanism of MvBOx immobilization and provide theoretical support for BOx-based bioelectrode design.

Single Molecule Force Spectroscopy and Molecular Dynamics Simulations as a Combined Platform for Probing Protein Face-Specific Binding

Biomolecular interactions frequently occur in orientation-specific manner. For example, prior nuclear magnetic resonance spectroscopy experiments in our lab have suggested the presence of a group of strongly binding residues on a particular face of the protein ubiquitin for interactions with Capto MMC multimodal ligands ("Capto" ligands) (Srinivasan, K.; et al. Langmuir 2014, 30 (44), 13205-13216). We present a clear confirmation of those studies by performing single-molecule force spectroscopy (SMFS) measurements of unbinding complemented with molecular dynamics (MD) calculations of the adsorption free energy of ubiquitin in two distinct orientations with self-assembled monolayers (SAMs) functionalized with "Capto" ligands. These orientations were maintained in the SMFS experiments by tethering ubiquitin mutants to SAM surfaces through strategically located cysteines, thus exposing the desired faces of the protein. Analogous orientations were maintained in MD simulations using suitable constraining methods. Remarkably, despite differences between the finer details of experimental and simulation methodologies, they confirm a clear preference for the previously hypothesized binding face of ubiquitin. Furthermore, MD simulations provided significant insights into the mechanism of protein binding onto this multimodal surface. Because SMFS and MD simulations both directly probe protein-surface interactions, this work establishes a key link between experiments and simulations at molecular scale through the determination of protein face-specific binding energetics. Our approach may have direct applications in biophysical systems where face- or orientation-specific interactions are important, such as biomaterials, sensors, and biomanufacturing.

Secondary Structure Determination of Peptides and Proteins After Immobilization

The presentation of immobilized peptides and other small biomolecules attached to surfaces can be greatly affected by the attachment chemistry and linking moieties, resulting in altered activity and specificity. For this reason, it is critical to understand how the various aspects of surface immobilization-underlying substrate properties, tether structure, and site of linkage-affect the secondary and quaternary structures of the immobilized species. Here, we present methods for attaching cysteine-containing peptides to quartz surfaces and determining the secondary structure of surface-immobilized peptides. We specifically show that, even when covalently immobilized, changes in peptide conformation can still occur, with measurement occurring in real time.

Investigation into the molecular and thermodynamic basis of protein interactions in multimodal chromatography using functionalized nanoparticles

Although multimodal chromatography offers significant potential for bioseparations, there is a lack of molecular level understanding of the nature of protein binding in these systems. In this study a nanoparticle system is employed that can simulate a chromatographic resin surface while also being amenable to isothermal titration calorimetry (ITC) and solution NMR. ITC and NMR titration experiments are carried out with (15)N-labeled ubiquitin to investigate the interactions of ubiquitin with nanoparticles functionalized with two industrially important multimodal ligands. The ITC results suggest that binding to both multimodal ligand surfaces is entropically driven over a range of temperatures and that this is due primarily to the release of surface bound waters. In order to reveal structural details of the interaction process, binding-induced chemical shift changes obtained from the NMR experiments are employed to obtain dissociation constants of individual amino acid residues on the protein surface. The residue level information obtained from NMR is then used to identify a preferred binding face on ubiquitin for interaction to both multimodal ligand surfaces. In addition, electrostatic potential and spatial aggregation propensity maps are used to determine important protein surface property data that are shown to correlate well with the molecular level information obtained from NMR. Importantly, the data demonstrate that the cluster of interacting residues on the protein surface act co-operatively to give rise to multimodal binding affinities several orders of magnitude greater than those obtained previously for interactions with free solution ligands. The use of NMR and ITC to study protein interactions with functionalized nanoparticles offers a new tool for obtaining important molecular and thermodynamic insights into protein affinity in multimodal chromatographic systems.

Computational prediction of circular dichroism spectra and quantification of helicity loss upon peptide adsorption on silica

Circular dichroism (CD) spectroscopy is one of the few experimental techniques sensitive to the structural changes that peptides undergo when they adsorb on inorganic material surfaces, a problem of deep significance in medicine, biotechnology, and materials science. Although the theoretical calculation of the CD spectrum of a molecule in a given conformation can be routinely performed, the inverse problem of extracting atomistic structural details from a measured spectrum is not uniquely determined. Especially complicated is the case of oligopeptides, whose folding/unfolding energy landscapes are often very broad and shallow. This means that the CD spectra measured for either dissolved or adsorbed peptides arise from a multitude of different structures, each present with a probability dictated by their relative free-energy variations, according to Boltzmann statistics. Here we present a modeling method based on replica exchange with solute tempering in combination with metadynamics, which allows us to predict both the helicity loss of a small peptide upon interaction with silica colloids in water and to compute the full CD spectra of the adsorbed and dissolved states, in quantitative agreement with experimental measurements. In our method, the CD ellipticity Θ for any given wavelength λ is calculated as an external collective variable by means of reweighting the biased trajectory obtained using the peptide-SiO2 surface distance and the structural helicity as two independent, internal collective variables. Our results also provide support for the often-employed hypothesis that the Θ intensity at λ = 222 nm is linearly correlated with the peptides' fractional helicity.

Circular dichroism analysis of cyclic β-helical peptides adsorbed on planar fused quartz

Conformational changes of three cyclic β-helical peptides upon adsorption onto planar fused-quartz substrates were detected and analyzed by far-ultraviolet (UV) circular dichroism (CD) spectroscopy. In trifluoroethanol (TFE), hydrophobic peptides, Leu β and Val β, form left- and right-handed helices, respectively, and water-soluble peptide WS β forms a left-handed helix. Upon adsorption, CD spectra showed a mixture of folded and unfolded conformations for Leu β and Val β and predominantly unfolded conformations for WS β. X-ray photoelectron spectroscopy (XPS) provided insight about the molecular mechanisms governing the conformational changes, revealing that ca. 40% of backbone amides in Leu β and Val β were interacting with the hydrophilic substrate, while only ca. 15% of the amines/amides in WS β showed similar interactions. In their folded β-helical conformations, Leu β and Val β present only hydrophobic groups to their surroundings; hydrophilic surface groups can only interact with backbone amides if the peptides change their conformation. Conversely, as a β helix, WS β presents hydrophilic side chains to its surroundings that could, in principle, interact with hydrophilic surface groups, with the peptide retaining its folded structure. Instead, the observed unfolded surface conformation for WS β and the relatively small percentage of surface-bound amides (15 versus 40% for Leu β and Val β) suggest that hydrophilic surface groups induce unfolding. Upon this surface-induced unfolding, WS β interacts with the surface preferentially via hydrophilic side chains rather than backbone amides. In contrast, the unfolded β-hairpin-like form of WS β does not irreversibly adsorb on fused quartz from water, highlighting that solvation effects can be more important than initial conformation in governing peptide adsorption. Both label-free methods demonstrated in this work are, in general, applicable to structural analysis of a broad range of biomolecules adsorbed on transparent planar substrates, the surface properties of which could be customized.

Adsorption of diblock polypeptides on polystyrene latex

The adsorption of peptides at solid/liquid interfaces is affected by peptide/surface and peptide/peptide hydrophobic and electrostatic forces. Three diblock copolypeptides and two homopeptides were adsorbed on poly(styrene) nanospheres from water, water/methanol, and water/glycerol mixtures at different pH's to study both of these effects. Peptides with one hydrophilic (glutamic acid or lysine) and one nonpolar block (alanine) or with both hydrophilic blocks with opposite charges (glutamic acid and lysine) were chemically synthesized and used as adsorbates in this study. The amount adsorbed was determined, and dynamic light scattering (DLS) was used to measure the adsorbed layer thickness. It was found that peptide/surface and peptide/peptide electrostatic interactions dominate the adsorption process. Hydrophobic forces also play a role, but secondary to electrostatic forces. Positively charged blocks show high affinity for the surface, whereas negatively charged blocks were excluded from it. Poly(Lys) has the highest affinity by the surface, while (Glu)(14)-b-(Ala)(5) has the lowest. Adsorption of all peptides was inhibited by methanol and promoted by glycerol. The adsorption for (Lys)(5)-b-(Glu)(6) was extremely sensitive to pH, irrespective of cosolvent, whereas the thickness for (Lys)(30)-b-(Ala)(41) was sensitive to pH as well as cosolvent. Aggregation was observed in the presence of the nanosurfaces but not in the bulk peptides under some pH and solvent conditions.

Multiple aspects of the interaction of biomacromolecules with inorganic surfaces

The understanding of the mechanisms involved in the interaction of biological systems with inorganic materials is of interest in both fundamental and applied disciplines. The adsorption of proteins modulates the formation of biofilms onto surfaces, a process important in infections associated to medical implants, in dental caries, in environmental technologies. The interaction with biomacromolecules is crucial to determine the beneficial/adverse response of cells to foreign inorganic materials as implants, engineered or accidentally produced inorganic nanoparticles. A detailed knowledge of the surface/biological fluids interface processes is needed for the design of new biocompatible materials. Researchers involved in the different disciplines face up with similar difficulties in describing and predicting phenomena occurring at the interface between solid phases and biological fluids. This review represents an attempt to integrate the knowledge from different research areas by focussing on the search for determinants driving the interaction of inorganic surfaces with biological matter.

Nanostructure-biomolecule interactions: implications for tissue regeneration and nanomedicine

Great strides are being made worldwide in our ability to synthesize and assemble nanoscale building blocks to create advanced materials with novel properties and functionalities. The novel properties of nanostructures are derived from their confined sizes and their very large surface-to-volume ratios. Nanostructured surfaces have also been shown to elicit more favorable and selective biomolecule and cellular responses than surfaces at coarser length scales. In the case of nanoscale ceramics and osteoblasts, for example, the benefit results from protein (vitronectin) unfolding at the nanostructured surface. These nanoscale attributes are enabling a variety of nanostructures to form the bases for a new field--nanomedicine. A fundamental issue in much of nanomedicine, and especially tissue regeneration, is to understand and to eventually control nanostructure-biomolecule interactions. To elucidate the fundamental bases for changes of protein conformation and function on nanostructured surfaces, and hence select responses including those of stem cells, a number of model experiments have been carried out. The results of these studies are presented and discussed in the context of the fundamental driving forces for protein conformation changes associated with nanostructures, their relationship to modified cell responses and tissue engineering, and our present knowledge regarding nanostructure properties.

Tensile mechanics of alanine-based helical polypeptide: force spectroscopy versus computer simulations

In nature, an alpha-helix is commonly used to build thermodynamically stable and mechanically rigid protein conformations. In view of growing interest in the mechanical rigidity of proteins, we measured the tensile profile of an alanine-based alpha-helical polypeptide on an atomic-force microscope to investigate the basic mechanics of helix extension with minimal interference from side-chain interactions. The peptide was extended to its maximum contour length with much less force than in reported cases of poly-L-Glu or poly-L-Lys, indicating that chain stiffness strongly depended on the physicochemical properties of side chains, such as their bulkiness. The low tensile-force extension originated presumably in locally unfolded parts because of spontaneous structural fluctuations. In 50% trifluoroethanol, the well-known helix-promoting agent, the rigidity of the sample polypeptide was markedly increased. Computer simulations of the peptide-stretching process showed that a majority of constituent residues underwent a transition from an alpha-helical to an extended conformation by overcoming an energy barrier around psi approximately 0 degrees on the Ramachandran plot. The observed lability of an isolated helix signified the biological importance of the lateral bundling of helices to maintain a rigid protein structure.

Engineering the nanoparticle-biomacromolecule interface

Monolayer-protected nanoparticles feature tunable size, surface functionality and core material, providing scaffolds for targeting biomacromolecules. This review highlights recent advances in nanoparticle-biomacromolecule interactions, focusing on two key areas: (1) The modulation of structure and function of biomacromolecules through engineered interactions with nanoparticle surfaces; (2) The use of biomacromolecules as building blocks for nanostructured materials.

Monolayer-protected nanoparticle–protein interactions

Monolayer-protected nanoparticles provide an appealing artificial receptor scaffold for targeting proteins and related biomacromolecules. During the past two years, multiple efforts have focused on the engineering and application of nanoparticle-protein interactions. These investigations include the molecular recognition of proteins with nanoparticles in aqueous media, self-assembly of proteins and nanoparticles either in solution or on surface, and construction of nanoparticle-based protein sensors.

High-resolution 2D 1H-15N NMR characterization of persistent structural alterations of proteins induced by interactions with silica nanoparticles

The binding of protein to solid surfaces often induces changes in the structure, and to investigate these matters we have selected two different protein-nanoparticle systems. The first system concerns the enzyme human carbonic anhydrase II which binds essentially irreversibly to the nanoparticles, and the second system concerns human carbonic anhydrase I which alternate between the adsorbed and free state upon interaction with nanoparticles. Application of the TROSY pulse sequence has allowed high-resolution NMR analysis for both of the protein-nanoparticle systems. For HCAII it was possible to observe spectra of protein when bound to the nanoparticles. The results indicated that HCAII undergoes large rearrangements, forming an ensemble of molten globule-like structures on the surface. The spectra from the HCAI-nanoparticle system are dominated by HCAI molecules in solution. A comparative analysis of variations in intensity from 97 amide resonances in a 1H-15N TROSY spectrum revealed the effects from interaction with nanoparticle on the protein structure at amino acid resolution.

Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation

Proteins often undergo changes in internal conformation upon interacting with a surface. We investigate the thermodynamics of surface induced conformational change in a lattice model protein using a multicanonical Monte Carlo method. The protein is a linear heteropolymer of 27 segments (of types A and B) confined to a cubic lattice. The segmental order and nearest neighbor contact energies are chosen to yield, in the absence of an adsorbing surface, a unique 3x3x3 folded structure. The surface is a plane of sites interacting either equally with A and B segments (equal affinity surface) or more strongly with the A segments (A affinity surface). We use a multicanonical Monte Carlo algorithm, with configuration bias and jump walking moves, featuring an iteratively updated sampling function that converges to the reciprocal of the density of states 1/Omega(E), E being the potential energy. We find inflection points in the configurational entropy, S(E)=k ln Omega(E), for all but a strongly adsorbing equal affinity surface, indicating the presence of free energy barriers to transition. When protein-surface interactions are weak, the free energy profiles F(E)=E-TS(E) qualitatively resemble those of a protein in the absence of a surface: a free energy barrier separates a folded, lowest energy state from globular, higher energy states. The surface acts in this case to stabilize the globular states relative to the folded state. When the protein surface interactions are stronger, the situation differs markedly: the folded state no longer occurs at the lowest energy and free energy barriers may be absent altogether.

Protein adsorption onto silica nanoparticles: conformational changes depend on the particles' curvature and the protein stability

We have analyzed the adsorption of protein to the surfaces of silica nanoparticles with diameters of 6, 9, and 15 nm. The effects upon adsorption on variants of human carbonic anhydrase with differing conformational stabilities have been monitored using methods that give complementary information, i.e., circular dichroism (CD), nuclear magnetic resonance (NMR), analytical ultracentrifugation (AUC), and gel permeation chromatography. Human carbonic anhydrase I (HCAI), which is the most stable of the protein variants, establishes a dynamic equilibrium between bound and unbound protein following mixture with silica particles. Gel permeation and AUC experiments indicate that the residence time of HCAI is on the order of approximately 10 min and slowly increases with time, which allows us to study the effects of the interaction with the solid surface on the protein structure in more detail than would be possible for a process with faster kinetics. The effects on the protein conformation from the interaction have been characterized using CD and NMR measurements. This study shows that differences in particle curvature strongly influence the amount of the protein's secondary structure that is perturbed. Particles with a longer diameter allow formation of larger particle-protein interaction surfaces and cause larger perturbations of the protein's secondary structure upon interaction. In contrast, the effects on the tertiary structure seem to be independent of the particles' curvature.

Effects of temperature and pH on the helicity of a peptide adsorbed to colloidal silica

The conformation of a cationic alpha-helical peptide (DDDDAAAARRRRR) adsorbed to anionic colloidal silica has been investigated by circular dichroism (CD) spectroscopy as a function of temperature and pH in order to examine how the structure of an adsorbed molecule responds to two simultaneous perturbations. Increased temperature destabilizes the helicity of the peptide in solution, while pH changes alter the substrate surface charge and the corresponding strength of the interaction with the peptide. Near neutral pH, the helicity of the adsorbed peptide, which is determined from the intensity of the CD signal at 222 nm, decreases with increasing temperature, similarly to the temperature-dependent behavior observed for the peptide in aqueous solution. By contrast, at basic pH and a strongly negative surface charge, the helicity of the adsorbed peptide increases with temperature. In order to elucidate the origin of the reversal of the temperature dependence of helicity, a statistical model for the conformation of the adsorbed peptide has been formulated based on the Lifson-Roig model for the helix-coil transition of the peptide in solution. The model provides insight into the trends in fractional helicity and reveals that the temperature dependence of the helicity of the adsorbed peptide results from a competition between the intramolecular interactions that promote helicity and the intermolecular interactions with the surface. The statistical model also enables estimation of the free energy contributions from specific aspects of the adsorption process. Through identification of a connection between the conformation of adsorbed peptide and the interactions of the peptide with the surface, this work suggests a route for the control of adsorbate conformation through peptide and surface engineering.

The interaction of proteins with solid surfaces

The interaction of proteins with solid surfaces is a fundamental phenomenon with implications for nanotechnology, biomaterials and biotechnological processes. Kinetic and thermodynamic studies have long indicated that significant conformational changes may occur as a protein encounters a surface; new techniques are measuring and modeling these changes. Combinatorial and directed evolution techniques have created new peptide sequences that bind specifically to solid surfaces, similar to the natural proteins that regulate crystal growth. Modeling efforts capture kinetics and thermodynamics on the colloidal scale, but detailed treatments of atomic structure are still in development and face the usual challenges of protein modeling. Opportunities abound for fundamental discovery, as well as breakthroughs in biomaterials, biotechnology and nanotechnology.