Determination of peptide-surface adsorption free energy for material surfaces not conducive to SPR or QCM using AFM

The interactions between peptides and proteins with material surfaces are of primary importance in many areas of biotechnology. While surface plasmon resonance spectroscopy (SPR) and quartz crystal microbalance (QCM) methods have proven to be very useful in measuring fundamental properties characterizing adsorption behavior, such as the free energy of adsorption for peptide-surface interactions, these methods are largely restricted to use for materials that can readily form nanoscale-thick films over the respective sensor surfaces. Many materials including most polymers, ceramics, and inorganic glasses, however, are not readily suitable for use with SPR or QCM methods. To overcome these limitations, we recently showed that desorption forces (F(des)) obtained using a standardized AFM method linearly correlate to standard-state adsorption free energy values (ΔG°(ads)) measured from SPR in phosphate buffered saline (PBS: phosphate buffered 140 mM NaCl, pH 7.4). This approach thus provides a means to determine ΔG°(ads) for peptide adsorption using AFM that can be applied to any flat material surface. In this present study, we investigated the F(des)-ΔG°(ads) correlation between AFM and SPR data in PBS for a much broader range of systems including eight different types of peptides on a set of eight different alkanethiol self-assembled monolayer (SAM) surfaces. The resulting correlation was then used to estimate ΔG°(ads) from F(des) determined by AFM for selected bulk polymer and glass/ceramic materials such as poly(methyl methacrylate) (PMMA), high-density polyethylene (HDPE), fused silica glass, and a quartz (100) surface. The results of these studies support our previous findings regarding the strong correlation between F(des) measured by AFM and ΔG°(ads) determined by SPR, and provides a means to estimate ΔG°(ads) for peptide adsorption on macroscopically thick samples of materials that are not conducive for use with SPR or QCM.     

Molecular hydrophobic attraction and ion-specific effects studied by molecular dynamics

Much is written about "hydrophobic forces" that act between solvated molecules and nonpolar interfaces, but it is not always clear what causes these forces and whether they should be labeled as hydrophobic. Hydrophobic effects roughly fall in two classes, those that are influenced by the addition of salt and those that are not. Bubble adsorption and cavitation effects plague experiments and simulations of interacting extended hydrophobic surfaces and lead to a strong, almost irreversible attraction that has little or no dependence on salt type and concentration. In this paper, we are concerned with hydrophobic interactions between single molecules and extended surfaces and try to elucidate the relation to electrostatic and ion-specific effects. For these nanoscopic hydrophobic forces, bubbles and cavitation effects play only a minor role and even if present cause no equilibration problems. In specific, we study the forced desorption of peptides from nonpolar interfaces by means of molecular dynamics simulations and determine the adsorption potential of mean force. The simulation results for peptides compare well with corresponding AFM experiments. An analysis of the various contributions to the total peptide-surface interactions shows that structural effects of water as well as van der Waals interactions between surface and peptide are important. Hofmeister ion effects are studied by separately determining the effective interaction of various ions with hydrophobic surfaces. An extension of the Poisson-Boltzmann equation that includes the ion-specific potential of mean force yields surface potentials, interfacial tensions, and effective interactions between hydrophobic surfaces. There, we also analyze the energetic contributions to the potential of mean force and find that the most important factor determining ion-specific adsorption at hydrophobic surfaces can best be described as surface-modified ion hydration.     

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united-atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit solvation method (C22 with GBMV), and an all-atom explicit solvation method (C22 with TIP3P). The adsorption behavior of each peptide was characterized by the calculation of the potential of mean force as a function of peptide-surface separation distance. The results from the C22/TIP3P model suggest that hydrophobic peptides exhibit relatively strong adsorption behavior, polar and positively-charged peptides exhibit negligible to relatively weak favorable interactions with the surface, and negatively-charged peptides strongly resist adsorption. Compared to the TIP3P model, the ACE and GBMV implicit solvent models predict much stronger attractions for the hydrophobic peptides as well as stronger repulsions for the negatively-charged peptides on the CH(3)-SAM surface. These comparisons provide a basis from which each of these implicit solvation methods may be reparameterized to provide closer agreement with explicitly represented solvation in simulations of peptide and protein adsorption to functionalized surfaces.     

Determination of the adsorption free energy for peptide-surface interactions by SPR spectroscopy

To understand and predict protein adsorption behavior, we must first understand the fundamental interactions between the functional groups presented by the amino acid residues making up a protein and the functional groups presented by the surface. Limited quantitative information is available, however, on these types of submolecular interactions. The objective of this study was therefore to develop a reliable method to determine the standard state adsorption free energy (delta Go ads) of amino acid residue-surface interactions using surface plasma resonance (SPR) spectroscopy. Two problems are commonly encountered when using SPR for peptide adsorption studies: the need to account for "bulk-shift" effects and the influence of peptide-peptide interactions at the surface. Bulk-shift effects represent the contribution of the bulk solute concentration to the SPR response that occurs in addition to the response due to adsorption. Peptide-peptide interactions, which are assumed to be zero for Langmuir adsorption, can greatly skew the isotherm shape and result in erroneous calculated values of delta Go ads. To address these issues, we have developed a new approach for the determination of delta Go ads using SPR that is based on the chemical potential. In this article, we present the development of this new approach and its application for the calculation of delta Go ads for a set of peptide-surface systems where the peptide has a host-guest amino acid sequence of TGTG-X-GTGT (where G and T are glycine and threonine residues and X represents a variable residue) and the surface consists of alkanethiol self-assembled monolayers (SAMs) with methyl (CH 3) and hydroxyl (OH) functionality. This new approach enables bulk-shift effects to be directly determined from the raw SPR versus peptide concentration data plots and the influence of peptide-peptide interaction effects to be minimized, thus providing a very straightforward and accurate method for the determination of delta Go ads for peptide adsorption. Further studies are underway to characterize delta Go ads for a large library of peptide-SAM combinations.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Comparison of antibody--antigen interactions on collagen measured by conventional immunological techniques and atomic force microscopy

We have developed a means of using atomic force microscopy (AFM) to repeatedly localize a small area of interest (4 x 4 microm(2)) within a 0.5-cm(2) area on a heterogeneous sample, to obtain and localize high-resolution images and force measurements on nonideal samples (i.e., samples that better reflect actual biological systems, not prepared on atomically flat surfaces). We demonstrate the repeated localization and measurement of unbinding forces associated with antibody--antigen (ab--ag) interactions, by applying AFM in air and in liquid to visualize and measure polyclonal ab--ag interactions, using chicken collagen as a model system. We demonstrate that molecular interactions, in the form of ab--ag complexes, can be visualized by AFM when secondary antibodies are conjugated to 20-nm colloidal gold particles. We then compare those results with established immunological techniques, to demonstrate broader application of AFM technology to other systems. Data from AFM studies are compared with results obtained using immunological methods traditionally employed to investigate ab--ag interactions, including enzyme-linked immunosorbent assay, immunoblotting, and in situ immunofluorescence. Finally, using functionalized AFM tips with a flexible tether [poly(ethylene glycol) 800] to which a derivatized antibody was attached, we analyzed force curve data to measure the unbinding force of collagen antibody from its antigen, obtaining a value of approximately 90 +/- 40 pN with a MatLab code written to automate the analyses of force curves obtained in force--volume mode. The methodology we developed for embedded collagen sections can be readily applied to the investigation of other receptor--ligand interactions.     

Aspects of the physical chemistry of polymers, biomaterials and mineralised tissues investigated with atomic force microscopy (AFM)

Beyond being merely a tool for measuring surface topography, atomic force microscopy (AFM) has made significant contributions to various scientific areas dealing with physical chemistry processes. This paper presents aspects of the physical chemistry at surfaces and interfaces of polymers, biomaterials and tissues investigated with AFM. Selected examples presented include surface induced self-assembly of polymer blends, copolymer interfacial reinforcement of immiscible homopolymers, protein adsorption on biomaterials and erosion of mineralised human tissues. In these areas, AFM is a useful and versatile tool to study structural or dynamic sample properties including thermodynamically driven surface evolution of polymer surfaces, lateral surface composition of interfaces, adsorption processes, and the metrology of demineralisation phenomena.     

Relationship between interfacial forces measured by colloid-probe atomic force microscopy and protein resistance of poly(ethylene glycol)-grafted poly(L-lysine) adlayers on niobia surfaces

Adsorbed layers of "comb-type" copolymers consisting of PEG chains grafted onto a poly(l-lysine) (PLL) backbone on niobium oxide substrates were studied by colloid-probe AFM in order to characterize the interfacial forces associated with coatings of varying architectures (PEG/PLL ratios and PEG chain lengths) and their relevance to protein resistance. The steric and electrostatic forces measured varied substantially with the architecture of the PLL-g-PEG copolymers. Varying the ionic strength of the buffer solutions enabled discrimination between electrostatic and steric-entropic contributions to the net interfacial force. For high PEG grafting densities the steric component was most prominent, but at low ionic strengths and high grafting densities, a repulsive electrostatic surface force was also observed; its origin was assigned to the niobia charges beneath the copolymer, as insufficient protonated amine groups in the PLL backbone were available for compensation of the oxide surface charges. For lower grafting densities and lower ionic strengths there was a substantial attractive electrostatic contribution arising from interaction of the electrical double layer arising from the protonated amine groups, with that of the silica probe surface (as under low ionic strength conditions, the electrical double layer was thicker than the PEG layer). For these PLL-g-PEG coatings the net interfacial force can thus be a markedly varying superposition of electrostatic and steric-entropic contributions, depending on various factors. The force curves correlate with protein adsorption data, demonstrating the utility of AFM colloid-probe force measurements for quantitative analysis of surface forces and how they determine interfacial interactions with proteins. Such characterization of the net interfacial forces is essential to elucidate the multiple types of interfacial forces relevant to the interactions between PLL-g-PEG coatings and proteins and to advance interpretation of protein adsorption or repellence beyond the oversimplified steric barrier model; in particular, our data demonstrate the importance of an ionic-strength-dependent minimum PEG layer thickness to screen the electrostatic interactions of charged interfaces.     

Surface heterogeneity of polystyrene latex particles determined by dynamic force microscopy

Atomic force microscopy (AFM) was employed to characterize the surface chemistry distribution on individual polystyrene latex particles. The particles were obtained by surfactant-free emulsion polymerization and contained hydrophilic quaternary ammonium chloride, sodium sulfonate, or hydroxyethyl groups. The phase shift in dynamic force mode AFM is sensitive to charge/chemical interactions between an oscillating atomic force microscope tip and a sample surface. In this work, the phase imaging technique distinguished phase domains of 50-100 nm on the surfaces of dried latex particles in ambient air. The domains are attributed to the separation of ion-rich and ion-poor components of the polymer on the particle surface.     

Adsorption and conformation behavior of biotinylated fibronectin on streptavidin-modified TiO(X) surfaces studied by SPR and AFM

It is well-known that protein-modified implant surfaces such as TiO(2) show a higher bioconductivity. Fibronectin is a glycoprotein from the extracellular matrix (ECM) with a major role in cell adhesion. It can be applied on titanium oxide surfaces to accelerate implant integration. Not only the surface concentration but also the presentation of the protein plays an important role for the cellular response. We were able to show that TiO(X) surfaces modified with biotinylated fibronectin adsorbed on a streptavidin-silane self-assembly multilayer system are more effective regarding osteoblast adhesion than surfaces modified with nonspecifically bound fibronectin. The adsorption and conformation behavior of biotinylated and nonbiotinylated (native) fibronectin was studied by surface plasmon resonance (SPR) spectroscopy and atomic force microscopy (AFM). Imaging of the protein modification revealed that fibronectin adopts different conformations on nonmodified compared to streptavidin-modified TiO(X) surfaces. This conformational change of biotinylated fibronectin on the streptavidin monolayer delivers a fibronectin structure similar to the conformation inside the ECM and therefore explains the higher cell affinity for these surfaces.     

Determination of solid surface tension from particle-substrate pull-off forces measured with the atomic force microscope

Atomic force microscopy (AFM) is capable of solid surface characterization at the microscopic and submicroscopic scales. It can also be used for the determination of surface tension of solids (gamma) from pull-off force (F) measurements, followed by analysis of the measured F values using contact mechanics theoretical models. Although a majority of the literature gamma results was obtained using either Johnson-Kendall-Roberts (JKR) or Derjaguin-Muller-Toporov (DMT) models, re-analysis of the published experimental data presented in this paper indicates that these models are regularly misused. Additional complication in determination of gamma values using the AFM technique is that the measured pull-off forces have poor reproducibility. Reproducible and meaningful F values can be obtained with strict control over AFM experimental conditions during the pull-off force measurements (low humidity level, controlled and known loads) for high quality substrates and probes (surfaces should be free of heterogeneity, roughness, and contamination). Any probe or substrate imperfections complicate the interpretation of experimental results and often reduce the quality of the generated data. In this review, surface imperfection in terms of roughness and heterogeneity that influence the pull-off force are analyzed based upon the contact mechanics models. Simple correlations are proposed that could guide in selection and preparation of AFM probes and substrates for gamma determination and selection of loading conditions during the pull-off force measurements. Finally, the possibility of AFM measurements of solid surface tension using materials with rough surfaces is discussed.     

Cleaning and hydrophilization of atomic force microscopy silicon probes

The silicon surface of commercial atomic force microscopy (AFM) probes loses its hydrophilicity by adsorption of airborne and package-released hydrophobic organic contaminants. Cleaning of the probes by acid piranha solution or discharge plasma removes the contaminants and renders very hydrophilic probe surfaces. Time-of-flight secondary-ion mass spectroscopy and X-ray photoelectron spectroscopy investigations showed that the native silicon oxide films on the AFM probe surfaces are completely covered by organic contaminants for the as-received AFM probes, while the cleaning methods effectively remove much of the hydrocarbons and silicon oils to reveal the underlying oxidized silicon of the probes. Cleaning procedures drastically affect the results of adhesive force measurements in water and air. Thus, cleaning of silicon surfaces of the AFM probe and sample cancelled the adhesive force in deionized water. The significant adhesive force values observed before cleaning can be attributed to formation of a bridge of hydrophobic material at the AFM tip-sample contact in water. On the other hand, cleaning of the AFM tip and sample surfaces results in a significant increase of the adhesive force in air. The presence of water soluble contaminants at the tip-sample contact lowers the capillary pressure in the water bridge formed by capillary condensation at the AFM tip-sample contact, and this consequently lowers the adhesive force.     

A case study on biological activity in a surface-bound multicomponent system: the biotin-streptavidin-peroxidase system

The adsorption of multiple protein layers on biotinylated organic surfaces has been characterized using surface plasmon resonance (SPR) and atomic force microscopy (AFM). Diffusion-limited loading of the biotinylated self-assembled monolayers (SAMs) ensures a precise control of the streptavidin surface density. For the subsequent interaction with biotinylated peroxidase, SPR data hint at a streptavidin density dependent orientation during peroxidase adsorption. Microcontact printed well-defined two-dimensional patterned surfaces of biotinylated organothiols and protein-resistant OEG-thiols allow an in-situ differentiation of specific and nonspecific adsorption (e.g., mono- vs multilayer adsorption). Additionally, the very important issue of biological activity of surface-bound enzymes is addressed by comparing the enzyme activities in solution with that for surface-bound species.     

The dynamic nature of contact angles as measured by atomic force microscopy

Atomic force microscopy appears to be a useful tool for determining the contact angle for small particles. It is shown in this paper that the contact angle of a spherical polyethylene particle changes with the speed of the AFM piezoelectric translator. Such dynamic behavior of the contact angle and other uncertainties such as the position of the three-phase contact on the particle surface during bubble-particle interaction make it difficult to decide whether or not the AFM single-particle contact angle can be used to describe the hydrophobic state of the particle surface.     

Dynamic force spectroscopy of the specific interaction between the PDZ domain and its recognition peptides

To characterize the molecular basis of specific interactions of PDZ proteins, dynamic force spectroscopy (DFS) for the PDZ protein Tax-interacting protein-1 (TIP-1) and its recognition peptide (PDZ-pep) derived from beta-catenin was performed using an atomic force microscope (AFM), together with measurement of thermodynamic and kinetic parameters using surface plasmon resonance (SPR). The unbinding force of this pair was measured under different conditions of AFM tip-retraction velocity. The relationship between the unbinding force and the logarithmic force-loading rate, that is, the dynamic force spectrum, exhibited two different rate regimes, for each of which the forces increased linearly with the force-loading rate. On the basis of the theoretical treatment of the Bell-Evans model, the positions of two different activation barriers in the reaction coordinate and dissociation rate constants in each barrier were evaluated from slopes and x-intercepts of the two linear regimes (first barrier: 0.04 nm and 1.10 x 10 s(-1); second barrier: 0.21 nm and 2.77 x 10(-2) s(-1), respectively). Although two-step unbinding kinetics between TIP-1 and PDZ-pep was suggested from the DFS analysis, SPR results showed single-step dissociation kinetics with a rate constant of 2.89 x 10(-1) s(-1). Different shapes of the free energy profile of the unbinding process were deduced from each result of DFS and SPR. The reason for such topographic differences in the energy landscape is discussed in relation to the differences in the pathways of forced unbinding and spontaneous dissociation.     

Quantitative analysis of protein adsorption via atomic force microscopy and surface plasmon resonance

Surface properties have a significant influence on the performance of biomedical devices. The influence of surface chemistry on the amount and distribution of adsorbed proteins has been evaluated by a combination of atomic force microscopy (AFM) and surface plasmon resonance (SPR). Adsorption of albumin, fibrinogen, and fibronectin was analyzed under static and dynamic conditions, employing self-assembled monolayers (SAMs) as model surfaces. AFM was performed in tapping mode with antibody-modified tips. Phase-contrast images showed protein distribution on SAMs and phase-shift entity provided information on protein conformation. SPR analysis revealed substrate-specific dynamics in each system investigated. When multi-protein solutions and diluted human plasma interacted with SAMs, SPR data suggested that surface chemistry governs the equilibrium composition of the protein layer.     

Influence of antibody immobilization strategy on molecular recognition force microscopy measurements

A systematic evaluation of the effects of antibody immobilization strategy on the binding efficiency and selectivity (e.g., ability to distinguish between specific and nonspecific interactions) of immunosurfaces prepared with F(ab') antibody fragments of rabbit Immunoglobulin G (IgG) is described. F(ab') was attached to gold surfaces either (1) directly via the formation of a gold-thiolate bond or (2) indirectly through a series of a bifunctional linkers containing an alkane chain or ethylene glycol spacer. Immobilization of F(ab') via the sulfhydryl reactive group located opposite the antigen binding site ensured optimum orientation of the antigen binding site. X-ray photoelectron spectroscopy (XPS) and surface plasmon resonance (SPR) were used to confirm surface modification with the bifunctional linkers and antibody immobilization, respectively. Binding efficiency assays performed with SPR indicated that increasing the length of the linker increased the antigen binding efficiency. Atomic force microscopy (AFM) adhesion force measurements indicated that AFM probes functionalized with directly immobilized F(ab') more effectively discriminated between specific and nonspecific surface-bound proteins than probes modified indirectly via linker-immobilized F(ab'). In addition, a greater number of antibody-antigen binding events were observed with directly immobilized F(ab')-functionalized probes.     

The electrical double layer on gold probed by electrokinetic and surface force measurements

Gold surfaces, obtained by vacuum deposition of 15-nm gold films on glass and silica wafers, were studied in aqueous solutions by streaming potential measurements and colloidal-probe AFM force measurements. In the force measurements both a bare and a gold-coated silica particle (6 microm in diameter) have been used as colloidal probes. From the streaming potential measurements we determined the zeta-potential of the gold surface, while from the force measurements the diffuse double-layer potential psi(d) was obtained by fitting the data to the DLVO theory or to the nonlinear Poisson-Boltzmann equation. Measured interactions were found to be entirely due to overlap of electric double layers with no indication of attractive Van der Waals forces. Results of both types of measurements are in good agreement. The double layer potential strongly depends on the pH, probably as a result of the presence of oxide species on the gold surface. Insight in the double layer potential of polarizable interfaces such as the gold/electrolyte solution interface is the first step for understanding the effect of externally applied potentials on the adsorption behavior of charged species.     

Oriented binding of the His6-tagged carboxyl-tail of the L-type Ca2+ channel alpha1-subunit to a new NTA-functionalized self-assembled monolayer

Oriented stable binding of functional proteins on surfaces is of fundamental interest for receptor/ligand studies in atomic force microscopy (AFM) and surface plasmon resonance (SPR) experiments. Here we have chosen the His6-tagged carboxyl-tail (C-tail) of the alpha1c-subunit of the L-type Ca2+ channel and calmodulin (CaM) as its cognitive partner as a model system to develop a new functional surface. Covalently attached self-assembled monolayers on ultraflat gold containing NTA-thiols to which the His6-tagged C-tail was bound and thiols with triethylene-glycol groups as matrix-thiols represented the system of choice. The topography of this surface was characterized using AFM; its ability to bind C-tail proteins oriented and stable was confirmed by SPR measurements and by complementary force spectroscopy experiments with a CaM4-construct covalently attached to the tip. The developed anchoring strategy can now be used to study receptor/ligand interactions in general applying force spectroscopy and SPR on His6-tagged proteins oriented immobilized onto this new NTA-functionalized self-assembled monolayer.