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

High Antifouling Performance of Weakly Hydrophilic Polymer Brushes: A Molecular Dynamics Study

The antifouling performance of polymer brushes usually improves with increasing hydrophilicity of the grafted polymer. However, in some cases, less hydrophilic polymers show comparable or better antifouling performance than do more hydrophilic polymers. We investigate the mechanism of this anomalous behavior using molecular dynamics (MD) simulations of coarse-grained (CG) models of weakly and strongly hydrophilic polymers. The antifouling performance is evaluated from the potential of mean force of a model protein. The strongly hydrophilic polymer exhibits a better antifouling performance than the weakly hydrophilic polymer when the substrate of the polymer brush is repulsive. However, when the substrate is sufficiently attractive, the weakly hydrophilic polymer brush becomes more effective than the strongly hydrophilic brush in a certain range of grafting density. This is because the weakly hydrophilic polymer chains form a tightly packed layer that prevents the adsorbate molecule from contacting the substrate. We also perform all-atom (AA) MD simulations for several standard polymers to examine the correspondence with the CG polymer models. The weakly hydrophilic CG polymer is found to be similar to poly[N-(2-hydroxypropyl)methacrylamide] and poly(2-hydroxyethyl methacrylate), both of which have a hydroxyl group in a monomer unit. The strongly hydrophilic CG polymer resembles zwitterionic poly(carboxybetaine methacrylate). A discussion referring to the adsorption free energies of proteins on surfaces calculated in previous AA MD studies suggests that the higher antifouling performance of less hydrophilic polymer brushes can be realized for various combinations of protein and surface.

Surface plasmon resonance biosensor chips integrated with MoS2-MoO3 hybrid microflowers for rapid CFP-10 tuberculosis detection

This study reports on the modification of surface plasmon resonance (SPR) chips with molybdenum disulfide-molybdenum trioxide (MoS2-MoO3) microflowers to detect the tuberculosis (TB) markers of CFP-10. The MoS2-MoO3 microflowers were prepared by hydrothermal methods with variations in the pH and amount of trisodium citrate (Na3Ct), which were projected to influence the shape and size of microflower particles. The analysis shows that optimum MoS2-MoO3 hybrid microflowers were obtained at neutral pH using 0.5 g Na3Ct. The modified SPR biosensor exhibits a ten times higher response than the bare Au. Moreover, increasing MoS2-MoO3 thickness results in a higher detection response, sensitivity, and a smaller limit of detection (LOD). Using the optimized material composition, the Au/MoS2-MoO3-integrated SPR sensor can demonstrate sensitivity and LOD of 1.005 and 3.45 ng mL-1, respectively. This biosensor also has good selectivity, stability, and reproducibility based on cross-sensitivity characterization with other analytes and repeated measurements on several chips with different storing times and fabrication batch. Therefore, this proposed SPR biosensor possesses high potential to be further developed and applied as a detection technology for CFP-10 in monitoring and diagnosing TB.

Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins

The initiation of infection of host tissues by Staphylococcus aureus requires a family of staphylococcal adhesive proteins containing serine-aspartate repeat (SDR) domains, such as ClfA. The O-linked glycosylation of the long-chain SDR domain mediated by SdgB and SdgA is a key virulence factor that protects the adhesive SDR proteins against host proteolytic attack in order to promote successful tissue colonization, and has also been implicated in staphylococcal agglutination, which leads to sepsis and an immunodominant epitope for a strong antibody response. Despite the biological significance of these two glycosyltransferases involved in pathogenicity and avoidance of the host innate immune response, their structures and the molecular basis of their activity have not been investigated. This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodimer and as a heterodimer with SdgA. Overall, these findings not only elucidate the putative role of the three domains of SdgB in recognizing donor and acceptor substrates, but also provide new mechanistic insights into glycosylation of the SDR domain, which can serve as a starting point for the development of antibacterial drugs against staphylococcal infections.

Modelling peptide adsorption energies on gold surfaces with an effective implicit solvent and surface model

The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technological applications. A rational approach to design peptides for specific surfaces would build on amino-acid and surface specific interaction models, which are difficult to characterize experimentally or by modeling. Even with such a model at hand, the large number of possible sequences and the large conformation space of peptides make comparative simulations challenging. Here we present a computational protocol, the effective implicit surface model (EISM), for efficient in silico evaluation of the binding affinity trends of peptides on parameterized surface, with a specific application to the widely studied gold surface. In EISM the peptide surface interactions are modeled with an amino-acid and surface specific implicit solvent model, which permits rapid exploration of the peptide conformational degrees of freedom. We demonstrate the parametrization of the model and compare the results with all-atom simulations and experimental results for specific peptides.

Structural Basis of Inhibition of DCLK1 by Ruxolitinib

Given the functional attributes of Doublecortin-like kinase 1 (DCLK1) in tumor growth, invasion, metastasis, cell motility, and tumor stemness, it is emerging as a therapeutic target in gastrointestinal cancers. Although a series of specific or nonspecific ATP-competitive inhibitors were identified against DCLK1, different types of scaffolds that can be utilized for the development of highly selective inhibitors or structural understanding of binding specificities of the compounds remain limited. Here, we present our work to repurpose a Janus kinase 1 inhibitor, ruxolitinib as a DCLK1 inhibitor, showing micromolar binding affinity and inhibitory activity. Furthermore, to gain an insight into its interaction mode with DCLK1, a crystal structure of the ruxolitinib-complexed DCLK1 has been determined and analyzed. Ruxolitinib as a nonspecific DCLK1 inhibitor characterized in this work is anticipated to provide a starting point for the structure-guided discovery of selective DCLK1 inhibitors.

Atomistic Perspective on Biomolecular Adsorption on Functionalized Carbon Nanomaterials under Ambient Conditions

The use of carbon-based nanomaterials is tremendously increasing in various areas of technological, bioengineering, and biomedical applications. The functionality of carbon-based nanomaterials can be further broadened via chemical functionalization of carbon nanomaterial surfaces. On the other hand, concern is rising on possible adverse effects when nanomaterials are taken up by biological organisms. In order to contribute into understanding of interactions of carbon-based nanomaterials with biological matter, we have investigated adsorption of small biomolecules on nanomaterials using enhanced sampling molecular dynamics. The biomolecules included amino acid side chain analogues, fragments of lipids, and sugar monomers. The adsorption behavior on unstructured amorphous carbon, pristine graphene and its derivatives (such as few-layer graphene, graphene oxide, and reduced graphene oxide) as well as pristine carbon nanotubes, and those functionalized with OH-, COOH-, COO-, NH2-, and NH3+ groups was investigated with respect to surface concentration. An adsorption profile, that is, the free energy as a function of distance from the nanomaterial surfaces, was determined for each molecule and surface using the Metadynamics approach. The results were analyzed in terms of chemical specificity, surface charge, and surface concentration. It was shown that although morphology of the nanomaterial has a limited effect on the adsorption properties, functionalization of the surface by various molecular groups can drastically change the adsorption behavior that can be used in the design of nanosurfaces with highly selective adsorption properties and safe for human health and environment.

Multimodal spectroscopic investigation of the conformation and local environment of biomolecules at an electrified interface

The complex and dynamic interfacial regions between biological samples and electronic components pose many challenges for characterization, including their evolution over multiple temporal and spatial scales. Spectroscopic probes of buried interfaces employing mid-infrared plasmon resonances and time-resolved fluorescence detection in the visible range are used to study the properties of polypeptides adsorbed at the surface of a working electrode. Information from these complementary spectroscopic probes reveals the interplay of solvation, electric fields, and ion concentration on their resulting macromolecular conformations.

Fundamental Principles of the Thermodynamics and Kinetics of Protein Adsorption to Material Surfaces

Protein adsorption is important for essentially any process that involves the contact of a protein-containing solution and a material surface, with the resulting formation of the adsorbed layer of protein determined by the thermodynamics and kinetics of the system involved. This paper presents an overview of the fundamentals of these processes. First, the hierarchical structure of proteins and the types of bonding that stabilize a protein's native-state structure are presented. This section is then followed by a section presenting the thermodynamic driving forces that influence the way that proteins adsorb and conformationally change for three characteristically different types of surface chemistries: nonpolar (hydrophobic) surfaces, neutral hydrophilic surfaces, and charged surfaces. The final section of this paper addresses how kinetics and thermodynamics combine together to influence protein adsorption behavior, followed by concluding remarks.

Association of Model Neurotransmitters with Lipid Bilayer Membranes

Aimed at reproducing the results of electrophysiological studies of synaptic signal transduction, conventional models of neurotransmission are based on the specific binding of neurotransmitters to ligand-gated receptor ion channels. However, the complex kinetic behavior observed in synaptic transmission cannot be reproduced in a standard kinetic model without the ad hoc postulation of additional conformational channel states. On the other hand, if one invokes unspecific neurotransmitter adsorption to the bilayer-a process not considered in the established models-the electrophysiological data can be rationalized with only the standard set of three conformational receptor states that also depend on this indirect coupling of neurotransmitters via their membrane interaction. Experimental verification has been difficult because binding affinities of neurotransmitters to the lipid bilayer are low. We quantify this interaction with surface plasmon resonance to measure equilibrium dissociation constants in neurotransmitter membrane association. Neutron reflection measurements on artificial membranes, so-called sparsely tethered bilayer lipid membranes, reveal the structural aspects of neurotransmitters' association with zwitterionic and anionic bilayers. We thus establish that serotonin interacts nonspecifically with the membrane at physiologically relevant concentrations, whereas γ-aminobutyric acid does not. Surface plasmon resonance shows that serotonin adsorbs with millimolar affinity, and neutron reflectometry shows that it penetrates the membrane deeply, whereas γ-aminobutyric is excluded from the bilayer.

Counterion Exchange in Peptide-Complexed Core-Shell Microgels

The complexation of polyvalent macroions with oppositely charged polyelectrolyte microgels can lead to core-shell structures. The shell is believed to be highly deswollen with a high concentration of counter-macroions. The core is believed to be relatively free of macroions but under a uniform compressive stress due to the deswollen shell. We use cryo-scanning electron microscopy (SEM) with X-ray microanalysis to confirm this understanding. We study poly(acrylic acid) (PAA) microgels which form a core-shell structure when complexed with a small cationic antimicrobial peptide (L5). We follow the spatial distribution of polymer, water, Na counterions, and peptide based on the characteristic X-ray intensities of C, O, Na, and N, respectively. Frozen-hydrated microgel suspensions include buffers of known composition from which calibration curves can be generated and used to quantify both the microgel water and sodium concentrations, the latter with a minimum quantifiable concentration less than 0.048 M. We find that as-synthesized PAA microgels are enriched in Na relative to the surrounding buffer as anticipated from established ideas of counterion shielding of electrostatic charge. The shell in L5-complexed microgels is depleted in Na and enriched in peptide and contains relatively little water. Our measurements furthermore show that shell/core interface is diffuse over a length scale of a few micrometers. Within the limits of detection, the core Na concentration is the same as that in as-synthesized microgels, and the core is free of peptide. The core has a slightly lower water concentration than as-synthesized controls, consistent with the hypothesis that the core is under compression from the shell.

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

Solid-Phase Nucleic Acid Sequence-Based Amplification and Length-Scale Effects during RNA Amplification

Solid-phase oligonucleotide amplification is of interest because of possible applications to next-generation sequencing, multiplexed microarray-based detection, and cell-free synthetic biology. Its efficiency is, however, less than that of traditional liquid-phase amplification involving unconstrained primers and enzymes, and understanding how to optimize the solid-phase amplification process remains challenging. Here, we demonstrate the concept of solid-phase nucleic acid sequence-based amplification (SP-NASBA) and use it to study the effect of tethering density on amplification efficiency. SP-NASBA involves two enzymes, avian myeloblastosis virus reverse transcriptase (AMV-RT) and RNase H, to convert tethered forward and reverse primers into tethered double-stranded DNA (ds-DNA) bridges from which RNA^- amplicons can be generated by a third enzyme, T7 RNA polymerase. We create microgels on silicon surfaces using electron-beam patterning of thin-film blends of hydroxyl-terminated and biotin-terminated poly(ethylene glycol) (PEG-OH, PEG-B). The tethering density is linearly related to the PEG-B concentration, and biotinylated primers and molecular beacon detection probes are tethered to streptavidin-activated microgels. While SP-NASBA is very efficient at low tethering densities, the efficiency decreases dramatically with increasing tethering density due to three effects: (a) a reduced hybridization efficiency of tethered molecular beacon detection probes; (b) a decrease in T7 RNA polymerase efficiency;

Molecular Structure Inhibiting Synergism in Charged Surfactant Mixtures: An Atomistic Molecular Dynamics Simulation Study

Synergistic and nonsynergistic surfactant-water mixtures of sodium dodecyl sulfate (SDS), lauryl betaine (C12B), and cocoamidopropyl betaine (CAPB) systems are studied using molecular simulation to understand the role of interactions among headgroups, tailgroups, and water on structural and thermodynamic properties at the air-water interface. SDS is an anionic surfactant, while C12B and CAPB are zwitterionic; CAPB differs from C12B by an amide group in the tail. While the lowest surface tensions at high surface concentrations in the SDS-C12B synergistic system could not be reproduced by simulation, estimated partitioning between surface and bulk shows trends consistent with synergism. Structural analysis shows the influence of the SDS headgroup pulling C12B to the surface, resulting in closely packed structures compared to their respective homomolecular-surfactant systems. The SDS-CAPB system, on the other hand, is nonsynergistic when the surfactants are mixed on account of the tilted structure of the CAPB tail. The translational excess entropy due to the tailgroup interactions discriminates between the synergistic and nonsynergistic systems. The implications of such interactions on surfactant effects in complex, multicomponent atmospheric aerosols are discussed.

Binding Affinity of a Highly Sensitive Au/Ag/Au/Chitosan-Graphene Oxide Sensor Based on Direct Detection of Pb2+ and Hg2+ Ions

The study of binding affinity is essential in surface plasmon resonance (SPR) sensing because it allows researchers to quantify the affinity between the analyte and immobilised ligands of an SPR sensor. In this study, we demonstrate the derivation of the binding affinity constant, K, for Pb²⁺ and Hg²⁺ ions according to their SPR response using a gold/silver/gold/chitosan-graphene oxide (Au/Ag/Au/CS-GO) sensor for the concentration range of 0.1-5 ppm. The higher affinity of Pb²⁺ to binding with the CS-GO sensor explains the outstanding sensitivity of 2.05 °ppm^-1 against 1.66 °ppm^-1 of Hg²⁺. The maximum signal-to-noise ratio (SNR) upon detection of Pb²⁺ is 1.53, and exceeds the suggested logical criterion of an SNR. The Au/Ag/Au/CS-GO SPR sensor also exhibits excellent repeatability in Pb²⁺ due to the strong bond between its functional groups and this cation. The adsorption data of Pb²⁺ and Hg²⁺ on the CS-GO sensor fits well with the Langmuir isotherm model where the affinity constant, K, of Pb²⁺ and Hg²⁺ ions is computed. The affinity of Pb²⁺ ions to the Au/Ag/Au/CS-GO sensor is significantly higher than that of Hg²⁺ based on the value of K, 7 × 10⁵ M^-1 and 4 × 10⁵ M^-1, respectively. The higher shift in SPR angles due to Pb²⁺ and Hg²⁺ compared to Cr³⁺, Cu²⁺ and Zn²⁺ ions also reveals the greater affinity of the CS-GO SPR sensor to them, thus supporting the rationale for obtaining K for these two heavy metals. This study provides a better understanding on the sensing performance of such sensors in detecting heavy metal ions.

Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation

We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface

The use of standard molecular dynamics simulation methods to predict the interactions of a protein with a material surface have the inherent limitations of lacking the ability to determine the most likely conformations and orientations of the adsorbed protein on the surface and to determine the level of convergence attained by the simulation. In addition, standard mixing rules are typically applied to combine the nonbonded force field parameters of the solution and solid phases the system to represent interfacial behavior without validation. As a means to circumvent these problems, the authors demonstrate the application of an efficient advanced sampling method (TIGER2A) for the simulation of the adsorption of hen egg-white lysozyme on a crystalline (110) high-density polyethylene surface plane. Simulations are conducted to generate a Boltzmann-weighted ensemble of sampled states using force field parameters that were validated to represent interfacial behavior for this system. The resulting ensembles of sampled states were then analyzed using an in-house-developed cluster analysis method to predict the most probable orientations and conformations of the protein on the surface based on the amount of sampling performed, from which free energy differences between the adsorbed states were able to be calculated. In addition, by conducting two independent sets of TIGER2A simulations combined with cluster analyses, the authors demonstrate a method to estimate the degree of convergence achieved for a given amount of sampling. The results from these simulations demonstrate that these methods enable the most probable orientations and conformations of an adsorbed protein to be predicted and that the use of our validated interfacial force field parameter set provides closer agreement to available experimental results compared to using standard CHARMM force field parameterization to represent molecular behavior at the interface.

Aqueous Peptide-TiO2 Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms

A major barrier to the systematic improvement of biomimetic peptide-mediated strategies for the controlled growth of inorganic nanomaterials in environmentally benign conditions lies in the lack of clear conceptual connections between the sequence of the peptide and its surface binding affinity, with binding being facilitated by noncovalent interactions. Peptide conformation, both in the adsorbed and in the nonadsorbed state, is the key relationship that connects peptide-materials binding with peptide sequence. Here, we combine experimental peptide-titania binding characterization with state-of-the-art conformational sampling via molecular simulations to elucidate these structure/binding relationships for two very different titania-binding peptide sequences. The two sequences (Ti-1, QPYLFATDSLIK; Ti-2, GHTHYHAVRTQT) differ in their overall hydropathy, yet via quartz-crystal microbalance measurements and predictions from molecular simulations, we show these sequences both support very similar, strong titania-binding affinities. Our molecular simulations reveal that the two sequences exhibit profoundly different modes of surface binding, with Ti-1 acting as an entropically driven binder while Ti-2 behaves as an enthalpically driven binder. The integrated approach presented here provides a rational basis for peptide sequence engineering to achieve the in situ growth and organization of titania nanostructures in aqueous media and for the design of sequences suitable for a range of technological applications that involve the interface between titania and biomolecules.

Influence of Solvent in Controlling Peptide-Surface Interactions

Protein binding to surfaces is an important phenomenon in biology and in modern technological applications. Extensive experimental and theoretical research has been focused in recent years on revealing the factors that govern binding affinity to surfaces. Theoretical studies mainly focus on examining the contribution of the individual amino acids or, alternatively, the binding potential energies of the full peptide, which are unable to capture entropic contributions and neglect the dynamic nature of the system. We present here a methodology that involves the combination of nonequilibrium dynamics simulations with strategic mutation of polar residues to reveal the different factors governing the binding free energy of a peptide to a surface. Using a gold-binding peptide as an example, we show that relative binding free energies are a consequence of the balance between strong interactions of the peptide with the surface and the ability for the bulk solvent to stabilize the peptide.

Estimation of the free energy of adsorption of a polypeptide on amorphous SiO2 from molecular dynamics simulations and force spectroscopy experiments

Estimating the free energy of adsorption of materials-binding peptides is fundamental to quantify their interactions across bio/inorganic interfaces, but is difficult to achieve both experimentally and theoretically. We employ a combination of molecular dynamics (MD) simulations and dynamical force-spectroscopy experiments based on atomic force microscopy (AFM) to estimate the free energy of adsorption ΔGads of a (GCRL) tetrapeptide on amorphous SiO2 in pure water. The results of both equilibrium, advanced sampling MD and non-equilibrium, steered MD are compared with those of two different approaches used to extract ΔGads from the dependence of experimentally measured adhesion forces on the applied AFM loading rates. In order to obtain unambiguous peak forces and bond loading rates from steered MD trajectories, we have developed a novel numerical protocol based on a piecewise-harmonic fit of the adhesion work profile along each trajectory. The interpretation of the experiments has required a thorough quantitative characterization of the elastic properties of polyethylene glycol linker molecules used to tether (GCRL)15 polypeptides to AFM cantilevers, and of the polypeptide itself. All obtained ΔGads values fall within a relatively narrow window between -5 and -9 kcal mol(-1), but can be associated with large relative error bars of more than 50%. Among the different approaches compared, Replica Exchange with Solute Tempering simulations augmented with MetaDynamics (RESTMetaD) and fitting of dynamic force spectroscopy experiments with the model of Friddle and De Yoreo lead to the most reliable ΔGads estimates.

Elucidating the mechanism of interaction between peptides and inorganic surfaces

Understanding the mechanism of interaction between peptides and inorganic materials is of high importance for the development of new composite materials. Here, we combined an experimental approach along with molecular simulations in order to gain insights into this binding process. Using single molecule force spectroscopy by atomic force microscopy and molecular simulations we studied the binding of a peptide towards an inorganic substrate. By performing alanine scan we examined the propensity of each amino acid in the peptide sequence to bind the substrate (mica). Our results indicate that this binding is not controlled by the specific sequence of the peptide, but rather by its conformational freedom in solution versus its freedom when it is in proximity to the substrate. When the conformational freedom of the peptide is identical in both environments, the peptide will not adhere to the substrate. However, when the conformational freedom is reduced, i.e., when the peptide is in close proximity to the substrate, binding will occur. These results shed light on the interaction between peptides and inorganic materials.

Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface

The association of proteins and peptides with inorganic material has vast technological potential. An understanding of the adsorption of peptides at liquid/solid interfaces on a molecular-level is fundamental to fully realising this potential. Combining our prior work along with the statistical analysis of 100+ molecular dynamics simulations of adsorption of an experimentally identified graphite binding peptide, GrBP5, at the water/graphite interface has been used here to propose a model for the adsorption of a peptide at a liquid/solid interface. This bottom-up model splits the adsorption process into three reversible phases: biased diffusion, anchoring and lockdown. Statistical analysis highlighted the distinct roles played by regions of the peptide studied here throughout the adsorption process: the hydrophobic domain plays a significant role in the biased diffusion and anchoring phases suggesting that the initial impetus for association between the peptide and the interface may be hydrophobic in origin; aromatic residues dominate the interaction between the peptide and the surface in the adsorbed state and the polar region in the middle of the peptide affords a high conformational flexibility allowing strongly interacting residues to maximise favourable interactions with the surface. Reversible adsorption was observed here, unlike in our prior work focused on a more strongly interacting surface. However, this reversibility is unlikely to be seen once the peptide-surface interaction exceeds 10 kcal mol(-1).

Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG-X-GTGT host-guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5 kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard-Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid-liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation.

Fundamentals of nanoscale polymer-protein interactions and potential contributions to solid-state nanobioarrays

Protein adsorption onto polymer surfaces is a very complex, ubiquitous, and integrated process, impacting essential areas of food processing and packaging, health devices, diagnostic tools, and medical products. The nature of protein-surface interactions is becoming much more complicated with continuous efforts toward miniaturization, especially for the development of highly compact protein detection and diagnostic devices. A large body of literature reports on protein adsorption from the perspective of ensemble-averaged behavior on macroscopic, chemically homogeneous, polymeric surfaces. However, protein-surface interactions governing the nanoscale size regime may not be effectively inferred from their macroscopic and microscopic characteristics. Recently, research efforts have been made to produce periodically arranged, nanoscopic protein patterns on diblock copolymer surfaces solely through self-assembly. Intriguing protein adsorption phenomena are directly probed on the individual biomolecule level for a fundamental understanding of protein adsorption on nanoscale surfaces exhibiting varying degrees of chemical heterogeneity. Insight gained from protein assembly on diblock copolymers can be effectively used to control the surface density, conformation, orientation, and biofunctionality of prebound proteins in highly miniaturized applications, now approaching the nanoscale. This feature article will highlight recent experimental and theoretical advances made on these fronts while focusing on single-biomolecule-level investigations of protein adsorption behavior combined with surface chemical heterogeneity on the length scale commensurate with a single protein. This article will also address advantages and challenges of the self-assembly-driven patterning technology used to produce protein nanoarrays and its implications for ultrahigh density, functional, and quantifiable protein detection in a highly miniaturized format.

Perspectives on the simulation of protein-surface interactions using empirical force field methods

Protein-surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein-surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation.

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.

Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors

Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomolecules and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomolecules and inorganic nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, molecular-level understanding of biomolecule-inorganic nanoparticle interactions. Here, we introduce an integrated method for building this understanding using experimental measurements and advanced molecular simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quantitatively demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in our laboratories to a range of inorganic nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.

Evaluating protocols and analytical methods for peptide adsorption experiments

This paper evaluates analytical techniques that are relevant for performing reliable quantitative analysis of peptide adsorption on surfaces. Two salient problems are addressed: determining the solution concentrations of model GG-X-GG, X5, and X10 oligopeptides (G = glycine, X = a natural amino acid), and quantitative analysis of these peptides following adsorption on surfaces. To establish a uniform methodology for measuring peptide concentrations in water across the entire GG-X-GG and X n series, three methods were assessed: UV spectroscopy of peptides having a C-terminal tyrosine, the bicinchoninic acid (BCA) protein assay, and amino acid (AA) analysis. Due to shortcomings or caveats associated with each of the different methods, none were effective at measuring concentrations across the entire range of representative model peptides. In general, reliable measurements were within 30% of the nominal concentration based on the weight of as-received lyophilized peptide. In quantitative analysis of model peptides adsorbed on surfaces, X-ray photoelectron spectroscopy (XPS) data for a series of lysine-based peptides (GGKGG, K5, and K10) on Au substrates, and for controls incubated in buffer in the absence of peptides, suggested a significant presence of aliphatic carbon species. Detailed analysis indicated that this carbonaceous contamination adsorbed from the atmosphere after the peptide deposition. The inferred adventitious nature of the observed aliphatic carbon was supported by control experiments in which substrates were sputter-cleaned by Ar(+) ions under ultra-high vacuum (UHV) then re-exposed to ambient air. In contrast to carbon contamination, no adventitious nitrogen species were detected on the controls; therefore, the relative surface densities of irreversibly-adsorbed peptides were calculated by normalizing the N/Au ratios by the average number of nitrogen atoms per residue.

Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass

Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.

Peptide-surface adsorption free energy comparing solution conditions ranging from low to medium salt concentrations

Multi-technique methods involving surface plasmon resonance spectroscopy and atomic force microscopy provide experimental data for the characterization of peptide adsorption on self-assembled monolayers. A comparative study is carried out in phosphate-buffered saline (PBS) and potassium phosphate-buffered (PPB) water to determine the influence of the salt concentration on the adsorption behavior (see figure; ΔG(0)(ads) : free energy of peptide adsorption, F(des) : force required for peptide desorption).

Self-assembled poly(ethylene glycol)-co-acrylic acid microgels to inhibit bacterial colonization of synthetic surfaces

We explored the use of self-assembled microgels to inhibit the bacterial colonization of synthetic surfaces both by modulating surface cell adhesiveness at length scales comparable to bacterial dimensions (∼1 μm) and by locally storing/releasing an antimicrobial. Poly(ethylene glycol) [PEG] and poly(ethylene glycol)-co-acrylic acid [PEG-AA] microgels were synthesized by suspension photopolymerization. Consistent with macroscopic gels, a pH dependence of both zeta potential and hydrodynamic diameter was observed in AA-containing microgels but not in pure PEG microgels. The microgels were electrostatically deposited onto poly(l-lysine) (PLL) primed silicon to form submonolayer surface coatings. The microgel surface density could be controlled via the deposition time and the microgel concentration in the parent suspension. In addition to their intrinsic antifouling properties, after deposition, the microgels could be loaded with a cationic antimicrobial peptide (L5) because of favorable electrostatic interactions. Loading was significantly higher in PEG-AA microgels than in pure PEG microgels. The modification of PLL-primed Si by unloaded PEG-AA microgels reduced the short-term (6 h) S. epidermidis surface colonization by a factor of 2, and the degree of inhibition increased when the average spacing between microgels was reduced. Postdeposition L5 peptide loading into microgels further reduced bacterial colonization to the extent that, after 10 h of S. epidermidis culture in tryptic soy broth, the colonization of L5-loaded PEG-AA microgel-modified Si was comparable to the very small level of colonization observed on macroscopic PEG gel controls. The fact that these microgels can be deposited by a nonline-of-sight self-assembly process and hinder bacterial colonization opens the possibility of modifying the surfaces of topographically complex biomedical devices and reduces the rate of biomaterial-associated infection.

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior

Fixed-charge empirical force fields have been developed and widely used over the past three decades for all-atom molecular simulations. Most simulation programs providing these methods enable only one set of force field parameters to be used for the entire system. Whereas this is generally suitable for single-phase systems, the molecular environment at the interface between two phases may be sufficiently different from the individual phases to require a different set of parameters to be used to accurately represent the system. Recently published simulations of peptide adsorption to material surfaces using the CHARMM force field have clearly demonstrated this issue by revealing that calculated values of adsorption free energy substantially differ from experimental results. Whereas nonbonded parameters could be adjusted to correct this problem, this cannot be done without also altering the conformational behavior of the peptide in solution, for which CHARMM has been carefully tuned. We have developed a dual-force-field approach (Dual-FF) to address this problem and implemented it in the CHARMM simulation package. This Dual-FF method provides the capability to use two separate sets of nonbonded force field parameters within the same simulation: one set to represent intraphase interactions and a separate set to represent interphase interactions. Using this approach, we show that interfacial parameters can be adjusted to correct errors in peptide adsorption free energy without altering peptide conformational behavior in solution. This program thus provides the capability to enable both intraphase and interphase molecular behavior to be accurately and efficiently modeled in the same simulation.

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.

Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms

When performing molecular dynamics simulations for a system with constrained (fixed) atoms, traditional isobaric algorithms (e.g., NPT simulation) often cannot be used. In addition, the calculation of the internal pressure of a system with fixed atoms may be highly inaccurate due to the nonphysical nature of the atomic constraints and difficulties in accurately defining the volume occupied by the unconstrained atoms in the system. The inability to properly set and control pressure can result in substantial problems for the accurate simulation of condensed-phase systems if the behavior of the system (e.g., peptide/protein adsorption) is sensitive to pressure. To address this issue, the authors have developed an approach to accurately determine the internal pressure for a system with constrained atoms. As the first step in this method, a periodically extendable portion of the mobile phase of the constrained system (e.g., the solvent atoms) is used to create a separate unconstrained system for which the pressure can be accurately calculated. This model system is then used to create a pressure calibration plot for an intensive local effective virial parameter for a small volume cross section or "slab" of the system. Using this calibration plot, the pressure of the constrained system can then be determined by calculating the virial parameter for a similarly sized slab of mobile atoms. In this article, the authors present the development of this method and demonstrate its application using the CHARMM molecular simulation program to characterize the adsorption behavior of a peptide in explicit water on a hydrophobic surface whose lattice spacing is maintained with atomic constraints. The free energy of adsorption for this system is shown to be dramatically influenced by pressure, thus emphasizing the importance of properly maintaining the pressure of the system for the accurate simulation of protein-surface interactions.

A versatile method for functionalizing surfaces with bioactive glycans

Microarrays and biosensors owe their functionality to our ability to display surface-bound biomolecules with retained biological function. Versatile, stable, and facile methods for the immobilization of bioactive compounds on surfaces have expanded the application of high-throughput "omics"-scale screening of molecular interactions by nonexpert laboratories. Herein, we demonstrate the potential of simplified chemistries to fabricate a glycan microarray, utilizing divinyl sulfone (DVS)-modified surfaces for the covalent immobilization of natural and chemically derived carbohydrates, as well as glycoproteins. The bioactivity of the captured glycans was quantitatively examined by surface plasmon resonance imaging (SPRi). Composition and spectroscopic evidence of carbohydrate species on the DVS-modified surface were obtained by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), respectively. The site-selective immobilization of glycans based on relative nucleophilicity (reducing sugar vs amine- and sulfhydryl-derived saccharides) and anomeric configuration was also examined. Our results demonstrate straightforward and reproducible conjugation of a variety of functional biomolecules onto a vinyl sulfone-modified biosensor surface. The simplicity of this method will have a significant impact on glycomics research, as it expands the ability of nonsynthetic laboratories to rapidly construct functional glycan microarrays and quantitative biosensors.

Correlation between desorption force measured by atomic force microscopy and adsorption free energy measured by surface plasmon resonance spectroscopy for peptide-surface interactions

Surface plasmon resonance (SPR) spectroscopy is a useful technique for thermodynamically characterizing peptide-surface interactions; however, its usefulness is limited to the types of surfaces that can readily be formed as thin layers on the nanometer scale on metallic biosensor substrates. Atomic force microscopy (AFM), on the other hand, can be used with any microscopically flat surface, thus making it more versatile for studying peptide-surface interactions. AFM, however, has the drawback of data interpretation due to questions regarding peptide-to-probe-tip density. This problem could be overcome if results from a standardized AFM method could be correlated with SPR results for a similar set of peptide-surface interactions so that AFM studies using the standardized method could be extended to characterize peptide-surface interactions for surfaces that are not amenable for characterization by SPR. In this article, we present the development and application of an AFM method to measure adsorption forces for host-guest peptides sequence on surfaces consisting of alkanethiol self-assembled monolayers (SAMs) with different functionality. The results from these studies show that a linear correlation exists between these data and the adsorption free energy (ΔG(o)(ads)) values associated with a similar set of peptide-surface systems available from SPR measurements. These methods will be extremely useful to characterize thermodynamically the adsorption behavior for peptides on a much broader range of surfaces than can be used with SPR to provide information related to understanding protein adsorption behavior to these surfaces and to provide an experimental database that can be used for the evaluation, modification, and validation of force field parameters that are needed to represent protein adsorption behavior accurately for molecular simulations.

Functionalized periodic mesoporous organosilicas for enhanced and selective peptide enrichment

The analysis of peptides by the mass spectrometry (MS) technique is important in modern life science. The enrichment of peptides can increase the detection efficiency and is sometimes indispensable for collecting the information on proteins with low-abundance. Herein, we first report that functionalized periodic mesoporous organosilica (PMO) materials have a superior peptide enrichment property. It is demonstrated that the PMO materials with an organo-bridged (-CH(2)-) hybrid wall composition display a highly enhanced peptide enrichment ability compared to the pure silica material (SBA-15) with similar mesostructured parameters and morphology. More importantly, by surface modification of PMO with amino groups (denoted NH(2)-PMO), PMO and NH(2)-PMO with opposite charged surfaces (-25.2 and +39.0 mV, respectively) show selective affinities for positively and negatively charged peptides, respectively. By directly adding PMO, NH(2)-PMO as well as pure silica materials to the peptides solution with a low concentration (1-2 fmol/microL), 36 and 28 peptides can be detected from the BSA digestion in the presence of PMO and NH(2)-PMO, respectively, while only 6 and 4 are monitored in the case of SBA-15 enrichment and from solution without enrichment, respectively. Moreover, 69.4% (25 of 36) of enriched peptides by PMO have pI > or = 6 and 80% (21 of 28) of enriched peptides by NH(2)-PMO possess pI < or = 6. Combining the results from the NH(2)-PMO and PMO enrichment together, 51 peptides can be identified with a MOWSE score of 333. It is also noted that similar conclusions can also be obtained from the peptides solution originated from other proteins. This might be an important contribution to the understanding of the interaction between peptides and porous hosts, and the proposed method is promising for the development of both material science and biotechnology.

Assessment of the transferability of a protein force field for the simulation of peptide-surface interactions

In order to evaluate the transferability of existing empirical force fields for all-atom molecular simulations of protein adsorption behavior, we have developed and applied a method to calculate the adsorption free energy (DeltaG(ads)) of model peptides on functionalized surfaces for comparison with available experimental data. Simulations were conducted using the CHARMM program and force field using a host-guest peptide with the sequence TGTG-X-GTGT (where G and T are glycine and threonine amino acid residues, respectively, with X representing valine, threonine, aspartic acid, phenylalanine or lysine) over nine different functionalized alkanethiol self-assembled monolayer (SAM) surfaces with explicitly represented solvent. DeltaG(ads) was calculated using biased-energy replica exchange molecular dynamics to adequately sample the conformational states of the system. The simulation results showed that the CHARMM force-field was able to represent DeltaG(ads) within 1 kcal/mol of the experimental values for most systems, while deviations as large as 4 kcal/mol were found for others. In particular, the simulations reveal that CHARMM underestimates the strength of adsorption on the hydrophobic and positively charged amine surfaces. These results clearly show that improvements in force field parameterization are needed in order to accurately represent interactions between amino acid residues and functional groups of a surface and they provide a means for force field evaluation and modification for the eventual development and validation of an interfacial force field for the accurate simulation of protein adsorption behavior.

Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'

Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.

Biological Responses to New Advanced Surface Modifications of Endosseous Medical Implants

Implantable medical devices are increasingly important in the practice of modern medicine. However, patients with severely poor bone quality and quantity require highest implant osseointegration for the long-term success. A number of newly-developed advanced surface modifications of medical implants have recently been introduced to the medical implant system. Understanding the mechanisms by which osteogenic cells respond to such materials is therefore of major importance in developing the most effective materials to promote functional osseointegration. Diverse studies using materials with a wide range of new surface modification techniques have demonstrated the pivotal role of surface treatments in cell adhesion, proliferation and lineage specific differentiation. These events underlie the tissue responses required for bone healing following implant placement, with the interaction between adsorbed proteins on the implant surface and surrounding cells eliciting body responses to the treated implant surface. This review illustrates tissue responses to the implant material following implant placement and highlights cellular responses to new advanced implant surface modifications. Such information is of utmost importance to further develop several new advanced surface modifications to be used in the new era medical implantable devices.

Benchmark experimental data set and assessment of adsorption free energy for peptide-surface interactions

With the increasing interest in protein adsorption in fields ranging from bionanotechnology to biomedical engineering, there is a growing need to understand protein-surface interactions at a fundamental level, such as the interaction between individual amino acid residues of a protein and functional groups presented by a surface. However, relatively little data are available that experimentally provide a quantitative, comparative measure of these types of interactions. To address this deficiency, the objective of this study was to generate a database of experimentally measured standard state adsorption free energy (DeltaGoads) values for a wide variety of amino acid residue-surface interactions using a host-guest peptide and alkanethiol self-assembled monolayers (SAMs) with polymer-like functionality as the model system. The host-guest amino acid sequence was synthesized in the form of TGTG-X-GTGT, where G and T are glycine and threonine amino acid residues and X represents a variable residue. In this paper, we report DeltaGoads values for the adsorption of 12 different types of the host-guest peptides on a set of nine different SAM surfaces, for a total of 108 peptide-surface systems. The DeltaGoads values for these 108 peptide-surface combinations show clear trends in adsorption behavior that are dependent on both peptide composition and surface chemistry. These data provide a benchmark experimental data set from which fundamental interactions that govern peptide and protein adsorption behavior can be better understood and compared.