Modeling of peptide adsorption interactions with a poly(lactic acid) surface

Globular Proteins and Where to Find Them within a Polymer Brush-A Case Study

Protein adsorption by polymerized surfaces is an interdisciplinary topic that has been approached in many ways, leading to a plethora of theoretical, numerical and experimental insight. There is a wide variety of models trying to accurately capture the essence of adsorption and its effect on the conformations of proteins and polymers. However, atomistic simulations are case-specific and computationally demanding. Here, we explore universal aspects of the dynamics of protein adsorption through a coarse-grained (CG) model, that allows us to explore the effects of various design parameters. To this end, we adopt the hydrophobic-polar (HP) model for proteins, place them uniformly at the upper bound of a CG polymer brush whose multibead-spring chains are tethered to a solid implicit wall. We find that the most crucial factor affecting the adsorption efficiency appears to be the polymer grafting density, while the size of the protein and its hydrophobicity ratio come also into play. We discuss the roles of ligands and attractive tethering surfaces to the primary adsorption as well as secondary and ternary adsorption in the presence of attractive (towards the hydrophilic part of the protein) beads along varying spots of the backbone of the polymer chains. The percentage and rate of adsorption, density profiles and the shapes of the proteins, alongside with the respective potential of mean force are recorded to compare the various scenarios during protein adsorption.

Preparation and characterization of ferulic acid-modified water soluble chitosan and poly (γ-glutamic acid) polyelectrolyte films through layer-by-layer assembly towards protein adsorption

In this study, ferulic acid-modified water soluble chitosan and poly (γ-glutamic acid) polyelectrolyte multilayers films were constructed through the layer-by-layer (LBL) self-assembly technique. Chitosan (CS) or ferulic acid modified chitosan (MCS) and Poly (γ-glutamic acid) (PGA) was alternately deposited on the surface of glass substrate for the enhancement of surface modification. The obtained films were characterized by Fourier transform spectroscopy (FTIR), X-ray diffractometry (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), UV-vis spectroscopy and water contact angle to study its physico-chemical properties including protein absorption. The (PGA/MCS) films showed intense deposition of multilayers built upon the surface roughness and an increase in the exponential growth of multilayer films by UV-vis spectroscopy. Water contact angle indicated that the (PGA/MCS) films performed well with good wettability due to the increase in the number of layers. The LBL multilayer coatings of (PGA/MCS) films surface possessed a reduced amount of protein adsorption. These results indicated that it can resist the protein adsorption and can enhance the biocompatibility towards the biomedical application through the protein interaction. The (PGA/MCS) films has the potential to utilization as a good biomaterial for biomedical purposes to intensify the bio-active surface.

Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets

A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 k_BT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations.

Measuring interaction energies from experimentally measured single-molecular interactions is challenging. Here, the authors report a gamma work distribution applied to single molecule pulling events for estimating peptide absorption free energy.

An In Vitro Evaluation of the Red Cell Damage and Hemocompatibility of Different Central Venous Catheters

Background

The aim of our study was to evaluate the damaging impact of characteristics of the central venous catheters (CVCs) on red blood cells.

Methods

CVCs from three different manufacturers were analyzed, including the presence of coating, tunnel geometry, length, lumen diameter, and number of lumens with two respective flow rates (33 mL/min and 500 mL/min). Blood cell damage was defined by analyzing microparticle (MP) and hematologic analysis. MPs were isolated by ultracentrifugation of erythrocyte concentrate and analyzed on a flow cytometer.

Results

Characteristics of catheters were not associated with blood cell damage at a low flow rate but showed an effect with a high flow rate. CVCs with a polyhexanide methacrylate coating have caused statistically less blood cell damage than noncoated CVCs. The length of lumens, diameter, and geometry of the tunnel showed no differences in blood cell damage. Meanwhile, the number of lumens was predicted to have a greater effect on the erythrocyte damage, which was revealed with the formation of MPs and hematological parameters. CVCs with five lumens caused significantly less damage to the blood cells than CVCs with a single lumen. Moreover, a high flow rate of 500 mL/min caused less damage to the blood cells than a low rate of 33 mL/min.

Conclusion

Properties of CVCs are an important factor for quality patient care, especially when transfusing blood with high flow rates, as we want to provide a patient with high-quality blood with as few damaged cells as possible.

A Bespoke Force Field To Describe Biomolecule Adsorption at the Aqueous Boron Nitride Interface

Reliable manipulation of the interface between 2D nanomaterials and biomolecules represents a current frontier in nanoscience. The ability to resolve the molecular-level structures of these biointerfaces would provide a fundamental data set that is needed to enable systematic and knowledge-based progress in this area. These structures are challenging to obtain via experiment alone, and molecular simulations offer a complementary approach to address this problem. Compared with graphene, the interface between hexagonal boron nitride (h-BN) and biomolecules is relatively understudied at present. While several force fields are currently available for modeling the h-BN/water interface, there is a lack of a suitable force field that can describe the interactions between h-BN, liquid water, and biomolecules. Here, we use density functional theory calculations to create a force field, BoNi-CHARMM, to describe biomolecular interactions at the aqueous h-BN interface. Verifying our force field presents an additional challenge, given the scarcity of available experimental data for these interfaces. We test our force field against experimental evidence regarding the water/surface contact angle and confirm that the force field provides experimentally consistent values. We also present preliminary data regarding predictions of the free energy of adsorption of a selection of amino acids at the aqueous h-BN interface, revealing arginine and tryptophan to be among the strongest binders. This force field provides an opportunity to initiate a systematic progression in our current understanding of how to capture the intermolecular interactions at the h-BN biointerface.

Peptide interactions with zigzag edges in graphene

Recognition and manipulation of graphene edges enable the control of physical properties of graphene-based devices. Recently, the authors have identified a peptide that preferentially binds to graphene edges from a combinatorial peptide library. In this study, the authors examine the functional basis for the edge binding peptide using experimental and computational methods. The effect of amino acid substitution, sequence context, and solution pH value on the binding of the peptide to graphene has been investigated. The N-terminus glutamic acid residue plays a key role in recognizing and binding to graphene edges. The protonation, substitution, and positional context of the glutamic acid residue impact graphene edge-binding. Our findings provide insights into the binding mechanisms and the design of peptides for recognizing and functionalizing graphene edges.

Modeling and simulation of protein-surface interactions: achievements and challenges

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Strong Electrostatic Interactions Lead to Entropically Favorable Binding of Peptides to Charged Surfaces

Thermodynamic analyses can provide key insights into the origins of protein self-assembly on surfaces, protein function, and protein stability. However, obtaining quantitative measurements of thermodynamic observables from unbiased classical simulations of peptide or protein adsorption is challenging because of sampling limitations brought on by strong biomolecule/surface binding forces as well as time scale limitations. We used the parallel tempering metadynamics in the well-tempered ensemble (PTMetaD-WTE) enhanced sampling method to study the adsorption behavior and thermodynamics of several explicitly solvated model peptide adsorption systems, providing new molecular-level insight into the biomolecule adsorption process. Specifically studied were peptides LKα14 and LKβ15 and trpcage miniprotein adsorbing onto a charged, hydrophilic self-assembled monolayer surface functionalized with a carboxylic acid/carboxylate headgroup and a neutral, hydrophobic methyl-terminated self-assembled monolayer surface. Binding free energies were calculated as a function of temperature for each system and decomposed into their respective energetic and entropic contributions. We investigated how specific interfacial features such as peptide/surface electrostatic interactions and surface-bound ion content affect the thermodynamic landscape of adsorption and lead to differences in surface-bound conformations of the peptides. Results show that upon adsorption to the charged surface, configurational entropy gains of the released solvent molecules dominate the configurational entropy losses of the bound peptide. This behavior leads to an apparent increase in overall system entropy upon binding and therefore to the surprising and seemingly nonphysical result of an apparent increased binding free energy at elevated temperatures. Opposite effects and conclusions are found for the neutral surface. Additional simulations demonstrate that by adjusting the ionic strength of the solution, results that show the expected physical behavior, i.e., peptide binding strength that decreases with increasing temperature or is independent of temperature altogether, can be recovered on the charged surface. On the basis of this analysis, an overall free energy for the entire thermodynamic cycle for peptide adsorption on charged surfaces is constructed and validated with independent simulations.

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.

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.

Advances in surfaces and osseointegration in implantology. Biomimetic surfaces

The present work is a revision of the processes occurring in osseointegration of titanium dental implants according to different types of surfaces -namely, polished surfaces, rough surfaces obtained from subtraction methods, as well as the new hydroxyapatite biomimetic surfaces obtained from thermochemical processes. Hydroxyapatite’s high plasma-projection temperatures have proven to prevent the formation of crystalline apatite on the titanium dental implant, but lead to the formation of amorphous calcium phosphate (i.e., with no crystal structure) instead. This layer produce some osseointegration yet the calcium phosphate layer will eventually dissolve and leave a gap between the bone and the dental implant, thus leading to osseointegration failure due to bacterial colonization. A new surface -recently obtained by thermochemical processes- produces, by crystallization, a layer of apatite with the same mineral content as human bone that is chemically bonded to the titanium surface. Osseointegration speed was tested by means of minipigs, showing bone formation after 3 to 4 weeks, with the security that a dental implant can be loaded. This surface can be an excellent candidate for immediate or early loading procedures.

Key words:Dental implants, implants surfaces, osseointegration, biomimetics surfaces.

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.

Molecular-level understanding of protein adsorption at the interface between water and a strongly interacting uncharged solid surface

Although protein adsorption on solids is of immense relevance, experimental limitations mean there is still a remarkable lack of understanding of the adsorption mechanism, particularly at a molecular level. By subjecting 240+ molecular dynamics simulations of two peptide/water/solid surface systems to statistical analysis, a generalized molecular level mechanism for peptide adsorption has been identified for uncharged surfaces that interact strongly with the solution phase. This mechanism is composed of three phases: (1) biased diffusion of the peptide from the bulk phase toward the surface; (2) anchoring of the peptide to the water/solid interface via interaction of a hydrophilic group with the water adjacent to the surface or a strongly interacting hydrophobic group with the surface; and (3) lockdown of the peptide on the surface via a slow, stepwise and largely sequential adsorption of its residues, which we term 'statistical zippering'. The adsorption mechanism is dictated by the existence of water layers adjacent to the solid and orientational ordering therein. By extending the solid into the solution by ~8 Å and endowing it with a charged character, the water layers ensure the peptide feels the effect of the solid at a range well beyond the dispersion force that arises from it, thus inducing biased diffusion from afar. The charging of the interface also facilitates anchoring of the peptide near the surface via one of its hydrophilic groups, allowing it time it would otherwise not have to rearrange and lockdown. Finally, the slowness of the lockdown process is dictated by the need for the peptide groups to replace adjacent tightly bound interfacial water.

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.

Exhaustively sampling peptide adsorption with metadynamics

Simulating the adsorption of a peptide or protein and obtaining quantitative estimates of thermodynamic observables remains challenging for many reasons. One reason is the dearth of molecular scale experimental data available for validating such computational models. We also lack simulation methodologies that effectively address the dual challenges of simulating protein adsorption: overcoming strong surface binding and sampling conformational changes. Unbiased classical simulations do not address either of these challenges. Previous attempts that apply enhanced sampling generally focus on only one of the two issues, leaving the other to chance or brute force computing. To improve our ability to accurately resolve adsorbed protein orientation and conformational states, we have applied the Parallel Tempering Metadynamics in the Well-Tempered Ensemble (PTMetaD-WTE) method to several explicitly solvated protein/surface systems. We simulated the adsorption behavior of two peptides, LKα14 and LKβ15, onto two self-assembled monolayer (SAM) surfaces with carboxyl and methyl terminal functionalities. PTMetaD-WTE proved effective at achieving rapid convergence of the simulations, whose results elucidated different aspects of peptide adsorption including: binding free energies, side chain orientations, and preferred conformations. We investigated how specific molecular features of the surface/protein interface change the shape of the multidimensional peptide binding free energy landscape. Additionally, we compared our enhanced sampling technique with umbrella sampling and also evaluated three commonly used molecular dynamics force fields.

Free energy of adsorption for a peptide at a liquid/solid interface via nonequilibrium molecular dynamics

Protein adsorption is of wide interest including in many technological applications such as tissue engineering, nanotechnology, biosensors, drug delivery, and vaccine production among others. Understanding the fundamentals of such technologies and their design would be greatly aided by an ability to efficiently predict the conformation of an adsorbed protein and its free energy of adsorption. In the study reported here, we show that this is possible when data obtained from nonequilibrium thermodynamic integration (NETI) combined with steered molecular dynamics (SMD) is subject to bootstrapping. For the met-enkephalin pentapeptide at a water-graphite interface, we were able to obtain accurate predictions for the location of the adsorbed peptide and its free energy of adsorption from around 50 and 80 SMD simulations, respectively. It was also shown that adsorption in this system is both energetically and entropically driven. The free energy of adsorption was also decomposed into that associated with formation of the cavity in the water near the graphite surface sufficient to accommodate the adsorbed peptide and that associated with insertion of the peptide into this cavity. This decomposition reveals that the former is modestly energetically and entropically unfavorable, whereas the latter is the opposite in both regards to a much greater extent.

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.

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.

Protein adsorption in three dimensions

Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the "protein-adsorption problem" to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations C(B). This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume V(I) by expulsion of either-or-both interphase water and initially adsorbed protein. Interphase protein concentration C(I) increases as V(I) decreases, resulting in slow reduction in interfacial energetics. Steady state is governed by a net partition coefficient P=(C(I)/C(B)). In the process of occupying space within the interphase, adsorbing protein molecules must displace an equivalent volume of interphase water. Interphase water is itself associated with surface-bound water through a network of transient hydrogen bonds. Displacement of interphase water thus requires an amount of energy that depends on the adsorbent surface chemistry/energy. This "adsorption-dehydration" step is the significant free energy cost of adsorption that controls the maximum amount of protein that can be adsorbed at steady state to a unit adsorbent surface area (the adsorbent capacity). As adsorbent hydrophilicity increases, adsorbent capacity monotonically decreases because the energetic cost of surface dehydration increases, ultimately leading to no protein adsorption near an adsorbent water wettability (surface energy) characterized by a water contact angle θ→65(°). Consequently, protein does not adsorb (accumulate at interphase concentrations greater than bulk solution) to more hydrophilic adsorbents exhibiting θ<65(°). For adsorbents bearing strong Lewis acid/base chemistry such as ion-exchange resins, protein/surface interactions can be highly favorable, causing protein to adsorb in multilayers in a relatively thick interphase. A straightforward, three-component free energy relationship captures salient features of protein adsorption to all surfaces predicting that the overall free energy of protein adsorption ΔG(ads)(o) is a relatively small multiple of thermal energy for any surface chemistry (except perhaps for bioengineered surfaces bearing specific ligands for adsorbing protein) because a surface chemistry that interacts chemically with proteins must also interact with water through hydrogen bonding. In this way, water moderates protein adsorption to any surface by competing with adsorbing protein molecules. This Leading Opinion ends by proposing several changes to the protein-adsorption paradigm that might advance answers to the three core questions that frame the "protein-adsorption problem" that is so fundamental to biomaterials surface science.

Coating and release of an anti-inflammatory hormone from PLGA microspheres for tissue engineering

Many biomaterials used in tissue engineering cause a foreign body response in vivo, which left untreated can severely reduce the effectiveness of tissue regeneration. In this study, an anti-inflammatory hormone α-melanocyte stimulating hormone (α-MSH) was physically adsorbed to the surface of biodegradable poly (lactic-co-glycolic) acid (PLGA) microspheres to reduce inflammatory responses to this material. The stability and adsorption isotherm of peptide binding were characterized. The peptide secondary structure was not perturbed by the adsorption and subsequent desorption process. The α-MSH payload was released over 72 h and reduced the expression of the inflammatory cytokine, Tumor necrosis factor-α (TNF-α) in lipopolysaccharide activated RAW 264.7 macrophage cells, indicating that the biological activity of α-MSH was preserved. α-MSH coated PLGA microspheres also appeared to reduce the influx of inflammatory cells in a subcutaneous implantation model in rats. This study demonstrates the potential of α-MSH coatings for anti-inflammatory delivery and this approach may be applied to other tissue engineering applications.

The Goldilocks surface

A minimum in the biological response to materials that is observed to occur within a narrow surface energy range is related to the properties of water at these biology-contacting surfaces. Wetting energetics are calculated using a published theory from which it is further estimated that water molecules bind to these special surfaces through a single hydrogen bond, leaving three other hydrogen bonds to interact with proximal water molecules. It is concluded that, at this Goldilocks Surface, the local chemical environment of surface-bound water is nearly identical to that experienced in bulk water; neither deprived of hydrogen bond opportunities, as it is in contact with a more hydrophobic surface, nor excessively hydrogen bonded to a more hydrophilic surface. A minimum in the biological response occurs because water vicinal (near) to the Goldilocks Surface is not chemically different than bulk water. A more precise definition of the relative terms hydrophobic and hydrophilic for use in biomaterials becomes evident from calculations: >1.3 kJ/mole-of-surface-sites is expended in wetting a hydrophilic surface whereas <1.3 kJ/mole-of-surface-sites is expended in wetting hydrophobic surfaces; hydrophilic surfaces wet with >1 hydrogen bond per water molecule whereas hydrophobic surfaces wet with <1 hydrogen bond per water molecule.

Molecular dynamics simulations of the interactions of kinin peptides with an anionic POPG bilayer

We have performed molecular dynamics simulations of peptide hormone bradykinin (BK) and its fragment des-Arg9-BK in the presence of an anionic lipid bilayer, with an aim toward delineating the mechanism of action related to their bioactivity. Starting from the initial aqueous environment, both of the peptides are quickly adsorbed and stabilized on the cell surface. Whereas BK exhibits a stronger interaction with the membrane and prefers to stay on the interface, des-Arg9-BK, with the loss of C-terminal Arg, penetrates further. The heterogeneous lipid-water interface induces β-turn-like structure in the otherwise inherently flexible peptides. In the membrane-bound state, we observed C-terminal β-turn formation in BK, whereas for des-Arg9-BK, with the deletion of Arg9, turn formation occurred in the middle of the peptide. The basic Arg residues anchor the peptide to the bilayer by strong electrostatic interactions with charged lipid headgroups. Simulations with different starting orientations of the peptides with respect to the bilayer surface lead to the same observations, namely, the relative positioning of the peptides on the membrane surface, deeper penetration of the des-Arg9-BK, and the formation of turn structures. The lipid headgroups adjacent to the bound peptides become substantially tilted, causing bilayer thinning near the peptide contact region and increase the degree of disorder in nearby lipids. Again, because of hydrogen bonding with the peptide, the neighboring lipid's polar heads exhibit considerably reduced flexibility. Corroborating findings from earlier experiments, our results provide important information about how the lipid environment promotes peptide orientation/conformation and how the peptide adapts to the environment.

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.

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.

Volumetric interpretation of protein adsorption: kinetics of protein-adsorption competition from binary solution

The standard solution-depletion method is implemented with SDS-gel electrophoresis as a multiplexing, separation-and-quantification tool to measure competition between two proteins (i and j) for adsorption to the same hydrophobic adsorbent particles (either octyl sepharose or silanized glass) immersed in binary-protein solutions. Adsorption kinetics reveals an unanticipated slow protein-size-dependent competition that controls steady-state adsorption selectivity. Two sequential pseudo-steady-state adsorption regimes (State 1 and State 2) are frequently observed depending on i, j solution concentrations. State 1 and State 2 are connected by a smooth transition, giving rise to sigmoidally-shaped adsorption-kinetic profiles with a downward inflection near 60 min of solution/adsorbent contact. Mass ratio of adsorbed i, j proteins (m(i)/m(j)) remains nearly constant between States 1 and 2, even though both m(i) and m(j) decrease in the transition between states. State 2 is shown to be stable for 24 h of continuous-adsorbent contact with stagnant solution whereas State 2 is eliminated by continuous mixing of adsorbent with solution. In sharp contrast to binary-competition results, adsorption to hydrophobic adsorbent particles from single-protein solutions (pure i or j) exhibits no detectable kinetics within the timeframe of experiment from either stagnant or continuously mixed solution, quickly achieving a single steady-state value in proportion to solution concentration. Comparison of binary competition between dissimilarly-sized protein pairs chosen to span a broad molecular-weight (MW) range demonstrates that selectivity between i and j scales with MW ratio that is proportional to protein-volume ratio (ubiquitin, Ub, MW=10.7 kDa; human serum albumin, HSA, MW=66.3 kDa; prothrombin, FII, 72 kDa; immunoglobulin G, IgG, MW=160 kDa; fibrinogen, Fib, MW=341 kDa). Results are interpreted in terms of a kinetic model of adsorption that has protein molecules rapidly diffusing into an inflating interphase that is spontaneously formed by bringing a protein solution into contact with a physical surface (State 1). State 2 follows by rearrangement of proteins within this interphase to achieve the maximum interphase concentration (dictated by energetics of interphase dehydration) within the thinnest (lowest volume) interphase possible by ejection of interphase water and initially-adsorbed proteins. Implications for understanding biocompatibility are discussed using a computational example relevant to the problem of blood-plasma coagulation.

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.