A theoretical analysis of the thermodynamic contributions for the adsorption of individual protein residues on functionalized surfaces

Orienting proteins by nanostructured surfaces: evidence of a curvature-driven geometrical resonance

Experimental and theoretical reports have shown that nanostructured surfaces have a dramatic effect on the amount of protein adsorbed and the conformational state and, in turn, on the performances of the related devices in tissue engineering strategies. Here we report an innovative method to prepare silica-based nanostructured surfaces with a reproducible, well-defined local curvature, consisting of ordered hexagonally packed arrays of curved hemispheres, from nanoparticles of different diameters (respectively 147 nm, 235 nm and 403 nm). The nanostructured surfaces have been made chemically homogeneous by partially embedding silica nanoparticles in poly(hydroxymethylsiloxane) films, further modified by means of UV-O3 treatments. This paper has been focused on the experimental and theoretical study of laminin, taken as a model protein, to study the nanocurvature effects on the protein configuration at nanostructured surfaces. A simple model, based on the interplay of electrostatic interactions between the charged terminal domains of laminin and the nanocurved charged surfaces, closely reproduces the experimental findings. In particular, the model suggests that nanocurvature drives the orientation of rigid proteins by means of a "geometrical resonance" effect, involving the matching of dimensions, charge distribution and spatial arrangement of both adsorbed molecules and adsorbent nanostructures. Overall, the results pave the way to unravel the nanostructured surface effects on the intra- and inter-molecular organization processes of proteins.

Change of the isoelectric point of hemoglobin at the air/water interface probed by the orientational flip-flop of water molecules

Nonlinear vibrational spectroscopy reveals that the isoelectric point of proteins can largely change when the proteins are adsorbed at the air/water interface.

Predicting the Structure-Activity Relationship of Hydroxyapatite-Binding Peptides by Enhanced-Sampling Molecular Simulation

Understanding the molecular structural and energetic basis of the interactions between peptides and inorganic surfaces is critical to their applications in tissue engineering and biomimetic material synthesis. Despite recent experimental progresses in the identification and functionalization of hydroxyapatite (HAP)-binding peptides, the molecular mechanisms of their interactions with HAP surfaces are yet to be explored. In particular, the traditional method of molecular dynamics (MD) simulation suffers from insufficient sampling at the peptide-inorganic interface that renders the molecular-level observation dubious. Here we demonstrate that an integrated approach combining bioinformatics, MD, and metadynamics provides a powerful tool for investigating the structure-activity relationship of HAP-binding peptides. Four low charge density peptides, previously identified by phage display, have been considered. As revealed by bioinformatics and MD, the binding conformation of the peptides is controlled by both the sequence and the amino acid composition. It was found that formation of hydrogen bonds between lysine residue and phosphate ions on the surface dictates the binding of positively charged peptide to HAP. The binding affinities of the peptides to the surface are estimated by free energy calculation using parallel-tempering metadynamics, and the results compare favorably to measurements reported in previous experimental studies. The calculation suggests that the charge density of the peptide primarily controls the binding affinity to the surface, while the backbone secondary structure that may restrain side chain orientation toward the surface plays a minor role. We also report that the application of enhanced-sampling metadynamics effects a major advantage over the steered MD method by significantly improving the reliability of binding free energy calculation. In general, our novel integration of diverse sampling techniques should contribute to the rational design of surface-recognition peptides in biomedical applications.

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.

Correlating single-molecule and ensemble-average measurements of peptide adsorption onto different inorganic materials

The coating of solid-binding peptides (SBPs) on inorganic material surfaces holds significant potential for improved surface functionalization at nano-bio interfaces. In most related studies, the goal has been to engineer peptides with selective and high binding affinity for a target material. The role of the material substrate itself in modulating the adsorption behavior of a peptide molecule remains less explored and there are few studies that compare the interaction of one peptide with different inorganic substrates. Herein, using a combination of two experimental techniques, we investigated the adsorption of a 16 amino acid-long random coil peptide to various inorganic substrates - gold, silicon oxide, titanium oxide and aluminum oxide. Quartz crystal microbalance-dissipation (QCM-D) experiments were performed in order to measure the peptide binding affinity for inorganic solid supports at the ensemble average level, and atomic force microscopy (AFM) experiments were conducted in order to determine the adhesion force of a single peptide molecule. A positive trend was observed between the total mass uptake of attached peptide and the single-molecule adhesion force on each substrate. Peptide affinity for gold was appreciably greater than for the oxide substrates. Collectively, the results obtained in this study offer insight into the ways in which inorganic materials can differentially influence and modulate the adhesion of SBPs.

Myoglobin on silica: a case study of the impact of adsorption on protein structure and dynamics

If protein structure and function changes upon adsorption are well documented, modification of adsorbed protein dynamics remains a blind spot, despite its importance in biological processes. The adsorption of metmyoglobin on a silica surface was studied by isotherm measurements, microcalorimetry, circular dichroïsm, and UV-visible spectroscopy to determine the thermodynamic parameters of protein adsorption and consequent structure modifications. The mean square displacement and the vibrational densities of states of the adsorbed protein were measured by elastic and inelastic neutron scattering experiments. A decrease of protein flexibility and depletion in low frequency modes of myoglobin after adsorption on silica was observed. Our results suggest that the structure loss itself is not the entropic driving force of adsorption.

Strong resistance of (tridecafluoro-1,1,2,2-tetrahydrooctyl)triethoxysilane (TTS) nanofilm to protein adsorption

In this report, the properties of fluorocarbon-containing (tridecafluoro-1,1,2,2-tetrahydrooctyl)triethoxysilane (TTS) (C14 H19 F13 O3 Si) nanofilm coated on silicon surface and its potential to resist protein adsorption were examined. Thickness and wettability of the silicon surface before and after TTS nanofilm coating were examined by ellipsometry and contact angle goniometry, respectively. The same techniques were used to examine protein layer on nonmodified and TTS-coated silicon surface. In addition, bright-field optical microscopy and fluorescence spectrophotometry were used to provide visual, qualitative description of adsorbed proteins and the specific signal of fluorescence-labeled bovine serum albumin (BSA), respectively, on bare and TTS-coated silicon surface. Single-component protein solution of four model proteins, namely BSA, human fibrinogen, bovine serum immunoglobulin G, and fibronectin, was prepared, and the adsorption responses of these four proteins on TTS nanofilm were examined, using nonmodified silicon surface as comparison. TTS substantially reduces the adsorption of all four proteins tested. Our results indicate that fluorocarbon-containing TTS, once coated on surfaces, is an effective molecule for resisting protein adsorption. This will open up potential applications, particularly for silicon-containing implant devices such as glass.

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.

Comparison between empirical protein force fields for the simulation of the adsorption behavior of structured LK peptides on functionalized surfaces

All-atom empirical molecular mechanics protein force fields, which have been developed to represent the energetics of peptide folding behavior in aqueous solution, have not been parameterized for protein interactions with solid material surfaces. As a result, their applicability for representing the adsorption behavior of proteins with functionalized material surfaces should not be assumed. To address this issue, we conducted replica-exchange molecular dynamics simulations of the adsorption behavior of structured peptides to functionalized surfaces using three protein force fields that are widely used for the simulation of peptide adsorption behavior: CHARMM22, AMBER94, and OPLS-AA. Simulation results for peptide structure both in solution and when adsorbed to the surfaces were compared to experimental results for similar peptide-surface systems to provide a means of evaluating and comparing the performance of these three force fields for this type of application. Substantial differences in both solution and adsorbed peptide conformations were found amongst these three force fields, with the CHARMM22 force field found to most closely match experimental results.

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.

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.

Neutral vs zwitterionic glycine forms at the water/silica interface: structure, energies, and vibrational features from B3LYP periodic simulations

B3LYP periodic calculations with a triple-xi-polarized Gaussian basis set have been used to study adsorption of glycine on a hydroxylated silica surface (2.2 OH/nm2) model derived from the (001) surface of edingtonite. The simulation envisages glycine adsorbed either as a gas-phase molecule or when microsolvated by up to five H20 molecules. Both neutral and zwitterionic forms of glycine have been considered and their structural, energetic, and spectroscopic vibrational features compared internally and with experiments. As a gas phase glycine sticks in its neutral form at the silica surface, the zwitterion being highly unstable and with transition-state character. When glycine is microsolvated at the silica interface, two H20 molecules render the zwitterion population comparable to that of the neutral form whereas with four H2O molecules the neutral glycine population is wiped out in favor of the zwitterion. With four H20 molecules the most stable structure shows no direct contact between glycine and the silica surface, H20 acting as a mediator via H-bond interactions. The B3LYP energies and structural data were also supported by comparing the scaled harmonic vibrational features with literature FTIR data of glycine adsorbed on an amorphous silica surface either from the gas phase or in water solution.

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

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

Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

The adsorption behavior of a biomolecule, such as a peptide or protein, to a functionalized surface is of fundamental importance for a broad range of applications in biotechnology. The adsorption free energy for these types of interactions can be determined from a molecular dynamics simulation using the partitioning between adsorbed and nonadsorbed states, provided that sufficient sampling of both states is obtained. However, if interactions between the solute and the surface are strong, the solute will tend to be trapped near the surface during the simulation, thus preventing the adsorption free energy from being calculated by this method. This situation occurs even when using an advanced sampling algorithm such as replica-exchange molecular dynamics (REMD). In this paper, the authors demonstrate the fundamental basis of this problem using a model system consisting of one sodium ion (Na(+)) as the solute positioned over a surface functionalized with one negatively charged group (COO(-)) in explicit water. With this simple system, the authors show that sufficient sampling in the coordinate normal to the surface cannot be obtained by conventional REMD alone. The authors then present a method to overcome this problem through the use of an adaptive windowed-umbrella sampling technique to develop a biased-energy function that is combined with REMD. This approach provides an effective method for the calculation of adsorption free energy for solute-surface interactions.

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

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

Interaction of glycine with isolated hydroxyl groups at the silica surface: first principles B3LYP periodic simulation

The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the (001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the Gamma point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH(2) group plays only a minor role as a weak hydrogen bond donor.

Adsorption of fluorescently labeled protein residues on poly(ethylene-co-acrylic acid) films modified with affinity functionalities

Poly(ethylene-co-acrylic acid) (EAA) films were reacted with glycine, 12-aminododecanoic acid, aspartic acid, 5-aminoisophthalic acid, ethanolamine, diethylamine, dimethylamine, N-isopropylamine, and dimethylaminoethyleneamine to prepare EAA films with negatively charged, non-charged, hydrophilic, and hydrophobic functionalities. Attenuated total reflectance Fourier transform infrared spectroscopy, differential scanning calorimetry, and contact angle measurements were used to characterize the modified EAA films. Analyses revealed that the films were modified on the surfaces and also in the bulk; therefore, bulk properties such as cohesive energy density were changed even though the surfaces remained hydrophobic. Adsorption studies were performed for two fluorescently labeled protein residues, dansyl-L-phenylalanine (dansyl-F) and dansyl-L-glutamine (dansyl-Q), from pH 7.4 buffer solutions. The adsorption results revealed that dimethylaminoethyleneamine functionality gave the highest uptake among the functionalities studied, and adsorption was more favorable for dansyl-F than dansyl-Q. Adsorption behavior is discussed in terms of hydrophobic-hydrophobic (dispersion) interactions and Coulombic interactions.

Comparison of implicit solvent models for the simulation of protein–surface interactions

Empirical force field-based molecular simulations can provide valuable atomistic-level insights into protein-surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface-separation distance for peptide-surface interactions using different empirical force field-based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self-consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement.

Soft-Landing of Peptides onto Self-Assembled Monolayer Surfaces

Mass-selected peptide ions produced by electrospray ionization were deposited as ions by soft-landing (SL) onto fluorinated and hydrogenated self-assembled monolayer (FSAM and HSAM) surfaces using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially designed for studying collisions of large ions with surfaces. Analysis of modified surfaces was performed in situ by combining 2 keV Cs(+) secondary ion mass spectrometry with FT-ICR detection of the sputtered ions (FT-ICR-SIMS). Similar SIMS spectra obtained following SL at different collision energies indicate that peptide fragmentation occurred in the analysis step (SIMS) rather than during ion deposition. The effect of the surface on SL was studied by comparing the efficiencies of SL on gold, FSAM, HSAM, and COOH-terminated SAM surfaces. It was found that FSAM surfaces are more efficient in retaining ions than their HSAM analogues, consistent with their larger polarizability. The efficiency of soft-landing of different peptides on the FSAM surface increases with the charge state of the ion, also consistent with an ion-polarizable molecule model for the initial stage of soft-landing on SAM surfaces. The gradual decrease of peptide ion deposition efficiency with an increase in collision energy found experimentally was quantitatively rationalized using the hard-cube model.

Surface energy components of a dye-ligand immobilized pHEMA membranes: Effects of their molecular attracting forces for non-covalent interactions with IgG and HSA in aqueous media

In the present paper, we report the study of the adsorption behaviour of human immunoglobulin G (IgG), human serum albumin (HSA) and polyethylenimine (PEI) onto surfaces of Procion Green HE-4BD (PG) immobilized poly(hydroxyethylmethacrylate) (pHEMA) membranes. The adsorption behaviour of the IgG and HSA onto surfaces of the PG-PEI complexed membrane was also studied. Surface wettability and hydrophilicity of all the membranes were investigated by static contact angle measurements. The measurements of the contact angle to various test liquids, i.e., water, glycerol, formamide, diiodomethane (DIM) and ethylene glycol on the investigated membranes were made by sessile drop method. In accordance to the Young equation, the smaller the surface tension of the test liquid, the smaller becomes the contact angles measured on all the investigated membranes surfaces. The highest contact angles were obtained with water, whereas ethylene glycol gave the lowest contact angles for all the tested membranes. Component and parameters of the surface free energy of all the investigated membranes were calculated from measured contact angle values using two methods (the geometric mean by Fowkes and acid-base by van Oss). HSA adsorption was enhanced after complexation of PEI with the immobilized dye-ligand. The adsorption of proteins and PEI significantly changed both the contact angles and component of surface free energies of the investigated membranes.

Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation

When simulating protein adsorption behavior, decisions must first be made regarding how the protein should be oriented on the surface. To address this problem, we have developed a molecular simulation program that combines an empirical adsorption free energy function with an efficient configurational search method to calculate orientation-dependent adsorption free energies between proteins and functionalized surfaces. The configuration space is searched systematically using a quaternion rotation technique, and the adsorption free energy is evaluated using an empirical energy function with an efficient grid-based calculational method. In this paper, the developed method is applied to analyze the preferred orientations of a model protein, lysozyme, on various functionalized alkanethiol self-assembled monolayer (SAM) surfaces by the generation of contour graphs that relate adsorption free energy to adsorbed orientation, and the results are compared with experimental observations. As anticipated, the adsorbed orientation of lysozyme is predicted to be dependent on the discrete organization of the functional groups presented by the surface. Lysozyme, which is a positively charged protein, is predicted to adsorb on its 'side' on both hydrophobic and negatively charged surfaces. On surfaces with discrete positively charged sites, attractive interaction energies can also be obtained due to the presence of discrete local negative charges present on the lysozyme surface. In this case, 'end-on' orientations are preferred. Additionally, SAM surface models with mixed functionality suggest that the interactions between lysozyme and surfaces could be greatly enhanced if individual surface functional groups are able to access the catalytic cleft region of lysozyme, similar to ligand-receptor interactions. The contour graphs generated by this method can be used to identify low-energy orientations that can then be used as starting points for further simulations to investigate conformational changes induced in protein structure following initial adsorption.

Electrostatic Contributions to Protein Retention in Ion-Exchange Chromatography. 2. Proteins with Various Degrees of Structural Differences

The relation of protein structure to retention provides a framework within which to investigate chromatographic adsorption mechanisms. Protein sets with varying degrees of structural differences were studied to relate variations in protein properties to retention behavior. To explore molecular contributions to protein adsorption in ion-exchange chromatography, protein-adsorbent electrostatic interactions were modeled using a continuum approach. The calculations qualitatively capture the chromatographic differentiation of closely related subtilisin variants. Descriptions of the electrostatic interactions of FGF-1 vs FGF-2 with cation exchangers were obtained, and aid in rationalizing differences in experimental retention trends across a set of adsorbents based on different adsorption mechanisms linked to the adsorbent structure. Comparative calculations for proteins with differences in local or overall arginine-lysine composition, including subtilisin variants G166R/G166K and lysozyme/cytochrome c, suggest that continuum electrostatics is not adequate to capture the full quantitative characteristics of the chromatographic retention of proteins. To allow more accurate description of retention, additional molecular interactions, specifically hydration effects, must be incorporated in the model.

Molecular dynamics simulations of peptide-surface interactions

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

Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment

Implants invoke inflammatory responses from the body even if they are chemically inert and nontoxic. It has been shown that a crucial precedent event in the inflammatory process is the spontaneous adsorption of fibrinogen (Fg) on implant surfaces, which is typically followed by the presence of phagocytic cells. Interactions between the phagocyte integrin Mac-1 and two short sequences within the fibrinogen gamma chain, gamma190-202 and gamma377-395, may partially explain phagocyte accumulation at implant surfaces. These two sequences are believed to form an integrin binding site that is inaccessible when Fg is in its soluble-state structure but then becomes available for Mac-1 binding following adsorption, presumably due to adsorption-induced conformational changes. The objective of this research was to theoretically investigate this possibility by using molecular dynamics simulations of the gamma-chain fragment of Fg over self-assembled monolayer (SAM) surfaces presenting different types of surface chemistry. The GROMACS software package was used to carry out the molecular simulations in an explicit solvation environment over a 5 ns period of time. The adsorption of the gamma-chain of fibrinogen was simulated on five types of SAM surfaces. The simulations showed that this protein fragment exhibits distinctly different adsorption behavior on the different surface chemistries. Although the trajectory files showed that significant conformational changes did not occur in this protein fragment over the time frame of the simulations, it was predicted that the protein does undergo substantial rotational and translational motions over the surface prior to stabilizing in various preferred orientations. This suggests that the kinetics of surface-induced conformational changes in a protein's structure might be much slower than the kinetics of orientational changes, thus enabling the principles of adsorption thermodynamics to be used to guide adsorbing proteins into defined orientations on surfaces before large conformational changes can occur. This finding may be very important for biomaterial surface design as it suggests that surface chemistry can potentially be used to directly control the orientation of adsorbing proteins in a manner that either presents or hides specific bioactive sites contained within a protein's structure, thereby providing a mechanism to control cellular responses to the adsorbed protein layer.

A molecular modeling study of the effect of surface chemistry on the adsorption of a fibronectin fragment spanning the 7-10th type III repeats

Although it is well documented that proteins adsorb onto biomaterial surfaces, relatively little is quantitatively understood about the effects of adsorption on protein orientation and conformation. Because this is the primary determining factor of protein bioactivity, the ability to accurately predict a protein's orientation and conformation following adsorption will be essential for the rational design of biomaterial surfaces to control biological responses. Force field-based computational chemistry methods provide an excellent means to theoretically address this issue, with the nontrivial requirement that the force field must be tailored to appropriately represent protein adsorption behavior. Accordingly, we have modified an existing force field (CHARMm) based on semiempirical quantum-mechanical peptide adsorption data to enable it to simulate protein adsorption behavior in an implicit aqueous environment. This modified force field was then applied to predict the adsorption behavior of the 7-10 type III repeats of fibronectin on functionalized surfaces. Predicted changes in adsorption energy and adsorption-induced conformation as a function of surface chemistry were found to correlate well with experimentally observed trends for these same systems. This work represents a first attempt towards the development of a molecular mechanics force field that is specifically parameterized to accurately simulate protein adsorption to biomaterial surfaces.

Thermodynamic Measurements and Predictions of the Adsorption of Short-Chain Peptides on Nanothin Polymer Films

This contribution describes experimental measurements of submolecular-level interaction energies involved in the process of peptide adsorption on polymer films. The objective of this study was to use surface plasmon resonance (SPR) spectroscopy to measure the Gibbs energy change on adsorption (DeltaG(ad)) for pairs of various homopeptides on highly uniform, nanothin polymer films and to use these data, along with the principle of additivity, to predict DeltaG(ad) for homologous homopeptides, as well as for a mixed-residue peptide. By using a graft polymerization methodology, a nanothin poly(2-vinylpyridine) film was prepared and adsorption energies were measured first for a homologous series of tyrosine (Y) homopeptides on this film to determine submolecular-level interaction energies. By using SPR, adsorption isotherms were measured for YY and YYY peptides; analysis of these isotherms provided DeltaG(ad) data for a midchain tyrosine unit and a set of chain-end tyrosine units; values were -0.75 +/- 0.07 kcal/mol and -2.12 +/- 0.04 kcal/mol, respectively. Combining the thermodynamic contributions for adsorption of individual tyrosine units allowed a predictive estimate of -5.12 +/- 0.32 kcal/mol for the adsorption energy for YYYYYY; this estimate deviated by only 2.3% from its measured value of -5.24 +/- 0.06 kcal/mol. Similarly, adsorption energies were found for phenylalanine, glycine, and tyrosine-leucine peptides. Combining the thermodynamic contributions for adsorption of individual residue units allowed a predictive estimate of -3.24 +/- 0.38 kcal/mol for a pentapeptide, leucine enkephalin; this estimate deviated by only 3.0% from its measured value of -3.34 +/-0.11 kcal/mol.

The interaction of proteins with solid surfaces

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