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.     

Research of protein adsorption on the different surface topography of the zinc oxide

The effect of the surface topography on the protein adsorption process is of great significance for designing biomaterial surfaces and the biocompatibility for specific biomedical applications. In this work, we have systematically investigated the mono‐protein adsorption kinetics of bovine serum albumin (BSA) and fibrinogen (Fg) adsorbed on the four different surface topographies (nanoparticles (NPs), nanorods (NRs), nanosheets (NSs) and nanobeams (NBs) of Zinc oxide (ZnO), respectively. The competition of multi‐protein adsorbed on them has been studied as well. Results showed that each protein had a singular process of adsorption that fitted well by Spreading Particle Model (SPM). It confirmed that ZnO NRs compared with other samples had more adsorption sites, which could provide more opportunities for the interaction between material and protein molecules. In addition, the Fg compared to the BSA could be more tightly adsorbed to the surface, both of which existed slight conformational changes by Fourier transform infrared (FTIR) and circular dichroism spectra (CD). Taken together, all these consequences well demonstrated that NRs may have wider applications in designing biomaterial surfaces and the biocompatibility for implanted biomaterials. Copyright © 2014 John Wiley & Sons, Ltd.     

Control of protein adsorption: molecular level structural and spatial variables

The adsorption of fibrinogen (Fb) and bovine serum albumin onto polycrystalline Au coated with HS(CH2)3O(CH2CH2O)5CH3 was determined by surface plasmon resonance from bare Au (0% coverage) to the complete ( approximately 100% coverage) self-assembled monolayer (SAM). Both proteins exhibit similar adsorption curves with common onset ( approximately 60% coverage) and range ( approximately 60% to 80% coverage) of minimal protein adsorption. Reflection-absorption infrared spectroscopic data show that widespread order is not present in the films over this range of coverage, indicating loosely packed, bound oligomers that are uniformly distributed and fully screen the underlying substrate. On the basis of our data, we propose a mechanism of protein rejection by oligo(ethylene oxide) (OEO)-modified surfaces in terms of changes in free energy (DeltaGsystem; system = protein + surface) due to oligomer conformational constriction over an area greater than the contact area. Minimal protein adsorption corresponds to the maximum DeltaGsystem for a given compression. This controlled study of protein adsorption provides insights into the molecular level understanding of protein adsorption unavailable from previous polymer and comparative SAM studies.     

Surface tailoring for controlled protein adsorption: effect of topography at the nanometer scale and chemistry

Protein adsorption behavior is at the heart of many of today's research fields including biotechnology and materials science. With understanding of protein-surface interactions, control over the conformation and orientation of immobilized species may ultimately allow tailor-made surfaces to be generated. In this contribution protein-surface interactions have been examined with particular focus on surface curvature with and without surface chemistry effects. Silica spheres with diameters in the range 15-165 nm with both hydrophilic and hydrophobic surface chemistries have been used as model substrates. Two proteins differing in size and shape, bovine serum albumin (BSA) and bovine fibrinogen (Fg), have been used in model studies of protein binding with detailed secondary structure analysis being performed using infrared spectroscopy (IR) on surface-bound proteins. Although trends in binding affinity and saturation values were similar for both proteins, albumin is increasingly less ordered on larger substrates, while fibrinogen, in contrast, loses secondary structure to a greater extent when adsorbing onto particles with high surface curvature. These effects are compounded by surface chemistry, with both proteins becoming more denatured on hydrophobic surfaces. Both surface chemistry and topography play key roles in determining the structure of the bound proteins. A model of the binding characteristics of these two proteins onto surfaces having differing curvature and chemistry is presented. We propose that properties of an adsorbed protein layer may be guided through careful consideration of surface structure, allowing the fabrication of materials/surface coatings with tailored bioactivity.     

Poly(N-vinylpyrrolidone)-modified surfaces repel plasma protein adsorption

The present work aimed to study the interaction between plasma proteins and PVP-modified surfaces under more complex protein conditions.In the competitive adsorption of fibrinogen(Fg) and human serum albumin(HSA),the modified surfaces showed preferential adsorption of HSA.In 100%plasma,the amount of Fg adsorbed onto PVP-modified surfaces was as low as 10 ng/cm~2,suggesting the excellent protein resistance properties of the modified surfaces.In addition, immunoblots of proteins eluted from the modified surfaces after plasma contact confirmed that PVP-modified surfaces can repel most plasma proteins,especially proteins that play important roles in the process of blood coagulation.     

Adsorption of fibrinogen on a biomedical-grade stainless steel 316LVM surface: a PM-IRRAS study of the adsorption thermodynamics, kinetics and secondary structure changes

Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) was employed to investigate the interaction of serum protein fibrinogen with a biomedical-grade 316LVM stainless steel surface, in terms of the adsorption thermodynamics, kinetics and secondary structure changes of the protein. Apparent Gibbs energy of adsorption values indicated a highly spontaneous and strong adsorption of fibrinogen onto the surface. The kinetics of fibrinogen adsorption were successfully modeled using a pseudo first-order kinetic model. Deconvolution of the amide I bands indicated that the adsorption of fibrinogen on 316LVM results in significant changes in the protein's secondary structure that occur predominantly within the first minute of adsorption. Among the investigated structures, the alpha-helix structure undergoes the smallest changes, while the beta-sheet and beta-turns structures undergo significant changes. It was shown that lateral interactions between the adsorbed molecules do not play a role in controlling the secondary structure changes. An increase in temperature induced changes in the secondary structure of the protein, characterized by a loss of the alpha-helical content and its transformation into the beta-turns structure.     

Influence of PEG architecture on protein adsorption and conformation

Poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG) copolymers with various grafting ratios were adsorbed to niobium pentoxide-coated silicon wafers and characterized before and after protein adsorption using X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Three proteins of different sizes, myoglobin (16 kD), albumin (67 kD), and fibrinogen (340 kD), were studied. XPS was used to quantify the amount of protein adsorbed to the bare and PEGylated surfaces. ToF-SIMS and principal component analysis (PCA) were used to study protein conformational changes on these surfaces. The smallest protein, myoglobin, generally adsorbed in higher numbers than the much larger fibrinogen. Protein adsorption was lowest on the surfaces with the highest PEG chain surface density and increased as the PEG layer density decreased. The highest adsorption was found on lysine-coated and bare niobium surfaces. ToF-SIMS and PCA data evaluation provided further information on the degree of protein denaturation, which, for a particular protein, were found to decrease with increasing PEG surface density and increase with decreasing protein size.     

Surface grafted sulfobetaine polymers via atom transfer radical polymerization as superlow fouling coatings

One of the sulfobetaine methacrylate (SBMA) monomers, N-(3-sulfopropyl)-N-(methacryloxyethyl)-N,N-dimethylammonium betaine, was polymerized onto initiator-covered gold surfaces using atom transfer radical polymerization (ATRP) to form uniform polymer brushes. Self-assembled monolayers (SAMs) with ATRP initiators were characterized by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The thickness of grafted poly(SBMA) films was measured by ellipsometry. Fibrinogen adsorption on poly(SBMA) grafted surfaces was measured with a surface plasmon resonance (SPR) sensor. Two approaches were compared to graft ATRP initiators onto gold surfaces for surface polymerization and subsequent protein adsorption on these polymer grafted surfaces. The first was to prepare a SAM from omega-mercaptoundecyl bromoisobutyrate onto a gold surface. Superlow fouling surfaces with well-controlled poly(SBMA) brushes were achieved using this approach (e.g., fibrinogen adsorption <0.3 ng/cm2). The second approach was to react bromoisobutyryl bromide with a hydroxyl-terminated SAM on a gold surface. Although protein adsorption decreased as the density of surface initiators increased, the surface prepared using the second approach was not able to achieve as low protein adsorption as the first approach. Key parameters to achieve superlow fouling surfaces were studied and discussed.     

Polymer surface reorientation after protein adsorption

Surface side-chain orientation changes of two polymers have been observed upon protein adsorption using sum frequency generation vibrational spectroscopy. Side-chain-deuterated poly(ethyl methacrylate) and poly(n-butyl methacrylate) were contacted with five protein solutions: albumin, fibrinogen, ubiquitin, cytochrome c, and lysozyme. The CD(3)/CD(2) symmetric stretch ratios of the surface polymer side chains in contact with these different media were compared to each other and to that of the polymer contacting air or phosphate buffered saline. The adsorption of different proteins to the surfaces resulted in polymer side-chain orientations slightly different from each other, with orientations between the air and buffer cases.     

Understanding the nonfouling mechanism of surfaces through molecular simulations of sugar-based self-assembled monolayers

This paper presents a molecular simulation study of the interactions of a protein (lysozyme) with self-assembled monolayers (SAMs) of mannitol and sorbitol terminated alkanethiols in the presence of explicit water molecules and ions. The all-atom simulations were performed to calculate the force generated on the protein as a function of its distance above the SAM surfaces. The structural and dynamic properties of water molecules both above the SAM surfaces and around the SAM head groups were analyzed to provide a better understanding of the nonfouling behavior of the sugar-based SAM surfaces. Results from this work suggest that both mannitol and sorbitol SAMs generate a tightly bound, structured water layer around the SAM chains. This hydration layer creates a repulsive force on the protein when it approaches the surface, resulting in a nonfouling surface despite the presence of hydrogen-bond donor groups. This work demonstrates the importance of strong surface-water interactions for surface resistance to nonspecific protein adsorption.     

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.     

Fibrinogen adsorption on blocked surface of albumin

We have investigated the adsorption of albumin and fibrinogen onto PET (polyethylene terephthalate) and glass surfaces and how pre-adsorption of albumin onto these surfaces can affect the adsorption of later added fibrinogen. For materials and devices being exposed to blood, adsorption of fibrinogen is often a non-wanted event, since fibrinogen is part of the clotting cascade and unspecific adsorption of fibrinogen can have an influence on the activation of platelets. Albumin is often used as blocking agent for avoiding unspecific protein adsorption onto surfaces in devices designed to handle biological samples, including protein solutions. It is based on the assumption that proteins adsorbs as a monolayer on surfaces and that proteins do not adsorb on top of each other. By labelling albumin and fibrinogen with two different radioactive iodine isotopes that emit gamma radiation with different energies, the adsorption of both albumin and fibrinogen has been monitored simultaneously on the same sample. Information about topography and coverage of adsorbed protein layers has been obtained using AFM (Atomic Force Microscopy) analysis in liquid. Our studies show that albumin adsorbs in a multilayer fashion on PET and that fibrinogen adsorbs on top of albumin when albumin is pre-adsorbed on the surfaces.     

Colloid probe AFM investigation of interactions between fibrinogen and PEG-like plasma polymer surfaces

Interaction forces between surfaces designed to be protein resistant and fibrinogen (Fg) were investigated in phosphate-buffered saline with colloid probe atomic force microscopy. The surfaces of the silica probes were coated with a layer of fibrinogen molecules by adsorption from the buffer. The technique of low-power, pulsed AC plasma polymerization was used to make poly(ethylene glycol) (PEG)-like coatings on poly(ethylene teraphthalate) by using diethylene glycol vinyl ether as the monomer gas. The degree of PEG-like nature of the films was controlled by use of a different effective plasma power in the chamber for each coating, ranging from 0.6 to 3.6 W. This produced a series of thin films with a different number of ether carbons, as assessed by X-ray photoelectron spectroscopy. The interaction force measurements are discussed in relation to trends observed in the reduction of fibrinogen adsorption, as determined quantitatively by (125)I radio-labeling. The plasma polymer coatings with the greatest protein-repelling properties were the most PEG-like in nature and showed the strongest repulsion in interaction force measurements with the fibrinogen-coated probe. Once forced into contact, all the surfaces showed increased adhesion with the protein layer on the probe, and the strength and extension length of adhesion was dependent on both the applied load and the plasma polymer surface chemistry. When the medium was changed from buffer to water, the adhesion after contact was eliminated and only appeared at much higher loads. This indicates that the structure of the fibrinogen molecules on the probe is changed from an extended conformation in buffer to a flat conformation in water, with the former state allowing for stronger interaction with the polymer chains on the surface. These experiments underline the utility of aqueous surface force measurements toward understanding protein-surface interactions, and developing nonfouling surfaces that confer a steric barrier against protein adsorption.     

Difference in electrophoretic mobility and plasmic digestion profile between four recombinant fibrinogens, gamma 308K, gamma 308I, gamma 308A, and wild type (gamma 308N)

We have produced recombinant gamma-chain variant fibrinogens, gamma308K, gamma308I, and gamma308A simultaneously with wild-type fibrinogen, gamma-308N, by genetic protein engineering using Chinese hamster ovary cells. Although all three variant fibrinogens are a result of a single amino acid substitution, the aberrant gamma-chains of gamma308K and gamma308I fibrinogens migrated faster than gamma308N. Furthermore, plasmic digestion profiles were examined in the presence of 5 mM ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) or 1 mM CaCl2. In the presence of EGTA, the three variant fibrinogens were digested into D1 and D2 fragments slightly faster than wild type. In addition, the D2 fragment derived from gamma308K was further digested into D3 by plasmin much faster than that from gamma308N. These data suggest that cleavage of gamma356Lys-gamma357Ala bond by plasmin in gamma308K, gamma308I, and gamma308A is slightly accelerated and the gamma302Lys-gamma303Phe bond is cleaved by plasmin rapidly in only the gamma308K variant. Furthermore, the substitution of Lys for gamma308Asn results in the generation of a new plasmin cleavage site between gamma308Lys and gamma309Gly in the presence of EGTA. In conclusion, a substitution at residue gamma308Asn may cause a conformational change in the gammachain of fragment D affecting polymerization and plasmin cleavage.     

Interfacial energetics of protein adsorption from aqueous buffer to surfaces with varying hydrophilicity

Adsorption isotherms constructed from time-and-concentration-dependent advancing contact angles thetaa show that the profound biochemical diversity among ten different blood proteins with molecular weight spanning 10-1000 kDa has little discernible effect on the amount adsorbed from aqueous phosphate-buffered saline (PBS) solution after 1 h contact with a particular test surface selected from the full range of observable water wettability (as quantified by PBS adhesion tension tauoa=gammaolv cos thetaoa; where gammaolv is the liquid-vapor interfacial tension and thetaoa is the advancing PBS contact angle). The maximum advancing spreading pressure, Pimaxa, determined from adsorption isotherms decreases systematically with tauoa for methyl-terminated self-assembled monolayers (CH3 SAM, tauo=-15 mN/m), polystyrene spun-coated onto electronic-grade SiOx wafers (PS, tauo=7.2 mN/m), aminopropyltriethoxysilane-treated SiOx surfaces (APTES, tauo = 42 mN/m), and fully water wettable SiOx (tauo=72 mN/m). Likewise, the apparent Gibbs' surface excess [Gammasl-Gammasv], which measures the difference in the amount of protein adsorbed Gamma (mol/cm2) at solid-vapor (SV) and solid-liquid (SL) interfaces, decreases with tauo from maximal values measured on the CH3 SAM surface through zero (no protein adsorption in excess of bulk solution concentration) near tauo=30 mN/m (thetaa=65 degrees). These latter results corroborate the conclusion drawn from independent studies that water is too strongly bound to surfaces with tauo>or=30 mN/m to be displaced by adsorbing protein and that, as a consequence, protein does not accumulate within the interfacial region of such surfaces at concentrations exceeding that of bulk solution ([Gammasl-Gammasv]=0 at tauo=30 mN/m). Results are collectively interpreted to mean that water controls protein adsorption to surfaces and that the mechanism of protein adsorption can be understood from this perspective for a diverse set of proteins with very different amino acid compositions.     

Monte Carlo Simulations of Copolymer Adsorption at Planar Chemically Patterned Surfaces: Effect of Interfacial Interaction

Summary: Monte Carlo simulation utilizing the bond fluctuation model in conjunction with single and configurational biased Monte Carlo moves is used to study the adsorption of diblock (A‐block‐B) and alternating (A‐alt‐B) copolymers at flat, chemically heterogeneous surfaces comprising C and D domains. The main objective of this work is to address the effect of the strength of attraction between the adsorbing surface domains, D, and the copolymer adsorbing segments, B, on the copolymer's ability to recognize the chemical pattern on the surface. The results of our simulations reveal that both block and alternating copolymers have the ability to recognize the surface motif and transcribe it into the bulk material. The extent to which diblock copolymers transfer the chemical pattern from the surface to the bulk is relatively unaffected when the attractive B‐D potential is increased beyond a certain critical value. This behavior stems from the brush‐like conformation adopted by the diblock copolymer at the substrate. In contrast to the diblock copolymer, the adsorption of the alternating copolymer is influenced by the strength of the attraction between the copolymer's adsorbing segments and the adsorbing domains on the surface. Since the B segments are distributed evenly along the backbone, the alternating copolymers are more likely to adopt conformations in which the whole chain is “zipped” to the surface. The resultant entropic frustration is then alleviated through an increased formation of loops with little change to their length. Such conformational changes endow the alternating copolymer with the ability to invert the substrate pattern as the distance away from the surface is increased.

     

The effect of surface microtopography of poly(dimethylsiloxane) on protein adsorption, platelet and cell adhesion

Chemical homogeneous poly(dimethylsiloxane) (PDMS) surface with dot-like protrusion pattern was used to investigate the individual effect of surface microtopography on protein adsorption and subsequent biological responses. Fibrinogen (Fg) and fibronectin (Fn) were chosen as model proteins due to their effect on platelet and cell adhesion, respectively. Fg labeled with ¹²⁵I and fluorescein isothiocyanate (FITC) was used to study its adsorption on flat and patterned surfaces. Patterned surface has a 46% increase in the adsorption of Fg when compared with flat surface. However, the surface area of the patterned surface was only 8% larger than that of the flat surface. Therefore, the increase in the surface area was not the only factor responsible for the increase in protein adsorption. Clear fluorescent pattern was visualized on patterned surface, indicating that adsorbed Fg regularly distributed and adsorbed most on the flanks and valleys of the protrusions. Such distribution and local enrichment of Fg presumably caused the specific location of platelets adhered from platelet-rich plasma (PRP) and flowing whole blood (FWB) on patterned surface. Furthermore, the different combination of surface topography and pre-adsorbed Fn could influence the adhesion of L929 cells. The flat surface with pre-adsorbed Fn was the optimum substrate while the virgin patterned surface was the poor substrate in terms of L929 cells spread.     

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

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

Recognition of multiblock copolymers on nanopatterned surfaces: insight from molecular simulations

The recognition of multiblock copolymers on nanopatterned surfaces has been investigated by molecular simulations. All the copolymers (AnB12-n)5 are composed of 60 square-well segments, but with various architectures by changing n. Segment density profiles, radii of gyration, pattern transfer parameters, and three adsorption conformations (tail, loop, and train) are examined quantitatively. It is found that the copolymer can recognize the adsorbing stripes on surface and the surface vicinity. The recognition affinity becomes stronger with increasing the stripe width, the adsorption strength, and the number of adsorbing segments in copolymer chain. From surface to bulk phase, the shape of copolymer changes from elongated to elliptical, and finally to globular. Among the three adsorption conformations, tail has the greatest average size while train has the smallest. With the increased number of nonadsorbing segments, the average size shows an increase in tail but a decrease in train.