Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces

A molecular dynamics study on pH response of protein adsorbed on peptide-modified polyvinyl alcohol hydrogel

Molecular dynamics simulation of the protein adsorption on peptide modified PVA hydrogel and the response of hydrogel chains to different pHs.

Development of injectable organic/inorganic colloidal composite gels made of self-assembling gelatin nanospheres and calcium phosphate nanocrystals

Colloidal gels are a particularly attractive class of hydrogels for applications in regenerative medicine, and allow for a "bottom-up" fabrication of multi-functional biomaterials by employing micro- or nanoscale particles as building blocks to assemble into shape-specific bulk scaffolds. So far, however, the synthesis of colloidal composite gels composed of both organic and inorganic particles has hardly been investigated. The current study has focused on the development of injectable colloidal organic-inorganic composite gels using calcium phosphate (CaP) nanoparticles and gelatin (Gel) nanospheres as building blocks. These novel Gel-CaP colloidal composite gels exhibited a strongly enhanced gel elasticity, shear-thinning and self-healing behavior, and gel stability at high ionic strengths, while chemical - potentially cytotoxic - functionalizations were not necessary to introduce sufficiently strong cohesive interactions. Moreover, it was shown in vitro that osteoconductive CaP nanoparticles can be used as an additional tool to reduce the degradation rate of otherwise fast-degradable gelatin nanospheres and fine-tune the control over the release of growth factors. Finally, it was shown that these colloidal composite gels support attachment, spreading and proliferation of cultured stem cells. Based on these results, it can be concluded that proof-of-principle has been obtained for the design of novel advanced composite materials made of nanoscale particulate building blocks which exhibit great potential for use in regenerative medicine.

Molecular docking characterization of a four-domain segment of human fibronectin encompassing the RGD loop with hydroxyapatite

Fibronectin adsorption on biomaterial surfaces plays a key role in the biocompatibility of biomedical implants. In the current study, the adsorption behavior of the 7–10th type III modules of fibronectin (FN-III_7–10) in the presence of hydroxyapatite (HAP) was systematically investigated by using molecular docking approach. It was revealed that the FN-III₁₀ is the most important module among FN-III_7–10 in promoting fibronectin binding to HAP by optimizing the interaction energy; the arginine residues were observed to directly interact with the hydroxyl group of HAP through electrostatic forces and hydrogen bonding. Moreover, it was found that the HAP-binding sites on FN-III₁₀ are mainly located at the RGD loop region, which does not affect the interaction between the fibronectin protein and its cognate receptors on the cell surface.

A scalable approach to obtain mesenchymal stem cells with osteogenic potency on apatite microcarriers

Bone tissue engineering, which relies on the interactions between stem cells and suitable scaffold materials, represents a highly desirable alternative to currently used allograft or autograft strategies for the treatment of bone defects caused by injury or disease, with one of the major challenges being to generate sufficient quantities of stem cells to bring about the intended therapeutic effect. However, conventional cell culture to achieve sufficient cell numbers faces limitations of low efficiency and diminished efficacy of stem cells due to repeated passaging. Furthermore, current microcarriers available may not be suitable for therapeutic implantation. Here, the authors featured an apatite-based microcarrier intended for bone tissue engineering applications. These apatite microcarriers have a diameter of ∼230 µm, and exhibited porous and rough surface morphology. Peaks obtained from X-ray diffractometry (XRD) corresponded to hydroxyapatite (HA) with high crystallinity. Fourier transform infrared spectrophotometry (FTIR) showed that no residues of alginate remained, and all bands observed belong to phosphate and hydroxyl groups of HA. To evaluate the cytocompatibility of these microcarriers, in vitro proliferation studies were conducted and compared with conventional monolayer as well as Cytodex 3. The authors found that human foetal mesenchymal stem cells (hfMSCs) cultured on apatite microcarriers exhibited comparable growth characteristics, achieving 1.4-fold higher live cells than Cytodex 3 over a 9-day culture period. As these microcarriers were hypothesised to offer enhanced osteogenic potency over conventional monolayer culture, alkaline phosphatase (ALP), type I collagen and osteocalcin expression of hfMSCs cultured on the apatite microcarriers were evaluated over a 12-day period. ALP expression for hfMSCs seeded on apatite microcarriers was 2.7-fold higher than that of adherent monolayer culture (p < 0.001). Additionally, type I collagen and osteocalcin expression were 1.8- and 1.5-fold higher than that of adherent monolayer culture on day 12, respectively (p < 0.001).

Synthesis and characterization of novel elastomeric poly(D,L-lactide urethane) maleate composites for bone tissue engineering

Here, we report the synthesis and characterization of a novel 4-arm poly(lactic acid urethane)-maleate (4PLAUMA) elastomer and its composites with nano-hydroxyapatite (nHA) as potential weight-bearing composite. The 4PLAUMA/nHA ratios of the composites were 1:3, 2:5, 1:2 and 1:1. FTIR and NMR characterization showed urethane and maleate units integrated into the PLA matrix. Energy dispersion and Auger electron spectroscopy confirmed homogeneous distribution of nHA in the polymer matrix. Maximum moduli and strength of the composites of 4PLAUMA/nHA, respectively, are 1973.31 ± 298.53 MPa and 78.10 ± 3.82 MPa for compression, 3630.46 ± 528.32 MPa and 6.23 ± 1.44 MPa for tension, 1810.42 ± 86.10 MPa and 13.00 ± 0.72 for bending, and 282.46 ± 24.91 MPa and 5.20 ± 0.85 MPa for torsion. The maximum tensile strains of the polymer and composites are in the range of 5% to 93%, and their maximum torsional strains vary from 0.26 to 0.90. The composites exhibited very slow degradation rates in aqueous solution, from approximately 50% mass remaining for the pure polymer to 75% mass remaining for composites with high nHA contents, after a period of 8 weeks. Increase in ceramic content increased mechanical properties, but decreased maximum strain, degradation rate, and swelling of the composites. Human bone marrow stem cells and human endothelial cells adhered and proliferated on 4PLAUMA films and degradation products of the composites showed little-to-no toxicity. These results demonstrate that novel 4-arm poly(lactic acid urethane)-maleate (4PLAUMA) elastomer and its nHA composites may have potential applications in regenerative medicine.

Interactions between inorganic and organic phases in bone tissue as a source of inspiration for design of novel nanocomposites

Mimicking the nanostructure of bone and understanding the interactions between the nanoscale inorganic and organic components of the extracellular bone matrix are crucial for the design of biomaterials with structural properties and a functionality similar to the natural bone tissue. Generally, these interactions involve anionic and/or cationic functional groups as present in the organic matrix, which exhibit a strong affinity for either calcium or phosphate ions from the mineral phase of bone. This study reviews the interactions between the mineral and organic extracellular matrix components in bone tissue as a source of inspiration for the design of novel nanocomposites. After providing a brief description of the various structural levels of bone and its main constituents, a concise overview is presented on the process of bone mineralization as well as the interactions between calcium phosphate (CaP) nanocrystals and the organic matrix of bone tissue. Bioinspired synthetic approaches for obtaining nanocomposites are subsequently addressed, with specific focus on chemical groups that have affinity for CaPs or are involved in stimulating and controlling mineral formation, that is, anionic functional groups, including carboxyl, phosphate, sulfate, hydroxyl, and catechol groups.

Trastuzumab-Peptide interactions: mechanism and application in structure-based ligand design

Understanding of protein-ligand interactions and its influences on protein stability is necessary in the research on all biological processes and correlative applications, for instance, the appropriate affinity ligand design for the purification of bio-drugs. In this study, computational methods were applied to identify binding site interaction details between trastuzumab and its natural receptor. Trastuzumab is an approved antibody used in the treatment of human breast cancer for patients whose tumors overexpress the HER2 (human epidermal growth factor receptor 2) protein. However, rational design of affinity ligands to keep the stability of protein during the binding process is still a challenge. Herein, molecular simulations and quantum mechanics were used on protein-ligand interaction analysis and protein ligand design. We analyzed the structure of the HER2-trastuzumab complex by molecular dynamics (MD) simulations. The interaction energies of the mutated peptides indicate that trastuzumab binds to ligand through electrostatic and hydrophobic interactions. Quantitative investigation of interactions shows that electrostatic interactions play the most important role in the binding of the peptide ligand. Prime/MM-GBSA calculations were carried out to predict the binding affinity of the designed peptide ligands. A high binding affinity and specificity peptide ligand is designed rationally with equivalent interaction energy to the wild-type octadecapeptide. The results offer new insights into affinity ligand design.

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.

Surface topography effects in protein adsorption on nanostructured carbon allotropes

We report a molecular dynamics (MD) simulation study of protein adsorption on the surface of nanosized carbon allotropes, namely single-walled carbon nanotubes (SWNT) considering both the convex outer surface and the concave inner surface, together with a graphene sheet for comparison. These systems are chosen to investigate the effect of the surface curvature on protein adsorption at the same surface chemistry, given by sp(2) carbon atoms in all cases. The simulations show that proteins do favorably interact with these hydrophobic surfaces, as previously found on graphite which has the same chemical nature. However, the main finding of the present study is that the adsorption strength does depend on the surface topography: in particular, it is slightly weaker on the outer convex surfaces of SWNT and is conversely enhanced on the inner concave SWNT surface, being therefore intermediate for flat graphene. We additionally find that oligopeptides may enter the cavity of common SWNT, provided their size is small enough and the tube diameter is large enough for both entropic and energetic reasons. Therefore, we suggest that proteins can effectively be used to solubilize in water single-walled (and by analogy also multiwalled) carbon nanotubes through adsorption on the outer surface, as indeed experimentally found, and to functionalize them after insertion of oligopeptides within the cavity of nanotubes of appropriate size.

Dispersion of graphene sheets in aqueous solution by oligodeoxynucleotides

Applications of graphene sheets in the fields of biosensors and biomedical devices are limited by their insolubility in water. Consequently, understanding the dispersion mechanism of graphene in water and exploring an effective way to prepare stable dispersions of graphene sheets in water is of vital importance for their application in biomaterials, biosensors, biomedical devices, and drug delivery. Herein, a method for stable dispersion of graphene sheets in water by single-stranded oligodeoxynucleotides (ssODNs) is studied. Owing to van der Waals interactions between graphene sheets, they undergo layer-to-layer (LtL) aggregation in water. Molecular dynamics simulations show that, by disrupting van der Waals interaction of graphene sheets with ssODNs, LtL aggregation of graphene sheets is prevented, and water molecules can be distributed stably between graphene sheets. Thus, graphene sheets are dispersed stably in water in the presence of ssODNs. The effects of size and molarity of ssODNs and noncovalent modification of graphene sheets are also discussed.

Fracture mechanics of hydroxyapatite single crystals under geometric confinement

Geometric confinement to the nanoscale, a concept that refers to the characteristic dimensions of structural features of materials at this length scale, has been shown to control the mechanical behavior of many biological materials or their building blocks, and such effects have also been suggested to play a crucial role in enhancing the strength and toughness of bone. Here we study the effect of geometric confinement on the fracture mechanism of hydroxyapatite (HAP) crystals that form the mineralized phase in bone. We report a series of molecular simulations of HAP crystals with an edge crack on the (001) plane under tensile loading, and we systematically vary the sample height whilst keeping the sample and the crack length constant. We find that by decreasing the sample height the stress concentration at the tip of the crack disappears for samples with a height smaller than 4.15nm, below which the material shows a different failure mode characterized by a more ductile mechanism with much larger failure strains, and the strength approaching that of a flaw-less crystal. This study directly confirms an earlier suggestion of a flaw-tolerant state that appears under geometric confinement and may explain the mechanical stability of the reinforcing HAP platelets in bone.

Protein diffusion and long-term adsorption states at charged solid surfaces

The diffusion pathways of lysozyme adsorbed to a model charged ionic surface are studied using fully atomistic steered molecular dynamics simulation. The simulations start from existing protein adsorption trajectories, where it has been found that one particular residue, Arg128 at the N,C-terminal face, plays a crucial role in anchoring the lysozyme to the surface [Langmuir 2010 , 26 , 15954 - 15965]. We first investigate the desorption pathway for the protein by pulling the Arg128 side chain away from the surface in the normal direction, and its subsequent readsorption, before studying diffusion pathways by pulling the Arg128 side chain parallel to the surface. We find that the orientation of this side chain plays a decisive role in the diffusion process. Initially, it is oriented normal to the surface, aligning in the electrostatic field of the surface during the adsorption process, but after resorption it lies parallel to the surface, being unable to return to its original orientation due to geometric constraints arising from structured water layers at the surface. Diffusion from this alternative adsorption state has a lower energy barrier of ∼0.9 eV, associated with breaking hydrogen bonds along the pathway, in reasonable agreement with the barrier inferred from previous experimental observation of lysozyme surface clustering. These results show the importance of studying protein diffusion alongside adsorption to gain full insight into the formation of protein clusters and films, essential steps in the future development of functionalized surfaces.

Molecular simulation of flavin adenine dinucleotide immobilized on charged single-walled carbon nanotubes for biosensor applications

The reconstitution of apo-glucose oxidase (apo-GOx) on single-walled carbon nanotubes (SWNTs) functionalized with the cofactor, flavin adenine dinucleotide (FAD), greatly improved electron transfer turnover rate of the redox reactions in glucose sensing with glucose sensors. The research reported here is aimed to better understand molecular details of affection of the charging SWNT to the conformational changes of FAD, in order to find a rational design and selection scheme of SWNT which is suitable for the FAD and apo-GOx to perform their reconstitution. In this report, molecular simulations of FAD functionalized differently charged SWNTs were carried outin an aqueous environment, with counterions to maintain total charge neutrality. The conformation and orientation changes were observed by both trajectory and quantitative analyses. The simulation results showed that in both uncharged and positively charged SWNT situations, FAD adsorbed onto SWNT at the end of the simulations, which increased the steric resistance of molecules and hindered the reconstitution of apo-GOx and FAD to some degree. By contrast, FAD functionalized negatively charged SWNT maintained its original conformation largely. In addition, negatively charged SWNT may be the best choice for electron transfer mediator for the reconstitution of apo-GOx on relay-cofactor units associated with electrodes.

Molecular simulation of fibronectin adsorption onto polyurethane surfaces

Poly(ethylene glycol)-based polyurethanes have been widely used in biomedical applications; however, they are prone to swelling. A natural polyol, castor oil, can be incorporated into these polyurethanes to control the degree of the swelling, which alters mechanical properties and protein adsorption characteristic of the polymers. In this work, we modeled poly(ethylene glycol) and castor oil copolymers of hexamethylene diisocyanate-based polyurethanes (PEG-HDI and CO-HDI, respectively) and compared their mechanisms for fibronectin adsorption using molecular mechanics and molecular dynamics simulations. Results showed that the interplay between the hydrophobic residues concentrated at the N-terminal end of the protein, the surface roughness, and the hydrophilicity of the polymer surface determine the overall protein adsorption affinity. Incorporating explicit water molecules in the simulations results in higher affinity for fibronectin adsorption to more hydrophobic surface of CO-HDI surfaces, emphasizing the role that water molecules play during adsorption. We also observed that the strain energies that are indicative of flexibility and consequently entropy are significantly affected by the changes in the patterns of β-sheet formation/breaking. Our study lends supports to the view that while castor oil controls the degree of swelling, it increases the adsorption of fibronectin to a limited extent due to the interplay between its hydrophobicity and its surface roughness, which needs to be taken into account during the design of polyurethane-based biomaterials.

The development of fibronectin-functionalised hydroxyapatite coatings to improve dermal fibroblast attachment in vitro

The success of long-term transcutaneous implants depends on dermal attachment to prevent downgrowth of the epithelium and infection. Hydroxyapatite (HA) coatings and fibronectin (Fn) have independently been shown to regulate fibroblast activity and improve attachment. In an attempt to enhance this phenomenon we adsorbed Fn onto HA-coated substrates. Our study was designed to test the hypothesis that adsorption of Fn onto HA produces a surface that will increase the attachment of dermal fibroblasts better than HA alone or titanium alloy controls.

Iodinated Fn was used to investigate the durability of the protein coating and a bioassay using human dermal fibroblasts was performed to assess the effects of the coating on cell attachment. Cell attachment data were compared with those for HA alone and titanium alloy controls at one, four and 24 hours. Protein attachment peaked within one hour of incubation and the maximum binding efficiency was achieved with an initial droplet of 1000 ng. We showed that after 24 hours one-fifth of the initial Fn coating remained on the substrates, and this resulted in a significant, three-, four-, and sevenfold increase in dermal fibroblast attachment strength compared to uncoated controls at one, four and 24 hours, respectively.

Study of protein adsorption on octacalcium phosphate surfaces by molecular dynamics simulations

This study numerically studies absorption of human serum albumin (HSA) and basic protein lysozyme (LSZ) on crystallographic planes of octacalcium phosphate (OCP), an essential bioactive calcium phosphate. The molecular simulations include constructing atomic structure of OCP crystallographic planes and representative segments of HSA and LSZ with three different initiate orientations respect to OCP planes. The simulation reveals the dynamic process of the protein absorption. The absorption behavior of proteins is quantified by the interaction energy between proteins and OCP planes and the strain energy of proteins in absorption. The results show that absorption interaction energy of basic LSZ is higher than that of acidic HSA, which indicates that LSZ is more favorable to adsorb onto OCP surface than HSA. The interaction energies change with the OCP crystallographic planes, the trend of changes for both proteins are similar, that is OCP (001) > OCP (111) > OCP (110) > OCP (100), which is corrected with surface energy variation of crystallographic planes. The strain energy strongly depends on the orientations of the proteins before absorption, but weakly depends on crystallographic planes. The simulation results provide useful significant information for predicting/designing interface between bioceramic materials and organic tissues as well as for understanding the mechanism of the osteoinductivity at an atomic level.

Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs

This paper reports a molecular modelling study of the adsorption of protein subdomains with unlike secondary structures on different surfaces of ceramic titanium dioxide (TiO(2)), forming a passivating film on titanium biomaterials that provides the interface between the bulk metal and the physiological environment, affecting its biocompatibility and performance. Using molecular dynamics methods, we study the effect of the nanoscale structure of the common TiO(2) polymorphs (rutile, anatase and brookite) on the adsorption of an albumin subdomain and on two connected fibronectin modules, respectively containing α-helices and β-sheets. We find that the larger protein subdomain shows a stronger adsorption, as expected because of its size, but also that the three surfaces behave differently. In particular, brookite shows the weakest adsorption, whereas anatase leads to the strongest intrinsic adsorption, in particular for the fibronectin modules. Moreover, the simulations indicate a significant conformational change of the adsorbed protein subdomains with extensive surface nanopatterning. These results show that classical molecular dynamics methods can provide useful information about the influence of nanostructure and topology on protein physisorption at a fixed surface chemistry.

Ab initio modelling of protein-biomaterial interactions: influence of amino acid polar side chains on adsorption at hydroxyapatite surfaces

The adsorption from the gas phase of five different amino acids (AAs), namely Gly, Ser, Lys, Gln and Glu, on three surface models of hexagonal hydroxyapatite (HA) has been studied at B3LYP level with Gaussian type basis set within a periodic approach. The AA adsorption was simulated on the (001) and (010) stoichiometric surfaces, the latter both in its pristine and water-reacted form. Low/high AA coverage has been studied by doubling the HA unit cell size. The AAs have been docked to the HA surfaces following the electrostatic complementarity between the electrostatic potentials of AA and the bare HA. Gly adsorbs as a zwitterion at the (001) surface, whereas at the (010) ones, the proton of the COOH group is transferred to the surface resulting in an HA(+)/Gly(-) ion pair. For the other AAs, the common COOH-CH-NH(2) moiety behaves like in Gly, while the specific side-chain functionalities adsorb at the HA surfaces by maximizing electrostatic and H-bond interactions. The interactions between the side chains and the HA surface impart a higher stability compared with the Gly case, with Glu being the strongest adsorbate owing to its high Ca affinity and H-bond donor propensity. For AAs of large size, the adsorption is more favourable in conditions of low coverage as repulsion between adjacent AAs is avoided. For all considered AAs, the strongest interaction is always established on the (010) faces rather than on the (001) one, therefore suggesting an easier growth along the c-direction of HA crystals from AA solutions.

A review of protein adsorption on bioceramics

Bioceramics, because of its excellent biocompatible and mechanical properties, has always been considered as the most promising materials for hard tissue repair. It is well know that an appropriate cellular response to bioceramics surfaces is essential for tissue regeneration and integration. As the in vivo implants, the implanted bioceramics are immediately coated with proteins from blood and body fluids, and it is through this coated layer that cells sense and respond to foreign implants. Hence, the adsorption of proteins is critical within the sequence of biological activities. However, the biological mechanisms of the interactions of bioceramics and proteins are still not well understood. In this review, we will recapitulate the recent studies on the bioceramic-protein interactions.

Thickness of hydroxyapatite nanocrystal controls mechanical properties of the collagen-hydroxyapatite interface

Collagen-hydroxyapatite interfaces compose an important building block of bone structures. While it is known that the nanoscale structure of this elementary building block can affect the mechanical properties of bone, a systematic understanding of the effect of the geometry on the mechanical properties of this interface between protein and mineral is lacking. Here we study the effect of geometry, different crystal surfaces, and hydration on the mechanical properties of collagen-hydroxyapatite interfaces from an atomistic perspective, and discuss underlying deformation mechanisms. We find that the presence of hydroxyapatite significantly enhances the tensile modulus and strength compared with a tropocollagen molecule alone. The stiffening effect is strongly dependent on the thickness of the mineral crystal until a plateau is reached at 2 nm crystal thickness. We observe no significant differences due to the mineral surface (Ca surface vs OH surface) or due to the presence of water. Our result shows that the hydroxyapatite crystal with its thickness confined to the nanometer size efficiently increases the tensile modulus and strength of the collagen-hydroxyapatite composite, agreeing well with experimental observations that consistently show the existence of extremely thin mineral flakes in various types of bones. We also show that the collagen-hydroxyapatite interface can be modeled with an elastic network model which, based on the results of atomistic simulations, provides a good estimate of the surface energy and other mechanical features.

Modelling of lysozyme binding to a cation exchange surface at atomic detail: the role of flexibility

Different approaches were made to predict the adsorbed orientation based on rigid, flexible, or a mixture of both models. To determine the role of flexibility during adsorption, the orientation of lysozyme adsorbed to a negatively charged ligand surface was predicted by a rigid and a flexible model based on two differing protein structures at atomic resolution. For the rigid model, the protein structures were placed at different distances from the ligand surface and the electrostatic interaction energy was calculated for all possible orientations. The results were compared to a flexible model where the binding to the ligand surface was modeled by multiple molecular dynamics simulations starting with 14 initial orientations. Different aspects of the adsorption process were not covered by the rigid model and only detectable by the flexible model. Whereas the results of the rigid model depended sensitively on the protein-surface distance and the protein structure, the preferred orientation obtained by the flexible model was closer to a previous experimental determined orientation, robust toward the initial orientation and independent of the initial protein structure. Additionally, it was possible to obtain insights into the preferred binding process of lysozyme on a negatively charged surface by the flexible model.

Advantages of RGD peptides for directing cell association with biomaterials

Despite many years of in vitro research confirming the effectiveness of RGD in promoting cell attachment to a wide variety of biomaterials, animal studies evaluating tissue responses to implanted RGD-functionalized substrates have yielded more variable results. The goals of this report are to present some of the reasons why cell culture studies may not always reliably predict in vivo responses, and more importantly, to highlight potential applications that may benefit from the use of RGD peptides.

Expression, functional, and structural analysis of proteins critical for otoconia development

Otoconia, developed during late gestation and perinatal stages, couple mechanic force to the sensory hair cells in the vestibule for motion detection and bodily balance. In the present work, we have investigated whether compensatory deposition of another protein(s) may have taken place to partially alleviate the detrimental effects of Oc90 deletion by analyzing a comprehensive list of plausible candidates, and have found a drastic increase in the deposition of Sparc-like 1 (aka Sc1 or hevin) in Oc90 null versus wt otoconia. We show that such up-regulation is specific to Sc1, and that stable transfection of Oc90 and Sc1 full-length expression constructs in NIH/3T3 cells indeed promotes matrix calcification. Analysis and modeling of Oc90 and Sc1 protein structures show common features that may be critical requirements for the otoconial matrix backbone protein. Such information will serve as the foundation for future regenerative purposes.

Mineralization, biodegradation, and drug release behavior of gelatin/apatite composite microspheres for bone regeneration

Gelatin microspheres are well-known for their capacity to release growth factors in a controlled manner, but gelatin microspheres do not calcify in the absence of so-called bioactive substances that induce deposition of calcium phosphate (CaP) bone mineral. This study has investigated if CaP nanocrystals can be incorporated into gelatin microspheres to render these inert microspheres bioactive without compromising the drug releasing properties of gelatin microspheres. Incorporation of CaP nanocrystals into gelatin microspheres resulted into reduced biodegradation and drug release rates, whereas their calcifying capacity increased strongly compared to inert gelatin microspheres. The reduced drug release rate was correlated to the reduced degradation rate as caused by a physical cross-linking effect of CaP nanocrystals dispersed in the gelatin matrix. Consequently, these composite microspheres combine beneficial drug-releasing properties of organic gelatin with the calcifying capacity of a dispersed CaP phase.

Modeling Pressure-Driven Transport of Proteins through a Nanochannel

Reducing the size of a nanofluidic channel not only creates new opportunities for high-precision manipulation of biological macromolecules, but also makes the performance of the entire nanofluidic system more susceptible to undesirable interactions between the transported biomolecules and the walls of the channel. In this manuscript, we report molecular dynamics simulations of a pressure-driven flow through a silica nanochannel that characterized, with atomic resolution, adsorption of a model protein to its surface. Although the simulated adsorption of the proteins was found to be nonspecific, it had a dramatic effect on the rate of the protein transport. To determine the relative strength of the protein-silica interactions in different adsorbed states, we simulated flow-induced desorption of the proteins from the silica surface. Our analysis of the protein conformations in the adsorbed states did not reveal any simple dependence of the adsorption strength on the size and composition of the protein-silica contact, suggesting that the heterogeneity of the silica surface may be a important factor.

Molecular understanding of conformational dynamics of a fibronectin module on rutile (110) surface

The conformational dynamics of the 10th type-III module of fibronectin (FN-III(10)) adsorbed on the perfect and three reduced rutile TiO(2)(110) surfaces with different types of defects was investigated by molecular dynamics (MD) simulations. Stable protein-surface complexes were presented in the four simulated models and were derived from the contributions of direct and indirect interactions of various functional groups in FN-III(10) with the metal oxide layers. A detailed analysis to characterize the overall structural stability of the adsorbed FN-III(10) molecule suggests that the bonding strength and the loss of protein secondary structure vary widely, depending on the topology of the substrate surface. The additional adsorption sites exhibiting higher activity, provided by the reduced surfaces, are responsible for the stronger FN-III(10)-TiO(2) interactions, but too high an interaction energy will cause a severe conformational deformation and therefore a significant loss of bioactivity of the adsorbed protein.

A density functional theory study of the interaction of collagen peptides with hydroxyapatite surfaces

Density functional theory calculations were applied to investigate the binding of four peptide strands, which are important in the collagen protein, to the bone and tooth mineral hydroxyapatite: amphiphilic PRO-HYP-GLY and HYP-PRO-GLY, and hydrophobic PRO-LYS-GLY and PRO-HYL-GLY. The particular peptide sequences are chosen for their different functional groups, containing (i) hydrophobic; (ii) uncharged polar; and (iii) charged polar side groups, thus allowing direct comparison of the general effect of these carboxylic acid and amine functional groups, as well as hydroxylation and charge, on their interactions with two major hydroxyapatite surfaces, (0001) and (0110). The calculated results are consistent with experiments, confirming that the terminal carboxyl groups and amine groups mainly contribute to the adsorption of the peptides to the hydroxyapatite surfaces and primarily to the (0110) surface rather than the dominant (0001) plane. Of the side groups in the tripeptide motifs representing the collagen protein, the -OH and positively charged -NH(3)(+) groups in particular bind strongly to the surfaces, and their presence should therefore promote hydroxyapatite growth.

Influence of crystallite size of nanophased hydroxyapatite on fibronectin and osteonectin adsorption and on MC3T3-E1 osteoblast adhesion and morphology

The characteristic topographical features (crystallite dimensions, surface morphology and roughness) of bioceramics may influence the adsorption of proteins relevant to bone regeneration. This work aims at analyzing the influence of two distinct nanophased hydroxyapatite (HA) ceramics, HA725 and HA1000 on fibronectin (FN) and osteonectin (ON) adsorption and MC3T3-E1 osteoblast adhesion and morphology. Both substrates were obtained using the same hydroxyapatite nanocrystals aggregates and applying the sintering temperatures of 725°C and 1000°C, respectively. The two proteins used in this work, FN as an adhesive glycoprotein and ON as a counter-adhesive protein, are known to be involved in the early stages of osteogenesis (cell adhesion, mobility and proliferation). The properties of the nanoHA substrates had an important role in the adsorption behavior of the two studied proteins and clearly affected the MC3T3-E1 morphology, distribution and metabolic activity. HA1000 surfaces presenting slightly larger grain size, higher root-mean-square roughness (Rq), lower surface area and porosity, allowed for higher amounts of both proteins adsorbed. These substrates also revealed increased number of exposed FN cell-binding domains as well as higher affinity for osteonectin. Regarding the osteoblast adhesion results, improved viability and cell number were found for HA1000 surfaces as compared to HA725 ones, independently of the presence or type of adsorbed protein. Therefore the osteoblast adhesion and metabolic activity seemed to be more sensitive to surfaces morphology and roughness than to the type of adsorbed proteins.