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Highest scoring binding sites for top 4 binding clusters between FN (stick) and HAP (ball). The bold sticks show the direct bonding amino acids.
Source publication
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-III7-10) in the presence of hydroxyapatite (HAP) was systematically investigated by using molecular docking approach. It was revealed that the...
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... binding sites and interaction free energies between the FN-III 7–10 and HAP were further examined using the tool suite of AutoDock 4 [19]. Both the ligand and the receptor were treated as rigid and we only explored the six degrees of translational and rotational freedom, hence excluding any kind of flexibility. There were multiple binding sites detected at every binding cluster and ten sites of minimum binding energy were selected. The resulting binding sites are shown in Figure 2. A total of 13 predicted binding clusters in FN-III 7–10 were detected, which separately locate at the FN-III 8 , FN-III 9 , FN-III 10 and the hinge region. While the sites with the lowest binding energy were in FN-III 10 , and there were no sites found in FN-III 7 . All the results were consistent with the results predicted by MPK2. For each binding cluster, the sites of the lowest binding energy were further investigated with respect to their interacting amino acids. The residues Arg1493, Arg1445, Gly1494, Lys1324, Arg1403, Arg1371, Phe1366, Ser1367 and Gly1368 were from cluster 1–4 (Figure 3), which formed the lowest binding energy sites in all clusters. Arginine is the most important amino acid in the binding of HAP ...
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Citations
... [15a] To gain an in-depth understanding of the initial stereoselectivity between the nanocomposite membrane and adhesive ligands, classical molecular dynamic (MD) simulations modeled on FN-III7-10, as the key cell-binding domains of fibronectin (FN) were performed. [16] Within the simulation models, the BTNF nanocomposite membrane exhibited greater numbers of absorbed residues than that of the BTNP nanocomposite membrane (Table S3, Supporting Information), which indicates that FN adsorbed on the surface of the BTNF composite membrane with stronger affinity. Interestingly, the BTNF-12 nanocomposite membrane exhibited minimal distance between the FN-III7-10 protein and nanocomposite membrane in the first 2000 ps of MD simulation ( Figure S7, Supporting Information), thus indicating that the FN-III7-10 protein was initially stably adsorped on the surface of the BTNF-12 nanocomposite membrane. ...
The heterogeneity of extracellular matrix (ECM) topology, stiffness and architecture is a key factor modulating cellular behavior and osteogenesis. However, the effects of heterogeneous ECM electric potential at the micro- and nanoscale on cellular behavior and osteogenesis remain to be elucidated. Here, the heterogeneous distributions of surface electrical potential is established by incorporating ferroelectric BaTiO3 nanofibers (BTNF) into poly(vinylidene fluoridetrifluoroethylene) (P(VDF-TrFE)) matrix based on phase-field simulation and first-principles simulation. By optimizing the aspect ratios of BTNF fillers, the anisotropic distribution of surface potential on BTNF/P(VDF-TrFE) nanocomposite membranes can be achieved by strong spontaneous electric polarization of BTNF fillers. Our results indicate that heterogeneous surface potential distribution leads to a meshwork pattern of fibronectin (FN) aggregation, which increased FN-III7-10 (FN fragment) focal flexibility and anchor points as predicted by molecular dynamics simulation. Furthermore, integrin clustering, focal adhesion formation, cell spreading and adhesion were enhanced sequentially. Increased traction of actin fibers amplifies mechanotransduction by promoting nuclear translocation of YAP/Runx2, which enhances osteogenesis in vitro and bone regeneration in vivo. Our work thus provides fundamental insights into the biological effects of surface potential heterogeneity at the micro- and nanoscale on osteogenesis, and also develops a new strategy to optimize the performance of electroactive biomaterials for tissue regenerative therapies. This article is protected by copyright. All rights reserved.
... The diversity of biological molecules and interactions makes it challenging to construct universal scoring functions. Blended scoring functions show potential, but their accuracy and generalizability can be improved (Guo et al., 2014). ...
Drug discovery and molecular biology can be advanced through the synergistic combination of bioinformatics techniques and molecular docking. This research attempts to investigate the most recent developments in this multidisciplinary subject, emphasizing enhancing the efficiency and accuracy of predictions. The process entails a thorough literature review and an analysis of significant advancements in search algorithms, machine learning integration, and scoring systems. Notable discoveries include improved search and scoring algorithms powered by machine learning methods that enhance protein flexibility and binding affinity predictions. The report highlights issues like data availability and computational complexity and suggests policy solutions, such as data-sharing programs, computational infrastructure investments, and regulatory guidelines for AI-driven drug discovery. This study highlights the revolutionary potential of bioinformatics docking synergy, opening the door for faster therapeutic advancements in the biomedical sciences and personalized medicine.
... The significance of this study was that misfolded or degraded proteins could be recognised by leukocyte-expressing receptors, which is not only engendered by bacterial challenges, but present in ECM remodelling processes [160]. In particular, fibrinogen is commonly investigated because it can bind several integrins through its arginine-glycine-aspartic acid (RGD) sequence [161], which is also found in other integrin ligands [155,162] such as fibronectin [163] and vitronectin [164]. Interestingly, fibrinogen absorbed onto the biomaterial may alter its conformation due to chemical and physical properties, exposing RGD for leukocyte recognition via Mac-1, and initiate integrin signalling [165][166][167]. ...
Biomaterial implants are an established part of medical practice, encompassing a broad range of devices that widely differ in function and structural composition. However, one common property amongst biomaterials is the induction of the foreign body response: an acute sterile inflammatory reaction which overlaps with tissue vascularisation and remodelling and ultimately fibrotic encapsulation of the biomaterial to prevent further interaction with host tissue. Severity and clinical manifestation of the biomaterial-induced foreign body response are different for each biomaterial, with cases of incompatibility often associated with loss of function. However, unravelling the mechanisms that progress to the formation of the fibrotic capsule highlights the tightly intertwined nature of immunological responses to a seemingly noncanonical "antigen." In this review, we detail the pathways associated with the foreign body response and describe possible mechanisms of immune involvement that can be targeted. We also discuss methods of modulating the immune response by altering the physiochemical surface properties of the biomaterial prior to implantation. Developments in these areas are reliant on reproducible and effective animal models and may allow a "combined" immunomodulatory approach of adapting surface properties of biomaterials, as well as treating key immune pathways to ultimately reduce the negative consequences of biomaterial implantation.
... FN intermediates its biological function through binding to the integrin, a transmembrane heterodimer [38]. Guo et al [39] investigated the interaction of the 7-10th type III modules of FN (FN-III 7-10 ) with HA by a molecular docking approach, and revealed that the FN-III 10 is the most important module among FN-III 7-10 in promoting FN binding to HA due to the RGD sequence. The Arg residues of RGD directly interact with the HA through electrostatic forces and H-bonds. ...
Biomaterial surfaces and interfaces are intrinsically complicated systems because they involve biomolecules, implanted biomaterials, and complex biological environments. It is difficult to understand the interaction mechanism between biomaterials and biomolecules through conventional experimental methods. Computer simulation is an effective way to study the interaction mechanism at the atomic and molecular levels. In this review, we summarized the recent studies on the interaction behaviors of biomolecules with three types of the most widely used biomaterials: hydroxyapatite (HA), titanium oxide (TiO2), and graphene(G)/graphene oxide(GO). The effects of crystal forms, crystallographic planes, surface defects, doping atoms, and water environments on biomolecules adsorption are discussed in detail. This review provides valuable theoretical guidance for biomaterial designing and surface modification.
... f La HA presenta interacciones muy fuertes con las sustancias que tienen grupos funcionales de carácter iónico, tales como las proteínas y los ácidos nucleicos (figura 7), por este motivo se utiliza en procesos de separación, extracción y purificación de algunos materiales. 63 de los péptidos y de los ácidos nucleicos por la superficie de la HA, conocida como la capacidad máxima adsorbente (qm). 65,66 Figura 7 Modelo que sugiere un posible mecanismo de interacción entre los ácidos nucleicos y la superficie de la hidroxiapatita para formar una capa unimolecular de recubrimiento con ADN. ...
Synthetic nanoparticles are used in the field of medicine for the diagnosis, prevention and treatment of disease. Some of the most relevant applications of these biomaterials in nanotechnology include fluorescent tracing, targeted gene transport and drug delivery, the biodetection of pathogens, as well as tissue engineering, among others. Hydroxyapatite is a mineral with empirical formula Ca 10 (PO4 )6 (OH) 2 that has been widely used in the field of biomedical research, given that the level of compatibility with the cells of various tissues has been very high while toxicity is very low. These nanoparticles have found application in several treatments such as: prosthetics and bone grafts, coating of metal surfaces used in manufacturing implants, reinforcement of compound materials and, more recently, as delivery systems for the release of bioactive substances, including drugs, peptides and nucleic acids. The main goal of this project is to evaluate the biocompatibility of synthetic hydroxyapatite nanoparticles with murine macrophages RAW 264.7 through in vitro assays, and to describe the interaction of this nanomaterial with DNA, as well as to assess its applicability for use as a molecular delivery system. For this purpose, hydroxyapatite nanoparticles were synthesized using electrochemical and coprecipitation methods, materials were characterized by means of X-ray diffraction analysis, infrared spectroscopy, Z potential and size of the particles in suspension. Cell viability tests were also conducted using the MTT reagent. The maximum DNA adsorption capacity of hydroxyapatite was determined by measuring adsorption isotherms and cell transfection trials were performed and compared using fluorescence microscopy and flow cytometry. The results show that hydroxyapatite is biocompatible with RAW 264.7 cells and has an affinity to DNA molecules, with a maximum adsorption capacity of 679 μg/mg. Likewise, was shown that hydroxyapatite nanoparticles could work as a transfection vector, which allows using this inorganic nanomaterial to deliver nucleic acids within cells.
Objective:
In this study, dentine surface was analysed through Environmental-scanning-electron-microscopy (ESEM) with energy-dispersive-X-ray-spectrometry (EDX) and Fourier-transform-infrared-spectroscopy (FTIR) with attenuated total-reflectance (ATR) to assess the morpho-chemical changes and variations in mineralization degree after demineralizing treatment, after five toothpastes application (HA & Citrate toothpaste, Zinc-HA toothpaste, Calcium Sodium Phosphosilicate toothpaste, Arginine & Calcium carbonate toothpaste, Colgate-Triple-Action, and Control toothpaste), after soaking in artificial saliva and after citric acid attack.
Methods:
Ca/P, Ca/N and P/N ratios were calculated from EDX atomic data to evaluate the mineralization degree of dentine surface. The IR calcium phosphate (CaP)/collagen and carbonate/collagen ratios has been evaluated to assess the remineralization changes in dentine; the carbonate/collagen IR ratio was calculated to identify the nucleation of B-type-carbonated apatite and calcium carbonate.
Results:
ESEM-EDX and ATR-FTIR showed residuals of toothpastes after the treatments in all cases, with a general increase in the mineralization degree after soaking in artificial saliva and a decrease after acid attack. Treatment with Arginine & Calcium carbonate toothpaste showed the highest Ca/P value after treatment (Ca/P 1.62) and acid attack (Ca/P 1.5) in confirmation, IR showed the highest amount of carbonate after treatment and soaking in artificial saliva. Arginine and calcium carbonate toothpaste and HA and citrate toothpaste remained to a higher extent on the dentine surface and revealed a higher remineralization activity. These formulations showed higher resistance to demineralization attack, as demonstrated by a higher ICaP /IAmide II intensity ratio than those obtained after EDTA treatment.
Conclusions:
Toothpastes that remained to a higher extent on dentine surface (arginine and calcium carbonate toothpaste in particular) were more able to promote remineralization. The formed calcium phosphate (CaPs) phase was intimately bound to dentine rather than a simple deposit.
Among synthetic biomaterials, calcium phosphate (CaP)-based bioceramics, specifically hydroxyapatite (HA) and tricalcium phosphate (TCP) as well as biphasic calcium phosphate (BCP), are widely investigated in the biomedical community. The arrangement of different ions in the CaP crystal structure allows one to dope with metal ions, while tailoring the properties. The present article reviews some of the multifaceted research in the field of (multi)-ion-doped BCP, particularly on the aspects of biomedical applications. After summarizing different synthesis methods, a brief overview of experimental techniques and results to probe the dopant site and local structure surrounding the dopants has been provided, with an emphasis on the XRD-based Rietveld refinement and EXAFS (extended X-ray absorption fine structure) method. The effect of ion substitution on the functional properties, such as dielectric and magnetic behavior, of BCP has also been discussed. Importantly, in vitro and in vivo biocompatibility of doped BCP has been elucidated along with in silico studies on the biomaterial–biomolecule interaction. Toward the end, the results of the published clinical trial study and limited commercialization efforts will be illustrated.
The theoretically possible stable conformer of the cyclic heptapeptide, that has significant anti-metastatic activity, was examined by conformational analysis followed by DFT calculations. Experimental infrared and Raman spectroscopy, together with theoretical DFT (6-31G (d,p) basis set)-based quantum chemical calculations, have been used to understand the structural and spectral characteristics of cyclo(Gly-Arg-Gly-Asp-Ser-Pro-Ala) {cyclo(GRGDSPA)}. A complete analysis of the vibrational spectrum has been reported on the basis of potential energy distribution (PED %) data of the vibrational modes. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound. The simulated spectra satisfactorily coincide with the experimental spectra. In addition, molecular electrostatic potential and frontier molecular orbital analysis were investigated using theoretical calculations. The stability of the molecule, arising from hyperconjugative interaction and charge delocalization, has been analyzed using natural bond orbital analysis and a high E(2) value reveals the presence of strong interaction between donors and acceptors. Molecular docking studies with fibronectin were performed on cyclo(GRGDSPA) in order to understand its inhibitory nature. The results indicate that the docked ligand {cyclo(GRGDSPA)} forms a stable complex with human fibronectin and gives a binding affinity value of -7.7 kcal/mol, which points out that cyclo(GRGDSPA) might exhibit inhibitory activity against the attachment of melanoma cells to human fibronectin.
