Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Pan, Haihua

doi:10.1016/j.biomaterials.2007.10.016

Cited by 255 publications

(219 citation statements)

References 51 publications

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“…Dong et al (2007) adapted these HAP parameters for the standard biomolecule FF for modeling the adsorption dynamics of the BMP-2 protein on a HAP (001) surface. In other studies, the Lennard-Jones and Coulomb parameters proposed by Hauptmann et al (2003) were combined with CHARMM parameters for the protein using the standard mixing rule in order to study the adsorption of fibronectin on HAP (001) (Shen et al 2008) and with OPLS-AA parameters for simulating the HAP-water interface (Zahn & Hochrein, 2003). …”

Section: Mineral Surfacesmentioning

confidence: 99%

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

191

199

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

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Section: Mineral Surfacesmentioning

confidence: 99%

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

191

199

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“…The bond, angle and dihedral parameters were derived from both quantum-mechanics calculations and experimental data. The force field has been validated in earlier works (Bhowmik et al, 2007;Dubey and Tomar, 2009;Hauptmann et al, 2003;Qin et al, 2012;Shen et al, 2008).…”

Section: Force Fieldmentioning

confidence: 99%

Mechanics of collagen–hydroxyapatite model nanocomposites

Libonati

Nair

Vergani

et al. 2014

Mechanics Research Communications

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a b s t r a c tBone is a hierarchical biological composite made of a mineral component (hydroxyapatite crystals) and an organic part (collagen molecules). Small-scale deformation phenomena that occur in bone are thought to have a significant influence on the large scale behavior of this material. However, the nanoscale behavior of collagen-hydroxyapatite composites is still relatively poorly understood. Here we present a molecular dynamics study of a bone model nanocomposite that consist of a simple sandwich structure of collagen and hydroxyapatite, exposed to shear-dominated loading. We assess how the geometry of the composite enhances the strength, stiffness and capacity to dissipate mechanical energy. We find that Hbonds between collagen and hydroxyapatite play an important role in increasing the resistance against catastrophic failure by increasing the fracture energy through a stick-slip mechanism.

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“…But because the acetic acid is weaker acid than acrylic acid, CS was found to interact more on the surface of HA. The intensity and area of -COO -and -NH 3 + groups in the XPS spectra of all nanocomposite samples is proportional to the interaction energy with HA surfaces [27].…”

Section: Egypt J Phys Vol 45 (2017) the Effect Of Different Solvementioning

confidence: 94%

“…It has been reported by Shen et al [27] that both charged -COO -and -NH 3 + groups are the major functional groups of amino acid in protein sequence that facilitate the interaction with HA surface. Hence, in the case of acrylic acid, the strong interaction between its carboxylate group and HA surface might be responsible for blocking the adsorption sites of the amine groups of CS.…”

Section: Egypt J Phys Vol 45 (2017) the Effect Of Different Solvementioning

confidence: 99%

The Effect of Different Solvents for Chitosan Solubilization on The Crystal Growth of in situ Prepared Hydroxyapatite

2017

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C HITOSAN/hydroxyapatite (CS/HA) nanocomposites have been widely fabricated for potential use in bone defects due to their high biocompatibility and similarity to the natural bone. In the current study, HA nanocrystals were prepared by co-precipitation method in CS which was initially dissolved in different concentrations of acrylic acid and acetic acid (2 and 4 %). The effect of chitosan solvents on the morphology of HA nanocrystals, the crystallite sizes, and the physical binding with CS were investigated by different techniques including Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and transmission electron microscope (TEM). The FT-IR and XPS results showed that the interaction between CS and HA in the nanocomposites is predominantly dependent on the type of solvent used to dissolve CS. When acetic acid was used, the interaction between CS and HA was stronger when compared to acrylic acid. Quantitative XPS results showed that the atomic percentage of nitrogen (N1s) of the amine groups of CS was less in the case of the composites prepared after dissolving CS in acrylic acid compared to acetic acid. The amine groups of CS (−NH 2 ) can start the nucleation of HA crystals and remain bounded to the surface of the grown crystal through chelation with calcium ions on the crystal facets. In both organic solvents, HA crystals were found to grow along their c-axis direction into rodshape but the growth in the width was more restricted in case of acetic acid. The results in the current study indicated that the type of CS solvents is determining the strength of the physical interaction between the CS and HA. This might be a crucial factor to control and enhance the mechanical and the biological behaviors of the nanocomposites.

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Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces

Cited by 255 publications

References 51 publications

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

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

Mechanics of collagen–hydroxyapatite model nanocomposites

The Effect of Different Solvents for Chitosan Solubilization on The Crystal Growth of in situ Prepared Hydroxyapatite

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