Molecular Dynamics Simulation of Free and Forced BSA Adsorption on a Hydrophobic Graphite Surface

Mücksch, Christian; Urbassek, Herbert M.

doi:10.1021/la201972f

Cited by 85 publications

(97 citation statements)

References 26 publications

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“…Circular dichroism (CD) spectroscopic study by Sivaraman et al demonstrated that adsorption of albumin on hydrophobic CH 3 -SAM induced greater conformational change than on hydrophilic surfaces (OH-, COOH-, NH 2 -SAMs) [34]. Conformational change of adsorbed proteins on hydrophobic surfaces is also shown by molecular simulation [35] and Fourier transform infrared spectroscopy [36]. While strongly (or irreversibly) adsorbing albumin to CH 3 -SAM would inhibit displacement with other proteins in liquid phase, weakly (or reversibly) adsorbing albumin to hydrophilic SAMs would allow for the displacement [32,37].…”

Section: Discussionmentioning

confidence: 98%

Preferential adsorption of cell adhesive proteins from complex media on self-assembled monolayers and its effect on subsequent cell adhesion

Arima

Iwata

2015

Acta Biomaterialia

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Adsorption of cell adhesive proteins including fibronectin (Fn) and vitronectin (Vn) plays an important role in cell adhesion to artificial materials. However, for the development of biomaterials that contact with biological fluids, it is important to understand adsorption of Fn and Vn in complex media containing many kinds of proteins. Here, we focused on adsorption of Fn and Vn from complex media including mixed solution with albumin and fetal bovine serum, and its role on cell adhesion using self-assembled monolayers (SAMs). Our result demonstrates that SAMs carrying carboxylic acid or amine allow for both cell adhesion and cell spreading because of preferentially adsorbed Vn. The result provides insights into surface design of cell culture substrates and tissue engineering scaffolds.

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Section: Discussionmentioning

confidence: 98%

Preferential adsorption of cell adhesive proteins from complex media on self-assembled monolayers and its effect on subsequent cell adhesion

Arima

Iwata

2015

Acta Biomaterialia

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“…These disturbances may lead to uncertainties in experimental measurements. Particularly, SMD simulations conducted to investigate the effect of the tip of an AFM showed that pushing a molecule towards a surface with an AFM tip will bias the results by increasing adhesion, as the force exerted on the molecule leads it to spread more on the surface (Horinek et al 2008;Mücksch & Urbassek, 2011). With SMD simulations, the adsorption mechanisms of peptides and proteins on different types of surfaces have been investigated (Alvarez-Paggi et al 2010;Dong et al 2007;Emami et al 2014b;Friedrichs et al 2013;Hamdi et al 2008;Shen et al 2008;Utesch et al 2011;Yang & Zhao, 2007) and compared with experimental measurements (Schneider & Colombi Ciacchi, 2010.…”

Section: Non-equilibrium Methodsmentioning

confidence: 99%

“…To alter the hydrophobicity, surface modifications with surface defects and polar groups have been suggested, but these affect the stability of the materials as well as their mechanical and electrical properties (Scida et al 2011). Computational studies of protein-carbon surface interactions have mostly focused on graphene/graphite (Mereghetti & Wade, 2011;Mücksch & Urbassek, 2011;Raffaini & Ganazzoli, 2010;Kang et al 2013;Sun et al 2014b;Yu et al 2012b), CNT (Balamurugan et al 2010;Chen et al 2009b;Tallury & Pasquinelli, 2010;Wang et al 2003) and fullerenes (Durdagi et al 2008;Kraszewski et al 2010;Noon et al 2002).…”

Section: Carbon Allotropesmentioning

confidence: 99%

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

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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“…Gold in particular can be modeled in common simulation codes such as GROMACS and NAMD using either the GolP atomistic force field [67] or the METAL/INTERFACE force field [68]. Additional materials of interest for bioelectrochemistry can be modeled such as silica [69], but also graphite [70] or carbon nanotubes [71]. These latter materials cannot be considered as planar surfaces, however.…”

Section: Conductive Electrode Surfacesmentioning

confidence: 99%

Controlling Redox Enzyme Orientation at Planar Electrodes

et al. 2018

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Abstract:Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.

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Molecular Dynamics Simulation of Free and Forced BSA Adsorption on a Hydrophobic Graphite Surface

Cited by 85 publications

References 26 publications

Preferential adsorption of cell adhesive proteins from complex media on self-assembled monolayers and its effect on subsequent cell adhesion

Preferential adsorption of cell adhesive proteins from complex media on self-assembled monolayers and its effect on subsequent cell adhesion

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

Controlling Redox Enzyme Orientation at Planar Electrodes

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