Titanium binding dodecapeptides and the impact of water structure

Friedrichs, Wenke; Köppen, Susan; Langel, Walter

doi:10.1016/j.susc.2013.07.010

Cited by 17 publications

(20 citation statements)

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“…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. In addition to accelerating the sampling of certain events, the SMD method is used to calculate free energy differences.…”

Section: Non-equilibrium Methodsmentioning

confidence: 99%

“…Studies have shown that the concentration of silanol groups (Si-OH) and the degree of their ionization define the hydrophobicity of silicon dioxide (silica) surfaces and govern their adsorption properties and thus also, the behavior of silica-based materials in processes such as biomolecular adhesion and biomineralization (Sumper & Brunner, 2008;Voskerician et al 2003). In computational studies of protein-oxide surface interactions, ionization may be represented explicitly (Friedrichs et al 2013;Köppen & Langel, 2010;Patwardhan et al 2012;Tosaka et al 2010), or by assigning uniform partial charges to selected surface atoms (Kubiak-Ossowska & Mulheran, 2012). Köppen & Langel (2010) showed that the adhesion energies of peptides on titanium dioxide surfaces are sensitive to the values of the partial charges of the surface hydroxyl groups.…”

Section: Ionization and Hydrationmentioning

confidence: 99%

“…In computational studies of protein–oxide surface interactions, ionization may be represented explicitly (Friedrichs et al . 2013; Köppen & Langel, 2010; Patwardhan et al . 2012; Tosaka et al .…”

Section: Which Surface Properties Need Consideration In Modeling?mentioning

confidence: 99%

See 2 more Smart Citations

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

195

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: Non-equilibrium Methodsmentioning

confidence: 99%

Section: Ionization and Hydrationmentioning

confidence: 99%

See 1 more Smart Citation

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

195

199

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show abstract

“…When used in simulations with three-dimensional periodicity and the Ewald summation for electrostatic calculations, as we do here, this creates the desired electric field across the water space of the simulation cell as illustrated in Figure 1. In our simulations, the silica ions are frozen in place to maintain the electric field above the surface; using rigid surface model is a common simulation strategy 37 . This allows us to simulate the adsorption of a protein onto the model negatively charged silica surface.…”

Section: Methodsmentioning

confidence: 99%

Steering protein adsorption at charged surfaces: electric fields and ionic screening

2016

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“…46 Therefore, molecular simulation, when carefully performed, and done in close partnership with experimental approaches, can bring valuable insights into the structurebinding relationships inherent to these versatile and widely-used materials. 17,23,[47][48][49] Here, we have examined the binding behavior of two TiO2 binders, Ti-1 and Ti-2, previously used in the biomineralization of crystalline, sub-10 nm sized TiO2 nanoparticles from water (pH 7.4) or Tris buffer particles 37 (see Table 1 for peptide sequences). The peptides were originally identified by panning against 100 nm titanium nanoparticles.…”

Section: Introductionmentioning

confidence: 99%

Aqueous Peptide–TiO₂ Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms

Sultan

Westcott

Hughes

et al. 2016

ACS Appl. Mater. Interfaces

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A major barrier to the systematic improvement of biomimetic peptide-mediated strategies for the controlled growth of inorganic nanomaterials in environmentally benign conditions lies in the lack of clear conceptual connections between the sequence of the peptide and its surface binding affinity, with binding being facilitated by non-covalent interactions. Peptide conformation, both in the adsorbed and non-adsorbed state, is the key relationship that connects peptide-materials binding with peptide sequence. Here, we combine experimental peptide-titania binding characterization with state-of-the-art conformational sampling via molecular simulations to elucidate these structure/binding relationships for two very different titania-binding peptide sequences. The two sequences (Ti-1: QPYLFATDSLIK and Ti-2:GHTHYHAVRTQT) differ in their overall hydropathy, yet via quartz-crystal microbalance measurements and predictions from molecular simulations, we show these sequences both support very similar, strong titania-binding affinities. Our molecular simulations reveal that the two sequences exhibit profoundly different modes of surface binding, with Ti-1 acting as an entropically-driven binder while Ti-2 behaves as an enthalpically-driven binder. The integrated approach presented here provides a rational basis for peptide sequence engineering to achieve the in-situ growth and organization of titania nanostructures in aqueous media and for the design of sequences suitable for a range of technological applications that involve the interface between titania and biomolecules.3

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Titanium binding dodecapeptides and the impact of water structure

Cited by 17 publications

References 50 publications

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

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

Steering protein adsorption at charged surfaces: electric fields and ionic screening

Aqueous Peptide–TiO₂ Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms

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Titanium binding dodecapeptides and the impact of water structure

Cited by 17 publications

References 50 publications

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

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

Steering protein adsorption at charged surfaces: electric fields and ionic screening

Aqueous Peptide–TiO2 Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms

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Product

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Aqueous Peptide–TiO₂ Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms