Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations

Hoefling, Martin; Iori, Federico; Corni, Stefano; Gottschalk, Kay‐Eberhard

doi:10.1021/la904765u

Cited by 187 publications

(264 citation statements)

References 45 publications

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“…Juffer et al (1996) applied thermodynamic integration to compute the adsorption free energies of the enzyme cutinase and its variants to a charged surface in the presence of explicit ions. Hoefling et al (2010a) applied the method to obtain the PMF profiles of amino acids adsorbing on an Au(111) surface. Further, Schneider & Colombi Ciacchi (2010) employed thermodynamic integration, along with the umbrella sampling/WHAM method, to compare the free energy profiles of adsorption of RGD peptides on oxidized Ti obtained by the two methods.…”

Section: Equilibrium Methodsmentioning

confidence: 99%

“…This parameterization can be directly used in standard MM force-fields. The GolP FF has been applied in MD simulations of the adsorption of amino acids, as well as several proteins, on gold Cohavi et al 2011;Hoefling et al 2010aHoefling et al , b, 2011Kokh et al 2010). Furthermore, the ProMetCS (Kokh et al 2010) continuum solvent model describes proteinsurface interactions in atomic detail using the GolP Lennard-Jones interaction parameters together with an image charge model for protein-metal surface electrostatic interactions.…”

Section: Metal Surfacesmentioning

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.

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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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Section: Equilibrium Methodsmentioning

confidence: 99%

Section: Metal Surfacesmentioning

confidence: 99%

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

Self Cite

197

199

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“…18,25,27,30,35,39,40 Here, AuBP2 sequence is rich in polar hydroxyl-containing (S, Y) amino acid residues, which have been previously reported to recognize the Au lattice. 25,26,35,41,42 Most recently, aromatic (Y, F, W) and basic amino acids (R, K) were computationally predicted and experimentally verified to adsorb to Au surfaces with even higher affinity and strength compared to traditional metal-binding amino acids (C, H). 41,43 Thus, the presence of aromatic and basic amino acids (W, Y, R) in AuBP2 potentially implies a novel gold-binding mechanism.…”

mentioning

confidence: 99%

“…25,26,35,41,42 Most recently, aromatic (Y, F, W) and basic amino acids (R, K) were computationally predicted and experimentally verified to adsorb to Au surfaces with even higher affinity and strength compared to traditional metal-binding amino acids (C, H). 41,43 Thus, the presence of aromatic and basic amino acids (W, Y, R) in AuBP2 potentially implies a novel gold-binding mechanism. At the same time, a lack of individual Cys and His amino acids eliminates the obvious well known metal-binding mechanisms by which peptides can attach non-specifically to metal surfaces.…”

mentioning

confidence: 99%

Peptide-directed co-assembly of nanoprobes on multimaterial patterned solid surfaces

Hnilova

Ören

et al. 2012

Soft Matter

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Biocombinatorially selected solid-binding peptides, through their unique material affinity and selectivity, are a promising platform for building up complex hierarchical assemblies of nanoscale materials and molecular probes, targeted to specific practical solid surfaces. Here, we demonstrate the material-specific characteristics of engineered gold-binding and silica-binding peptides through coassembly onto micro-and nano-patterned gold surfaces on silica substrates. To build hierarchical nanostructures on patterned solid surfaces, we utilize peptides as molecular tools and monitor their behavior by either conjugating biotin to them for specific affinity to streptavidin-coated QDot nanoparticles or labelling them with small fluorescent labels. This biomimetic peptide-based approach could be used as an alternative to conventional chemical coupling and surface functionalization techniques with substantial advantages, allowing simultaneous assembly of two or more inorganic nano-entities and/or molecular probes onto patterned inorganic solid substrates. The results have significant implications in a wide range of potential applications, including controlled assembly of hybrid nanostructures in bionanophotonic and biosensing devices.

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“…Although much of this work has been designed to isolate properties contributing to successful binding (e.g., flexibility, electrostatics, solvent interactions), it has remained difficult to distill this into a concise set of design principles. 36,53,54 In order to probe the origins of the predominance of hydroxyl-containing amino acids with gold surfaces, Calzolari et al 55 performed ab initio molecular dynamics (AIMD) of a hydroxyl containing b-sheet-forming peptide, and found that cooperativity between serine side chains and solvent molecules contributed to successful 57 suggested that Tyr, Met, and Phe are strong binders, while serine breaks through the hydration layer to form an anchor point. Verde et al 58 performed further molecular dynamics to study the role of flexibility and stability in adsorption of known gold-binding and non-gold-binding peptides.…”

Section: Gold-binding Peptidesmentioning

confidence: 99%

Functional and Selective Bacterial Interfaces Using Cross-Scaffold Gold Binding Peptides

Adams

Hurley

Jahnke

et al. 2015

JOM

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We investigated the functional and selective activity of three phage-derived gold-binding peptides on the Escherichia coli (E. coli) bacterial cell surface display scaffold (eCPX) for the first time. Gold-binding peptides, p3-Au12 (LKAHLPPSRLPS), p8#9 (VSGSSPDS), and Midas-2 (TGTSVLIATPYV), were compared side-by-side through experiment and simulation. All exhibited strong binding to an evaporated gold film, with approximately a 4-log difference in binding between each peptide and the control sample. The increased affinity for gold was also confirmed by direct visualization of samples using Scanning Electron Microscopy (SEM). Peptide dynamics in solution were performed to analyze innate structure, and all three were found to have a high degree of flexibility. Preferential binding to gold over silicon for all three peptides was demonstrated, with up to four orders of magnitude selectivity exhibited by p3-Au12. The selectivity was also clearly evident through SEM analysis of the boundary between the gold film and silicon substrate. Functional activity of bound E. coli cells was further demonstrated by stimulating filamentation and all three peptides were characterized as prolific relative to control samples. This work shows great promise towards functional and active bacterial-hybrid gold surfaces and the potential to enable the next generation living material interfaces.

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Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations

Cited by 187 publications

References 45 publications

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

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

Peptide-directed co-assembly of nanoprobes on multimaterial patterned solid surfaces

Functional and Selective Bacterial Interfaces Using Cross-Scaffold Gold Binding Peptides

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