Chimeric peptides as implant functionalization agents for titanium alloy implants with antimicrobial properties

The final publication is available at Springer via http://dx.doi.org/10.1007/s11837-015-1350-7.Implant-associated infections can have severe effects on the longevity of implant devices and they also represent a major cause of implant failures. Treating these infections associated with implants by antibiotics is not always an effective strategy due to poor penetration rates of antibiotics into biofilms. Additionally, emerging antibiotic resistance poses serious concerns. There is an urge to develop effective antibacterial surfaces that prevent bacterial adhesion and proliferation. A novel class of bacterial therapeutic agents, known as antimicrobial peptides (AMP’s), are receiving increasing attention as an unconventional option to treat septic infection, partly due to their capacity to stimulate innate immune responses and for the difficulty of microorganisms to develop resistance towards them. While host- and bacterial- cells compete in determining the ultimate fate of the implant, functionalization of implant surfaces with antimicrobial peptides can shift the balance and prevent implant infections. In the present study, we developed a novel chimeric peptide to functionalize the implant material surface. The chimeric peptide simultaneously presents two functionalities, with one domain binding to a titanium alloy implant surface through a titanium-binding domain while the other domain displays an antimicrobial property. This approach gains strength through control over the bio-material interfaces, a property built upon molecular recognition and self-assembly through a titanium alloy binding domain in the chimeric peptide. The efficiency of chimeric peptide both in-solution and absorbed onto titanium alloy surface was evaluated in vitro against three common human host infectious bacteria, S. mutans, S. epidermidis, and E. coli. In biological interactions such as occurs on implants, it is the surface and the interface that dictate the ultimate outcome. Controlling the implant surface by creating an interface composed chimeric peptides may therefore open up new possibilities to cover the implant site and tailor it to a desirable bioactivity

Interaction of β-Sheet Folds with a Gold Surface

The adsorption of proteins on inorganic surfaces is of fundamental biological importance. Further, biomedical and nanotechnological applications increasingly use interfaces between inorganic material and polypeptides. Yet, the underlying adsorption mechanism of polypeptides on surfaces is not well understood and experimentally difficult to analyze. Therefore, we investigate here the interactions of polypeptides with a gold(111) surface using computational molecular dynamics (MD) simulations with a polarizable gold model in explicit water. Our focus in this paper is the investigation of the interaction of polypeptides with β-sheet folds. First, we concentrate on a β-sheet forming model peptide. Second, we investigate the interactions of two domains with high β-sheet content of the biologically important extracellular matrix protein fibronectin (FN). We find that adsorption occurs in a stepwise mechanism both for the model peptide and the protein. The positively charged amino acid Arg facilitates the initial contact formation between protein and gold surface. Our results suggest that an effective gold-binding surface patch is overall uncharged, but contains Arg for contact initiation. The polypeptides do not unfold on the gold surface within the simulation time. However, for the two FN domains, the relative domain-domain orientation changes. The observation of a very fast and strong adsorption indicates that in a biological matrix, no bare gold surfaces will be present. Hence, the bioactivity of gold surfaces (like bare gold nanoparticles) will critically depend on the history of particle administration and the proteins present during initial contact between gold and biological material. Further, gold particles may act as seeds for protein aggregation. Structural re-organization and protein aggregation are potentially of immunological importance

Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets

A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 kBT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations

Cementomimetics—constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides

This is the published version. Copyright 2012 Nature Publishing GroupCementum is the outer-, mineralized-tissue covering the tooth root and an essential part of the system of periodontal tissue that anchors the tooth to the bone. Periodontal disease results from the destructive behavior of the host elicited by an infectious biofilm adhering to the tooth root and left untreated, may lead to tooth loss. We describe a novel protocol for identifying peptide sequences from native proteins with the potential to repair damaged dental tissues by controlling hydroxyapatite biomineralization. Using amelogenin as a case study and a bioinformatics scoring matrix, we identified regions within amelogenin that are shared with a set of hydroxyapatite-binding peptides (HABPs) previously selected by phage display. One 22-amino acid long peptide regions referred to as amelogenin-derived peptide 5 (ADP5) was shown to facilitate cell-free formation of a cementum-like hydroxyapatite mineral layer on demineralized human root dentin that, in turn, supported attachment of periodontal ligament cells in vitro. Our findings have several implications in peptide-assisted mineral formation that mimic biomineralization. By further elaborating the mechanism for protein control over the biomineral formed, we afford new insights into the evolution of protein–mineral interactions. By exploiting small peptide domains of native proteins, our understanding of structure–function relationships of biomineralizing proteins can be extended and these peptides can be utilized to engineer mineral formation. Finally, the cementomimetic layer formed by ADP5 has the potential clinical application to repair diseased root surfaces so as to promote the regeneration of periodontal tissues and thereby reduce the morbidity associated with tooth loss

Direct interaction of ligand–receptor pairs specifying stomatal patterning

Plant stomata—the epidermis valves used for efficient gas exchange—are patterned by positional cues. In this study, Torii and colleagues describe the long-sought-after nature of ligand–receptor interplay during stomatal development. Employing newly developed receptor biosensor chips, they demonstrate that the EPIDERMAL PATTERNING FACTOR ligands EPF1 and EPF2 can directly and robustly bind ERECTA family receptor kinases. Using bioactive peptides that elicit unique developmental responses, they further delineate the in vivo specificity for these ligand–receptor pairs, revealing a new mode of action in plant receptor kinase signaling

Multifunctional Protein-Enabled Patterning on Arrayed Ferroelectric Materials

This study demonstrates a biological route to programming well-defined protein-inorganic interfaces with an arrayed geometry via modular peptide tag technology. To illustrate this concept, we designed a model multifunctional fusion protein, which simultaneously displays a maltose-binding protein (MBP), a green fluorescence protein (GFPuv) and an inorganic-binding peptide (AgBP2C). The fused combinatorially selected AgBP2C tag controls and site-directs the multifunctional fusion protein to immobilize on silver nanoparticle arrays that are fabricated on specific domain surfaces of ferroelectric LiNbO₃ via photochemical deposition and in situ synthesis. Our combined peptide-assisted biological and ferroelectric lithography approach offers modular design and versatility in tailoring surface reactivity for fabrication of nanoscale devices in environmentally benign conditions

GolP-CHARMM : first-principles based force fields for the interaction of proteins with Au(111) and Au(100)

Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field, compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and first-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of gold atoms, chemisorbing species, and the interaction between sp2 hybridized carbon atoms and gold. A systematic study of small molecule adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401–1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the first time, gives unique insights into facet selectivity of gold binding in vacuo. Energetic and spatial trends observed in our DFT calculations are reproduced by the force field under the same conditions. Finally, we use the new force field to calculate adsorption energies, under aqueous conditions, for a representative set of amino acids. These data are found to agree with experimental findings