Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.

Understanding the adsorption of salmon calcitonin, antimicrobial peptide AP114 and polymyxin B onto lipid nanocapsules

International audience

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Labaditin, a cyclic peptide with rich biotechnological potential: preliminary toxicological studies and structural changes in water and lipid membrane environment

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Improving diagnosis and oral vaccination strategies against bovine tuberculosis

In this work peptide antigens [ESAT-6,p45 in water (1ml, 1mg/ml)] have been adsorbed onto 10mg inorganic substrates (hydroxyapatite (MHA P201;P120, CHA), polystyrene, calcium carbonate and glass microspheres) and in vitro release characteristics were determined. The aim of formulation was to enhance the interaction of peptides with antigen presenting cells and to achieve rapid peptide release from the carrier compartment system in a mildly acidic environment. Hydroxyapatite microparticle P201 has a greater surface area and thus has the largest peptide adsorption compared to the P120. CHA gave a further higher adsorption due to larger surface area than that available on microparticles. These particles were incorporated into the BOVIGAMTM assay to determine if they improve the sensitivity. After overnight incubation the blood plasma was removed and the amount of IFN-g in each plasma sample was estimated. CHA and MHA P201 gave a significantly higher immune response at low peptide concentration compared to the free peptide, thus indicating that these systems can be used to evaluate Tuberculosis (TB) amongst cattle using the BOVIGAMTM assay. Badgers are a source of TB and pass infection to cattle. At the moment vaccination against TB in badgers is via the parenteral route and requires a trained veterinary surgeon as well as catching the badgers. This process is expensive and time consuming; consequently an oral delivery system for delivery of BCG vaccines is easier and cheaper. The initial stage involved addition of various surfactants and suspending agents to disperse BCG and the second stage involved testing for BCG viability. Various copolymers of Eudragit were used as enteric coating systems to protect BCG against the acidic environment of the stomach (SGF, 0.1M HCl pH 1.2 at 37oC) while dissolving completely in the alkaline environment of the small intestine (SIF, IM PBS solution pH 7.4 at 37oC). Eudragit L100 dispersed in 2ml PBS solution and 0.9ml Tween 80 (0.1%w/v) gave the best results remaining intact in SGF loosing only approximately 10-15% of the initial weight and dissolving completely within 3 hours. BCG was incorporated within the matrix formulation adjusted to pH 7 at the initial formulation stage containing PBS solution and Tween 80. It gave viability of x106 cfu/ml at initial formulation stage, freezing and freeze-drying stages. After this stage the matrix was compressed at 4 tons for 3 mins and placed in SGF for 2 hours and then in SIF until dissolved. The BCG viability dropped to x106 cfu/ml. There is potential to develop it further for oral delivery of BCG vaccine.

Influences of the pH on the adsorption properties of an antimicrobial peptide on titanium surfaces

The adsorption behavior of the Tet-124 antimicrobial peptide and the Tet-124 peptide modified at the C- and N-terminus with the sequence glycine-3,4-dihydroxyphenylalanine-glycine (G-DOPA-G) on titanium surfaces was studied using quartz crystal micro balance with dissipation (QCM-D). At a low pH level (4.75) Tet-124 and Tet-124-G-DOPA-G form rigid layers. This is attributed to the electrostatic interactions of the positively charged lysine and arginine residues in the peptide sequence with the negatively charged titanium oxide layer. At an elevated pH level (6.9) Tet-124 shows a lower mass adsorption at the surface than Tet-124-G-DOPA-G. This is attributed to the interaction of the catechol due to the formation of complexes with the titanium oxide and titanium surface layer. The C terminal and N terminal modification with the sequence G-DOPA-G shows similar adsorption rate and mass adsorption coverage at saturation; however it is presented a more loosely layers on the G-DOPA-G-TeT-124. Fibroblast adhesion and the biocompatibility test of both the surfaces following modification with Tet-124-G-DOPA-G and the titanium alloy control showed similar results. In addition, no changes in the adhesion of E. coli bacteria due to the modification of the surface were detected.

Peptide interfacial adsorption is kinetically limited by the thermodynamic stability of self association

We present a study of the adsorption of two peptides at the octane–water interface. The first peptide, Lac21, exists in mixed monomer–tetramer equilibrium in bulk solution with an appreciable monomer concentration. The second peptide, Lac28, exists as a tetramer in solution, with minimal exposed hydrophobic surface. A kinetic limitation to interfacial adsorption exists for Lac28 at moderate to high surface coverage that is not observed for Lac21. We estimate the potential energy barrier for Lac28 adsorption to be 42 kJ/mol and show that this is comparable to the expected free energy barrier for tetramer dissociation. This finding suggests that, at moderate to high surface coverage, adsorption is kinetically limited by the availability of interfacially active monomeric “domains” in the subinterfacial region. We also show how the commonly used empirical equation for protein adsorption dynamics can be used to estimate the potential energy barrier for adsorption. Such an approach is shown to be consistent with a formal description of diffusion–adsorption, provided a large potential energy barrier exists. This work demonstrates that the dynamics of interfacial adsorption depend on protein thermodynamic stability, and hence structure, in a quantifiable way.

The harnessing of peptide-monolith constructs for single step plasmid DNA purification

The availability of synthetic peptides has paved the way for their use in tailor-made interactions with biomolecules. In this study, a 16mer LacI-based peptide was used as an affinity ligand to examine the scale up feasibility for plasmid DNA purification. First, the peptide was designed and characterized for the affinity purification of lacO containing plasmid DNA, to be employed as a high affinity ligand for the potential capturing of plasmid DNA in a single unit operation. It was found there were no discernible interactions with a control plasmid that did not encode the lacO nucleotide sequence. The dissociation equilibrium constant of the binding between the 16mer peptide and target pUC19 was 5.0 ± 0.5 × 10-8 M as assessed by surface plasmon resonance. This selectivity and moderated affinity indicate that the 16mer is suitable for the adsorption and chromatographic purification of plasmid DNA. The suitability of this peptide was then evaluated using a chromatography system with the 16mer peptide immobilized to a customized monolith to purify plasmid DNA, obtaining preferential purification of supercoiled pUC19. The results demonstrate the applicability of peptide-monolith supports to scale up the purification process for plasmid DNA using designed ligands via a biomimetic approach.

LacO-LacI interaction in affinity adsorption of plasmid DNA

Current approaches for purifying plasmids from bacterial production systems exploit the physiochemical properties of nucleic acids in non-specific capture systems. In this study, an affinity system for plasmid DNA (pDNA) purification has been developed utilizing the interaction between the lac operon (lacO) sequence contained in the pDNA and a 64mer synthetic peptide representing the DNA-binding domain of the lac repressor protein, LacI. Two plasmids were evaluated, the native pUC19 and pUC19 with dual lacO3/lacOs operators (pUC19lacO3/lacOs), where the lacOs operator is perfectly symmetrical. The DNA-protein affinity interaction was evaluated by surface plasmon resonance using a Biacore system. The affinity capture of DNA in a chromatography system was evaluated using LacI peptide that had been immobilized to Streamline™ adsorbent. The KD-values for double stranded DNA (dsDNA) fragments containing lacO1 and lacO3 and lacOs and lacO3 were 5.7 ± 0.3 × 10 -11 M and 4.1 ± 0.2 × 10-11 M respectively, which compare favorably with literature reports of 5 × 10-10 - 1 × 10-9 M for native laCO1 and 1-1.2 × 10-10 M for lacO1 in a saline buffer. Densitometric analysis of the gel bands from the affinity chromatography run clearly showed a significant preference for capture of the supercoiled fraction from the feed pDNA sample. The results indicate the feasibility of the affinity approach for pDNA capture and purification using native protein-DNA interaction.

Immobilized metal-ion chelating capillary microreactor for peptide mapping analysis of proteins by matrix assisted laser desorption/ionization-time of flight-mass spectrometry

Peptide mass mapping analysis, utilizing a regenerable enzyme microreactor with metal-ion chelated adsorption of enzyme, combined with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was developed. Different procedures from the conventional approaches were adopted to immobilize the chelator onto the silica supports, that is, the metal chelating agent of iminodiacetic acid (IDA) was reacted with glycidoxypropyltrimethoxysilane (GLYMO) before its immobilization onto the inner wall of the fused-silica capillary pretreated with NH4HF2. The metal ion of copper and subsequently enzyme was specifically adsorbed onto the surface to form the immobilized enzyme capillary microreactor, which was combined with MALDI-TOF-MS to apply for the mass mapping analysis of nL amounts of protein samples. The results revealed that the peptide mapping could routinely be generated from 0.5 pmol protein sample in 15 min at 50degreesC, even 20 fmol cytochrome c could be well digested and detected.

On the adsorption of hexaammineruthenium (III) at anionic self-assembled monolayers

The binding of the electroactive hexaammineruthenium (III) complex ions to anionic self-assembled monolayers (SAMs) has been investigated by means of chronocoulometry and ac voltammetry. From chronocoulometric data recorded in 10-2 M LiClO4 containing different [Ru(NH3)6]3+ concentrations, we have established the adsorption isotherm of [Ru(NH3)6]3+ on a compact monolayer of 2-mercaptobenzimidazole-5-sulfonate (MBIS) self-assembled on Au(1 1 1). The data were satisfactorily fitted to the linearized Langmuir adsorption isotherm and a binding constant of 4.0 (±0.4) × 106 M-1 has been determined. The electrostatic binding of [Ru(NH3)6]3+ to a dilute PNA-DNA monolayer formed after hybridization on a PNA-modified gold electrode by self-assembly from a mixed solution of mercaptobutan-1-ol and PNA oligonucleotides has been studied by ac voltammetry. The admittance of the PNA-modified electrode after hybridization with complementary DNA was measured in 0.01 M Tris-HCl buffer containing different [Ru(NH3)6]3+ concentrations. Based on these data, a binding constant of [Ru(NH3)6]3+ to the surface-confined PNA-DNA duplex was derived from the Langmuir isotherm and amounts to 2.9 (±0.3) × 105 M-1. As the interactions between [Ru(NH3)6]3+ and the immobilized PNA-DNA hybrids on the gold surface are essentially electrostatic, the adsorption of the highly charged cationic redox complex at low concentrations to the negatively charged PNA-DNA modified surface is in large competition with other monovalent cations present in the electrolyte at higher concentrations. The influence of competing sodium cations was thus studied by adding different NaCl concentrations in the 0.01 M Tris-HCl electrolyte. © 2008 Elsevier Ltd. All rights reserved.

A comparison of gold nanoparticle surface co-functionalization approaches using Polyethylene Glycol (PEG) and the effect on stability, non-specific protein adsorption and internalization

To create clinically useful gold nanoparticle (AuNP) based cancer therapeutics it is necessary to co-functionalize the AuNP surface with a range of moieties; e.g. Polyethylene Glycol (PEG), peptides and drugs. AuNPs can be functionalized by creating either a mixed monolayer by attaching all the moieties directly to the surface using thiol chemistry, or by binding groups to the surface by means of a bifunctional polyethylene glycol (PEG) linker. The linker methodology has the potential to enhance bioavailability and the amount of functional agent that can be attached. While there is a large body of published work using both surface arrangements independently, the impact of attachment methodology on stability, non-specific protein adsorption and cellular uptake is not well understood, with no published studies directly comparing the two most frequently employed approaches. This paper compares the two methodologies by synthesizing and characterizing PEG and Receptor Mediated Endocytosis (RME) peptide co-functionalized AuNPs prepared using both the mixed monolayer and linker approaches. Successful attachment of both PEG and RME peptide using the two methods was confirmed using Dynamic Light Scattering, Fourier Transform Infrared Spectroscopy and gel electrophoresis. It was observed that while the 'as synthesized' citrate capped AuNPs agglomerated under physiological salt conditions, all the mixed monolayer and PEG linker capped samples remained stable at 1M NaCl, and were stable in PBS over extended periods. While it was noted that both functionalization methods inhibited non-specific protein attachment, the mixed monolayer samples did show some changes in gel electrophoresis migration profile after incubation with fetal calf serum. PEG renders the AuNP stable in-vivo however, studies with MDA-MB-231 and MCF 10A cell lines indicated that functionalization with PEG, blocks cellular uptake. It was observed that co-functionalization with RME peptide using both the mixed monolayer and PEG linker methods greatly enhanced cellular internalization compared to PEG capped AuNPs.

Antimicrobial peptide-lipid binding interactions and binding selectivity

Surface pressure measurements, external reflection- Fourier transform infrared spectroscopy, and neutron re. flectivity have been used to investigate the lipid-binding behavior of three antimicrobial peptides: melittin, magainin II, and cecropin P1. As expected, all three cationic peptides were shown to interact more strongly with the anionic lipid, 1,2 dihexadecanoyl-sn-glycerol3-( phosphor-rac-( 1- glycerol)) ( DPPG), compared to the zwitterionic lipid, 1,2 dihexadecanoyl-sn-glycerol-3-phosphocholine ( DPPC). All three peptides have been shown to penetrate DPPC lipid layers by surface pressure, and this was confirmed for the melittin-DPPC interaction by neutron reflectivity measurements. Adsorption of peptide was, however, minimal, with a maximum of 0.4 mg m(-2) seen for melittin adsorption compared to 2.1 mg m(-2) for adsorption to DPPG ( from 0.7 mu M solution). The mode of binding to DPPG was shown to depend on the distribution of basic residues within the peptide alpha-helix, although in all cases adsorption below the lipid layer was shown to dominate over insertion within the layer. Melittin adsorption to DPPG altered the lipid layer structure observed through changes in the external reflection-Fourier transform infrared lipid spectra and neutron reflectivity. This lipid disruption was not observed for magainin or cecropin. In addition, melittin binding to both lipids was shown to be 50% greater than for either magainin or cecropin. Adsorption to the bare air-water interface was also investigated and surface activity followed the trend melittin. magainin. cecropin. External re. ection- Fourier transform infrared amide spectra revealed that melittin adopted a helical structure only in the presence of lipid, whereas magainin and cecropin adopted helical structure also at an airwater interface. This behavior has been related to the different charge distributions on the peptide amino acid sequences.

Nanostructured materials based on mesoporous silica and mesoporous silica/apatite as osteogenic growth peptide carriers

The aim of this work was the preparation of inorganic mesoporous materials from silica, calcium phosphate and a nonionic surfactant and to evaluate the incorporation and release of different concentrations of osteogenic growth peptide (OGP) for application in bone regeneration. The adsorption and release of the labeled peptide with 5,6-carboxyfluorescein (OGP-CF) from the mesoporous matrix was monitored by fluorescence spectroscopy. The specific surface area was 880 and 484 m2 g- 1 for pure silica (SiO) and silica/apatite (SiCaP), respectively; the area influenced the percentage of incorporation of the peptide. The release of OGP-CF from the materials in simulated body fluid (SBF) was dependent on the composition of the particles, the amount of incorporated peptide and the degradation of the material. The release of 50% of the peptide content occurred at around 4 and 30 h for SiCaP and SiO, respectively. In conclusion, the materials based on SiO and SiCaP showed in vitro bioactivity and degradation; thus, these materials should be considered as alternative biomaterials for bone regeneration. © 2013 Elsevier B.V.