MD simulation of a plastocyanin mutant adsorbed onto a gold surface

Multilayer Model of Gold Nanoparticles (AuNPs) and Its Application in the Classical Molecular Dynamics Simulation of Citrate-Capped AuNPs

Studies on the interaction between gold nanoparticles (AuNPs) and functional proteins have been useful in developing diagnostic and therapeutic agents. Such studies require a realistic computational model of AuNPs for successful molecular design works. This study offers a new multilayer model of AuNPs to address the inconsistency between its molecular mechanics' interpretation and AuNP's plasmonic nature. We performed partial charge quantum calculation of AuNPs using Au13 and Au55 models. The result showed that it has partial negative charges on the surface and partial positive charges on the inner part, indicating that the AuNP model should be composed of multiatom types. We tested the partial charge parameters of these gold (Au) atoms in classical molecular dynamics simulation (CMD) of AuNPs. The result showed that our parameters performed better in simulating the adsorption of Na+ and dicarboxy acetone in terms of consistency with surface charge density than the zero charges Au in the interface force field (IFF). We proposed that the multiple-charged AuNP model can be developed further into a simpler four-atom type of Au in a larger AuNP size.

Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study

A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.

Engineering the Aggregation of Dyes on Ligand-Shell Protected Gold Nanoparticles to Promote Plexcitons Formation

The ability to control the light–matter interaction in nanosystems is a major challenge in the field of innovative photonics applications. In this framework, plexcitons are promising hybrid light–matter states arising from the strong coupling between plasmonic and excitonic materials. However, strategies to precisely control the formation of plexcitons and to modulate the coupling between the plasmonic and molecular moieties are still poorly explored. In this work, the attention is focused on suspensions of hybrid nanosystems prepared by coupling cationic gold nanoparticles to tetraphenyl porphyrins in different aggregation states. The role of crucial parameters such as the dimension of nanoparticles, the pH of the solution, and the ratio between the nanoparticles and dye concentration was systematically investigated. A variety of structures and coupling regimes were obtained. The rationalization of the results allowed for the suggestion of important guidelines towards the control of plexcitonic systems.

Atomistic simulations of gold surface functionalization for nanoscale biosensors applications

A wide class of biosensors can be built via functionalization of gold surface with proper bio conjugation element capable of interacting with the analyte in solution, and the detection can be performed either optically, mechanically or electrically. Any change in physico-chemical environment or any slight variation in mass localization near the surface of the sensor can cause differences in nature of the transduction mechanism. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection of the analyte. Here, we employ molecular modeling techniques to assist the optimization of a gold-surface biosensor. The gold surface of a quartz-crystal-microbalance sensor is functionalized using polymeric chains of poly(ethylene glycol) (PEG) of 2 KDa molecular weight, which is an inert long chain amphiphilic molecule, supporting biotin molecules (bPEG) as the ligand molecules for streptavidin analyte. The PEG linkers are immobilized onto the gold surface through sulphur chemistry. Four gold surfaces with different PEG linker density and different biotinylation ratio between bPEG and PEG, are investigated by means of state-of-the art atomistic simulations and compared with available experimental data. Results suggest that the amount of biotin molecules accessible for the binding with the protein increases upon increasing the linkers density. At the high density a 1:1 ratio of bPEG/PEG can further improve the accessibility of the biotin ligand due to a strong repulsion between linker chains and different degree of hydrophobicity between bPEG and PEG linkers. The study provides a computaional protocol to model sensors at the level of single molecular interactions, and for optimizing the physical properties of surface conjugated ligand which is crucial to enhance output of the sensor.

Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles

A multiscale molecular dynamics simulation study has been carried out in order to provide in-depth information on the adsorption of hemoglobin, myoglobin, and trypsin over citrate-capped AuNPs of 15 nm diameter. In particular, determinants for single proteins adsorption and simultaneous adsorption of the three types of proteins considered have been studied by Coarse-Grained and Meso-Scale molecular simulations, respectively. The results, discussed in the light of the controversial experimental data reported in the current experimental literature, have provided a detailed description of the (i) recognition process, (ii) number of proteins involved in the early stages of corona formation, (iii) protein competition for AuNP adsorption, (iv) interaction modalities between AuNP and protein binding sites, and (v) protein structural preservation and alteration.

Structure, Dynamics, and Electron Transfer of Azurin Bound to a Gold Electrode

Blue copper redox protein azurin (AZ) constitutes an ideal active element for building bionano-optoelectronic devices based on the intriguing interplay among its electron transfer (ET), vibrational, and optical properties. A full comprehension of its dynamical and functional behavior is required for efficient applications. Here, AZ bound to gold electrode via its disulfide bridge was investigated by a molecular dynamics simulation approach taking into account for gold electron polarization which provides a more realistic description of the protein-gold interaction. Upon binding to gold, AZ undergoes slight changes in its secondary structure with the preservation of the copper-containing active site structure. Binding of AZ to gold promotes new collective motions, with respect to free AZ, as evidenced by essential dynamics. Analysis of the ET from the AZ copper ion to the gold substrate, performed by the Pathways model, put into evidence the main residues and structural motifs of AZ involved in the ET paths. During the dynamical evolution of the bionanosystem, transient contacts between some lateral protein atoms and the gold substrate occurred; concomitantly, the opening of additional ET channels with much higher rates was registered. These results provide new and detailed insights on the dynamics and ET properties of the AZ-gold system, by also helping to rationalize some imaging and conductive experimental evidences and also to design new bionanodevices with tailored features.

Structural properties of azobenzene self-assembled monolayers by atomistic simulations

Azobenzene self-assembled monolayers (SAMs) are examples of optomechanical nanostructures capable of producing mechanical work through the well-known azobenzene photoisomerization process. Experimental studies have provided information on their structural properties, but an atomistic description of the SAMs in both the cis and trans forms is still lacking. In this work, a computational investigation of the SAM structures is conducted by classical molecular dynamics with a dedicated force. Experimental data on the SAM unit cell is used to set up SAM models of different molecular densities. The optimal structures are identified through the comparison with structural data from X-ray photoelectron and near-edge X-ray absorption fine structure spectroscopies. The resulting SAM atomistic models are validated by comparing simulated and experimental scanning tunneling microscopy images.

Effect of the protonation degree of a self-assembled monolayer on the immobilization dynamics of a [NiFe] hydrogenase

Understanding the interaction and immobilization of [NiFe] hydrogenases on functionalized surfaces is important in the field of biotechnology and, in particular, for the development of biofuel cells. In this study, we investigated the adsorption behavior of the standard [NiFe] hydrogenase of Desulfovibrio gigas on amino-terminated alkanethiol self-assembled monolayers (SAMs) with different levels of protonation. Classical all-atom molecular dynamics (MD) simulations revealed a strong correlation between the adsorption behavior and the level of ionization of the chemically modified electrode surface. While the hydrogenase undergoes a weak but stable initial adsorption process on SAMs with a low degree of protonation, a stronger immobilization is observable on highly ionized SAMs, affecting protein reorientation and conformation. These results were validated by complementary surface-enhanced infrared absorption (SEIRA) measurements on the comparable [NiFe] standard hydrogenases from Desulfovibrio vulgaris Miyazaki F and allowed in this way for a detailed insight into the adsorption mechanism at the atomic level.

Electrically induced conformational change of peptides on metallic nanosurfaces

Surface immobilized biomolecular probes are used in many areas of biomedical research, such as genomics, proteomics, immunology, and pathology. Although the structural conformations of small DNA and peptide molecules in free solution are well studied both theoretically and experimentally, the conformation of small biomolecules bound on surfaces, especially under the influence of external electric fields, is poorly understood. Using a combination of molecular dynamics simulation and surface-enhanced Raman spectroscopy, we study the external electric field-induced conformational change of dodecapeptide probes tethered to a nanostructured metallic surface. Surface-tethered peptides with and without phosphorylated tyrosine residues are compared to show that peptide conformational change under electric field is sensitive to biochemical modification. Our study proposes a highly sensitive in vitro nanoscale electro-optical detection and manipulation method for biomolecule conformation and charge at bio-nano interfaces.

Redox-induced conformational change in mercaptoalkanoic acid multilayer films

We discuss the assembly, structure, and stability of multilayer molecular films formed from multiple mercaptoalkanoic acid monolayers ligated via carboxyl and thiol interactions with divalent copper ions. Using dual-polarization interferometry to study the assembly of multilayer films in real time, we observe a clear linear relationship between the number of layers within a film and the overall average film thickness. Unexpectedly, however, we find a restructuring of the lower monolayer upon association of the Cu(2+) ions to form the Cu carboxylate surface. In particular, the thickness of the lower monolayer was found to decrease significantly, accompanied by an increase in the film density. The conformation of the monolayer subsequently recovered to that observed originally following the reduction of the Cu ion to Cu(+) upon chemisorption of the adlayer. Comparable restructuring was also observed in molecular dynamics simulations of a bilayer film assembled on a gold surface. Our combined experimental and theoretical study suggests that the observed restructuring is a result of charge-charge interactions between adjacent Cu ions that exist in the +2 oxidation state in the copper carboxylate surface and in the +1 oxidation state following chemisorption of the adlayer.

Adsorption of sulfite oxidase on self-assembled monolayers from molecular dynamics simulations

Sulfite oxidase (SO) is an enzyme catalyzing the terminal step of the metabolism of sulfur-containing amino acids that is essential for almost all living organisms. The catalytic activity of SO in vertebrates strongly depends on the efficiency of the intramolecular electron transfer (IET) between the catalytic Moco domain and the cytochrome b5 (cyt b5) domain. The IET process is assumed to be mediated by large domain motions of the cyt b5 domains within the enzyme. Thus, the interaction of SO with charged surfaces may affect the mobility of the cyt b5 domain required for IET and consequently hinder SO activation. In this study, we present a molecular dynamics approach to investigating the ionic strength dependence of the initial surface adsorption of SO in two different conformations-the crystallographic structure and the model structure for an activated SO-onto mixed amino- and hydroxyl-terminated SAMs. The results show for both conformations at low ionic strengths a strong adsorption of the cyt b5 units onto the SAM, which inhibits the domain motion event required for IET. Under higher ion concentrations, however, the interaction with the surface is weakened by the negatively charged ions acting as a buffer and competing in adsorption with the cathodic cyt b5 domains. This competition prevents the immobilization of the cytochrome b5 units onto the surface, allowing the intramolecular domain motions favoring IET. Our predictions support the interpretation of recent experimental spectroelectrochemical studies on SO.

Direct monitoring of opto-mechanical switching of self-assembled monolayer films containing the azobenzene group

The potential for manipulation and control inherent in molecule-based motors holds great scientific and technological promise. Molecules containing the azobenzene group have been heavily studied in this context. While the effects of the cis-trans isomerization of the azo group in such molecules have been examined macroscopically by a number of techniques, modulations of the elastic modulus upon isomerization in self-assembled films were not yet measured directly. Here, we examine the mechanical response upon optical switching of bis[(1,1'-biphenyl)-4-yl]diazene organized in a self-assembled film on Au islands, using atomic force microscopy. Analysis of higher harmonics by means of a torsional harmonic cantilever allowed real-time extraction of mechanical data. Quantitative analysis of elastic modulus maps obtained simultaneously with topographic images show that the modulus of the cis-form is approximately twice that of the trans-isomer. Quantum mechanical and molecular dynamics studies show good agreement with this experimental result, and indicate that the stiffer response in the cis-form comprises contributions both from the individual molecular bonds and from intermolecular interactions in the film. These results demonstrate the power and insights gained from cutting-edge AFM technologies, and advanced computational methods.

Molecular dynamics of amicyanin reveals a conserved dynamical core for blue copper proteins

Molecular dynamics simulation has been carried out for the blue copper protein amicyanin from two different sources, Paracoccus denitrificans and Paraccocus versutus, to investigate the structural and dynamical properties common to the two molecules and to identify prominent features shared with proteins of the same family, the monomeric cupredoxins. The two amicyanins have almost identical secondary and tertiary structure. In the simulation, they differ for the number of hydrogen bonds in the main chain and the conformation of some beta-strands. However, they strictly maintain the arrangement of the portions of the beta-barrel that are conserved in the folding architecture of the blue copper proteins. Paracoccus versutus amicyanin equilibrates more rapidly, shows lower atomic deviation values, and is less rigid with respect to Paracoccus denitrificans amicyanin. Principal component analysis reveals that the conformational subspaces corresponding to eigenvectors with the same index for each of the two molecules are not necessarily equivalent. Nevertheless, a core scaffold with constrained dynamics exist for both amicyanins. In addition, two fairly flexible regions that are located on the opposite side with respect to the interaction sites with the partner molecules in the redox process have been evidenced in the protein structure. This description of amicyanin, with a few mobile regions remote from the active site and a rigid scaffold including most of the protein beta-barrel, has a close similarity with that of azurin and plastocyanin, two other cupredoxins previously investigated in simulation. Furthermore, similarities in the distribution of the atomic fluctuations indicate that amicyanin, azurin, and plastocyanin possess common dynamical features, in spite of differences in their structure. On the basis of these findings, we suggest that topological constraints imposed by the folding in correspondence of protein regions that are the most conserved determine the protein dynamics of the cupredoxin family. The dynamical properties of the cupredoxins might be controlled for functional advantages that include the binding mechanism with the biological partners and the collective inner motions of the protein matrix required for the electron transfer, whereas long-range conformational changes in the redox reaction should be excluded.

Molecular simulation of bovine beta-lactoglobulin adsorbed onto a positively charged solid surface

To obtain detailed insight into the mechanism of beta-lactoglobulin (beta-Lg) adsorption to a stainless steel surface at acidic pH, the adsorption of positively charged beta-Lg to a positively charged surface (Au (100) surface with virtual positive charge) was simulated using classical molecular dynamics. The initial orientation and position of beta-Lg on the surface were determined using Monte Carlo simulation using the implicit water system. Molecular dynamics simulation with the explicit water system was conducted for a 5 ns simulation time to monitor beta-Lg adsorption. To investigate surface charge density effects on adsorption of beta-Lg, the positive charge number per Au atom on the (100) surface, C, was varied from 0 to +0.0250|e|. Stable adsorption occurred in MD simulations when C was equal to or less than +0.0200|e|. Among these surface Au charge conditions, no large difference was observed in the vertical separation distance between the surface and the protein's center of mass, and the orientation angle. This fact indicates that the main interactions contributing to the adsorption were van der Waals interactions. The protein domain contacting the surface was near Thr125, agreeing with previous experimental studies. Considering simulation results and those previous experimental studies suggests a detailed adsorption mechanism of beta-Lg at acidic pH: beta-Lg molecule is adsorbed initially with the specific part of 125-135th residues close to the surface by van der Waals interactions. Simultaneously or subsequently, side carboxylic groups of acidic amino acid residues near the surface in 125-135th residues dissociate, leading to firmer adsorption by attractive electrostatic residue-surface interaction.

Quantification of ink diffusion in microcontact printing with self-assembled monolayers

Spreading of ink outside the desired printed area is one of the major limitations of microcontact printing (micro-CP) with alkanethiol self-assembled monolayers (SAMs) on gold. We use molecular dynamics (MD) computer simulations to quantify the temperature and concentration dependence of hexadecanethiol (HDT) ink spreading on HDT SAMs, modeling 18 distinct printing conditions using periodic simulation cells of approximately 7 nm edge length and printing conditions ranging from 7 ink molecules per cell at 270 K to 42 ink molecules per cell at 371K. The computed alkanethiol ink diffusion rates on the SAM are of the same order of magnitude as bulk liquid alkanethiol diffusion rates at all but the lowest ink concentrations and highest temperatures, with up to 20-30 times increases in diffusion rates at the lowest concentration-highest temperature conditions. We show that although alkanethiol surfaces are autophobic, autophobicity is not enough to pin the ink solutions on the SAM, and so any overinking of the SAM will lead to spreading of the printed pattern. Comparison of experimental and calculated diffusion data supports an interpretation of pattern broadening as a mixture of spreading on fully and partially formed SAMs, and the calculated spreading rates establish some of the fundamental limitations of mu-CP in terms of stamp contact time and desired pattern width.

Electronic coupling between azurin and gold at different protein/substrate orientations

By means of constrained classical molecular dynamics simulations, we have computed the structure of azurin deposited on a Au(111) surface at different possible orientations and the azimuthal forces acting on the protein at each sampled conformation. We have then evaluated the effect of the angular variation on the speed of electron tunneling between the protein redox site and the metal surface. We find that the azurin/gold electronic coupling has a strong dependence on the molecular orientation and is greatly enhanced by inclining the protein to lie as flat as possible on the surface. We discuss the implications of our results for scanning probe microscopy experiments in which tunneling currents are measured while the protein is subjected to mechanical forces exerted by the tip of the instrument.

Structural, dynamical and functional aspects of the inner motions in the blue copper protein azurin

Molecular dynamics was applied to dissect out the internal motions of azurin, a copper protein performing electron transfer. Simulations of 16.5 ns were analyzed in search of coordinated displacements of amino acid residues that are important for the protein function. A region with high conformational instability was found in the 'southern' end of the molecule, far away from the copper site and the binding sites for the redox partners of azurin. By excluding the 'southern' region from the subsequent analysis, correlated motions were identified in the hydrophobic patch that surrounds the protein active site. The simulation results are in excellent agreement with recent NMR data on azurin in solution [A. V. Zhuravleva, D. M. Korzhnev, E. Kupce, A. S. Arseniev, M. Billeter, V. Y. Orekhov, Gated electron transfers and electron pathways in azurin: a NMR dynamic study at multiple fields and temperatures, J. Mol. Biol. 342 (2004) 1599-1611] and suggest a rationale for cooperative displacements of protein residues that are thought to be critical for the electron transfer process. A number of other structural and dynamic features of azurin are discussed in the context of the blue copper protein family and an explanation is proposed to account for the variability/conservation of some regions in the cupredoxins.

Residue-specific immobilization of protein molecules by size-selected clusters

The atomic force microscope (AFM), operating in contact mode, has been employed in buffer solution to study two proteins; (i) green fluorescent protein (GFP), from the hydromedusan jellyfish Aequorea victoria; and (ii) human oncostatin M (OSM), in the presence of size-selected gold nanoclusters pinned on to a highly oriented pyrolytic graphite substrate. The AFM images have revealed immobilization of single molecules of OSM, which are strongly bound to the gold nanoclusters. Conversely, no strong immobilization has been observed for the GFP, as these molecules were easily displaced by the scanning tip. The contrasting behaviour of the two proteins can be explained by the exposed molecular surface area of their cysteine residues as modelled on the basis of their respective X-ray crystallographic data structures. GFP contains two cysteine residues, but neither is readily available to chemisorb on the gold clusters, because the cysteines are largely inaccessible from the surface of the protein. In contrast, OSM has a total of five cysteine residues, with different degrees of accessibility, which make the protein amenable to anchoring on the nanoclusters. Statistical analysis of the height of the OSM molecules bound to the nanoclusters is in accordance with crystallographic data, and suggests various configurations of the proteins on the clusters, associated with the presence of different cysteine anchoring sites. These results suggest that the three-dimensional conformation of protein molecules is preserved when they are chemisorbed to size-selected gold clusters, thus opening a new route towards oriented immobilization of individual protein molecules.

Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation

A classical molecular dynamics study of the electron transfer protein azurin, covalently bound to a gold substrate through its native disulphide group, is carried out at full hydration. With the aim of investigating the effects on the protein structure and dynamics as induced by the presence of an electric field, simulations are performed on neutral, positively and negatively charged substrates. A number of parameters, such as the average structure, the root mean square deviations and fluctuations, the intraprotein hydrogen bonds and solvent accessible surface of the protein, are monitored during 10 ns of run. The orientation, the height and the lateral size of the protein, with respect to the substrate are evaluated and compared with the experimental data obtained by scanning probe nanoscopies. The electron transfer properties between the copper redox center and the disulphide bridge bound to the substrate are investigated and briefly discussed.

A Combined Atomic Force Microscopy and Molecular Dynamics Simulation Study on a Plastocyanin Mutant Chemisorbed on a Gold Surface

A mutant of copper plastocyanin, covalently bound to an Au (111) surface through an engineered disulfide bridge, was investigated in aqueous medium by atomic force microscopy (AFM) and molecular dynamics (MD) simulations. Tapping-mode AFM images revealed adsorption of single molecules which are homogeneously distributed over the substrate and strongly bound to gold and display uniform lateral size. A statistical analysis of the height of the macromolecules on the gold substrate evidenced a distribution around a mean value consistent with that expected from the crystallographic data and with a relatively large standard deviation. A 10-ns classical MD simulation of mutated plastocyanin, hydrated by a layer of water, covalently bound to a gold surface by one or two sulfur atoms, was performed. The simulations indicate that the bound protein retains, in both cases, its overall tertiary structure during the dynamic evolution. Moreover, the macro-molecule can assume different orientations with respect to the gold substrate, which give rise to a distribution of heights on the gold substrate. Experimental and MD simulation results are compared and discussed in connection with the topological and dynamical properties of the protein system.