Anna Rita Bizzarri

Surface-Enhanced Resonance Raman Spectroscopy Signals from Single Myoglobin Molecules

The extremely large cross-section available from metallic surface enhancement has been exploited to investigate the Raman spectrum of heme myoglobin adsorbed on silver colloidal nanoparticles at very low concentrations. The study has been performed on particles both in solution and immobilized onto a polymer-coated glass surface. In both the cases, we have observed striking temporal fluctuations in the surface-enhanced resonance Raman spectroscopy (SERRS) spectra collected at short times. A statistical analysis of the temporal intensity fluctuations and of the associated correlations of the Raman signals has allowed us to verify that the single molecule limit is approached. The possible connections of these fluctuations with the entanglement of the biomolecule within the local minima of its rough energy landscape is discussed.

Probing the interaction between p53 and the bacterial protein azurin by single molecule force spectroscopy.

p53 is a human tumour suppressor which regulates multiple cellular processes, including cell growth, genomic stability and cell death. Recent works have demonstrated the bacterial redox protein azurin to enter cancer cells and induce apoptosis through p53 stabilization, resulting in a tumour growth regression. Azurin has been shown to bind p53 although many details of the complex formed by these two proteins are still poorly characterized. Here, we get insight into the kinetics of this complex formation, by exploring the interaction between p53 and azurin in their environment by single molecule force spectroscopy. To this aim, azurin has been linked to the atomic force microscope tip, whereas p53 has been immobilized onto a gold substrate. Therefore, by performing force‐distance cycles we have detected specific recognition events between p53 and azurin, displaying unbinding forces of around 70 pN for an applied loading rate of 3 nN s−1. The specificity of these events has been assessed by the significant reduction of their frequency observed after blocking the p53 sample by an azurin solution. Moreover, by measuring the rupture force as a function of the loading rate we have determined the dissociation rate constant of this complex to be ∼0.1 s−1. Our findings are here discussed in connection with results obtained in bulk experiments, with the aim of clarifying some molecular details of the p53‐azurin complex that may help designing new anticancer strategy. Copyright

Surface-enhanced Raman scattering detection of wild-type and mutant p53 proteins at very low concentration in human serum

The development of ultrasensitive and rapid approaches to detect tumor markers at very low concentrations even in a physiological environment represents a challenge in nano-medicine. The p53 protein is at the center of the cellular network that protects organisms against the insurgence of tumors, most of which are related to alteration of p53 expression. Therefore p53 is regarded as a valuable prognostic marker whose detection at high sensitivity may considerably contribute to early diagnosis of cancers. In this work we have applied an analytical method based on surface enhanced Raman spectroscopy with high sensitivity and rapidity to improve traditional bioaffinity techniques. The Raman reporter bifunctional linker 4-aminothiophenol (4-ATP) first assembled onto 50 nm gold nanoparticles (Nps) has then been azotated to bind low concentration wild-type and two mutated forms of p53 proteins. The Raman signal enhancement of the resulting p53-(4-ATP-Np) systems has been used to identify the p53 molecules captured on a recognition substrate constituted by the azurin (Az) protein monolayer. Az has shown a strong association for both wild-type and mutated p53 proteins, allowing us to selectively detect these proteins at concentrations as low as 500 fM, in a human serum environment.

Atomic Force Spectroscopy in Biological Complex Formation: Strategies and Perspectives

Atomic force spectroscopy has become a widely used technique for investigating forces, energies, and dynamics of biomolecular interactions. These studies provide dissociation kinetic parameters by pulling apart proteins involved in a complex. Biological complexes are studied under near-physiological conditions, without labeling procedures, and are probed one at time, the latter allowing to one obtain results which are not averaged over the ensemble. However, to gain reliable information, some experimental aspects have to be carefully controlled. In particular, the immobilization of molecular partners to AFM tips and supports, required to force the molecular dissociation, plays a crucial role in determining the success of the experiments. To actually resolve single interactions, multiple simultaneous complex dissociations have to be avoided, and nonspecific adhesions, commonly found in these studies, have to be recognized and discarded. This article is aimed at offering a critical revisitation of the atomic force spectroscopy technique applied to the study of biomolecular interactions, highlighting the critical points, identifying strategies to be adopted for a more reliable data extraction and interpretation, and pointing out the experimental and theoretical aspects which still need to be refined. To this purpose, we take advantage of the vast landscape of literature and then proceed into the details of our works. In this respect, we describe the general principles of the technique, the procedures for protein immobilization, and how they can affect the results. We emphasize the use of computational docking to predict molecular complex configurations, when unknown, as a useful approach to select proper anchorage architectures. Additionally, we deal with data acquirement and analysis, with regard to the force curve selection, to the force histograms interpretation, and to the theoretical frameworks used to extract kinetic parameters. Through this, we outline that AFS can be successfully used both to investigate complexes having very different affinities and also to reveal competitive binding mechanisms, thus gaining deeper information about molecular interactions.

Concerted motions in copper plastocyanin and azurin: an essential dynamics study

Essential dynamics analysis of molecular dynamics simulation trajectories (1.1 ns) of two copper containing electron transfer proteins, plastocyanin and azurin, has been performed. The protein essential modes have been analysed in order to identify large concerted motions which could be relevant for the electron transfer function exerted by these proteins. The analysis, conducted for temporal windows of different lengths along the protein trajectories, shows a rapid convergence and indicates that for both the proteins the predominant internal motions occur in a subspace of only a few degrees of freedom. Moreover, it is found that for both the proteins the likely binding sites (i.e. the hydrophobic and negative patches) with the reaction partners move in a concerted fashion with a few structural regions far from the active site. Such results are discussed in connection with the possible involvement of large concerted motions in the recognition and binding interaction with physiological electron transfer partners.

Water residence times around copper plastocyanin: a molecular dynamics simulation approach

Abstract In order to study the dynamical properties of the solvent-protein interface, a detailed analysis of the time-relaxation behaviour of the hydration shells around each atom of copper plastocyanin has been performed by means of a time correlation function technique. In computing the function, which allowed us to extract average water residence times and coordination numbers within atomic shells of a given radius, we focused on the short and long time limits of the function itself, also in connection with a detailed analysis of the statistical uncertainty. Water residence times distribution around plastocyanin has been calculated for the first coordination shell. Water residence times near charged and polar atoms were found to be longer than those of non-polar ones; moreover side-chain oxygens and nitrogens, which form hydrogen bonds with solvent molecules, show larger water residence times than other atom types and, for negatively and positively charged residues, these times correlate to the hydrogen bond average duration. The accessibility of the solvent to protein atoms, investigated in terms of coordination numbers, has been compared to the more standard Solvent Accessible Surface. The active site, including the copper atom and its ligands, has been studied in greater detail to better understand the connections between the water molecule dynamical properties and the protein biological functionality. In particular for copper site, which was believed to be inaccessible to the solvent, it has been found that at least one water molecule which does not exchange with bulk has permanent contact with the metal.

Incoherent neutron scattering of copper azurin: a comparison with molecular dynamics simulation results

Abstract The low-frequency dynamics of copper azurin has been studied at different temperatures for a dry and deuterium hydrated sample by incoherent neutron scattering and the experimental results have been compared with molecular dynamics (MD) simulations carried out in the same temperature range. Experimental Debye-Waller factors are consistent with a dynamical transition at approximately 200 K which appears partially suppressed in the dry sample. Inelastic and quasielastic scattering indicate that hydration water modulates both vibrational and diffusive motions. The low-temperature experimental dynamical structure factor of the hydrated protein shows an excess of inelastic scattering peaking at about 3 meV and whose position is slightly shifted downwards in the dry sample. Such an excess is reminiscent of the “boson peak” observed in glass-like materials. This vibrational peak is quite well reproduced by MD simulations, although at a lower energy. The experimental quasielastic scattering of the two samples at 300 K shows a two-step relaxation behaviour with similar characteristic times, while the corresponding intensities differ only by a scale factor. Also, MD simulations confirm the two-step diffusive trend, but the slow process seems to be characterized by a decay faster than the experimental one. Comparison with incoherent neutron scattering studies carried out on proteins having different structure indicates that globular proteins display common elastic, quasielastic and inelastic features, with an almost similar hydration dependence, irrespective of their secondary and tertiary structure.

Long-term molecular dynamics simulation of copper azurin: structure, dynamics and functionality.

A long-term molecular dynamics simulation (1.1 ns), at 300 K, of fully hydrated azurin has been performed to put into relationship the protein dynamics to functional properties with particular attention to those structural elements involved in the electron transfer process. A detailed analysis of the root mean square deviations and fluctuations and of the intraprotein H-bonding pattern has allowed us to demonstrate that a rigid arrangement of the beta-stranded protein skeleton is maintained during the simulation run, while a large mobility is registered in the solvent-exposed connecting regions (turns) and in the alpha-helix. Moreover, the structural elements, likely involved in the electron transfer path, show a stable H-bonding arrangement and low fluctuations. Analysis of the dynamical cross-correlation map has revealed the existence of correlated motions among residues connected by hydrogen bonds and of correlated and anti-correlated motions between regions which are supposed to be involved in the functional process, namely the hydrophobic patch and the regions close to the copper reaction center. The results are briefly discussed also in connection to the current through-bond tunneling model for the electron transfer process. Finally, a comparison with the structural and the dynamical behaviour of plastocyanin, whose structure and functional role are very similar to those of azurin, has been performed.

Origin of the anomalous diffusion observed by MD simulation at the protein-water interface

Abstract Our recent molecular dynamics simulations of water-plastocyanin systems have shown evidence of a sublinear trend in time, for long times, of the mean square displacements of water oxygens. In this Letter, we extensively analyze the role played by the spatial (protein surface roughness) and temporal (distribution of water residence times) disorder intrinsic to the systems investigated in determining the observed anomalous diffusion process. Moreover, the occurrence of a correlated motion of waters, due to the glassy character of the protein-water interface, is explored in the framework of mode coupling theory.

Temporal fluctuations in the SERRS spectra of single iron-protoporphyrin IX molecule

Abstract Surface enhanced resonance Raman spectra of Fe–protoporphyrin IX, adsorbed on silver colloidal nanoparticles immobilized onto a polymer-coated glass slide have been investigated at very low concentrations. The spectra exhibit drastic temporal fluctuations on a time scale of seconds in both line frequency and intensity; such a trend suggesting that the single molecule limit is approached. Sequences of spectra have been analyzed in terms of an underlying continuum and of Raman peaks superimposed on this continuum. A statistical analysis of the spectrum intensity has allowed us to put into evidence that main contribution to the intensity fluctuations arises from the continuum. In addition, a high correlation between the total integrated intensity and the intensity detected at different Raman peaks has been revealed. Furthermore, the ratio between the intensity detected in correspondence of different FePP vibrational modes shows a temporal variability likely reflecting the intrinsic dynamics of the molecule. All these findings have been ascribed to a desorption–adsorption mechanism of the molecules at the silver surface.