Combined NMR and Computational Study of Cysteine Oxidation during Nucleation of Metallic Clusters in Biological Systems

The widespread biomedical applications of silver and gold nanoparticles (AgNPs and AuNPs, respectively) prompt the need for mechanistic evaluation of their interaction with biomolecules. In biological media, metallic NPs are known to transform by various pathways, especially in the presence of thiols. The interplay between metallic NPs and thiols may lead to unpredictable consequences for the health status of an organism. This study explored the potential events occurring during biotransformation, dissolution, and reformation of NPs in the thiol-rich biological media. The study employed a model system evaluating the interaction of cysteine with small-sized AgNPs and AuNPs. The interplay of cysteine on transformation and reformation pathways of these NPs was experimentally investigated by nuclear magnetic resonance (NMR) spectroscopy and supported by light scattering techniques and transmission electron microscopy (TEM). As the main outcome, Ag- or Au-catalyzed oxidation of cysteine to cystine was found to occur through generation of reactive oxygen species (ROS). Computational simulations confirmed this mechanism and the role of ROS in the oxidative dimerization of biothiol during NPs reformation. The obtained results represent valuable mechanistic data about the complex events during the transport of metallic NPs in thiol-rich biological systems that should be considered for the future biomedical applications of metal-based nanomaterials.

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

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.

Assembly of a chiral amino acid on an unreactive surface: (S)-proline on Au(111)

The adsorption of (S)-proline on Au(111) at 300 K was studied by low-temperature scanning tunnelling microscopy, X-ray photoelectron spectroscopy, and high resolution electron energy loss spectroscopy. (S)-proline adsorbs to produce a 2-D gas phase at 300 K, which can be condensed to form ordered molecular assemblies on cooling to 77 K. The chemical nature of the self-assembled structures is discussed in light of the information provided by photoelectron and vibrational spectroscopies.

Ab initio studies of Ag-S bond formation during the adsorption of L-cysteine on Ag(111)

Ab initio studies of Ag-S bond formation during the adsorption of L-cysteine on Ag(111) have been performed by combining density functional theory with a quantum mechanical model developed in our group. The adsorbate-silver bond formation has been investigated by analyzing the projected density of states onto the different atoms of the molecule and by charge density difference calculations when the zwitterion radical approaches the surface. The polar character of the bond can be distinguished. For the first time, the coupling constants of the sulfur orbitals with the d and sp bands have been calculated by fitting the density of states. The role of the sp bands in the stabilization of the sulfur-silver bond is analyzed. The differences with the catalysis of hydrogen adsorption are discussed. Copper, gold, and silver are not good catalysts for the adsorption of hydrogen because of the position of the d bands lying too far below the Fermi level. However, the coin metals are excellent for the adsorption of thiols. The reason is that at the equilibrium position the sulfur atom is much farther from the surface than hydrogen, and thus the interactions with the sp bands stabilize its bond to the surface.

Ab initio studies of the electronic structure of L-cysteine adsorbed on Ag(111)

We have performed ab initio calculations for the adsorption of L-cysteine on Ag(111) using density functional theory. We have focused on two possible adsorbed species: the L-cysteine radical (•S-CH(2)-CH-NH(2)-COOH) adsorbed almost flat at a bridge site, slightly displaced toward an fcc location, and the zwitterionic radical Z-cysteine (•S-CH(2)-CH-NH(3)(+)-COO(-)) adsorbed at a bridge site, shifted to a hcp site forming a (4 × 4) unit cell (θ = 0.06) and a (√3 × √3) R 30° unit cell (θ = 0.33), respectively. Special attention has been paid to the electronic structure of the system. The adsorbate-silver bond formation has been exhaustively investigated by analyzing the density of states projected onto the different atoms of the molecule, and by charge density difference calculations. A complicated interplay between sp and d states of silver in the formation of bonds between the adsorbates and the surface has been found. The role of the carboxyl group in the interaction with the surface has been also analyzed.