Glutamate surface speciation on amorphous titanium dioxide and hydrous ferric oxide

The moonlighting activities of dihydrolipoamide dehydrogenase: Biotechnological and biomedical applications

Dihydrolipoamide dehydrogenase (DLDH) is a homodimeric flavin-dependent enzyme that catalyzes the NAD⁺ -dependent oxidation of dihydrolipoamide. The enzyme is part of several multi-enzyme complexes such as the Pyruvate Dehydrogenase system that transforms pyruvate into acetyl-co-A. Concomitantly with its redox activity, DLDH produces Reactive Oxygen Species (ROS), which are involved in cellular apoptotic processes. DLDH possesses several moonlighting functions. One of these is the capacity to adhere to metal-oxides surfaces. This was first exemplified by the presence of an exocellular form of the enzyme on the cell-wall surface of Rhodococcus ruber. This capability was evolutionarily conserved and identified in the human, mitochondrial, DLDH. The enzyme was modified with Arg-Gly-Asp (RGD) groups, which enabled its interaction with integrin-rich cancer cells followed by "integrin-assisted-endocytosis." This allowed harnessing the enzyme for cancer therapy. Combining the TiO₂ -binding property with DLDH's ROS-production, enabled us to develop several medical applications including improving oesseointegration of TiO₂ -based implants and photodynamic treatment for melanoma. The TiO₂ -binding sites of both the bacterial and human DLDH's were identified on the proteins' molecules at regions that overlap with the binding site of E3-binding protein (E3BP). This protein is essential in forming the multiunit structure of PDC. Another moonlighting activity of DLDH, which is described in this Review, is its DNA-binding capacity that may affect DNA chelation and shredding leading to apoptotic processes in living cells. The typical ROS-generation by DLDH, which occurs in association with its enzymatic activity and its implications in cancer and apoptotic cell death are also discussed.

Surface Complexation Modeling of Biomolecule Adsorptions onto Titania

The adsorption of nucleic acid components on the surface of nanocrystalline titaniumdioxide (anatase, pH_pzc = 6.5) in NaCl solutions was investigated using potentiometric titrationsand multibatch adsorption experiments over a wide range of pH and ionic strengths. The BasicStern surface complexation model was applied to experimental data to obtain quantitativeequilibrium reaction constants. Adsorption results suggest that there is a considerable difference inthe binding of nucleobases, nucleosides, and nucleotides with an anatase surface.

Pyrite surface environment drives molecular adsorption: cystine on pyrite(100) investigated by X-ray photoemission spectroscopy and low energy electron diffraction

We have demonstrated that the annealing process for cleaning pyrite surfaces is a critical parameter in promoting ordering on the surface and driving surface reactivity. Furthermore, we describe a spectroscopic surface characterization of the presence or absence of the surface ordering, as indicated by the Low Energy Electron Diffraction (LEED) pattern, as a function of the surface annealing process. Complementary X-ray photoemission spectroscopy (XPS) results provide evidence that longer annealing processes of over 3 hours repair the sulfur vacancies in the pyrite, making FeS species partially disappear in favor of FeS₂ species. These features play an important role in molecular adsorption. We show that in the case of the cystine amino acid on the (100) pyrite surface, the substrate structure is responsible for the chemical adsorption form. The presence of an ordered structure on the surface, as indicated by the LEED pattern, favors the cystine NH₃⁺ chemical form, whereas the absence of the surface ordering promotes cystine NH₂ adsorption due to the sulfur-deficient surface. The cystine molecule could then act by changing its chemical functionalities to compensate for the iron surface coordination. The chemical molecular adsorption form can be selected by the surface annealing conditions, implying that environmental conditions could drive molecular adsorption on mineral surfaces. These findings are relevant in several surface processes, and they could play a possible role in prebiotic chemistry surface reactions and iron-sulfur scenarios.

Surface force analysis of glycine adsorption on different crystal surfaces of titanium dioxide (TiO2)

Surface force analysis with atomic force microscope (AFM) in which a single amino acid residue was mounted on the tip apex of AFM probe was carried out for the first time at the molecular level on titanium dioxide (TiO₂) as a representative mineral surface for prebiotic chemical evolution reactions. The force analyses on surfaces with three different crystal orientations revealed that the TiO₂ (110) surface has unique characteristics for adsorbing glycine molecules showing different features compared to those on TiO₂ (001) and (100). To examine this difference, we investigated thermal desorption spectroscopy (TDS) and the interaction between the PEG cross-linker and the three TiO₂ surfaces. Our data suggest that the different single crystal surfaces would provide different chemical evolution field for amino acid molecules.

Adsorption of Amino Acids and Peptides on Metal and Oxide Surfaces in Water Environment: A Synthetic and Prospective Review

Amino acids and peptides are often used as "model" segments of proteins for studying their behavior in various types of environments, and/or elaborating functional surfaces. Indeed, though the protein behavior is much more complex than that of their isolated segments, knowledge of the binding mode as well as of the chemical structure of peptides on metal or oxide surfaces is a significant step toward the control of materials in a biological environment. Such knowledge has considerably increased in the past few years, thanks to the combination of advanced characterization techniques and of modeling methods. Investigations of biomolecule-surface interactions in water/solvent environments are quite numerous, but only in a few cases is it possible to reach an understanding of the molecule-(water)-surface interaction with a level of detail comparable to that of the UHV studies. This contribution aims at reviewing the recent data describing the amino acid and peptide interaction with metal or oxide surfaces in the presence of water.

Molecular-Scale Study of Aspartate Adsorption on Goethite and Competition with Phosphate

Knowledge of the interfacial interactions between aspartate and minerals, especially its competition with phosphate, is critical to understanding the fate and transport of amino acids in the environment. Adsorption reactions play important roles in the mobility, bioavailability, and degradation of aspartate and phosphate. Attenuated total reflectance Fourier-transform infrared (ATR-FTIR) measurements and density functional theory (DFT) calculations were used to investigate the interfacial structures and their relative contributions in single-adsorbate and competition systems. Our results suggest three dominant mechanisms for aspartate: bidentate inner-sphere coordination involving both α- and γ-COO(-), outer-sphere complexation via electrostatic attraction and H-bonding between aspartate NH2 and goethite surface hydroxyls. The interfacial aspartate is mainly governed by pH and is less sensitive to changes of ionic strength and aspartate concentration. The phosphate competition significantly reduces the adsorption capacity of aspartate on goethite. Whereas phosphate adsorption is less affected by the presence of aspartate, including the relative contributions of diprotonated monodentate, monoprotonated bidentate, and nonprotonated bidentate structures. The adsorption process facilitates the removal of bioavailable aspartate and phosphate from the soil solution as well as from the sediment pore water and the overlying water.

ATR-FTIR spectroscopic evidence for biomolecular phosphorus and carboxyl groups facilitating bacterial adhesion to iron oxides

Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy has been used to probe the binding of bacteria to hematite (α-Fe2O3) and goethite (α-FeOOH). In situ ATR-FTIR experiments with bacteria (Pseudomonas putida, Pseudomonas aeruginosa, Escherichia coli), mixed amino acids, polypeptide extracts, deoxyribonucleic acid (DNA), and a suite of model compounds were conducted. These compounds represent carboxyl, catecholate, amide, and phosphate groups present in siderophores, amino acids, polysaccharides, phospholipids, and DNA. Due in part to the ubiquitous presence of carboxyl groups in biomolecules, numerous IR peaks corresponding to outer-sphere or unbound (1400 cm(-1)) and inner-sphere (1310-1320 cm(-1)) coordinated carboxyl groups are noted following reaction of bacteria and biomolecules with α-Fe2O3 and α-FeOOH. However, the data also reveal that the presence of low-level amounts (i.e., 0.45-0.79%) of biomolecular phosphorous groups result in strong IR bands at ∼1043 cm(-1), corresponding to inner-sphere Fe-O-P bonds, underscoring the importance of bacteria associated P-containing groups in biomolecule and cell adhesion. Spectral comparisons also reveal slightly greater P-O-Fe contributions for bacteria (Pseudomonad, E. coli) deposited on α-FeOOH, as compared to α-Fe2O3. This data demonstrates that slight differences in bacterial adhesion to Fe oxides can be attributed to bacterial species and Fe-oxide minerals. However, more importantly, the strong binding affinity of phosphate in all bacteria samples to both Fe-oxides results in the formation of inner-sphere Fe-O-P bonds, signifying the critical role of biomolecular P in the initiation of bacterial adhesion.

Speciation of L-DOPA on nanorutile as a function of pH and surface coverage using surface-enhanced Raman spectroscopy (SERS)

The adsorption configuration of organic molecules on mineral surfaces is of great interest because it can provide fundamental information for both engineered and natural systems. Here we have conducted surface-enhanced Raman spectroscopy (SERS) measurements to probe the attachment configurations of DOPA on nanorutile particles under different pH and surface coverage conditions. The Raman signal enhancement arises when a charge transfer (CT) complex forms between the nanoparticles and adsorbed DOPA. This Raman signal is exclusively from the surface-bound complexes with great sensitivity to the binding and orientation of the DOPA attached to the TiO(2) surface. Our SERS spectra show peaks that progressively change with pH and surface coverage, indicating changing surface speciation. At low pH and surface coverage, DOPA adsorbs on the surface lying down, with probably three points of attachment, whereas at higher pH and surface coverage DOPA stands up on the surface as a species involving two attachment points via the two phenolic oxygens. Our results demonstrate experimentally the varying proportions of the two surface species as a function of environmental conditions consistent with published surface complexation modeling. This observation opens up the possibility to manipulate organic molecule attachment in engineered systems such as biodetection devices. Furthermore, it provides a perspective on the possible role of mineral surfaces in the chemical evolution of biomolecules on the early Earth. Adsorbed biomolecules on mineral surface in certain configurations may have had an advantage for subsequent condensation reactions, facilitating the formation of peptides.

Mineral-organic interfacial processes: potential roles in the origins of life

Life is believed to have originated on Earth ∼4.4-3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.

Adsorption and surface complexation study of L-DOPA on Rutile (α-TiO₂) in NaCl solutions

Dihydroxyphenylalanine (DOPA) and similar molecules are of considerable interest in studies of bioadhesion to minerals, solar cells involving titanium dioxide, and biomedical imaging. However, the extent and mechanisms of DOPA adsorption on oxides in salt solutions are unknown. We report measurements of DOPA adsorption on well-characterized rutile (α-TiO₂) particles over a range of pH, ionic strength, and surface coverage as well as a surface complexation model analysis establishing the stoichiometry, model surface speciation, and thermodynamic equilibrium constants, which permits predictions in more complex systems. DOPA forms two surface species on rutile, the proportions of which vary strongly with pH but weakly with ionic strength and surface loading. At pH < 4.5 a species involving four attachment points ("lying down") is important, whereas at pH > 4.5 a species involving only two attachment points via the phenolic oxygens ("standing up") predominates. Based on evidence of strong attachment of DOPA to titanium dioxide from single molecule AFM (Lee, H. et al., Proc. Natl. Acad. Sci.2006, 103, 12999-12003) and studies of catechol adsorption, one or more of the DOPA attachments for each species is inner-sphere, the others are likely to be H-bonds.

Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.

Evaluating glutamate and aspartate binding mechanisms to rutile (α-TiO2) via ATR-FTIR spectroscopy and quantum chemical calculations

Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy and quantum chemical calculations were used to elucidate the influence of solution chemistry (pH, amino acid concentration) on the binding mechanisms of glutamic and aspartic acid to rutile (α-TiO(2)). The amino acids, glutamate and aspartate, contain carboxyl and amine groups whose dissociation over a pH range results in changes of molecular charge and reactivity, including reactions with mineral surfaces. At pH 3, a decrease of IR bands corresponding to protonated carboxyl groups is observed upon reaction with TiO(2) and indicates involvement of distal carboxyl groups during sorption. In addition, decreased IR bands arising from carboxyl bonds at 1400 cm(-1), concomitant to shifts to higher wavenumbers for ν(as)(γ-COO(-)) and ν(as)(α-COO(-)) (particularly at low glutamate concentrations), are indicative of inner-sphere coordination of both carboxyl groups and therefore suggest a "lying down" surface species. IR spectra of aspartate reacted with rutile are similar to those of solution-phase samples, without peak shifts indicative of covalent bonding, and outer-sphere coordination is predicted. Quantum chemical calculations were carried out to assist in elucidating molecular mechanisms for glutamate binding to rutile and are in reasonable agreement with experimental data. The combined use of ATR-FTIR data and quantum calculations suggests three potential surface configurations, which include (1) bridging-bidentate where glutamate is "lying down" and binding occurs through inner-sphere coordination of both α- and γ-carboxyl groups; (2) chelating-monodentate in which glutamate binds through inner-sphere coordination with the γ-carboxyl group in a "standing up" configuration (with or without protonation of the α-carboxyl); and (3) another bridging-bidentate configuration where glutamate is binding to rutile via inner-sphere coordination of the α-carboxyl group and outer-sphere coordination with the γ-carboxyl ("lying down").

Mineral surfaces, geochemical complexities, and the origins of life

Crystalline surfaces of common rock-forming minerals are likely to have played several important roles in life's geochemical origins. Transition metal sulfides and oxides promote a variety of organic reactions, including nitrogen reduction, hydroformylation, amination, and Fischer-Tropsch-type synthesis. Fine-grained clay minerals and hydroxides facilitate lipid self-organization and condensation polymerization reactions, notably of RNA monomers. Surfaces of common rock-forming oxides, silicates, and carbonates select and concentrate specific amino acids, sugars, and other molecular species, while potentially enhancing their thermal stabilities. Chiral surfaces of these minerals also have been shown to separate left- and right-handed molecules. Thus, mineral surfaces may have contributed centrally to the linked prebiotic problems of containment and organization by promoting the transition from a dilute prebiotic "soup" to highly ordered local domains of key biomolecules.

Photoelectrochemical characterization of a robust TiO2/BDD heterojunction electrode for sensing application in aqueous solutions

Titanium dioxide (TiO(2)) and boron-doped diamond (BDD) are two of the most popular functional materials in recent years. In this work, TiO(2) nanoparticles were immobilized onto the BDD electrodes by a dip-coating technique. Continuous and uniform mixed-phase (anatase and rutile) and pure-anatase TiO(2)/BDD electrodes were obtained after calcination processes at 700 and 450 degrees C, respectively. The particle sizes of both types of TiO(2) film range from 20 to 30 nm. In comparison with a TiO(2)/indium tin oxide (ITO) electrode, the TiO(2)/BDD electrode demonstrates a higher photoelectrocatalytic activity toward the oxidation of organic compounds, such as glucose and potassium hydrogen phthalate. Among all the tested TiO(2) electrodes, the mixed-phase TiO(2)/BDD electrode demonstrated the highest photoelectrocatalytic activity, which can be attributed to the formation of the p-n heterojunction between TiO(2) and BDD. The electrode was subsequently used to detect a wide spectrum of organic compounds in aqueous solution using a steady-state current method. An excellent linear relationship between the steady-state photocurrents and equivalent organic concentrations was attained. The steady-state oxidation photocurrents of the mixed-phase TiO(2)/BDD electrode were insensitive to pH in the range of pH 2-10. Furthermore, the electrodes exhibited excellent robustness under strong acidic conditions that the TiO(2)/ITO electrodes cannot stand. These characteristics bestow the mixed-phase TiO(2)/BDD electrode to be a versatile material for the sensing of organic compounds.

Adsorption of nucleic acid components on rutile (TiO(2)) surfaces

Nucleic acids, the storage molecules of genetic information, are composed of repeating polymers of ribonucleotides (in RNA) or deoxyribonucleotides (in DNA), which are themselves composed of a phosphate moiety, a sugar moiety, and a nitrogenous base. The interactions between these components and mineral surfaces are important because there is a tremendous flux of nucleic acids in the environment due to cell death and horizontal gene transfer. The adsorption of mono-, oligo-, and polynucleotides and their components on mineral surfaces may have been important for the origin of life. We have studied here interactions of nucleic acid components with rutile (TiO(2)), a mineral common in many terrestrial crustal rocks. Our results suggest roles for several nucleic acid functional groups (including sugar hydroxyl groups, the phosphate group, and extracyclic functional groups on the bases) in binding, in agreement with results obtained from studies of other minerals. In contrast with recent studies of nucleotide adsorption on ZnO, aluminum oxides, and hematite, our results suggest a different preferred orientation for the monomers on rutile surfaces. The conformations of the molecules bound to rutile surfaces appear to favor specific interactions, which in turn may allow identification of the most favorable mineral surfaces for nucleic acid adsorption.

Attachment of L-glutamate to rutile (alpha-TiO(2)): a potentiometric, adsorption, and surface complexation study

Interactions between aqueous amino acids and mineral surfaces influence the bioavailability of amino acids in the environment, the viability of Ti implants in humans, and the role of mineral surfaces in the origin of life on Earth. We studied the adsorption of l-glutamate on the surface of rutile (alpha-TiO(2), pH(PPZC) = 5.4) in NaCl solutions using potentiometric titrations and batch adsorption experiments over a wide range of pH values, ligand-to-solid ratios, and ionic strengths. Between pH 3 and 5, glutamate adsorbs strongly, up to 1.4 micromol m(-2), and the adsorption decreases with increasing ionic strength. Potentiometric titration measurements of proton consumption for the combined glutamate-rutile-aqueous solution system show a strong dependence on glutamate concentration. An extended triple-layer surface complexation model of all the experimental results required at least two reaction stoichiometries for glutamate adsorption, indicating the possible existence of at least two surface glutamate complexes. A possible mode of glutamate attachment involves a bridging-bidentate species binding through both carboxyl groups, which can be thought of as "lying down" on the surface (as found previously for amorphous titanium dioxide and hydrous ferric oxide). Another involves a chelating species which binds only through the gamma-carboxyl group, that is, "standing up" at the surface. The calculated proportions of these two surface glutamate species vary strongly, particularly with pH and glutamate concentration. Overall, our results serve as a basis for a better quantitative understanding of how and under what conditions acidic amino acids bind to oxide mineral surfaces.