V. Renugopalakrishnan

A resolution-enhanced Fourier transform infrared spectroscopic study of the environment of the CO3(2-) ion in the mineral phase of enamel during its formation and maturation.

SummaryA resolution-enhanced Fourier Transform Infrared (FTIR) Spectroscopic study of the CO32− ion in pig enamel of increasing age and maturity has demonstrated the existence of four different, main carbonate locations. The major CO32− site arises as a result of the substitution of CO32− ions in the positions occupied by PO43− ions in the apatitic lattice. In addition, two minor locations have been identified in positions in which the CO32− ions substitute for OH− ions. The fourth carbonate group appears to be in an unstable location. Its concentration has been found to decrease with aging and maturation, during which there is a progressive increase in the amount of mineral deposited in the enamel. The distribution of the carbonate ions in the different apatitic sites varies randomly during the formation of the mineral phase in enamel and during its maturation. Although these changes have been shown to be related to changes in the composition of the mineral phase, a comparison of the parameters assessing the degree of crystallinity of the mineral phase from υ2CO32− and υ4PO32− infrared absorption data reveals a significant discrepancy related to the nonhomogeneous partition of the CO32− ion in the mineral phase. After maximum mineralization is reached, the composition of the mature mineral phase is decidedly different than that of the initial mineral deposited; the changes affect principally the concentrations of Ca2+, OH−, and HPO42− ions, but not the CO32− ions.

Arginine interactions with anatase TiO2 (100) surface and the perturbation of 49Ti NMR chemical shifts – a DFT investigation: relevance to Renu-Seeram bio solar cell

Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7 ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.

Role of Extracellular Glutamic Acids in the Stability and Energy Landscape of Bacteriorhodopsin

Bacteriorhodopsin (BR), a specialized nanomachine, converts light energy into a proton gradient to power Halobacterium salinarum. In this work, we analyze the mechanical stability of a BR triple mutant in which three key extracellular residues, Glu(9), Glu(194), and Glu(204), were mutated simultaneously to Gln. These three Glu residues are involved in a network of hydrogen bonds, in cation binding, and form part of the proton release pathway of BR. Changes in these features and the robust photocycle dynamics of wild-type (WT) BR are apparent when the three extracellular Glu residues are mutated to Gln. It is speculated that such functional changes of proteins go hand in hand with changes in their mechanical properties. Here, we apply single-molecule dynamic force spectroscopy to investigate how the Glu to Gln mutations change interactions, reaction pathways, and the energy barriers of the structural regions of WT BR. The altered heights and positions of individual energy barriers unravel the changes in the mechanical and the unfolding kinetic properties of the secondary structures of WT BR. These changes in the mechanical unfolding energy landscape cause the proton pump to choose unfolding pathways differently. We suggest that, in a similar manner, the changed mechanical properties of mutated BR alter the functional energy landscape favoring different reaction pathways in the light-induced proton pumping mechanism.

Ultrastructure of Dental Enamel afflicted with Hypoplasia: An Atomic Force Microscopic Study

The ultrastructure of the human tooth enamel from a patient diagnosed with hypoplasia (HYP) was investigated using atomic force microscopy (AFM) and compared with the surface of normal human tooth enamel. Hypoplasia is a hereditary defect of dental enamel in which the enamel is deficient in either quality or quantity. AFM results presented for the HYP tooth enamel clearly demonstrate that the apatite crystal morphology in hypoplasia tooth enamel is perturbed in the diseased state which could result from a defective synthesis of the extracellular matrix proteins, e.g., amelogenin, by the ameloblasts. HYP enamel consisting of loosely packed, very small grains does not present a tendency for association, as in the case of the normal healthy tooth. Indeed, the enamel surface affected by HYP is porous and is made of much smaller grains. In some samples, the HYP part of enamel surface appeared in the form of a point-defect, which we believe may be associated with the early stages of the HYP deformation.

Cross-linked glucose oxidase clusters for biofuel cell anode catalysts

The efficient localization of increased levels of active enzymes onto conducting scaffolds is important for the development of enzyme-based biofuel cells. Cross-linked enzyme clusters (CEC) of glucose oxidase (GOx) constrained to functionalized carbon nanotubes (CEC-CNTs) were generated in order to evaluate the potential of using CECs for developing GOx-based bioanodes functioning via direct electron transfer from the GOx active site to the CNT scaffold. CEC-CNTs generated from several weight-to-weight ratios of GOx:CNT were examined for comparable catalytic activity to free GOx into the solution, with CEC-CNTs generated from a 100% GOx solution displaying the greatest enzymatic activity. Scanning transmission electron microscopic analysis of CEC-CNTs generated from 100% GOx to CNT (wt/wt) ratios revealed that CEC clusters of ∼78 µm2 localized to the CNT surface. Electrochemical analysis indicates that the enzyme is engaged in direct electron transfer, and biofuel cells generated using GOx CEC-CNT bioanodes were observed to have a peak power density of ∼180 µW cm(-2). These data indicate that the generation of nano-to-micro-sized active enzyme clusters is an attractive option for the design of enzyme-specific biofuel cell powered implantable devices.

Effect of ethanol on the binding of conformationally rigid and labile ligands of opioid receptors to rat brain membranes

The effect of ethanol on the binding of conformationally rigid and labile ligands for mu and delta opioid receptors to rat brain membranes was determined. The mu ligands used for the studies were [3H]naltrexone and [3H]Tyr-D-Ala-Gly-N-MePhe-Gly-ol (DAGO), and delta ligands used were [3H]Tyr-D-Ser-Gly-Phe-Leu-Thr-OH (DSTLE) and [3H]Tyr-D-Ala-Gly-Phe-Leu (DADLE). The binding of all the opioid ligands was inhibited by ethanol in a concentration-dependent manner. For mu ligands the inhibition was greater for [3H]DAGO binding than for the binding of [3H]naltrexone. For delta ligands, the inhibition by ethanol of the binding of [3H]DADLE was greater than that of [3H]DSTLE. Fourier-transform infrared (FT-IR) spectroscopy was used to determine the conformation of opioid peptides. The data indicated that the conformation of peptides was altered in the presence of ethanol. The results suggest that ethanol inhibits the binding of both mu and delta opioid ligands with greater inhibition observed with conformationally labile ligands. Finally, the alteration in the conformation of the peptide ligands by ethanol, in addition to denaturation of the receptor protein, may also account for the observed inhibitory effect of ethanol on brain opioid receptors.

Ethanol induced conformational changes of the peptide ligands for the opioid receptors and their relevance to receptor interaction.

The FT-IR (Fourier Transform Infrared) Spectrum of [Met 5]-enkephalinamide in aqueous solution shows the presence of both the beta-turn and beta-sheet conformations. The beta-turn and beta-sheet conformations of enkephalins have been proposed to play a role in receptor selectivity. Addition of ethanol alters these secondary structural features and hence the effect of ethanol on ligand-receptor interaction may be mediated primarily through conformational changes of the ligand rather than those of the receptor.

Protein hot spots at bio-nano interfaces

Nanotechnology has influenced the direction of research across the sciences, medicine, and engineering. Carbon nanotubes (CNTs) and, more recently, protein nanotubes (PNTs) and protein-inorganic nanocomposites have received considerable attention due to their unique nanostructures that can be utilized as a scaffold to house proteins or create nanowires. A shift towards protein-inorganic interactions has numerous applications from biosensors to biofuel cells and bio-based nanodevices. We examine several systems where protein hot spots, the active domains on proteins and the interactive dynamics in them, play a critical role in the interactions at the interface of these unique systems.

Specialized Biology From Tandem β-Turns

Abstract Diverse forms of pathologies can be derived from the lack of flexibility in tissues and the absence of required concentrations of certain types of proteins (e.g., amelogenesis imperfecta). β-spirals using canonical proline-nucleated β-turns in diverse proteins allow for vital functions including structural (mucin and amelogenin), respiratory (elastin), muscular (titin), and that of genetic expression (RNA polymerase II). These confer particular physical and chemical properties to proteins and therefore to the tissues in which they are found, while the pervasive presence of tandem repeats in the genome sequence indicates their importance. This paper discusses the general biomedical relevance of this structure, focusing on several proteins found in humans.

Molecular effects of encapsulation of glucose oxidase dimer by graphene

Knowing the nature of the enzyme–graphene interface is critical for a design of graphene-based biosensors. Extensive contacts between graphene and enzyme could be obtained by employing a suitable encapsulation which does not impede its enzymatic reaction. We have performed molecular dynamics simulations to obtain an insight on many forms of contact between glucose oxidase dimer and the single-layer graphene nano-sheets. The unconnected graphene sheets tended to form a flat stack regardless of their initial positions around the enzyme, whereas the same graphene sheets linked together formed a flower-like shape engendering different forms of wrapping of the enzyme. During the encapsulation no core hydrophobic residues of the enzyme were exposed. Since the polar and charged amino acids populated the enzymes surface we also estimated, using DFT calculations, the interaction energies of individual polar and charged amino acid residues with graphene. It was found that the negatively charged residues can bind to graphene unexpectedly strongly; however, the main effect of encapsulation comes from the overlap of adjacent edges of graphene sheets.