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

Exactly soluble model of resonant energy transfer between molecules

F\"orster's theory of resonant energy transfer (FRET) predicts the strength and range of exciton transport between separated molecules. We introduce an exactly soluble model for FRET which reproduces F\"orster's results as well as incorporating quantum coherence effects. As an application the model is used to analyze a system composed of quantum dots and the protein bacteriorhodopsin.Comment: 10 pages, 2 figure

Bacteriorhodopsin Enhances Efficiency of Perovskite Solar Cells

Recently, halide perovskites have upstaged decades of solar cell development by reaching power conversion efficiencies that surpass the performance of polycrystalline silicon. The efficiency improvement in the perovskite cells is related to repeated recycling between photons and electron–hole pairs, reduced recombination losses, and increased carrier lifetimes. Here, we demonstrate a novel approach toward augmenting the perovskite solar cell efficiency by invoking the Förster Resonance Energy Transfer (FRET) mechanism. FRET occurs in the near-field region as the bacteriorhodopsin (bR) protein, and perovskite has similar optical gaps. Titanium dioxide functionalized with the bR protein is shown to accelerate the electron injection from excitons produced in the perovskite layer. FRET predicts the strength of long-range excitonic transport between the perovskite and bR layers. Solar cells incorporating TiO2/bR layers are found to exhibit much higher photovoltaic performance as compared to baseline cells without bR. These results open the opportunity to develop a new class of bioperovskite solar cells with improved performance and stability.Post-print / Final draf

Acetamide planarity revisited: Density functional and second order Moeller-Plesset perturbation studies

1092-109

Optical properties of Bacteriorhodopsin-Gold Bionano Interfaces

Monolayers of different mutants of bacteriorhodopsin (bR) with purple membranes are deposited on gold (Au) substrates. Optical measurements and density functional theory-based electronic structure calculations are reported for the first time for the bR chromophore, which is the retinal protonated Schiff base. The dielectric function of the chromophore is extracted using spectroscopic ellipsometry. Designed mutants of bR are used to investigate the bonding with the gold substrate and bR–Au bonding changes can be tracked using the optical properties of the retinal fragment.Post-print / Final draf

Aquaporin–graphene interface: relevance to point-of-care device for renal cell carcinoma and desalination

© 2018 The Author(s) Published by the Royal Society. All rights reserved. The aquaporin superfamily of hydrophobic integral membrane proteins constitutes water channels essential to the movement of water across the cell membrane, maintaining homeostatic equilibrium. During the passage of water between the extracellular and intracellular sides of the cell, aquaporins act as ultra-sensitive filters. Owing to their hydrophobic nature, aquaporins self-assemble in phospholipids. If a proper choice of lipids is made then the aquaporin biomimetic membrane can be used in the design of an artificial kidney. In combination with graphene, the aquaporin biomimetic membrane finds practical application in desalination and water recycling using mostly Escherichia coli AqpZ. Recently, human aquaporin 1 has emerged as an important biomarker in renal cell carcinoma. At present, the ultra-sensitive sensing of renal cell carcinoma is cumbersome. Hence, we discuss the use of epitopes from monoclonal antibodies as a probe for a point-of-care device for sensing renal cell carcinoma. This device works by immobilizing the antibody on the surface of a single-layer graphene, that is, as a microfluidic device for sensing renal cell carcinoma

EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts

BACKGROUND: A better understanding of the mechanisms of an enzyme's functionality and stability, as well as knowledge and impact of mutations is crucial for researchers working with enzymes. Though, several of the enzymes' databases are currently available, scientific literature still remains at large for up-to-date source of learning the effects of a mutation on an enzyme. However, going through vast amounts of scientific documents to extract the information on desired mutation has always been a time consuming process. In this paper, therefore, we describe an unique method, termed as EnzyMiner, which automatically identifies the PubMed abstracts that contain information on the impact of a protein level mutation on the stability and/or the activity of a given enzyme. RESULTS: We present an automated system which identifies the abstracts that contain an amino-acid-level mutation and then classifies them according to the mutation's effect on the enzyme. In the case of mutation identification, MuGeX, an automated mutation-gene extraction system has an accuracy of 93.1% with a 91.5 F-measure. For impact analysis, document classification is performed to identify the abstracts that contain a change in enzyme's stability or activity resulting from the mutation. The system was trained on lipases and tested on amylases with an accuracy of 85%. CONCLUSION: EnzyMiner identifies the abstracts that contain a protein mutation for a given enzyme and checks whether the abstract is related to a disease with the help of information extraction and machine learning techniques. For disease related abstracts, the mutation list and direct links to the abstracts are retrieved from the system and displayed on the Web. For those abstracts that are related to non-diseases, in addition to having the mutation list, the abstracts are also categorized into two groups. These two groups determine whether the mutation has an effect on the enzyme's stability or functionality followed by displaying these on the web

Elongated Polyproline Motifs Facilitate Enamel Evolution through Matrix Subunit Compaction

How does proline-repeat motif length in the proteins of teeth and bones relate to the evolution of vertebrates? Counterintuitively, longer repeat stretches are associated with smaller aggregated subunits within a supramolecular matrix, resulting in enhanced crystal length in mammalian versus amphibian tooth enamel