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

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

1092-109

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

Amelogenin Supramolecular Assembly in Nanospheres Defined by a Complex Helix-Coil-PPII Helix 3D-Structure

Tooth enamel, the hardest material in the human body, is formed within a self-assembled matrix consisting mostly of amelogenin proteins. Here we have determined the complete mouse amelogenin structure under physiological conditions and defined interactions between individual domains. NMR spectroscopy revealed four major amelogenin structural motifs, including an N-terminal assembly of four α-helical segments (S9-V19, T21-P33, Y39-W45, V53-Q56), an elongated random coil region interrupted by two 310 helices (∼P60-Q117), an extended proline-rich PPII-helical region (P118-L165), and a charged hydrophilic C-terminus (L165-D180). HSQC experiments demonstrated ipsilateral interactions between terminal domains of individual amelogenin molecules, i.e. N-terminal interactions with corresponding N-termini and C-terminal interactions with corresponding C-termini, while the central random coil domain did not engage in interactions. Our HSQC spectra of the full-length amelogenin central domain region completely overlapped with spectra of the monomeric Amel-M fragment, suggesting that the central amelogenin coil region did not involve in assembly, even in assembled nanospheres. This finding was confirmed by analytical ultracentrifugation experiments. We conclude that under conditions resembling those found in the developing enamel protein matrix, amelogenin molecules form complex 3D-structures with N-terminal α-helix-like segments and C-terminal PPII-helices, which self-assemble through ipsilateral interactions at the N-terminus of the molecule

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

A theoretical study of Na+ and Mg+2 binding to the carbonyl oxygen of N-methyl acetamide.

Molecular orbital calculations (CNDO/2) are reported for the interaction of Na+ and Mg+2 with the carbonyl of a model peptide moiety (N-methyl acetamide) as a function of the C--O ... Me distance and angle and with variation in the number of ligands for the purpose of determining the steepness of the distance dependence of the binding energy and for the purpose of determining the reduction of charge on the ion with increasing numbers of ligands. The greater energy derived on divalent ion binding and the steeper distance dependence indicate that selective, divalent over monovalent, ion binding will occur whenever the liganding system can provide a coordination shell of appropriate dimension. The calculations indicate that the preferred C--O ... Me angle is not 180 degrees. Of particular note is the decrease of charge on the cation on binding to N-methyl acetamide. One ligand bound to Na+ reduces the charge from 1.0 to 0.7 electron units and four ligands bound to Mg+2 reduces the charge from 2.0 to 0.7 electron units. This is of primary significance in carrier and channel mechanisms for cation permeation of lipid membranes; and although the numerical values are qualitative, the implication is for allowance of multiple occupancy of channels by monovalent cations

Stereochemistry of nucleic acids and polynucleotides III. Electronic charge distribution

Calculation of σ- and π-charges were made on nucleotides and nucleic acids. The σ-charges were calculated using LCAO MO method suggested by Del Re, making use of Berthod and Pullman parameters. The π-charges were calculated by Hückel's method, making use of suitable parameters which gave a good qualitative correlation of calculated bond orders with experimentally determined bond lengths. General features of the charge distribution are discussed