Multiway Analysis Reveals Hydrophobicity as the Sole Determinant of Dynamic Peptide-Acetonitrile-Water Association Behavior.

Multiway analysis, a class of techniques developed for the purpose of studying multi-dimensional multivariate data, has been applied to study the dynamical structure of the first solvation layer of Ace-Gly-X-Gly-Nme peptides (where X is any amino acid) perturbed with the increase in concentrations of acetonitrile. Separate MD simulations of each peptide were carried out in five different concentrations of acetonitrile. Association of peptide, water, and acetonitrile atoms was quantified in terms of the relative abundance of Delaunay tetrahedra whose vertices could be centered on either the peptide, acetonitrile, or water atoms. A three-way data set comprising nine types of Delaunay tetrahedra in the first dimension, five concentrations of acetonitrile in the second dimension, and 26 different peptides in the third dimension was subjected to two different multiway methods viz., the constrained PARAFAC and the unconstrained Tucker3 analysis. The results unequivocally show that the dynamic peptide-acetonitrile-water association behavior could be solely explained by the hydrophobicity of the central amino acid. The study also demonstrates the utility of multiway analysis for the integration and interpretation of large number of separate MD simulations.

Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family.

BACKGROUND: The first step of GPI anchor biosynthesis is catalyzed by PIG-A, an enzyme that transfers N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol. This protein is present in all eukaryotic organisms ranging from protozoa to higher mammals, as part of a larger complex of five to six 'accessory' proteins whose individual roles in the glycosyltransferase reaction are as yet unclear. The PIG-A gene has been shown to be an essential gene in various eukaryotes. In humans, mutations in the protein have been associated with paroxysomal noctural hemoglobuinuria. The corresponding PIG-A gene has also been recently identified in the genome of many archaeabacteria although genes of the accessory proteins have not been discovered in them. The present study explores the evolution of PIG-A and the phylogenetic relationship between this protein and other glycosyltransferases. RESULTS: In this paper we show that out of the twelve conserved motifs identified by us eleven are exclusively present in PIG-A and, therefore, can be used as markers to identify PIG-A from newly sequenced genomes. Three of these motifs are absent in the primitive eukaryote, G. lamblia. Sequence analyses show that seven of these conserved motifs are present in prokaryote and archaeal counterparts in rudimentary forms and can be used to differentiate PIG-A proteins from glycosyltransferases. Using partial least square regression analysis and data involving presence or absence of motifs in a range of PIG-A and glycosyltransferases we show that (i) PIG-A may have evolved from prokaryotic glycosyltransferases and lipopolysaccharide synthases, members of the GT4 family of glycosyltransferases and (ii) it is possible to uniquely classify PIG-A proteins versus glycosyltransferases. CONCLUSION: Besides identifying unique motifs and showing that PIG-A protein from G. lamblia and some putative PIG-A proteins from archaebacteria are evolutionarily closer to glycosyltransferases, these studies provide a new method for identification and classification of PIG-A proteins.

Comparison of methods for transfer of calibration models in near-infared spectroscopy: a case study based on correcting path length differences using fiber-optic transmittance probes in in-line near-infrared spectroscopy.

This article addresses problems related to transfer of calibration models due to variations in distance between the transmittance fiber-optic probes. The data have been generated using a mixture design and measured at five different probe distances. A number of techniques reported in the literature have been compared. These include multiplicative scatter correction (MSC), path length correction (PLC), finite impulse response (FIR), orthogonal signal correction (OSC), piecewise direct standardization (PDS), and robust calibration. The quality of the predictions was expressed in terms of root mean square error of prediction (RMSEP). Robust calibration gave good calibration transfer results, while the other methods did not give acceptable results.

OntoVisT: A general purpose Ontological Visualization Tool.

UNLABELLED: Ontologies have emerged as a fast growing research topic in the area of semantic web during last decade. Currently there are 204 ontologies that are available through OBO Foundry and BioPortal. Several excellent tools for navigating the ontological structure are available, however most of them are dedicated to a specific annotation data or integrated with specific analysis applications, and do not offer flexibility in terms of general-purpose usage for ontology exploration. We developed OntoVisT, a web based ontological visualization tool. This application is designed for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery. AVAILABILITY: The database is available for free at http://ccbb.jnu.ac.in/OntoVisT.html.