Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of C alpha Atoms

Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C alpha atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C alpha. We extend the method further to recognize potential protein-protein interface residues. Conclusion/Significance: Our approach to identify buried and exposed residues solely from the positions of C alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C alpha positions and all-atom models suggested that, recognition of interfacial residues using C alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only C alpha positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly.

Assessing vulnerability at the urban interface

House loss during unplanned bushfires is a complex phenomenon where design, configuration, material and siting, can significantly influence the loss. In collaboration with the Bushfire Cooperative Research Centre the CSIRO has developed a tool to assess the vulnerability of a specific house at the urban interface. The tool is based on a spatial profiling of urban assets including their design, material, surrounding objects and their relationship amongst one another. The analysis incorporates both probabilistic and deterministic parameters, and is based on the impact of radiant heat, flame and embers on the surrounding elements and the structure itself. It provides a breakdown of the attributes and design parameters that contribute to the vulnerability level. This paper describes the tool which allows the user to explore the vulnerability of a house to varying levels of bushfire attacks. The tool is aimed at government agencies interested in building design, town planning and community education for bushfire risk mitigation.

Computation of Thermal Stress Intensity Factors for Bimaterial Interface Cracks Using Domain Integral Method

The concept of domain integral used extensively for J integral has been applied in this work for the formulation of J(2) integral for linear elastic bimaterial body containing a crack at the interface and subjected to thermal loading. It is shown that, in the presence of thermal stresses, the J(k) domain integral over a closed path, which does not enclose singularities, is a function of temperature and body force. A method is proposed to compute the stress intensity factors for bimaterial interface crack subjected to thermal loading by combining this domain integral with the J(k) integral. The proposed method is validated by solving standard problems with known solutions.

Behaviour of Bi-material interface cracks in the presence of material nonlinearity of adherends

The well known features of crack face interpenetration/contact at the tip of an interface crack is re-examined using finite element analysis and assuming material nonlinear properties for the adherends. It was assumed in literature that the crack tips are fully open at all load levels in the presence of material nonlinearity of the adherends. Analysis for the case of remote tension shows that even in the presence of material nonlinearity, crack tip closes at small load levels and opens above a certain load level. Mixed-mode fracture parameters are evaluated for the situation when the crack tips are fully open. Due to the presence of nonlinearity, the mixed-mode fracture parameters are measured with the symmetric and anti-symmetric components of J-integral. The present analysis explains the sequence of events at the interface crack tip with progressively increasing remote tension load for the case of adherends with material nonlinear behaviour.

Middle-aged and elderly Finnish households considering moving, their preferences, and potential downsizing amidst changing life course and housing careers

We examine the moving and housing preferences of middle-aged and older in Finland, a country where population composition and movement through the life course are changing. A logistic regression reveals that middle-aged, moderate income residents, renters, those who have lived in their houses only a short time, and residents who are generally dissatisfied are most likely to consider moving. Downsizing appeals to residents with lower incomes who live alone, and who have been in their current houses longer. All potential movers agree on the importance of transportation access and a neighborhood grocery store; however, those preferring to downsize are also interested in house and neighborhood design as well as services that will allow aging in place. Income limitations may create affordability problems for some potential movers.

Kernel-based spatial-color modeling for fast moving object tracking

Visual tracking has been a challenging problem in computer vision over the decades. The applications of Visual Tracking are far-reaching, ranging from surveillance and monitoring to smart rooms. Mean-shift (MS) tracker, which gained more attention recently, is known for tracking objects in a cluttered environment and its low computational complexity. The major problem encountered in histogram-based MS is its inability to track rapidly moving objects. In order to track fast moving objects, we propose a new robust mean-shift tracker that uses both spatial similarity measure and color histogram-based similarity measure. The inability of MS tracker to handle large displacements is circumvented by the spatial similarity-based tracking module, which lacks robustness to object's appearance change. The performance of the proposed tracker is better than the individual trackers for tracking fast-moving objects with better accuracy.

Book Review: "The Interface: IBM and the Transformation of Corporate Design, 1945-1975", John Harwood, Minneapolis: University of Minnesota Press, 2011

Within the history of twentieth-century design, there are a number of well-known objects and stories that are invoked time and time again to capture a pivotal moment or summarize a much broader historical transition. For example, Marcel Breuer’s Model B3 chair is frequently used as a stand-in for the radical investigations of form and new industrial materials occurring at the Bauhaus in the mid-1920s. Similarly, Raymond Loewy’s streamlined pencil sharpener has become historical shorthand for the emergence of modern industrial design in the 1930s. And any discussion of the development of American postwar “organic design” seems incomplete without reference to Charles and Ray Eames’s molded plywood leg splint of 1942. Such objects and narratives are dear to historians of modern design. They are tangible, photogenic subjects that slot nicely into exhibitions, historical surveys, and coffee-table best sellers...

'Wet N2O oxidation' process and interface state density characterization of nanoscale nitrided SiO2 for flash memory application

In this paper we first present the 'wet N2O' furnace oxidation process to grow nitrided tunnel oxides in the thickness range 6 to 8 nm on silicon at a temperature of 800 degrees C. Electrical characteristics of MOS capacitors and MOSFETs fabricated using this oxide as gate oxide have been evaluated and the superior features of this oxide are ascertained The frequency response of the interface states, before and after subjecting the MOSFET gate oxide to constant current stress, is studied using a simple analytical model developed in this work.

Phase-Field Simulation of Fusion Interface Events during Solidification of Dissimilar Welds: Effect of Composition Inhomogeneity

We investigate the events near the fusion interfaces of dissimilar welds using a phase-field model developed for single-phase solidification of binary alloys. The parameters used here correspond to the dissimilar welding of a Ni/Cu couple. The events at the Ni and the Cu interface are very different, which illustrate the importance of the phase diagram through the slope of the liquidus curves. In the Ni side, where the liquidus temperature decreases with increasing alloying, solutal melting of the base metal takes place; the resolidification, with continuously increasing solid composition, is very sluggish until the interface encounters a homogeneous melt composition. The growth difficulty of the base metal increases with increasing initial melt composition, which is equivalent to a steeper slope of the liquidus curve. In the Cu side, the initial conditions result in a deeply undercooled melt and contributions from both constrained and unconstrained modes of growth are observed. The simulations bring out the possibility of nucleation of a concentrated solid phase from the melt, and a secondary melting of the substrate due to the associated recalescence event. The results for the Ni and Cu interfaces can be used to understand more complex dissimilar weld interfaces involving multiphase solidification.

The Use of Liquid-Liquid Interface (Biphasic) for the Preparation of Benzenetricarboxylate Complexes of Cobalt and Nickel

New metal-organic frameworks (MOFs) [Ni(C12N2H10)(H2O)][C6H3(COO)2(COOH)] (I), [Co2(H2O)6][C6H3(COO)3]2·(C4N2H12)(H2O)2 (II), [Ni2(H2O)6][C6H3(COO)3]2·(C4N2H12)(H2O)2 (III), [Ni(C13N2H14)(H2O)][C6H3(COO)2(COOH)] (IV), [Ni3(H2O)8][C6H3(COO)3] (V) and [Co(C4N2H4)(H2O)][C6H3(COO)3] (VI) {C6H3(COOH)3 = trimesic acid, C12N2H10 = 1,10-phenanthroline, C4N2H12 = piperazine dication, C13N2H14 = 1,3-bis(4-pyridyl)propane and C4N2H4 = pyrazine} have been synthesized by using an interface between two immiscible solvents, water and cyclohexanol. The compounds are constructed from the connectivity between the octahedral M2+ (M = Ni, Co) ions coordinated by oxygen atoms of carboxylate groups and water molecules and/or by nitrogen atoms of the ligand amines and the carboxylate units to form a variety of structures of different dimensionality. Strong hydrogen bonds of the type O-H···O are present in all the compounds, which give rise to supramolecularly organized higher-dimensional structures. In some cases ··· interactions are also observed. Magnetic studies indicate weak ferromagnetic interactions in I, IV and V and weak antiferromagnetic interactions in the other compounds (II, III and VI). All the compounds have been characterized by a variety of techniques.

Small-angle x-ray scattering study of the aggregation of gold nanoparticles during formation at the toluene-water interface

We report the results of an in situ small-angle x-ray scattering (SAXS) study of the aggregation of gold nanoparticles formed by an interfacial reaction at the toluene-water interface. The SAXS data provide a direct evidence for aggregate formation of nanoparticles having 1.3 nm gold core and an organic shell that gives a core-core separation of about 2.5 nm. Furthermore, the nanoparticles do not occupy all the cites of 13-member cluster. This occupancy decreases with reaction time and indicate reorganization of the clusters that generates planner disklike structures. A gradual increase in fractal dimension from 1.82 to 2.05 also indicate compactification of cluster aggregation with reaction time, the final exponent being close to 2 expected for disklike aggregates.

Covalent tethering of the dimer interface annuls aggregation in thymidylate synthase

Thymidylate synthase (TS), a dimeric enzyme, forms large soluble aggregates at concentrations of urea (3.3-5 M), well below that required for complete denaturation, as established by fluorescence and size-exclusion chromatography. In contrast to the wild-type enzyme, an engineered mutant of TS (T155C/E188C/C244T), TSMox, in which two subunits are crosslinked by disulfide bridges between residues 155-188' and 188-155', does not show this behavior. Aggregation behavior is restored upon disulfide bond reduction in the mutant protein, indicating the involvement of interface segments in forming soluble associated species. Intermolecular disulfide crosslinking has been used as a probe to investigate the formation of larger non-native aggregates. The studies argue for the formation of large multimeric species via a sticky patch of polypeptide from the dimer interface region that becomes exposed on partial unfolding. Covalent reinforcement of relatively fragile protein-protein interfaces may be a useful strategy in minimizing aggregation of non-native structures in multimeric proteins.

Use of the liquid-liquid interface for generating ultrathin nanocrystalline films of metals, chalcogenides, and oxides

The air-water interface has traditionally been employed to prepare particle assemblies and films of metals and semiconductors. The interface between water and an organic liquid, however, has not been investigated sufficiently for possible use in preparing nanocrystals and thin films of materials. In this article, we demonstrate the use of the liquid-liquid interface as a medium for preparing ultrathin films of metals, chalcogenides and oxides. The method involves the reaction at the interface between a metal-organic compound in the organic layer and an appropriate reagent for reduction, sulfidation, etc. in the aqueous layer. Some of the materials discussed are nanocrystalline films of gold, CuS, CuSe, CuO, and Cu(OH)(2) formed at the liquid-liquid interface. The results reported in this article should demonstrate the versatility and potential of the liquid-liquid interface for preparing nanomaterials and ultrathin films and encourage further research in this area. (c) 2005 Elsevier Inc. All rights reserved.

Fermi level depinning at the germanium Schottky interface through sulfur passivation

We demonstrate the depinning of Fermi level on both p- and n-type germanium after sulfur passivation by aqueous (NH4)(2)S treatment. Schottky contacts realized using metals with a wide range of work functions produce nearly ideal behavior confirming that the Fermi level is depinned. Examination of the passivated surface using x-ray photoelectron spectroscopy reveals bonding between Ge and sulfur.It is shown that good Ohmic contacts to n-type Ge and a hole barrier height (phi(Bp)) of 0.6 eV to p-type Ge can be achieved after this passivation treatment, with Zr Schottky contacts. This is the highest phi(Bp) reported so far.