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.

Unravelling the self-assembly of hydrogen bonded NDI semiconductors in 2D and 3D

Supramolecular ordering of organic semiconductors is the key factor defining their electrical characteristics. Yet, it is extremely difficult to control, particularly at the interface with metal and dielectric surfaces in semiconducting devices. We have explored the growth of n-type semiconducting films based on hydrogen-bonded monoalkylnaphthalenediimide (NDI-R) from solution and through vapor deposition on both conductive and insulating surfaces. We combined scanning tunneling and atomic force microscopies with X-ray diffraction analysis to characterize, at the submolecular level, the evolution of the NDI-R molecular packing in going from monolayers to thin films. On a conducting (graphite) surface, the first monolayer of NDI-R molecules adsorbs in a flat-lying (face-on) geometry, whereas in subsequent layers the molecules pack edge-on in islands (Stranski–Krastanov-like growth). On SiO2, the NDI-R molecules form into islands comprising edge-on packed molecules (Volmer–Weber mode). Under all the explored conditions, self-complementary H bonding of the imide groups dictates the molecular assembly. The measured electron mobility of the resulting films is similar to that of dialkylated NDI molecules without H bonding. The work emphasizes the importance of H bonding interactions for controlling the ordering of organic semiconductors, and demonstrates a connection between on-surface self-assembly and the structural parameters of thin films used in electronic devices.

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.

Structure and bonding of MCB5H7 and its sandwiched dimer CB5H6M–MCB5H6 (M = Si, Ge, Sn): Isomer stability and preference for slip distorted structure

We find sandwiched metal dimers CB5H6M–MCB5H6 (M = Si, Ge, Sn) which are minima in the potential energy surface with a characteristic M–M single bond. The NBO analysis and the M–M distances (Å) (2.3, 2.44 and 2.81 for M = Si, Ge, Sn) indicate substantial M–M bonding. Formal generation of CB5H6M–MCB5H6 has been studied theoretically. Consecutive substitution of two boron atoms in B7H−27 by M (Si, Ge, Sn) and carbon, respectively followed by dehydrogenation may lead to our desired CB5H6M–MCB5H6. We find that the slip distorted geometry is preferred for MCB5H7 and its dehydrogenated dimer CB5H6M–MCB5H6. The slip-distortion of M–M bond in CB5H6M–MCB5H6 is more than the slip distortion of M–H bond in MCB5H7. Molecular orbital analysis has been done to understand the slip distortion. Larger M–M bending (CB5H6M–MCB5H6) in comparison with M–H bending (MCB5H7) is suspected to be encouraged by stabilization of one of the M–M π bonding MO’s. Preference of M to occupy the apex of pentagonal skeleton of MCB5H7 over its icosahedral analogue MCB10H11 has been observed.

The Relational Self, the Social Bond and the Dynamics of Personal Relationships : A Sociological Analysis

This study analyses personal relationships linking research to sociological theory on the questions of the social bond and on the self as social. From the viewpoint of disruptive life events and experiences, such as loss, divorce and illness, it aims at understanding how selves are bound to their significant others as those specific people ‘close or otherwise important’ to them. Who form the configurations of significant others? How do different bonds respond in disruptions and how do relational processes unfold? How is the embeddedness of selves manifested in the processes of bonding, on the one hand, and in the relational formation of the self, on the other? The bonds are analyzed from an anti-categorical viewpoint based on personal citations of significance as opposed to given relationship categories, such as ‘family’ or ‘friendship’ – the two kinds of relationships that in fact are most frequently significant. The study draws from analysis of the personal narratives of 37 Finnish women and men (in all 80 interviews) and their entire configurations of those specific people who they cite as ‘close or otherwise important’. The analysis stresses the subjective experiences, while also investigating the actualized relational processes and configurations of all personal relationships with certain relationship histories embedded in micro-level structures. The research is based on four empirical sub-studies of personal relationships and a summary discussing the questions of the self and social bond. Discussion draws from G. H. Mead, C. Cooley, N. Elias, T. Scheff, G. Simmel and the contributors of ‘relational sociology’. Sub-studies analyse bonds to others from the viewpoint of biographical disruption and re-configuration of significant others, estranged family bonds, peer support and the formation of the most intimate relationships into exclusive and inclusive configurations. All analyses examine the dialectics of the social and the personal, asking how different structuring mechanisms and personal experiences and negotiations together contribute to the unfolding of the bonds. The summary elaborates personal relationships as social bonds embedded in wider webs of interdependent people and social settings that are laden with cultural expectations. Regarding the question of the relational self, the study proposes both bonding and individuality as significant. They are seen as interdependent phases of the relationality of the self. Bonding anchors the self to its significant relationships, in which individuality is manifested, for example, in contrasting and differentiating dynamics, but also in active attempts to connect with others. Individuality is not a fixed quality of the self, but a fluid and interdependent phase of the relational self. More specifically, it appears in three formats in the flux of relational processes: as a sense of unique self (via cultivation of subjective experiences), as agency and as (a search for) relative autonomy. The study includes an epilogue addressing the ambivalence between the social expectation of individuality in society and the bonded reality of selves.

Understanding Connectivity between Groundwater Chemistry Data and Geological Stratigraphy via 3D Sub-surface Visualization and Analysis

This paper describes the 3D Water Chemistry Atlas - an open source, Web-based system that enables the three-dimensional (3D) sub-surface visualization of ground water monitoring data, overlaid on the local geological model. Following a review of existing technologies, the system adopts Cesium (an open source Web-based 3D mapping and visualization interface) together with a PostGreSQL/PostGIS database, for the technical architecture. In addition a range of the search, filtering, browse and analysis tools were developed that enable users to interactively explore the groundwater monitoring data and interpret it spatially and temporally relative to the local geological formations and aquifers via the Cesium interface. The result is an integrated 3D visualization system that enables environmental managers and regulators to assess groundwater conditions, identify inconsistencies in the data, manage impacts and risks and make more informed decisions about activities such as coal seam gas extraction, waste water extraction and re-use.

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.

Elastic stress analysis of jointed half-planes

Using a Fourier-integral approach, the problem of stress analysis in a composite plane consisting of two half-planes of different elastic properties rigidly joined along their boundaries has been solved. The analysis is done for a force acting in one of the half-planes for both cases when the force acts parallel and perpendicular to the interface. As a particular case, the interface stresses are evaluated when the interface is smooth. Some properties of the normal stress at the interface are discussed both for plane stress and plane strain conditions.

The Role of Interface Modification on Thermal Degradation and Crystallization Behavior of Composites from Commingled Polypropylene Fiber and Banana Fiber

The thermal degradation behavior of banana fiber and polypropylene/banana fiber composites has been studied by thermogravimetric analysis. Banana fiber was found to be decomposing in two stages, first one around 320 degrees C and the second one around 450 degrees C. For chemically treated banana fiber, the decomposition process has been at a higher temperature, indicating thermal stability for the treated fiber. Activation energies for thermal degradation were estimated using Coats and Redfern method. Calorific value of the banana fiber was measured using a constant volume isothermal bomb calorimeter. rystallization studies exhibited an increase in the crystallization temperature and crystallinity of polypropylene upon the addition of banana fiber. POLYM. COMPOS., 31:1113-1123, 2010. (C) 2009 Society of Plastics Engineers.

Ring-Opening-Induced Toughening of a Low-Permittivity Polymer-Metal Interface

Integrating low dielectric permittivity (low-k) polymers to metals is an exacting fundamental challenge because poor bonding between low-polarizability moieties and metals precludes good interfacial adhesion. Conventional adhesion-enhancing methods such as using intermediary layers are unsuitable for engineering polymer/metal interfaces for many applications because of the collateral increase in dielectric permittivity. Here, we demonstrate a completely new approach without surface treatments or intermediary layers to obtain an excellent interfacial fracture toughness of > 13 J/m(2) in a model system comprising copper. and a cross-linked polycarbosilane with k similar to 2.7 obtained by curing a cyclolinear polycarbosilane in air.Our results suggest that interfacial oxygen catalyzed molecularring-opening and anchoring of the opened ring moieties of the polymer to copper is the main toughening mechanism. This novel approach of realizing adherent low-k polymer/metal structures without intermediary layers by activating metal-anchoring polymer moieties at the interface could be adapted for applications such as device wiring and packaging, and laminates and composites.

Emerging trends at the interface of chemistry and biology: Applications to the design of human therapeutics

This article describes recent developments in the design and implementation of various strategies towards the development of novel therapeutics using first principles from biology and chemistry. Strategies for multi-target therapeutics and network analysis with a focus on cancer and HIV are discussed. Methods for gene and siRNA delivery are presented along with challenges and opportunities for siRNA therapeutics. Advances in protein design methodology and screening are described, with a focus on their application to the design of antibody based therapeutics. Future advances in this area relevant to vaccine design are also mentioned.

Positional dependence of material flow in friction stir welding: analysis of joint line remnant and its relevance to dissimilar metal welding

Understanding material flow in friction stir welding is important for production of sound dissimilar metal welding that control the intermixing of two alloys being welded and consequent formation of new constituents which influences the weld properties. In the present experimental investigation material flow patterns are visualised using dissimilar and similar aluminium alloys using a simple innovative ,experiment. The experimental results reveal that only a portion of material transported from the leading edge undergoes chaotic flow and the remaining is deposited systematically in the trailing edge of the weld. Using this information it is shown that the formation of a friction stir welding defect, joint line remnant, does not occur only when the weld interface is on the advancing side. The material flow visualisation study has been utilised to analyse the mechanism of weld formation and its usefulness in improving fatigue properties and for dissimilar metal welds.

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/ PBE/.

An ab-initio study of the proton affinity of conjugated schiff-base and related nitrogen compounds: an analysis of the triggering site of bacteriorhodopsin

The chemical groups which take part in the proton transfer reaction in bacteriorhodopsin have been studied by ab initio quantum chemical methods. The various factors such as conjugation with a linear system, electron delocalization of the guanidine type, cis-trans isomerism, geometry distortion and hydrogen bonding with charged groups can influence the properties of a given chemical group. Several systems are studied at 4-31G and STO-3G levels. Some of the Schiff-base analogues and guanidine type molecules are characterized by their molecular orbital diagrams, energy levels and the nature of charge distribution. Also, the effects of the above-mentioned factors on proton affinity are studied. It is hoped that the values thus obtained can be helpful in evaluating various structural models for proton transfer.