An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

Rich data bearing on the structural and evolutionary principles of protein protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial `driver' mutations in oncogenesis. They also provide the foundation toward the design of protein protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. (C) 2014 Elsevier Ltd. All rights reserved.

Evolution of Aromatic beta-Glucoside Utilization by Successive Mutational Steps in Escherichia coli

The bglA gene of Escherichia coli encodes phospho-beta-glucosidase A capable of hydrolyzing the plant-derived aromatic beta-glucoside arbutin. We report that the sequential accumulation of mutations in bglA can confer the ability to hydrolyze the related aromatic beta-glucosides esculin and salicin in two steps. In the first step, esculin hydrolysis is achieved through the acquisition of a four-nucleotide insertion within the promoter of the bglA gene, resulting in enhanced steady-state levels of the bglA transcript. In the second step, hydrolysis of salicin is achieved through the acquisition of a point mutation within the bglA structural gene close to the active site without the loss of the original catabolic activity against arbutin. These studies underscore the ability of microorganisms to evolve additional metabolic capabilities by mutational modification of preexisting genetic systems under selection pressure, thereby expanding their repertoire of utilizable substrates.

Evolution of annealing texture in cryo-rolled copper

The present study addresses the evolution of texture and microstructure during annealing in a cryorolled copper. Transition from copper to brass texture during the cryo-rolling has been illustrated. Twinning and interaction between twins and shear bands have been found to play the important role in grain refinement and strengthening. The low temperature vacancy clustering and its effect on the recrystallization have been experimentally demonstrated. Fine scale twinning, and grain refinement have been attributed to the higher yield strength found in the case of samples subjected to cryo-rolling. (C) 2015 Elsevier B.V. All rights reserved.

Crustal Evolution of Kolli-Massif, Southern India

Southern India is a collage of numerous crustal fragments formed since the Archean (2500 Ma ago) and reworked several times during the geological history. A close look at these terrains provides a window to understand the crustal evolutionary processes experienced by the continental crust in the past, such as crustal growth (formation of crust through addition of new magma) and crustal reworking (modification of an already existing crust). Here we discuss the evolutionary history of such a crustal fragment from the Southern Granulite Terrain (SGT) in peninsular India, namely Kolli-massif. Geology, structural deformation through time, and the implications in crustal assembly of southern India are exponded.

The effect of structural dimensionality on the electrocatalytic properties of the nickel selenide phase

Nickel selenide (NiSe) nanostructures possessing different morphologies of wires, spheres and hexagons are synthesized by varying the selenium precursors, selenourea, selenium dioxide (SeO2) and potassium selenocyanate (KSeCN), respectively, and are characterized using X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, transmission electron microscopy and scanning electron microscopy techniques. Electrical measurements of a single nanowire and a hexagon carried out on devices fabricated by the focused ion beam (FIB) technique depict the semiconducting nature of NiSe and its ability to act as a visible light photodetector. The three different morphologies are used as catalysts for hydrogen evolution (HER), oxygen reduction (ORR) and glucose oxidation reactions. The wire morphology is found to be better than that of spheres and hexagons for all the reactions. Among the reactions studied, NiSe is found to be good for HER and glucose oxidation while ORR seems to terminate at the peroxide stage.

Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold

Heterodimeric proteins with homologous subunits of same fold are involved in various biological processes. The objective of this study is to understand the evolution of structural and functional features of such heterodimers. Using a non-redundant dataset of 70 such heterodimers of known 3D structure and an independent dataset of 173 heterodimers from yeast, we note that the mean sequence identity between interacting homologous subunits is only 23-24% suggesting that, generally, highly diverged paralogues assemble to form such a heterodimer. We also note that the functional roles of interacting subunits/domains are generally quite different. This suggests that, though the interacting subunits/domains are homologous, the high evolutionary divergence characterize their high functional divergence which contributes to a gross function for the heterodimer considered as a whole. The inverse relationship between sequence identity and RMSD of interacting homologues in heterodimers is not followed. We also addressed the question of formation of homodimers of the subunits of heterodimers by generating models of fictitious homodimers on the basis of the 3D structures of the heterodimers. Interaction energies associated with these homodimers suggests that, in overwhelming majority of the cases, such homodimers are unlikely to be stable. Majority of the homologues of heterodimers of known structures form heterodimers (51.8%) and a small proportion (14.6%) form homodimers. Comparison of 3D structures of heterodimers with homologous homodimers suggests that interfacial nature of residues is not well conserved. In over 90% of the cases we note that the interacting subunits of heterodimers are co-localized in the cell. Proteins 2015; 83:1766-1786. (c) 2015 Wiley Periodicals, Inc.

Electronic Structure Evolution across the Peierls Metal-Insulator Transition in a Correlated Ferromagnet

Transition metal compounds often undergo spin-charge-orbital ordering due to strong electron-electron correlations. In contrast, low-dimensional materials can exhibit a Peierls transition arising from low-energy electron-phonon-coupling-induced structural instabilities. We study the electronic structure of the tunnel framework compound K2Cr8O16, which exhibits a temperature-dependent (T-dependent) paramagnetic-to-ferromagnetic- metal transition at T-C = 180 K and transforms into a ferromagnetic insulator below T-MI = 95 K. We observe clear T-dependent dynamic valence (charge) fluctuations from above T-C to T-MI, which effectively get pinned to an average nominal valence of Cr+3.75 (Cr4+:Cr3+ states in a 3:1 ratio) in the ferromagnetic-insulating phase. High-resolution laser photoemission shows a T-dependent BCS-type energy gap, with 2G(0) similar to 3.5(k(B)T(MI)) similar to 35 meV. First-principles band-structure calculations, using the experimentally estimated on-site Coulomb energy of U similar to 4 eV, establish the necessity of strong correlations and finite structural distortions for driving the metal-insulator transition. In spite of the strong correlations, the nonintegral occupancy (2.25 d-electrons/Cr) and the half-metallic ferromagnetism in the t(2g) up-spin band favor a low-energy Peierls metal-insulator transition.

Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes

Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.

Microstructural evolution and strength variability in microwires

Tensile experiments on cold-drawn Ni microwires with diameters from similar to 115 to 50 gm revealed high strengths, with significant strength variability for finer wires with diameters less than similar to 50 gm. The wires showed pronounced necking at fracture. The coarser wires with diameters > 50 mu m exhibited conventional ductile cup-cone fracture, with dimples in the central zone and peripheral shear lips, whereas finer wires failed by shear with knife or chisel-edge fractures. Shear bands were observed in all samples. Further, through- section microscopy of selected fractured samples revealed that the shear bands did not go across the enitre specimen for the coarser wires. The shear bands led to grain fragmention, with a reduction in grain aspect ratio as well as rotations away from the initial < 111 > orientations. The strength data were analysed based on a Weibull approach. The data could be rationalized in terms of failure from volume defects in coarser wires, with a high Weibull modulus, and from surface defects in finer wires, with a low Weibull modulus and greater variability. (C) 2015 Elsevier B.V. All rights reserved.

Archean tectonics and crustal evolution of the Biligiri Rangan Block, southern India

The Southern Granulite Terrain in India is a collage of crustal blocks ranging in age from Archean to Neoproterozoic. This study investigate the tectonic evolution of one of the northernmost block- the Biligiri Block (BRB) through a multidisciplinary approach involving field investigation, petrographic studies, LA-ICPMS zircon U-Pb geochronology, Hf isotopic analyses, metamorphic P-T phase diagram computations, and crustal thickness modeling. The garnet bearing quartzofeldspathic gneiss from the central BRB preserve Mesoarchean magmatic zircons with ages between 3207 and 2806 Ma and positive epsilon Hf value (+2.7) which possibly indicates vestiges of a Mesoarchean primitive continental crust. The occurrence of quartzite-iron formation intercalation as well as ultramafic lenses along the western boundary of the BRB is interpreted to indicate that the Kollegal structural lineament is a possible paleo-suture. Phase diagram computation of a metagabbro from the southwestern periphery of the Kollegal suture zone reveals high-pressure (similar to 18.5 kbar) and medium-temperature (similar to 840 degrees C) metamorphism, likely during eastward subduction of the Western Dharwar oceanic crust beneath the Mesoarchean BRB. In the model presented here, slab subduction, melting and underplating processes generated arc magmatism and subsequent charnockitization within the BRB between ca. 2650 Ma and ca. 2498 Ma. These results thus reveal Meso- to Neoarchean tectonic evolution of the BRB. The spatial variation of crustal thickness, derived from flexure inversion technique, provides additional constraints on the tectonic linkage of the BRB with its surrounding terrains. In conjunction with published data, the Moyar and the Kollegal suture zones are considered to mark the trace of ocean closure along which the Nilgiri and Biligiri Rangan Blocks accreted on to the Western Dharwar Craton. (C) 2016 Elsevier B.V. All rights reserved.

Evolution of multivariant microstructures with anisotropic misfit: A phase field study

We study, in two dimensions, the effect of misfit anisotropy on microstructural evolution during precipitation of an ordered beta phase from a disordered alpha matrix; these phases have, respectively, 2- and 6-fold rotation symmetries. Thus, precipitation produces three orientational variants of beta phase particles, and they have an anisotropic (and crystallographically equivalent) misfit strain with the matrix. The anisotropy in misfit is characterized using a parameter t = epsilon(yy)/epsilon(xx), where epsilon(xx) and epsilon(yy) are the principal components of the misfit strain tensor. Our phase field, simulations show that the morphology of beta phase particles is significantly influenced by 1, the level of misfit anisotropy. Particles are circular in systems with dilatational misfit (t = 1), elongated along the direction of lower principal misfit when 0 < t < 1 and elongated along the invariant direction when - 1 <= t <= 0. In the special case of a pure shear misfit strain (t = - 1), the microstructure exhibits star, wedge and checkerboard patterns; these microstructural features are in agreement with those in Ti-Al-Nb alloys.

Nonlinear Enzyme Kinetics Can Lead to High Metabolic Flux Control Coefficients: Implications for the Evolution of Dominance

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can expect high values of control coefficients for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial ''default'' consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

Structural and lithium ion transport studies in sol-gel-prepared lithium silicophosphate glasses

Lithium silicophosphate glasses have been prepared by a sol-gel route over a wide range of compositions. Their structural and electrical properties have been investigated. Infrared spectroscopic studies show the presence of hydroxyl groups attached to Si and P. MAS NMR investigations provide evidence for the presence of different phosphatic units in the structure. The variations of de conductivities at 423 K and activation energies have been studied as a function of composition, and both exhibit an increasing trend with the ratio of nonbridging oxygen to bridging oxygen in the structure. Ac conductivity behavior shows that the power law exponent, s, is temperature dependent and exhibits a minimum. Relaxation behavior has been examined in detail using an electrical modulus formalism, and modulus data were fitted to Kohlraush-William-Watts stretched exponential function. A structural model has been proposed and the unusual properties exhibited by this unique system of glasses have been rationalized using this model. Ion transport in these glasses appears to be confined to unidimensional conduits defined by modified phosphate chains and interspersed with unmodified silica units.

Structural correlations in GexSe1-x glasses - a neutron diffraction study

Neutron diffraction measurement is carried out on GexSe1-x glasses, where 0.1 less than or equal to x less than or equal to 0.4, in a Q interval of 0.55-13.8 Angstrom(-1). The first sharp diffraction peak (FSDP) in the structure factor, S(Q), shows a systematic increase in the intensity and shifts to a lower Q with increasing Ge concentration. The coherence length of FSDP increases with x and becomes maximum for 0.33 less than or equal to x less than or equal to 0.4. The Monte-Carlo method, due to Soper, is used to generate S(Q) and also the pair correlation function, g(r). The generated S(Q) is in agreement with the experimental data for all x. Analysis of the first four peaks in the total correlation function, T(r), shows that the short range order in GeSe2 glass is due to Ge(Se-1/2)(4) tetrahedra, in agreement with earlier reports. Se-rich glasses contain Se-chains which are cross-linked with Ge(Se-1/2)(4) tetrahedra. Ge-2(Se-1/2)(6) molecular units are the basic structural units in Ge-rich, x = 0.4, glass. For x = 0.2, 0.33 and 0.4 there is evidence for some of the tetrahedra being in an edge-shared configuration. The number of edge-shared tetrahedra in these glasses increase with increasing Ge content.

Finite volume evolution Galerkin method for hyperbolic conservation laws with spatially varying flux functions

We present a generalization of the finite volume evolution Galerkin scheme [M. Lukacova-Medvid'ova,J. Saibertov'a, G. Warnecke, Finite volume evolution Galerkin methods for nonlinear hyperbolic systems, J. Comp. Phys. (2002) 183 533-562; M. Luacova-Medvid'ova, K.W. Morton, G. Warnecke, Finite volume evolution Galerkin (FVEG) methods for hyperbolic problems, SIAM J. Sci. Comput. (2004) 26 1-30] for hyperbolic systems with spatially varying flux functions. Our goal is to develop a genuinely multi-dimensional numerical scheme for wave propagation problems in a heterogeneous media. We illustrate our methodology for acoustic waves in a heterogeneous medium but the results can be generalized to more complex systems. The finite volume evolution Galerkin (FVEG) method is a predictor-corrector method combining the finite volume corrector step with the evolutionary predictor step. In order to evolve fluxes along the cell interfaces we use multi-dimensional approximate evolution operator. The latter is constructed using the theory of bicharacteristics under the assumption of spatially dependent wave speeds. To approximate heterogeneous medium a staggered grid approach is used. Several numerical experiments for wave propagation with continuous as well as discontinuous wave speeds confirm the robustness and reliability of the new FVEG scheme.