Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Cardiac remodeling in Drosophila arises from changes in actin gene expression and from a contribution of lymph gland-like cells to the heart musculature

Understanding the basis of normal heart remodeling can provide insight into the plasticity of the cardiac state, and into the potential for treating diseased tissue. In Drosophila, the adult heart arises during metamorphosis from a series of events, that include the remodeling of an existing cardiac tube, the elaboration of new inflow tracts, and the addition of a layer of longitudinal muscle fibers. We have identified genes active in all these three processes, and studied their expression in order to characterize in greater detail normal cardiac remodeling. Using a Transglutaminase-lacZ transgenic line, that is expressed in the inflow tracts of the larval and adult heart, we confirm the existence of five inflow tracts in the adult structure. In addition, expression of the Actin87E actin gene is initiated in the remodeling cardiac tube, but not in the longitudinal fibers, and we have identified an Act87E promoter fragment that recapitulates this switch in expression. We also establish that the longitudinal fibers are multinucleated, characterizing these cells as specialized skeletal muscles. Furthermore, we have defined the origin of the longitudinal fibers, as a subset of lymph gland cells associated with the larval dorsal vessel. These studies underline the myriad contributors to the formation of the adult Drosophila heart, and provide new molecular insights into the development of this complex organ. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Analysis of texture evolution in pure magnesium and the magnesium alloy AM30 during rod and tube extrusion

The evolution of microstructure and texture during extrusion of pure magnesium and its single phase alloy AM30 has been studied experimentally as well as by crystal plasticity simulation. Microstructure and micro-texture were characterized by electron back scattered diffraction (EBSD), bulk-texture was measured using X-ray diffraction and deformation texture simulations were carried out using visco-plastic self consistent (VPSC) model. In spite of clear indications of the occurrence of dynamic recrystallization (DRX), simulations were able to reproduce the experimental textures successfully. This was attributed to the fact that the textures were c-type fibers with their axis of rotation parallel to the c-axis and DRX leads to simply rotate the texture around the c-axis. (C) 2011 Elsevier B.V. All rights reserved.

Social selection and the evolution of cooperative groups: The example of the cellular slime moulds

In social selection the phenotype of an individual depends on its own genotype as well as on the phenotypes, and so genotypes, of other individuals. This makes it impossible to associate an invariant phenotype with a genotype: the social context is crucial. Descriptions of metazoan development, which often is viewed as the acme of cooperative social behaviour, ignore or downplay this fact. The implicit justification for doing so is based on a group-selectionist point of view. Namely, embryos are clones, therefore all cells have the same evolutionary interest, and the visible differences between cells result from a common strategy. The reasoning is flawed, because phenotypic heterogeneity within groups can result from contingent choices made by cells from a flexible repertoire as in multicellular development. What makes that possible is phenotypic plasticity, namely the ability of a genotype to exhibit different phenotypes. However, co-operative social behaviour with division of labour requires that different phenotypes interact appropriately, not that they belong to the same genotype, or have overlapping genetic interests. We sketch a possible route to the evolution of social groups that involves many steps: (a) individuals that happen to be in spatial proximity benefit simply by virtue of their number; (b) traits that are already present act as preadaptations and improve the efficiency of the group; and (c) new adaptations evolve under selection in the social context-that is, via interactions between individuals-and further strengthen group behaviour. The Dictyostelid or cellular slime mould amoebae (CSMs) become multicellular in an unusual way, by the aggregation of free-living cells. In nature the resulting group can be genetically homogeneous (clonal) or heterogeneous (polyclonal); in either case its development, which displays strong cooperation between cells (to the extent of so-called altruism) is not affected. This makes the CSMs exemplars for the study of social behaviour.

Asymptotic and finite element analyses of mode III dynamic crack growth at a ductile-brittle interface

In this work, dynamic crack growth along a ductile-brittle interface under anti-plane strain conditions is studied. The ductile solid is taken to obey the J(2) flow theory of plasticity with linear isotropic strain hardening, while the substrate is assumed to exhibit linear elastic behavior. Firstly, the asymptotic near-tip stress and velocity fields are derived. These fields are assumed to be variable-separable with a power singularity in the radial coordinate centered at the crack tip. The effects of crack speed, strain hardening of the ductile phase and mismatch in elastic moduli of the two phases on the singularity exponent and the angular functions are studied. Secondly, full-field finite element analyses of the problem under small-scale yielding conditions are performed. The validity of the asymptotic fields and their range of dominance are determined by comparing them with the results of the full-field finite element analyses. Finally, theoretical predictions are made of the variations of the dynamic fracture toughness with crack velocity. The influence of the bi-material parameters on the above variation is investigated.

Processing map for hot working of powder

The constitutive flow behavior of a metal matrix composite (MMC) with 2124 aluminum containing 20 vol pct silicon carbide particulates under hot-working conditions in the temperature range of 300 °C to 550 °C and strain-rate range of 0.001 to 1 s-1 has been studied using hot compression testing. Processing maps depicting the variation of the efficiency of power dissipation given by [2m/(m + 1)] (wherem is the strain-rate sensitivity of flow stress) with temperature and strain rate have been established for the MMC as well as for the matrix material. The maps have been interpreted on the basis of the Dynamic Materials Model (DMM). [3] The MMC exhibited a domain of superplasticity in the temperature range of 450 °C to 550 °C and at strain rates less than 0.1 s-1. At 500 °C and 1 s-1 strain rate, the MMC undergoes dynamic recrystallization (DRX), resulting in a reconstitution of microstructure. In comparison with the map for the matrix material, the DRX domain occurred at a strain rate higher by three orders of magnitude. At temperatures lower than 400 °C, the MMC exhibited dynamic recovery, while at 550 °C and 1 s-1, cracking occurred at the prior particle boundaries (representing surfaces of the initial powder particles). The optimum temperature and strain-rate combination for billet conditioning of the MMC is 500 °C and 1 s-1, while secondary metalworking may be done in the super- plasticity domain. The MMC undergoes microstructural instability at temperatures lower than 400 °C and strain rates higher than 0.1 s-1.

Characteristic water contents of a fine-grained soil-water system

This paper critically appraises the limitations of the liquid-limit water content of clayey soils determined conventionally either by percussion cup or by the cone penetration method. It is shown that the conventional liquid limit and plastic limit are arbitrary, strength-based water contents and that they cannot represent the plasticity limits, and that the state of the soil-water system at the conventional liquid limit does not correspond to a stress-free reference state. The present investigation identifies three characteristic limiting water contents for a soil-water system which have well-defined, unique mechanisms controlling them, namely the free swell limit, settling limit and shrinkage limit. Simple procedures for the determination of the free swell limit and settling limit of natural soils are presented. The settling limit is shown to be the 'real liquid limit' of any clayey soil. With a number of experimental illustrations, it is clearly shown that the settling limit represents the maximum water-holding capacity of clayey soils and that it corresponds to the stress-free reference state.

Mechanistic approach to the shear strength behaviour of allophanic soils

The presence of allophane minerals imparts special engineering features to the volcanic ash soils. This study examines the reasons for the allophanic soils exhibiting unusual shear strength properties in comparison to sedimentary clays. The theories of residual shear strength developed for natural soils and artificial soil mixtures and the unusual surface charge properties of the allophane particle are invoked to explain the high shear strength values of these residual soils. The lack of any reasonable correlation between phi' (effective stress-strength parameter) and plasticity index values for allophanic soils is explained on the basis of the unusual structure of the allophane particle. The reasons as to why natural soil slopes in allophanic soil areas (example, Dominica, West Indies) are stable at much steeper angles than natural slopes in sedimentary clay deposits (London clay areas) are explained in light of the hypothesis developed in this study.

Primary Sequence That Determines the Functional Overlap between Mitochondrial Heat Shock Protein 70 Ssc1 and Ssc3 of Saccharomyces cerevisiae

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can ``make or break'' mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

Water-mediated ionic interactions in protein structures

It is well known that water molecules play an indispensable role in the structure and function of biological macromolecules. The water-mediated ionic interactions between the charged residues provide stability and plasticity and in turn address the function of the protein structures. Thus, this study specifically addresses the number of possible water-mediated ionic interactions, their occurrence, distribution and nature found in 90% non-redundant protein chains. Further, it provides a statistical report of different charged residue pairs that are mediated by surface or buried water molecules to form the interactions. Also, it discusses its contributions in stabilizing various secondary structural elements of the protein. Thus, the present study shows the ubiquitous nature of the interactions that imparts plasticity and flexibility to a protein molecule.

Hidden order in serrated flow of metallic glasses

We report results of statistical and dynamic analysis of the serrated stress-time curves obtained from compressive constant strain-rate tests on two metallic glass samples with different ductility levels in an effort to extract hidden information in the seemingly irregular serrations. Two distinct types of dynamics are detected in these two alloy samples. The stress-strain curve corresponding to the less ductile Zr65Cu15Ni10Al10 alloy is shown to exhibit a finite correlation dimension and a positive Lyapunov exponent, suggesting that the underlying dynamics is chaotic. In contrast, for the more ductile Cu47.5Zr47.5Al5 alloy, the distributions of stress drop magnitudes and their time durations obey a power-law scaling reminiscent of a self-organized critical state. The exponents also satisfy the scaling relation compatible with self-organized criticality. Possible physical mechanisms contributing to the two distinct dynamic regimes are discussed by drawing on the analogy with the serrated yielding of crystalline samples. The analysis, together with some physical reasoning, suggests that plasticity in the less ductile sample can be attributed to stick-slip of a single shear band, while that of the more ductile sample could be attributed to the simultaneous nucleation of a large number of shear bands and their mutual interactions. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Assessing formability of sheet metals through advanced tensile and LASER speckle analysis

The ability of a metal to resist strain localisation and hence reduction in local thickness, is a most important forming property upon stretching. The uniform strain represents in this regard a critical factor to describe stretching ability - especially when the material under consideration exhibits negative strain rate sensitivity and dynamic strain ageing (DSA). A newly developed Laser Speckle Technique (LST), e.g. see [1], was used in-situ during tensile testing with two extensometers. The applied technique facilitates quantitative information on the propagating plasticity (i.e. the so-called PLC bands) known to take place during deformation where DSA is active. The band velocity (V-band), and the bandwidth (W-band) were monitored upon increasing accumulated strain. The knowledge obtained with the LST was useful for understanding the underlying mechanisms for the formability limit when DSA and negative strain rate sensitivity operate. The goal was to understand the relationship between PLC/DSA phenomena and the formability limit physically manifested as shear band formation. Two principally different alloys were used to discover alloying effects.

Constraint loss under dynamic loading in rate independent plastic solids

The objectives of this paper are to examine the loss of crack tip constraint in dynamically loaded fracture specimens and to assess whether it can lead to enhancement in the fracture toughness at high loading rates which has been observed in several experimental studies. To this end, 2-D plane strain finite element analyses of single edge notched (tension) specimen and three point bend specimen subjected to time varying loads are performed. The material is assumed to obey the small strain J(2) flow theory of plasticity with rate independent behaviour. The results demonstrate that a valid J-Q field exists under dynamic loading irrespective of the crack length and specimen geometry. Further, the constraint parameter Q becomes strongly negative at high loading rates, particularly in deeply cracked specimens. The variation of dynamic fracture toughness K-dc with stress intensity rate K for cleavage cracking is predicted using a simple critical stress criterion. It is found that inertia-driven constraint loss can substantially enhance K-dc for (K) over dot > 10(5) MPa rootm/s.

Analysis of deformation mechanisms in superplastic yttria-stabilized tetragonal zirconia

There have been extensive experimental observations of changes in the apparent rate controlling creep parameters in studies on superplastic materials. The three most common explanations associated with these changes in the stress exponent, n, the activation energy Q and the inverse grain size exponent, p involve the effect of concurrent grain growth, the operation of a threshold stress or transitions in creep mechanisms. Each of these factors may influence experimental creep data in a similar manner. Therefore, a careful analysis of the consequences of all three factors must involve the development of a consistent set of experimental observations in order to adequately distinguish the effects of each. This paper discusses the role of concurrent grain growth, a threshold stress and transitions in creep mechanisms in superplastic materials. Specific attention is given to the analysis of data on superplastic yttria-stabilized zirconia ceramics for which an increase in n has been observed at low applied stresses. It is demonstrated that neither concurrent grain growth nor a threshold stress can account for all the relevant experimental observations in this material. It is concluded that the changes in rate controlling creep parameters are associated with the operation of two distinct sequential mechanisms as part of a grain boundary sliding process.

Analysis of shear bands in slow granular flows using a frictional Cosserat model

The slow flow of granular materials is often marked by the existence of narrow shear layers, adjacent to large regions that suffer little or no deformation. This behaviour, in the regime where shear stress is generated primarily by the frictional interactions between grains, has so far eluded theoretical description. In this paper, we present a rigid-plastic frictional Cosserat model that captures thin shear layers by incorporating a microscopic length scale. We treat the granular medium as a Cosserat continuum, which allows the existence of localised couple stresses and, therefore, the possibility of an asymmetric stress tensor. In addition, the local rotation is an independent field variable and is not necessarily equal to the vorticity. The angular momentum balance, which is implicitly satisfied for a classical continuum, must now be solved in conjunction with the linear momentum balances. We extend the critical state model, used in soil plasticity, for a Cosserat continuum and obtain predictions for flow in plane and cylindrical Couette devices. The velocity profile predicted by our model is in qualitative agreement with available experimental data. In addition, our model can predict scaling laws for the shear layer thickness as a function of the Couette gap, which must be verified in future experiments. Most significantly, our model can determine the velocity field in viscometric flows, which classical plasticity-based model cannot.