Elastic proteins: biological roles and mechanical properties

The term 'elastic protein' applies to many structural proteins with diverse functions and mechanical properties so there is room for confusion about its meaning. Elastic implies the property of elasticity, or the ability to deform reversibly without loss of energy; so elastic proteins should have high resilience. Another meaning for elastic is 'stretchy', or the ability to be deformed to large strains with little force. Thus, elastic proteins should have low stiffness. The combination of high resilience, large strains and low stiffness is characteristic of rubber-like proteins (e.g. resilin and elastin) that function in the storage of elastic-strain energy. Other elastic proteins play very different roles and have very different properties. Collagen fibres provide exceptional energy storage capacity but are not very stretchy. Mussel byssus threads and spider dragline silks are also elastic proteins because, in spite of their considerable strength and stiffness, they are remarkably stretchy. The combination of strength and extensibility, together with low resilience, gives these materials an impressive resistance to fracture (i.e. toughness), a property that allows mussels to survive crashing waves and spiders to build exquisite aerial filters. Given this range of properties and functions, it is probable that elastic proteins will provide a wealth of chemical structures and elastic mechanisms that can be exploited in novel structural materials through biotechnology.     

Review of stochastic hybrid systems with applications in biological systems modeling and analysis

Stochastic hybrid systems (SHS) have attracted a lot of research interests in recent years. In this paper, we review some of the recent applications of SHS to biological systems modeling and analysis. Due to the nature of molecular interactions, many biological processes can be conveniently described as a mixture of continuous and discrete phenomena employing SHS models. With the advancement of SHS theory, it is expected that insights can be obtained about biological processes such as drug effects on gene regulation. Furthermore, combining with advanced experimental methods, in silico simulations using SHS modeling techniques can be carried out for massive and rapid verification or falsification of biological hypotheses. The hope is to substitute costly and time-consuming in vitro or in vivo experiments or provide guidance for those experiments and generate better hypotheses.     

Regulatory modules that generate biphasic signal response in biological systems

Biochemical networks might be composed of modules. It is still not clear how biochemical modules can be defined and characterised. Here we propose a functional approach to module definition, considering different classes of biphasic regulation modules, which effect optimal cell response to intermediate signal strength. Each regulation class might possess unique properties that make it especially suitable for particular biological functions.     

Mineral nutrition influences physiological responses of pear in vitro

Abnormal physiological responses of plant cultures such as shoot tip necrosis, callus, and hyperhydricity are some of the most difficult challenges in shoot micropropagation, and their causes are not well understood. Five Murashige and Skoog mineral salt factors, which influence the growth of pear shoot cultures, were tested in a five-dimensional surface response experimental design. Pyrus communis ‘Old Home × Farmingdale 87,’ ‘Horner 51,’ and ‘Winter Nelis’; Pyrus dimorphophylla; and Pyrus ussuriensis ‘Hang Pa Li’ shoot cultures were grown on 43 computer-designed treatments to represent the design space of all possible treatment combinations. Analysis of shoot response to these treatments identified the factors that both contributed to physiological disorders and remedied them. Undesirable callus formation was common for pear shoots cultured on standard medium and decreased on formulations with increased NH₄NO₃, Fe, and mesos (CaCl₂, KH₂PO₄, and MgSO₄) for most genotypes. Shoot tip necrosis varied with the genotype, but low mesos or low nitrogen concentrations contributed to the necrosis. Hyperhydricity was more prominent with low mesos or low NH₄NO₃. Hooked and upwardly curled new leaves were seen in most genotypes and resulted from use of low mesos in P. communis and low nitrogen for ‘Hang Pa Li’ and P. dimorphophylla. Fasciation and hypertrophy were seen infrequently and resulted from wide imbalances in several nutrients simultaneously. In general, standard concentrations of Murashige and Skoog iron and micros combined with high mesos and moderate nitrogen compounds produced normal shoots without physiological disorders.     

Isotope effects on electron tunneling reactions in biological systems conformational mobility of proteins

Effects of D2O substitution on electron transport reactions in proteins were analysed on the basis of generally adopted ideas of electronic vibration interactions and conformational mobility of macromolecules. At the molecular level, a mechanism for cytochrome c oxidation was established. On the basis of general viscosity and elasticity properties of proteins, the effects of temperature and chemical composition of the medium on conformational relaxation were analysed. For chromatophores of photosynthetising bacteria, a mechanism is discussed by which abnormal effects of temperature and abnormal isotope effects may be exercised on charge recombination.     

Mucous systems show a novel mechanical response to applied deformation

Mucous secretions have a wide range of biological functions that are intimately linked with their rheological properties. In addition, many mucous secretions are exposed to significant stress and deformation during physiological function. This study has examined the rheological response of three mucous systems, native pig gastric mucus, purified mucin gels, and mucin alginate gels, to increasing applied stress to a level sufficient to induce flow behavior. A novel, frequency-dependent stress hardening was observed in all three systems. This hardening behavior may play a significant role in the ability of mucous systems to resist mechanical disruption in the physiological state.     

Histidine kinases and response regulator proteins in two-component signaling systems.

Phosphotransfer-mediated signaling pathways allow cells to sense and respond to environmental stimuli. Autophosphorylating histidine protein kinases provide phosphoryl groups for response regulator proteins which, in turn, function as molecular switches that control diverse effector activities. Structural studies of proteins involved in two-component signaling systems have revealed a modular architecture with versatile conserved domains that are readily adapted to the specific needs of individual systems.     

Spatial proximity of proteins surrounding zyxin under force-bearing conditions

Sensing physical forces is a critical first step in mechano-transduction of cells. Zyxin, a LIM domain-containing protein, is recruited to force-bearing actin filaments and is thought to repair and strengthen them. Yet, the precise force-induced protein interactions surrounding zyxin remain unclear. Using BioID analysis, we identified proximal proteins surrounding zyxin under normal and force-bearing conditions by label-free mass spectrometry analysis. Under force-bearing conditions, increased biotinylation of α-actinin 1, α-actinin 4, and AFAP1 were detected, and these proteins accumulated along force-bearing actin fibers independently from zyxin, albeit at a lower intensity than zyxin. VASP also accumulated along force-bearing actin fibers in a zyxin-dependent manner, but the biotinylation of VASP remained constant regardless of force, supporting the model of a free zyxin–VASP complex in the cytoplasm being corecruited to tensed actin fibers. In addition, ARHGAP42, a RhoA GAP, was also identified as a proximal protein of zyxin and colocalized with zyxin along contractile actin bundles. The overexpression of ARHGAP42 reduced the rate of small wound closure, a zyxin-dependent process. These results demonstrate that the application of proximal biotinylation can resolve the proximity and composition of protein complexes as a function of force, which had not been possible with traditional biochemical analysis.     

Application of modular response analysis to medium- to large-size biological systems

The development of high-throughput genomic technologies associated with recent genetic perturbation techniques such as short hairpin RNA (shRNA), gene trapping, or gene editing (CRISPR/Cas9) has made it possible to obtain large perturbation data sets. These data sets are invaluable sources of information regarding the function of genes, and they offer unique opportunities to reverse engineer gene regulatory networks in specific cell types. Modular response analysis (MRA) is a well-accepted mathematical modeling method that is precisely aimed at such network inference tasks, but its use has been limited to rather small biological systems so far. In this study, we show that MRA can be employed on large systems with almost 1,000 network components. In particular, we show that MRA performance surpasses general-purpose mutual information-based algorithms. Part of these competitive results was obtained by the application of a novel heuristic that pruned MRA-inferred interactions a posteriori. We also exploited a block structure in MRA linear algebra to parallelize large system resolutions.     

Retrograde fluxes of focal adhesion proteins in response to cell migration and mechanical signals

Recent studies suggest that mechanical signals mediated by the extracellular matrix play an essential role in various physiological and pathological processes; yet, how cells respond to mechanical stimuli remains elusive. Using live cell fluorescence imaging, we found that actin filaments, in association with a number of focal adhesion proteins, including zyxin and vasodilator-stimulated phosphoprotein, undergo retrograde fluxes at focal adhesions in the lamella region. This flux is inversely related to cell migration, such that it is amplified in fibroblasts immobilized on micropatterned islands. In addition, the flux is regulated by mechanical signals, including stretching forces applied to flexible substrates and substrate stiffness. Conditions favoring the flux share the common feature of causing large retrograde displacements of the interior actin cytoskeleton relative to the substrate anchorage site, which may function as a switch translating mechanical input into chemical signals, such as tyrosine phosphorylation. In turn, the stimulation of actin flux at focal adhesions may function as part of a feedback mechanism, regulating structural assembly and force production in relation to cell migration and mechanical load. The retrograde transport of associated focal adhesion proteins may play additional roles in delivering signals from focal adhesions to the interior of the cell.     

The influences of task difficulty and response correctness on neural systems supporting fluid reasoning

This functional magnetic resonance imaging (fMRI) study examined neural contributions to managing task difficulty and response correctness during fluid reasoning. Previous studies investigate reasoning by independently varying visual complexity or task difficulty, or the specific domain. Under natural conditions these factors interact in a complex manner to support dynamic combinations of perceptual and conceptual processes. This study investigated fluid reasoning under circumstances that would represent the cognitive flexibility of real life decision-making. Results from a mixed effects analysis corrected for multiple comparisons indicate involvement of cortical and subcortical areas during fluid reasoning. A 2 × 2 ANOVA illustrates activity related to variances in task difficulty correlated with increased blood oxygenation level-dependent (BOLD)-signal in the left middle frontal gyrus (BA6). Activity related to response correctness correlated with increased BOLD-signal in a larger, distributed system including right middle frontal gyrus (BA6), right superior parietal lobule (BA7), left inferior parietal lobule (BA40), left lingual gyrus (BA19), and left cerebellum (Lobule VI). The dissociation of function in left BA 6 for task difficulty and right BA6 for response correctness and the involvement of a more diffuse network involving the left cerebellum in response correctness extends knowledge about contributions of classic motor and premotor areas supporting higher level cognition.     

P Nuclear magnetic resonance observations in biological systems II. Nucleic acids and proteins

³¹P nucleus has proven to be an extremely useful nmr probe of phosphates in biochemical systems. It provides information on their structure and environment; any changes in these two factors are reflected in 31P chemical shift perturbations. This approach has been most useful in studying the nucleic acids backbone conformation.     

Benchmarking yeast two‐hybrid systems using the interactions of bacterial motility proteins

Yeast two‐hybrid screens often produce vastly non‐overlapping interaction data when the screens are conducted in different laboratories, or use different vectors, strains, or reporter genes. Here we investigate the underlying reasons for such inconsistencies and compare the effect of seven different vectors and their yeast two‐hybrid interactions. Genome‐wide array screens with 49 motility‐related baits from Treponema pallidum yielded 77 and 165 interactions with bait vectors pLP‐GBKT7 and pAS1‐LP, respectively, including 21 overlapping interactions. In addition, 90 motility‐related proteins from Escherichia coli were tested in all pairwise combinations and yielded 140 interactions when tested with pGBKT7g/pGADT7g vectors but only 47 when tested with pDEST32/pDEST22. We discuss the factors that determine these effects, including copy number, the nature of the fusion protein, and species‐specific differences that explain non‐conserved interactions among species. The pDEST22/pDEST32 vectors produce a higher fraction of interactions that are conserved and that are biologically relevant when compared with the pGBKT7/pGADT7‐related vectors, but the latter appear to be more sensitive and thus detect more interactions overall.     

Self-organization in biological systems

Biological systems are considered that are capable of dynamic self-organization, i.e., spontaneous emergence of spatio-temporal order with the formation of various spatio-temporal patterns. A cell is involved in the organization of ontogenesis of all stages. Embryonic cells exhibit coordinated social behavior and generate ordered morphological patterns displaying variability and equifinality of development. Physical and topological patterns are essential for biological systems as an imperative that restricts and directs biological morphogenesis. Biological self-organization is directed and fixed by natural selection during which selection of the most sustainable, flexible, modular systems capable of adaptive self-organization occurs.