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Sample records for modular multifunctional protein

  1. Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein

    PubMed Central

    D'Auria, Giuseppe; Jiménez, Núria; Peris-Bondia, Francesc; Pelaz, Carmen; Latorre, Amparo; Moya, Andrés

    2008-01-01

    Background The repeats in toxin (Rtx) are an important pathogenicity factor involved in host cells invasion of Legionella pneumophila and other pathogenic bacteria. Its role in escaping the host immune system and cytotoxic activity is well known. Its repeated motives and modularity make Rtx a multifunctional factor in pathogenicity. Results The comparative analysis of rtx gene among 6 strains of L. pneumophila showed modularity in their structures. Among compared genomes, the N-terminal region of the protein presents highly dissimilar repeats with functionally similar domains. On the contrary, the C-terminal region is maintained with a fashionable modular configuration, which gives support to its proposed role in adhesion and pore formation. Despite the variability of rtx among the considered strains, the flanking genes are maintained in synteny and similarity. Conclusion In contrast to the extracellular bacteria Vibrio cholerae, in which the rtx gene is highly conserved and flanking genes have lost synteny and similarity, the gene region coding for the Rtx toxin in the intracellular pathogen L. pneumophila shows a rapid evolution. Changes in the rtx could play a role in pathogenicity. The interplay of the Rtx toxin with host membranes might lead to the evolution of new variants that are able to escape host cell defences. PMID:18194518

  2. Modular assembly of thick multifunctional cardiac patches

    PubMed Central

    Fleischer, Sharon; Shapira, Assaf; Feiner, Ron; Dvir, Tal

    2017-01-01

    In cardiac tissue engineering cells are seeded within porous biomaterial scaffolds to create functional cardiac patches. Here, we report on a bottom-up approach to assemble a modular tissue consisting of multiple layers with distinct structures and functions. Albumin electrospun fiber scaffolds were laser-patterned to create microgrooves for engineering aligned cardiac tissues exhibiting anisotropic electrical signal propagation. Microchannels were patterned within the scaffolds and seeded with endothelial cells to form closed lumens. Moreover, cage-like structures were patterned within the scaffolds and accommodated poly(lactic-co-glycolic acid) (PLGA) microparticulate systems that controlled the release of VEGF, which promotes vascularization, or dexamethasone, an anti-inflammatory agent. The structure, morphology, and function of each layer were characterized, and the tissue layers were grown separately in their optimal conditions. Before transplantation the tissue and microparticulate layers were integrated by an ECM-based biological glue to form thick 3D cardiac patches. Finally, the patches were transplanted in rats, and their vascularization was assessed. Because of the simple modularity of this approach, we believe that it could be used in the future to assemble other multicellular, thick, 3D, functional tissues. PMID:28167795

  3. Protein Multifunctionality: Principles and Mechanisms

    PubMed Central

    Zaretsky, Joseph Z.; Wreschner, Daniel H.

    2008-01-01

    In the review, the nature of protein multifunctionality is analyzed. In the first part of the review the principles of structural/functional organization of protein are discussed. In the second part, the main mechanisms involved in development of multiple functions on a single gene product(s) are analyzed. The last part represents a number of examples showing that multifunctionality is a basic feature of biologically active proteins. PMID:21566747

  4. A spectrum of modularity in multi-functional gene circuits.

    PubMed

    Jiménez, Alba; Cotterell, James; Munteanu, Andreea; Sharpe, James

    2017-04-27

    A major challenge in systems biology is to understand the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi-functional circuits contain modules which reflect the different functions? Here, we computationally survey a range of bi-functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit. Our analysis reveals two distinct classes: hybrid circuits which overlay two simpler mono-functional sub-circuits within their circuitry, and emergent circuits, which do not. In this second class, the bi-functionality emerges from more complex designs which are not fully decomposable into distinct modules and are consequently less intuitive to predict or understand. These non-intuitive emergent circuits are just as robust as their hybrid counterparts, and we therefore suggest that the common bias toward studying modular systems may hinder our understanding of real biological circuits. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

  5. Insect transferrins: multifunctional proteins.

    PubMed

    Geiser, Dawn L; Winzerling, Joy J

    2012-03-01

    Many studies have been done evaluating transferrin in insects. Genomic analyses indicate that insects could have more than one transferrin. However, the most commonly studied insect transferrin, Tsf1, shows greatest homology to mammalian blood transferrin. Aspects of insect transferrin structure compared to mammalian transferrin and the roles transferrin serves in insects are discussed in this review. Insect transferrin can have one or two lobes, and can bind iron in one or both. The iron binding ligands identified for the lobes of mammalian blood transferrin are generally conserved in the lobes of insect transferrins that have an iron binding site. Available information supports that the form of dietary iron consumed influences the regulation of insect transferrin. Although message is expressed in several tissues in many insects, fat body is the likely source of hemolymph transferrin. Insect transferrin is a vitellogenic protein that is down-regulated by Juvenile Hormone. It serves a role in transporting iron to eggs in some insects, and transferrin found in eggs appears to be endowed from the female. In addition to the roles of transferrin in iron delivery, this protein also functions to reduce oxidative stress and to enhance survival of infection. Future studies in Tsf1 as well as the other insect transferrins that bind iron are warranted because of the roles of transferrin in preventing oxidative stress, enhancing survival to infections and delivering iron to eggs for development. This article is part of a Special Issue entitled Transferrins: Molecular mechanisms of iron transport and disorders. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Can the Modular Engineer Battalion Headquarters Be Multifunctional?

    DTIC Science & Technology

    2009-08-01

    modular combat companies—are both located at Fort Leonard Wood, Mis- souri , under the 4th Maneuver Enhancement Brigade. In order to enable the...University and a master’s from the University of Missouri–Rolla (now Mis- souri University of Science and Technology). May-August 200970 Engineer Engineers clear and grub a road during construction operations.

  7. The Coronavirus Nucleocapsid Is a Multifunctional Protein

    PubMed Central

    McBride, Ruth; van Zyl, Marjorie; Fielding, Burtram C.

    2014-01-01

    The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. Recent studies have confirmed that N is a multifunctional protein. The aim of this review is to highlight the properties and functions of the N protein, with specific reference to (i) the topology; (ii) the intracellular localization and (iii) the functions of the protein. PMID:25105276

  8. The Modular Structure of Protein Networks

    NASA Astrophysics Data System (ADS)

    Rozenfeld, Hernán D.; Rybski, Diego; Havlin, Shlomo; Makse, Hernán A.

    2008-03-01

    The evolution of the human protein homology network (H-PHN) has led to a complex network that exhibits a surprisingly high level of modularity. Topologically, the H-PHN presents well connected groups (conformed by proteins of similar aminoacid structure) and weak connectivities between the groups. Here, we perform an empirical study of the H-PHN to characterize the degree of modularity in terms of scale-invariant laws using recently introduced box covering algorithms. We find that the exponent that determines the scale-invariance of the modularity is unexpectedly higher than the box dimension of the network. In addition, we perform a percolation analysis that gives insight into the evolutionary process that led to the modular organization and dynamics of the present H-PHN.

  9. Multifunctional Microtubule-Associated Proteins in Plants

    PubMed Central

    Krtková, Jana; Benáková, Martina; Schwarzerová, Kateřina

    2016-01-01

    Microtubules (MTs) are involved in key processes in plant cells, including cell division, growth and development. MT-interacting proteins modulate MT dynamics and organization, mediating functional and structural interaction of MTs with other cell structures. In addition to conventional microtubule-associated proteins (MAPs) in plants, there are many other MT-binding proteins whose primary function is not related to the regulation of MTs. This review focuses on enzymes, chaperones, or proteins primarily involved in other processes that also bind to MTs. The MT-binding activity of these multifunctional MAPs is often performed only under specific environmental or physiological conditions, or they bind to MTs only as components of a larger MT-binding protein complex. The involvement of multifunctional MAPs in these interactions may underlie physiological and morphogenetic events, e.g., under specific environmental or developmental conditions. Uncovering MT-binding activity of these proteins, although challenging, may contribute to understanding of the novel functions of the MT cytoskeleton in plant biological processes. PMID:27148302

  10. Modular protein switches derived from antibody mimetic proteins

    PubMed Central

    Nicholes, N.; Date, A.; Beaujean, P.; Hauk, P.; Kanwar, M.; Ostermeier, M.

    2016-01-01

    Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. PMID:26637825

  11. Modular protein switches derived from antibody mimetic proteins.

    PubMed

    Nicholes, N; Date, A; Beaujean, P; Hauk, P; Kanwar, M; Ostermeier, M

    2016-02-01

    Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Modularity in protein structures: study on all-alpha proteins.

    PubMed

    Khan, Taushif; Ghosh, Indira

    2015-01-01

    Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

  13. Linker design for the modular assembly of multifunctional and targeted platinum(ii)-containing anticancer agents.

    PubMed

    Ding, S; Bierbach, U

    2016-08-16

    A versatile and efficient modular synthetic platform was developed for assembling multifunctional conjugates and targeted forms of platinum-(benz)acridines, a class of highly cytotoxic DNA-targeted hybrid agents. The synthetic strategy involved amide coupling between succinyl ester-modified platinum compounds (P1, P2) and a set of 11 biologically relevant primary and secondary amines (N1-N11). To demonstrate the feasibility and versatility of the approach, a structurally and functionally diverse range of amines was introduced. These include biologically active molecules, such as rucaparib (a PARP inhibitor), E/Z-endoxifen (an estrogen receptor antagonist), and a quinazoline-based tyrosine kinase inhibitor. Micro-scale reactions in Eppendorf tubes or on 96-well plates were used to screen for optimal coupling conditions in DMF solution with carbodiimide-, uronium-, and phosphonium-based compounds, as well as other common coupling reagents. Reactions with the phosphonium-based coupling reagent PyBOP produced the highest yields and gave the cleanest conversions. Furthermore, it was demonstrated that the chemistry can also be performed in aqueous media and is amenable to parallel synthesis based on multiple consecutive reactions in DMF in a "one-tube" format. In-line LC-MS was used to assess the stability of the conjugates in physiologically relevant buffers. Hydrolysis of the conjugates occurs at the ester moiety and is facilitated by the aquated metal moiety under low-chloride ion conditions. The rate of ester cleavage greatly depends on the nature of the amine component. Potential applications of the linker technology are discussed.

  14. Modularity in the evolution of yeast protein interaction network

    PubMed Central

    Ogishima, Soichi; Tanaka, Hiroshi; Nakaya, Jun

    2015-01-01

    Protein interaction networks are known to exhibit remarkable structures: scale-free and small-world and modular structures. To explain the evolutionary processes of protein interaction networks possessing scale-free and small-world structures, preferential attachment and duplication-divergence models have been proposed as mathematical models. Protein interaction networks are also known to exhibit another remarkable structural characteristic, modular structure. How the protein interaction networks became to exhibit modularity in their evolution? Here, we propose a hypothesis of modularity in the evolution of yeast protein interaction network based on molecular evolutionary evidence. We assigned yeast proteins into six evolutionary ages by constructing a phylogenetic profile. We found that all the almost half of hub proteins are evolutionarily new. Examining the evolutionary processes of protein complexes, functional modules and topological modules, we also found that member proteins of these modules tend to appear in one or two evolutionary ages. Moreover, proteins in protein complexes and topological modules show significantly low evolutionary rates than those not in these modules. Our results suggest a hypothesis of modularity in the evolution of yeast protein interaction network as systems evolution. PMID:25914446

  15. RNA-Binding Proteins in Trichomonas vaginalis: Atypical Multifunctional Proteins.

    PubMed

    Figueroa-Angulo, Elisa E; Calla-Choque, Jaeson S; Mancilla-Olea, Maria Inocente; Arroyo, Rossana

    2015-11-26

    Iron homeostasis is highly regulated in vertebrates through a regulatory system mediated by RNA-protein interactions between the iron regulatory proteins (IRPs) that interact with an iron responsive element (IRE) located in certain mRNAs, dubbed the IRE-IRP regulatory system. Trichomonas vaginalis, the causal agent of trichomoniasis, presents high iron dependency to regulate its growth, metabolism, and virulence properties. Although T. vaginalis lacks IRPs or proteins with aconitase activity, possesses gene expression mechanisms of iron regulation at the transcriptional and posttranscriptional levels. However, only one gene with iron regulation at the transcriptional level has been described. Recently, our research group described an iron posttranscriptional regulatory mechanism in the T. vaginalis tvcp4 and tvcp12 cysteine proteinase mRNAs. The tvcp4 and tvcp12 mRNAs have a stem-loop structure in the 5'-coding region or in the 3'-UTR, respectively that interacts with T. vaginalis multifunctional proteins HSP70, α-Actinin, and Actin under iron starvation condition, causing translation inhibition or mRNA stabilization similar to the previously characterized IRE-IRP system in eukaryotes. Herein, we summarize recent progress and shed some light on atypical RNA-binding proteins that may participate in the iron posttranscriptional regulation in T. vaginalis.

  16. Domain organizations of modular extracellular matrix proteins and their evolution.

    PubMed

    Engel, J

    1996-11-01

    Multidomain proteins which are composed of modular units are a rather recent invention of evolution. Domains are defined as autonomously folding regions of a protein, and many of them are similar in sequence and structure, indicating common ancestry. Their modular nature is emphasized by frequent repetitions in identical or in different proteins and by a large number of different combinations with other domains. The extracellular matrix is perhaps the largest biological system composed of modular mosaic proteins, and its astonishing complexity and diversity are based on them. A cluster of minireviews on modular proteins is being published in Matrix Biology. These deal with the evolution of modular proteins, the three-dimensional structure of domains and the ways in which these interact in a multidomain protein. They discuss structure-function relationships in calcium binding domains, collagen helices, alpha-helical coiled-coil domains and C-lectins. The present minireview is focused on some general aspects and serves as an introduction to the cluster.

  17. Multifunctional ECM proteins in bone and teeth.

    PubMed

    Ravindran, Sriram; George, Anne

    2014-07-15

    The extracellular matrix (ECM) of all tissues and organs is a highly organized and complex structure unique to the specific organ type. The ECM contains structural and functional proteins that define cellular function, organization, behavior and ultimately organ characteristics and function. The ECM was initially thought to contain only a specific set of secretory proteins. However, our group and several other groups have shown that the ECM contains functional proteins that have been previously defined as solely intracellular. In the present review, we have focused on the ECM of mineralized tissues namely bone and dentin. We provide here, a brief review of some non-classical ECM proteins that have been shown to possess both intra and extracellular roles in the formation of these mineralized matrices.

  18. Multifunctional clickable and protein-repellent magnetic silica nanoparticles

    NASA Astrophysics Data System (ADS)

    Estupiñán, Diego; Bannwarth, Markus B.; Mylon, Steven E.; Landfester, Katharina; Muñoz-Espí, Rafael; Crespy, Daniel

    2016-01-01

    Silica nanoparticles are versatile materials whose physicochemical surface properties can be precisely adjusted. Because it is possible to combine several functionalities in a single carrier, silica-based materials are excellent candidates for biomedical applications. However, the functionality of the nanoparticles can get lost upon exposure to biological media due to uncontrolled biomolecule adsorption. Therefore, it is important to develop strategies that reduce non-specific protein-particle interactions without losing the introduced surface functionality. Herein, organosilane chemistry is employed to produce magnetic silica nanoparticles bearing differing amounts of amino and alkene functional groups on their surface as orthogonally addressable chemical functionalities. Simultaneously, a short-chain zwitterion is added to decrease the non-specific adsorption of biomolecules on the nanoparticles surface. The multifunctional particles display reduced protein adsorption after incubation in undiluted fetal bovine serum as well as in single protein solutions (serum albumin and lysozyme). Besides, the particles retain their capacity to selectively react with biomolecules. Thus, they can be covalently bio-functionalized with an antibody by means of orthogonal click reactions. These features make the described multifunctional silica nanoparticles a promising system for the study of surface interactions with biomolecules, targeting, and bio-sensing.Silica nanoparticles are versatile materials whose physicochemical surface properties can be precisely adjusted. Because it is possible to combine several functionalities in a single carrier, silica-based materials are excellent candidates for biomedical applications. However, the functionality of the nanoparticles can get lost upon exposure to biological media due to uncontrolled biomolecule adsorption. Therefore, it is important to develop strategies that reduce non-specific protein-particle interactions without losing the

  19. The application of modular protein domains in proteomics

    PubMed Central

    Jadwin, Joshua A.; Ogiue-Ikeda, Mari; Machida, Kazuya

    2012-01-01

    The ability of modular protein domains to independently fold and bind short peptide ligands both in vivo and in vitro has allowed a significant number of protein-protein interaction studies to take advantage of them as affinity and detection reagents. Here, we refer to modular domain based proteomics as “domainomics” to draw attention to the potential of using domains and their motifs as tools in proteomics. In this review we describe core concepts of domainomics, established and emerging technologies, and recent studies by functional category. Accumulation of domain-motif binding data should ultimately provide the foundation for domain-specific interactomes, which will likely reveal the underlying substructure of protein networks as well as the selectivity and plasticity of signal transduction. PMID:22710164

  20. Dps biomineralizing proteins: multifunctional architects of nature.

    PubMed

    Zeth, Kornelius

    2012-08-01

    Dps proteins are the structural relatives of bacterioferritins and ferritins ubiquitously present in the bacterial and archaeal kingdoms. The ball-shaped enzymes play important roles in the detoxification of ROS (reactive oxygen species), in iron scavenging to prevent Fenton reactions and in the mechanical protection of DNA. Detoxification of ROS and iron chaperoning represent the most archetypical functions of dodecameric Dps enzymes. Recent crystallographic studies of these dodecameric complexes have unravelled species-dependent mechanisms of iron uptake into the hollow spheres. Subsequent functions in iron oxidation at ferroxidase centres are highly conserved among bacteria. Final nucleation of iron as iron oxide nanoparticles has been demonstrated to originate at acidic residues located on the inner surface. Some Dps enzymes are also implicated in newly observed catalytic functions related to the formation of molecules playing roles in bacterium-host cell communication. Most recently, Dps complexes are attracting attention in semiconductor science as biomimetic tools for the technical production of the smallest metal-based quantum nanodots used in nanotechnological approaches, such as memory storage or solar cell development.

  1. Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages

    PubMed Central

    del Sol, Antonio; Araúzo-Bravo, Marcos J; Amoros, Dolors; Nussinov, Ruth

    2007-01-01

    Background Allosteric communications are vital for cellular signaling. Here we explore a relationship between protein architectural organization and shortcuts in signaling pathways. Results We show that protein domains consist of modules interconnected by residues that mediate signaling through the shortest pathways. These mediating residues tend to be located at the inter-modular boundaries, which are more rigid and display a larger number of long-range interactions than intra-modular regions. The inter-modular boundaries contain most of the residues centrally conserved in the protein fold, which may be crucial for information transfer between amino acids. Our approach to modular decomposition relies on a representation of protein structures as residue-interacting networks, and removal of the most central residue contacts, which are assumed to be crucial for allosteric communications. The modular decomposition of 100 multi-domain protein structures indicates that modules constitute the building blocks of domains. The analysis of 13 allosteric proteins revealed that modules characterize experimentally identified functional regions. Based on the study of an additional functionally annotated dataset of 115 proteins, we propose that high-modularity modules include functional sites and are the basic functional units. We provide examples (the Gαs subunit and P450 cytochromes) to illustrate that the modular architecture of active sites is linked to their functional specialization. Conclusion Our method decomposes protein structures into modules, allowing the study of signal transmission between functional sites. A modular configuration might be advantageous: it allows signaling proteins to expand their regulatory linkages and may elicit a broader range of control mechanisms either via modular combinations or through modulation of inter-modular linkages. PMID:17531094

  2. Multifunctional clickable and protein-repellent magnetic silica nanoparticles.

    PubMed

    Estupiñán, Diego; Bannwarth, Markus B; Mylon, Steven E; Landfester, Katharina; Muñoz-Espí, Rafael; Crespy, Daniel

    2016-02-07

    Silica nanoparticles are versatile materials whose physicochemical surface properties can be precisely adjusted. Because it is possible to combine several functionalities in a single carrier, silica-based materials are excellent candidates for biomedical applications. However, the functionality of the nanoparticles can get lost upon exposure to biological media due to uncontrolled biomolecule adsorption. Therefore, it is important to develop strategies that reduce non-specific protein-particle interactions without losing the introduced surface functionality. Herein, organosilane chemistry is employed to produce magnetic silica nanoparticles bearing differing amounts of amino and alkene functional groups on their surface as orthogonally addressable chemical functionalities. Simultaneously, a short-chain zwitterion is added to decrease the non-specific adsorption of biomolecules on the nanoparticles surface. The multifunctional particles display reduced protein adsorption after incubation in undiluted fetal bovine serum as well as in single protein solutions (serum albumin and lysozyme). Besides, the particles retain their capacity to selectively react with biomolecules. Thus, they can be covalently bio-functionalized with an antibody by means of orthogonal click reactions. These features make the described multifunctional silica nanoparticles a promising system for the study of surface interactions with biomolecules, targeting, and bio-sensing.

  3. Cooperativity and modularity in protein folding

    PubMed Central

    Sasai, Masaki; Chikenji, George; Terada, Tomoki P.

    2016-01-01

    A simple statistical mechanical model proposed by Wako and Saitô has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Muñoz and Eaton and has since been referred to as the Wako-Saitô-Muñoz-Eaton (WSME) model. The success of the WSME model in explaining the folding of many proteins has verified the hypothesis that the folding is dominated by native interactions, which makes the energy landscape globally biased toward native conformation. Using the WSME and other related models, Saitô emphasized the importance of the hierarchical pathway in protein folding; folding starts with the creation of contiguous segments having a native-like configuration and proceeds as growth and coalescence of these segments. The Φ-values calculated for barnase with the WSME model suggested that segments contributing to the folding nucleus are similar to the structural modules defined by the pattern of native atomic contacts. The WSME model was extended to explain folding of multi-domain proteins having a complex topology, which opened the way to comprehensively understanding the folding process of multi-domain proteins. The WSME model was also extended to describe allosteric transitions, indicating that the allosteric structural movement does not occur as a deterministic sequential change between two conformations but as a stochastic diffusive motion over the dynamically changing energy landscape. Statistical mechanical viewpoint on folding, as highlighted by the WSME model, has been renovated in the context of modern methods and ideas, and will continue to provide insights on equilibrium and dynamical features of proteins. PMID:28409080

  4. Modular enzymatically crosslinked protein polymer hydrogels for in situ gelation

    PubMed Central

    Davis, Nicolynn E.; Ding, Sheng; Forster, Ryan; Pinkas, Daniel M.; Barron, Annelise E.

    2012-01-01

    Biomaterials that mimic the extracellular matrix in both modularity and crosslinking chemistry have the potential to recapitulate the instructive signals that ultimately control cell fate. Toward this goal, modular protein polymer-based hydrogels were created through genetic engineering and enzymatic crosslinking. Animal derived tissue transglutaminase (tTG) and recombinant human transglutaminase (hTG) enzymes were used for coupling two classes of protein polymers containing either lysine or glutamine, which have the recognition substrates for enzymatic crosslinking, evenly spaced along the protein backbone. Utilizing tTG under physiological conditions, crosslinking occurred within two minutes, as determined by particle tracking microrheology. Hydrogel composition impacted the elastic storage modulus of the gel over 4-fold and also influenced microstructure and degree of swelling, but did not appreciably effect degradation by plasmin. Mouse 3T3 and primary human fibroblasts were cultured in both 2- and 3-dimensions without a decrease in cell viability and displayed spreading in 2D. The properties of these gels, which are controlled through the specific nature of the protein polymer precursors, render these gels valuable for in situ therapies. Furthermore, the modular hydrogel composition allows tailoring of mechanical and physical properties for specific tissue engineering applications. PMID:20609472

  5. Mining the modular structure of protein interaction networks.

    PubMed

    Berenstein, Ariel José; Piñero, Janet; Furlong, Laura Inés; Chernomoretz, Ariel

    2015-01-01

    Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis. We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera's cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns. As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge.

  6. Mining the Modular Structure of Protein Interaction Networks

    PubMed Central

    Furlong, Laura Inés; Chernomoretz, Ariel

    2015-01-01

    Background Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis. Methodology We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera’s cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns. Results As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge. PMID:25856434

  7. Modular microfluidics for point-of-care protein purifications

    SciTech Connect

    Millet, L. J.; Lucheon, J. D.; Standaert, R. F.; Retterer, S. T.; Doktycz, M. J.

    2015-01-01

    Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured to suit a variety of fluidic operations or biochemical processes. In conclusion, we demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.

  8. A Binding Model and Similarity for Flexible Modular Proteins

    NASA Astrophysics Data System (ADS)

    Máté, Gabriell; Feinauer, Christoph J.; Hofmann, Andreas; Goldt, Sebastian; Liu, Lei; Heermann, Dieter W.

    2013-03-01

    Modular proteins are one of the most commonly found disordered protein motifs. An example is CTCF, a protein that has been named the master waver of the genome i.e., the organizer of the 3D structure of the chromosomes. Using NMR and numerical simulations, much progress has been made in understanding their various functions and ways of binding. Modular proteins are often composed of protein modules interconnected by flexible linkers. They can be imagined as ``beads on a string.'' We argue that when the number of beads is small, these structures behave like a self avoiding random walk. Nevertheless, when binding to a target, linkers can fold in more ordered and stable states. At the same time, folding can influence functional roles. We show that the flexibility of the linkers can boost binding affinity. As a result of flexibility, the conformations of these proteins before and after binding are different. So this implies that generic binding site prediction methods may fail. To deal with this we introduce a new methodology to characterize and compare these flexible structures. Employing topological concepts we propose a method which intrinsically fuses topology and geometry. GM gratefully acknowledges support from the HGS-MathComp and the RTG 1653.

  9. Stimuli responsive smart-gels realized via modular protein design

    PubMed Central

    Grove, Tijana Z.; Osuji, Chinedum O.; Forster, Jason D.; Dufresne, Eric R.; Regan, Lynne

    2012-01-01

    Smart-gels have a variety of applications including tissue engineering and controlled drug delivery. Here we present a modular, bottom-up approach that permits the creation of protein-based smart-gels with encoded morphology, functionality, and responsiveness to external stimuli. The properties of these gels are encoded by the proteins from which they are synthesized. In particular, the strength and density of the network of intermolecular cross-links are specified by the interactions of the gel’s constituent protein modules with their cognate peptide ligands. Thus, these gels exhibit stimuli-responsive assembly and disassembly, dissolving (or gelling) under conditions that weaken (or strengthen) the protein-peptide interaction. We further demonstrate that such gels can encapsulate and release both proteins and small molecules and that their rheological properties are well suited for biomedical applications. PMID:20860358

  10. Multifunctional nanoparticles for protein detections in thin channels.

    PubMed

    Tsai, Hweiyan; Lin, Weimin; Chuang, Mingchieh; Lu, Yishuan; Fuh, C Bor

    2017-04-15

    This paper presents a method for simultaneous detection of two proteins by using multifunctional nanoparticles with a magnetic immunoassay in thin channels. Biofunctional magnetic graphene quantum dots (GQDs) combined with two biofunctional quantum dots (QDs) were used for simultaneously detecting two proteins. Magnetic GQDs enabled selective and quantitative nanoparticle deposition with blue emission. Biofunctional QDs confirmed the two protein detections with orange and green emissions. We used two model biomarkers [alpha-fetoprotein (AFP) and cancer antigen 125 (CA125)] to demonstrate the feasibility of the proposed method. The detection limits (0.06pg/mL AFP and 0.001U/mL CA125) and linear ranges (0.2pg/mL-0.68ng/mL AFP and 0.003-25U/mL CA125) of this method are the same as those of single protein detection within experimental errors. These detection limits are substantially lower and the linear ranges are considerably wider than those of enzyme-linked immunosorbent assay (ELISA) and other immunoassay methods. The differences between the proposed method and an ELISA method in AFP and CA125 measurements of serum samples were less than 12%. The proposed method demonstrates favorable detection of biomarkers with advantages of speed, sensitivity, selectivity, and throughput.

  11. Elongation factor Tu is a multifunctional and processed moonlighting protein.

    PubMed

    Widjaja, Michael; Harvey, Kate Louise; Hagemann, Lisa; Berry, Iain James; Jarocki, Veronica Maria; Raymond, Benjamin Bernard Armando; Tacchi, Jessica Leigh; Gründel, Anne; Steele, Joel Ricky; Padula, Matthew Paul; Charles, Ian George; Dumke, Roger; Djordjevic, Steven Philip

    2017-09-11

    Many bacterial moonlighting proteins were originally described in medically, agriculturally, and commercially important members of the low G + C Firmicutes. We show Elongation factor Tu (Ef-Tu) moonlights on the surface of the human pathogens Staphylococcus aureus (SaEf-Tu) and Mycoplasma pneumoniae (MpnEf-Tu), and the porcine pathogen Mycoplasma hyopneumoniae (MhpEf-Tu). Ef-Tu is also a target of multiple processing events on the cell surface and these were characterised using an N-terminomics pipeline. Recombinant MpnEf-Tu bound strongly to a diverse range of host molecules, and when bound to plasminogen, was able to convert plasminogen to plasmin in the presence of plasminogen activators. Fragments of Ef-Tu retain binding capabilities to host proteins. Bioinformatics and structural modelling studies indicate that the accumulation of positively charged amino acids in short linear motifs (SLiMs), and protein processing promote multifunctional behaviour. Codon bias engendered by an A + T rich genome may influence how positively-charged residues accumulate in SLiMs.

  12. The modular organization of domain structures: insights into protein-protein binding.

    PubMed

    del Sol, Antonio; Carbonell, Pablo

    2007-12-01

    Domains are the building blocks of proteins and play a crucial role in protein-protein interactions. Here, we propose a new approach for the analysis and prediction of domain-domain interfaces. Our method, which relies on the representation of domains as residue-interacting networks, finds an optimal decomposition of domain structures into modules. The resulting modules comprise highly cooperative residues, which exhibit few connections with other modules. We found that non-overlapping binding sites in a domain, involved in different domain-domain interactions, are generally contained in different modules. This observation indicates that our modular decomposition is able to separate protein domains into regions with specialized functions. Our results show that modules with high modularity values identify binding site regions, demonstrating the predictive character of modularity. Furthermore, the combination of modularity with other characteristics, such as sequence conservation or surface patches, was found to improve our predictions. In an attempt to give a physical interpretation to the modular architecture of domains, we analyzed in detail six examples of protein domains with available experimental binding data. The modular configuration of the TEM1-beta-lactamase binding site illustrates the energetic independence of hotspots located in different modules and the cooperativity of those sited within the same modules. The energetic and structural cooperativity between intramodular residues is also clearly shown in the example of the chymotrypsin inhibitor, where non-binding site residues have a synergistic effect on binding. Interestingly, the binding site of the T cell receptor beta chain variable domain 2.1 is contained in one module, which includes structurally distant hot regions displaying positive cooperativity. These findings support the idea that modules possess certain functional and energetic independence. A modular organization of binding sites confers

  13. Protein disulfide isomerase a multifunctional protein with multiple physiological roles

    NASA Astrophysics Data System (ADS)

    Ali Khan, Hyder; Mutus, Bulent

    2014-08-01

    Protein disulfide isomerase (PDI), is a member of the thioredoxin superfamily of redox proteins. PDI has three catalytic activities including, thiol-disulfide oxireductase, disulfide isomerase and redox-dependent chaperone. Originally, PDI was identified in the lumen of the endoplasmic reticulum and subsequently detected at additional locations, such as cell surfaces and the cytosol. This review will provide an overview of the recent advances in relating the structural features of PDI to its multiple catalytic roles as well as its physiological and pathophysiological functions related to redox regulation and protein folding.

  14. Modular microfluidics for point-of-care protein purifications

    DOE PAGES

    Millet, L. J.; Lucheon, J. D.; Standaert, R. F.; ...

    2015-01-01

    Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured tomore » suit a variety of fluidic operations or biochemical processes. In conclusion, we demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.« less

  15. Calcineurin homologous protein: a multifunctional Ca2+-binding protein family

    PubMed Central

    Vadnagara, Komal; Moe, Orson W.; Babich, Victor

    2012-01-01

    The calcineurin homologous protein (CHP) belongs to an evolutionarily conserved Ca2+-binding protein subfamily. The CHP subfamily is composed of CHP1, CHP2, and CHP3, which in vertebrates share significant homology at the protein level with each other and between other Ca2+-binding proteins. The CHP structure consists of two globular domains containing from one to four EF-hand structural motifs (calcium-binding regions composed of two helixes, E and F, joined by a loop), the myristoylation, and nuclear export signals. These structural features are essential for the function of the three members of the CHP subfamily. Indeed, CHP1–CHP3 have multiple and diverse essential functions, ranging from the regulation of the plasma membrane Na+/H+ exchanger protein function, to carrier vesicle trafficking and gene transcription. The diverse functions attributed to the CHP subfamily rendered an understanding of its action highly complex and often controversial. This review provides a comprehensive and organized examination of the properties and physiological roles of the CHP subfamily with a view to revealing a link between CHP diverse functions. PMID:22189947

  16. The generation of zinc finger proteins by modular assembly

    PubMed Central

    Bhakta, Mital; Segal, David J.

    2015-01-01

    The modular assembly (MA) method of generating engineered zinc finger proteins (ZFPs) was the first practical method for creating custom DNA-binding proteins. As such, MA has enabled a vast exploration of sequence-specific methods and reagents, ushering in the modern era of zinc finger-based applications that are described in this volume. The first zinc finger nuclease to cleave an endogenous site was created using MA, as was the first artificial transcription factor to enter phase II clinical trials. In recent years, other excellent methods have been developed that improved the affinity and specificity of the engineered ZFPs. However, MA is still used widely for many applications. This chapter will describe methods and give guidance for the creation of ZFPs using MA. Such ZFPs might be useful as starting materials to perform other methods described in this volume. Here, we also describe a single-strand annealing recombination assay for the initial testing of zinc finger nucleases. PMID:20680825

  17. Modular arrangement of proteins as inferred from analysis of homology.

    PubMed Central

    Sonnhammer, E. L.; Kahn, D.

    1994-01-01

    The structure of many proteins consists of a combination of discrete modules that have been shuffled during evolution. Such modules can frequently be recognized from the analysis of homology. Here we present a systematic analysis of the modular organization of all sequenced proteins. To achieve this we have developed an automatic method to identify protein domains from sequence comparisons. Homologous domains can then be clustered into consistent families. The method was applied to all 21,098 nonfragment protein sequences in SWISS-PROT 21.0, which was automatically reorganized into a comprehensive protein domain database, ProDom. We have constructed multiple sequence alignments for each domain family in ProDom, from which consensus sequences were generated. These nonreduntant domain consensuses are useful for fast homology searches. Domain organization in ProDom is exemplified for proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PEP:PTS) and for bacterial 2-component regulators. We provide 2 examples of previously unrecognized domain arrangements discovered with the help of ProDom. PMID:8019419

  18. Multifunctional cellulolytic auxiliary activity protein HcAA10-2 from Hahella chejuensis enhances enzymatic hydrolysis of crystalline cellulose.

    PubMed

    Ghatge, Sunil S; Telke, Amar A; Waghmode, Tatoba R; Lee, Yuno; Lee, Keun-Woo; Oh, Doo-Byoung; Shin, Hyun-Dong; Kim, Seon-Won

    2015-04-01

    The modular auxiliary activity (AA) family of proteins is believed to cause amorphogenesis in addition to oxidative cleavage of crystalline cellulose although the supporting evidence is limited. HcAA10-2 is a modular AA10 family protein (58 kDa) composed of a AA10 module and a family two carbohydrate binding module (CBM2), joined by a long stretch of 222 amino acids of unknown function. The protein was expressed in Escherichia coli and purified to homogeneity. Scanning electron microscopy and X-ray diffraction analysis of Avicel treated with HcAA10-2 provided evidence for the disruption of the cellulose microfibrils ("amorphogenesis") and reduction of the crystallinity index, resulting in a twofold increase of cellulase adsorption on the polysaccharide surface. HcAA10-2 exhibited weak endoglucanase-like activity toward soluble cellulose and cello-oligosaccharides with an optimum at pH 6.5 and 45 °C. HcAA10-2 catalyzed oxidative cleavage of crystalline cellulose released native and oxidized cello-oligosaccharides in the presence of copper and an electron donor such as ascorbic acid. Multiple sequence alignment indicated that His1, His109, and Phe197 in the AA10 module formed the conserved copper-binding site. The reducing sugar released from Avicel by the endoglucanase Cel5 and Celluclast accompanying HcAA10-2 was increased by four- and sixfold, respectively. Moreover, HcAA10-2 and Celluclast acted synergistically on pretreated wheat straw biomass resulting in a threefold increase in reducing sugar than Celluclast alone. Taken together, these results suggest that HcAA10-2 is a novel multifunctional modular AA10 protein possessing amorphogenesis, weak endoglucanase, and oxidative cleavage activities useful for efficient degradation of crystalline cellulose.

  19. Modular synthetic inverters from zinc finger proteins and small RNAs

    DOE PAGES

    Hsia, Justin; Holtz, William J.; Maharbiz, Michel M.; ...

    2016-02-17

    Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosenmore » parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.« less

  20. Modular synthetic inverters from zinc finger proteins and small RNAs

    SciTech Connect

    Hsia, Justin; Holtz, William J.; Maharbiz, Michel M.; Arcak, Murat; Keasling, Jay D.; Rao, Christopher V.

    2016-02-17

    Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.

  1. Protein linguistics - a grammar for modular protein assembly?

    PubMed

    Gimona, Mario

    2006-01-01

    The correspondence between biology and linguistics at the level of sequence and lexical inventories, and of structure and syntax, has fuelled attempts to describe genome structure by the rules of formal linguistics. But how can we define protein linguistic rules? And how could compositional semantics improve our understanding of protein organization and functional plasticity?

  2. Modularity of a carbon-fixing protein organelle.

    PubMed

    Bonacci, Walter; Teng, Poh K; Afonso, Bruno; Niederholtmeyer, Henrike; Grob, Patricia; Silver, Pamela A; Savage, David F

    2012-01-10

    Bacterial microcompartments are proteinaceous complexes that catalyze metabolic pathways in a manner reminiscent of organelles. Although microcompartment structure is well understood, much less is known about their assembly and function in vivo. We show here that carboxysomes, CO(2)-fixing microcompartments encoded by 10 genes, can be heterologously produced in Escherichia coli. Expression of carboxysomes in E. coli resulted in the production of icosahedral complexes similar to those from the native host. In vivo, the complexes were capable of both assembling with carboxysomal proteins and fixing CO(2). Characterization of purified synthetic carboxysomes indicated that they were well formed in structure, contained the expected molecular components, and were capable of fixing CO(2) in vitro. In addition, we verify association of the postulated pore-forming protein CsoS1D with the carboxysome and show how it may modulate function. We have developed a genetic system capable of producing modular carbon-fixing microcompartments in a heterologous host. In doing so, we lay the groundwork for understanding these elaborate protein complexes and for the synthetic biological engineering of self-assembling molecular structures.

  3. Synthetic Modularity of Protein-Metal-Organic Frameworks.

    PubMed

    Bailey, Jake B; Zhang, Ling; Chiong, Jerika A; Ahn, Sunhyung; Tezcan, F Akif

    2017-06-21

    Previously, we adopted the construction principles of metal-organic frameworks (MOFs) to design a 3D crystalline protein lattice in which pseudospherical ferritin nodes decorated on their C3 symmetric vertices with Zn coordination sites were connected via a ditopic benzene-dihydroxamate linker. In this work, we have systematically varied both the metal ions presented at the vertices of the ferritin nodes (Zn(II), Ni(II), and Co(II)) and the synthetic dihydroxamate linkers, which yielded an expanded library of 15 ferritin-MOFs with the expected body-centered (cubic or tetragonal) lattice arrangements. Crystallographic and small-angle X-ray scattering (SAXS) analyses indicate that lattice symmetries and dimensions of ferritin-MOFs can be dictated by both the metal and linker components. SAXS measurements on bulk crystalline samples reveal that some ferritin-MOFs can adopt multiple lattice conformations, suggesting dynamic behavior. This work establishes that the self-assembly of ferritin-MOFs is highly robust and that the synthetic modularity that underlies the structural diversity of conventional MOFs can also be applied to the self-assembly of protein-based crystalline materials.

  4. Diatom Adhesive Mucilage Contains Distinct Supramolecular Assemblies of a Single Modular Protein

    PubMed Central

    Dugdale, T. M.; Dagastine, R.; Chiovitti, A.; Wetherbee, R.

    2006-01-01

    A previous study used atomic force microscopy saw-tooth retraction curves to characterize the adhesive mucilage pads of the diatom Toxarium undulatum. The major mucilage component consisted of adhesive nanofibers (ANFs) made up of modular proteins arranged into cohesive units, each containing a set number of modular proteins aligned in parallel. This study shows that T. undulatum adhesive mucilage is a biocomposite containing four additional adhesive components, including single modular proteins that are likely to be the structural units from which the ANFs are assembled. Two further distinct supramolecular assemblies were observed to coexist with ANFs (ANFs II and III), along with a continuum of single modular proteins through oligomers made up of varying numbers of modular proteins arranged in parallel. All components of the adhesive biocomposite produce a characteristic force spectrum with the same interpeak distance (35.3 ± 0.3 (mean ± SE) nm), suggesting they are derived from discrete supramolecular assemblies of the same modular protein, but they are distinguishable from one another based on the rupture force, persistence length, and interpeak force measured from their saw-tooth curves. PMID:16443662

  5. Rethinking the capsid proteins of enveloped viruses: multifunctionality from genome packaging to genome transfection.

    PubMed

    Freire, João M; Santos, Nuno C; Veiga, Ana Salomé; Da Poian, Andrea T; Castanho, Miguel A R B

    2015-06-01

    Regardless of the debate on whether there is a place for viruses in the tree of life, it is consensual that they co-evolve with their hosts under the pressure of genome minimization. The abundance of multifunctional viral structural proteins is a consequence of this pressure. The molecular key to multifunctionality is the existence of intrinsically disordered domains together with ordered domains in the same protein. Capsid proteins, the hallmark of viruses, are not exceptions because they have coexisting ordered and disordered domains that are crucial for multifunctionality. It is also frequent to find supercharged proteins (i.e. proteins for which the net charge per unit molecular mass is > +0.75/kDa) among viral capsid proteins. All flaviviruses having annotated proteins in the ExPASy Viralzone database have supercharged capsid proteins. Moreover, cell-penetrating sequences/domains are frequent in viral proteins, even when they are not supercharged. Altogether, the findings strongly suggest that the ability to translocate membranes was acquired, conserved and optimized throughout the evolution of some viral proteins as part of their multifunctionality. The fitness of capsid proteins to translocate membranes carrying genomes was experimentally demonstrated with dengue virus capsid protein. This protein is potentially able to help the fusion process and translocate the RNA genome across the hemifused membrane formed by the viral envelope and the endosomal membrane. In addition, one of the cell-penetrating domains of the capsid protein also has antibacterial activity. This may be reminiscent of parasitic bacteria-bacteria competition for the same host and shed light on the origins of enveloped viruses. © 2015 FEBS.

  6. Design of Modular Protein Tags for Orthogonal Covalent Bond Formation at Specific DNA Sequences.

    PubMed

    Nguyen, Thang Minh; Nakata, Eiji; Saimura, Masayuki; Dinh, Huyen; Morii, Takashi

    2017-06-28

    Simultaneous formation of specific covalent linkages at nucleotides in given DNA sequences demand distinct orthogonal reactivity of DNA modification agents. Such highly specific reactions require well-balanced reactivity and affinity of the DNA modification agents. Conjugation of a sequence-specific DNA binding zinc finger protein and a self-ligating protein tag provides a modular adaptor that expedites formation of a covalent bond between the protein tag and a substrate-modified nucleotide at a specific DNA sequence. The modular adaptor stably locates a protein of interest fused to it at the target position on DNA scaffold in its functional form. Modular adaptors with orthogonal selectivity and fast reaction kinetics to specific DNA sequences enable site-specific location of different protein molecules simultaneously. Three different modular adaptors consisting of zinc finger proteins with distinct DNA sequence specificities and self-ligating protein tags with different substrate specificities achieved orthogonal covalent bond formation at respective sequences on the same DNA scaffold with an overall coassembly yield over 90%. Application of this unique set of orthogonal modular adaptors enabled construction of a cascade reaction of three enzymes from xylose metabolic pathway on DNA scaffold.

  7. Protein cofactor competition regulates the action of a multifunctional RNA helicase in different pathways

    PubMed Central

    Heininger, Annika U.; Hackert, Philipp; Andreou, Alexandra Z.; Boon, Kum-Loong; Memet, Indira; Prior, Mira; Clancy, Anne; Schmidt, Bernhard; Urlaub, Henning; Schleiff, Enrico; Sloan, Katherine E.; Deckers, Markus; Lührmann, Reinhard; Enderlein, Jörg; Klostermeier, Dagmar; Rehling, Peter; Bohnsack, Markus T.

    2016-01-01

    ABSTRACT A rapidly increasing number of RNA helicases are implicated in several distinct cellular processes, however, the modes of regulation of multifunctional RNA helicases and their recruitment to different target complexes have remained unknown. Here, we show that the distribution of the multifunctional DEAH-box RNA helicase Prp43 between its diverse cellular functions can be regulated by the interplay of its G-patch protein cofactors. We identify the orphan G-patch protein Cmg1 (YLR271W) as a novel cofactor of Prp43 and show that it stimulates the RNA binding and ATPase activity of the helicase. Interestingly, Cmg1 localizes to the cytoplasm and to the intermembrane space of mitochondria and its overexpression promotes apoptosis. Furthermore, our data reveal that different G-patch protein cofactors compete for interaction with Prp43. Changes in the expression levels of Prp43-interacting G-patch proteins modulate the cellular localization of Prp43 and G-patch protein overexpression causes accumulation of the helicase in the cytoplasm or nucleoplasm. Overexpression of several G-patch proteins also leads to defects in ribosome biogenesis that are consistent with withdrawal of the helicase from this pathway. Together, these findings suggest that the availability of cofactors and the sequestering of the helicase are means to regulate the activity of multifunctional RNA helicases and their distribution between different cellular processes. PMID:26821976

  8. The Modular Organization of Domain Structures: Insights into Protein–Protein Binding

    PubMed Central

    del Sol, Antonio; Carbonell, Pablo

    2007-01-01

    Domains are the building blocks of proteins and play a crucial role in protein–protein interactions. Here, we propose a new approach for the analysis and prediction of domain–domain interfaces. Our method, which relies on the representation of domains as residue-interacting networks, finds an optimal decomposition of domain structures into modules. The resulting modules comprise highly cooperative residues, which exhibit few connections with other modules. We found that non-overlapping binding sites in a domain, involved in different domain–domain interactions, are generally contained in different modules. This observation indicates that our modular decomposition is able to separate protein domains into regions with specialized functions. Our results show that modules with high modularity values identify binding site regions, demonstrating the predictive character of modularity. Furthermore, the combination of modularity with other characteristics, such as sequence conservation or surface patches, was found to improve our predictions. In an attempt to give a physical interpretation to the modular architecture of domains, we analyzed in detail six examples of protein domains with available experimental binding data. The modular configuration of the TEM1-β-lactamase binding site illustrates the energetic independence of hotspots located in different modules and the cooperativity of those sited within the same modules. The energetic and structural cooperativity between intramodular residues is also clearly shown in the example of the chymotrypsin inhibitor, where non–binding site residues have a synergistic effect on binding. Interestingly, the binding site of the T cell receptor β chain variable domain 2.1 is contained in one module, which includes structurally distant hot regions displaying positive cooperativity. These findings support the idea that modules possess certain functional and energetic independence. A modular organization of binding sites

  9. Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree.

    PubMed

    Moore, Andrew D; Grath, Sonja; Schüler, Andreas; Huylmans, Ann K; Bornberg-Bauer, Erich

    2013-05-01

    Modularity is a hallmark of molecular evolution. Whether considering gene regulation, the components of metabolic pathways or signaling cascades, the ability to reuse autonomous modules in different molecular contexts can expedite evolutionary innovation. Similarly, protein domains are the modules of proteins, and modular domain rearrangements can create diversity with seemingly few operations in turn allowing for swift changes to an organism's functional repertoire. Here, we assess the patterns and functional effects of modular rearrangements at high resolution. Using a well resolved and diverse group of pancrustaceans, we illustrate arrangement diversity within closely related organisms, estimate arrangement turnover frequency and establish, for the first time, branch-specific rate estimates for fusion, fission, domain addition and terminal loss. Our results show that roughly 16 new arrangements arise per million years and that between 64% and 81% of these can be explained by simple, single-step modular rearrangement events. We find evidence that the frequencies of fission and terminal deletion events increase over time, and that modular rearrangements impact all levels of the cellular signaling apparatus and thus may have strong adaptive potential. Novel arrangements that cannot be explained by simple modular rearrangements contain a significant amount of repeat domains that occur in complex patterns which we term "supra-repeats". Furthermore, these arrangements are significantly longer than those with a single-step rearrangement solution, suggesting that such arrangements may result from multi-step events. In summary, our analysis provides an integrated view and initial quantification of the patterns and functional impact of modular protein evolution in a well resolved phylogenetic tree. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.

  10. The Multifunctional Protein in Peroxisomal β-Oxidation

    PubMed Central

    Arent, Susan; Christensen, Caspar E.; Pye, Valerie E.; Nørgaard, Allan; Henriksen, Anette

    2010-01-01

    Plant fatty acids can be completely degraded within the peroxisomes. Fatty acid degradation plays a role in several plant processes including plant hormone synthesis and seed germination. Two multifunctional peroxisomal isozymes, MFP2 and AIM1, both with 2-trans-enoyl-CoA hydratase and l-3-hydroxyacyl-CoA dehydrogenase activities, function in mouse ear cress (Arabidopsis thaliana) peroxisomal β-oxidation, where fatty acids are degraded by the sequential removal of two carbon units. A deficiency in either of the two isozymes gives rise to a different phenotype; the biochemical and molecular background for these differences is not known. Structure determination of Arabidopsis MFP2 revealed that plant peroxisomal MFPs can be grouped into two families, as defined by a specific pattern of amino acid residues in the flexible loop of the acyl-binding pocket of the 2-trans-enoyl-CoA hydratase domain. This could explain the differences in substrate preferences and specific biological functions of the two isozymes. The in vitro substrate preference profiles illustrate that the Arabidopsis AIM1 hydratase has a preference for short chain acyl-CoAs compared with the Arabidopsis MFP2 hydratase. Remarkably, neither of the two was able to catabolize enoyl-CoA substrates longer than 14 carbon atoms efficiently, suggesting the existence of an uncharacterized long chain enoyl-CoA hydratase in Arabidopsis peroxisomes. PMID:20463021

  11. Controlling multi-function of biomaterials interfaces based on multiple and competing adsorption of functional proteins.

    PubMed

    Guan, Zhen-Yu; Huang, Chao-Wei; Huang, Mei-Ching; Wu, Chih-Yu; Liu, Hui-Yu; Ding, Shih-Torng; Chen, Hsien-Yeh

    2017-01-01

    Multifunctional biomaterial surfaces can be created by controlling the competing adsorption of multiple proteins. To demonstrate this concept, bone morphogenetic protein 2 (BMP-2) and fibronectin were adsorbed to the hydrophobic surface of polychloro-para-xylylene. The resulting adsorption properties on the surface depended on the dimensional and steric characteristics of the selected protein molecule, the degree of denaturation of the adsorbed proteins, the associated adsorption of interphase water molecules within the protein layers, and the aggregation of proteins in a planar direction with respect to the adsorbent surface. Additionally, a defined surface composition was formed by the competing adsorption of multiple proteins, and this surface composition was directly linked to the composition of the protein mixture in the solution phase. Although the mechanism of this complex competing adsorption process is not fully understood, the adsorbed proteins were irreversibly adsorbed and were unaffected by the further adsorption of homologous or heterologous proteins. Moreover, synergistic biological activities, including cell osteogenesis and proliferation independently and specifically induced by BMP-2 or fibronectin, were observed on the modified surface, and these biological activities were positively correlated with the surface composition of the multiple adsorbed proteins. These results provide insights and important design parameters for prospective biomaterials and biointerfaces for (multi)functional modifications. The ability to control protein/interface properties will be beneficial for the processing of biomaterials for clinical applications and industrial products.

  12. Trimeric Autotransporter Adhesins in Members of the Burkholderia Cepacia Complex: A Multifunctional Family of Proteins Implicated in Virulence

    PubMed Central

    Mil-Homens, Dalila; Fialho, Arsénio M.

    2011-01-01

    Trimeric autotransporter adhesins (TAAs) are multimeric surface proteins exclusively found in bacteria. They are involved in various biological traits of pathogenic Gram-negative bacteria including adherence, biofilm formation, invasion, survival within eukaryotic cells, serum resistance, and cytotoxicity. TAAs have a modular architecture composed by a conserved membrane-anchored C-terminal domain and a variable number of stalk and head domains. In this study, a bioinformatic approach has been used to analyze the distribution and architecture of TAAs among Burkholderia cepacia complex (Bcc) genomes. Fifteen genomes were probed revealing a total of 74 encoding sequences. Compared with other bacterial species, the Bcc genomes contain a large number of TAAs (two genes to up to eight genes, such as in B. cenocepacia). Phylogenetic analysis showed that the TAAs grouped into at least eight distinct clusters. TAAs with serine-rich repeats are clearly well separated from others, thereby representing a different evolutionary lineage. Comparative gene mapping across Bcc genomes reveals that TAA genes are inserted within conserved synteny blocks. We further focused our analysis on the epidemic strain B. cenocepacia J2315 in which seven TAAs were annotated. Among these, three TAA-encoding genes (BCAM019, BCAM0223, and BCAM0224) are organized into a cluster and are candidates for multifunctional virulence factors. Here we review the current insights into the functional role of BCAM0224 as a model locus. PMID:22919579

  13. The structural protein ODV-EC27 of Autographa californica nucleopolyhedrovirus is a multifunctional viral cyclin.

    PubMed

    Belyavskyi, M; Braunagel, S C; Summers, M D

    1998-09-15

    Two major characteristics of baculovirus infection are arrest of the host cell at G2/M phase of the cell cycle with continuing viral DNA replication. We show that Autographa californica nucleopolyhedrovirus (AcMNPV) encodes for a multifunctional cyclin that may partially explain the molecular basis of these important characteristics of AcMNPV (baculovirus) infection. Amino acids 80-110 of the viral structural protein ODV-EC27 (-EC27) demonstrate 25-30% similarity with cellular cyclins within the cyclin box. Immunoprecipitation results using antibodies to -EC27 show that -EC27 can associate with either cdc2 or cdk6 resulting in active kinase complexes that can phosphorylate histone H1 and retinoblastoma protein in vitro. The cdk6-EC27 complex also associates with proliferating cell nuclear antigen (PCNA) and we demonstrate that PCNA is a structural protein of both the budded virus and the occlusion-derived virus. These results suggest that -EC27 can function as a multifunctional cyclin: when associated with cdc2, it exhibits cyclin B-like activity; when associated with cdk6, the complex possesses cyclin D-like activity and binds PCNA. The possible roles of such a multifunctional cyclin during the life cycle of baculovirus are discussed, along with potential implications relative to the expression of functionally authentic recombinant proteins by using baculovirus-infected cells.

  14. Modular protein domains: an engineering approach toward functional biomaterials.

    PubMed

    Lin, Charng-Yu; Liu, Julie C

    2016-08-01

    Protein domains and peptide sequences are a powerful tool for conferring specific functions to engineered biomaterials. Protein sequences with a wide variety of functionalities, including structure, bioactivity, protein-protein interactions, and stimuli responsiveness, have been identified, and advances in molecular biology continue to pinpoint new sequences. Protein domains can be combined to make recombinant proteins with multiple functionalities. The high fidelity of the protein translation machinery results in exquisite control over the sequence of recombinant proteins and the resulting properties of protein-based materials. In this review, we discuss protein domains and peptide sequences in the context of functional protein-based materials, composite materials, and their biological applications.

  15. Multifunctional nature of the arenavirus RING finger protein Z.

    PubMed

    Fehling, Sarah Katharina; Lennartz, Frank; Strecker, Thomas

    2012-11-09

    Arenaviruses are a family of enveloped negative-stranded RNA viruses that can cause severe human disease ranging from encephalitis symptoms to fulminant hemorrhagic fever. The bi‑segmented RNA genome encodes four polypeptides: the nucleoprotein NP, the surface glycoprotein GP, the polymerase L, and the RING finger protein Z. Although it is the smallest arenavirus protein with a length of 90 to 99 amino acids and a molecular weight of approx. 11 kDa, the Z protein has multiple functions in the viral life cycle including (i) regulation of viral RNA synthesis, (ii) orchestration of viral assembly and budding, (iii) interaction with host cell proteins, and (iv) interferon antagonism. In this review, we summarize our current understanding of the structural and functional role of the Z protein in the arenavirus replication cycle.

  16. Multifunctional Nature of the Arenavirus RING Finger Protein Z

    PubMed Central

    Fehling, Sarah Katharina; Lennartz, Frank; Strecker, Thomas

    2012-01-01

    Arenaviruses are a family of enveloped negative-stranded RNA viruses that can cause severe human disease ranging from encephalitis symptoms to fulminant hemorrhagic fever. The bi‑segmented RNA genome encodes four polypeptides: the nucleoprotein NP, the surface glycoprotein GP, the polymerase L, and the RING finger protein Z. Although it is the smallest arenavirus protein with a length of 90 to 99 amino acids and a molecular weight of approx. 11 kDa, the Z protein has multiple functions in the viral life cycle including (i) regulation of viral RNA synthesis, (ii) orchestration of viral assembly and budding, (iii) interaction with host cell proteins, and (iv) interferon antagonism. In this review, we summarize our current understanding of the structural and functional role of the Z protein in the arenavirus replication cycle. PMID:23202512

  17. Analyzing the roles of multi-functional proteins in cells: The case of arrestins and GRKs.

    PubMed

    Gurevich, Vsevolod V; Gurevich, Eugenia V

    2015-01-01

    Most proteins have multiple functions. Obviously, conventional methods of manipulating the level of the protein of interest in the cell, such as over-expression, knockout or knockdown, affect all of its functions simultaneously. The key advantage of these methods is that over-expression, knockout or knockdown does not require any knowledge of the molecular mechanisms of the function(s) of the protein of interest. The disadvantage is that these approaches are inadequate to elucidate the role of an individual function of the protein in a particular cellular process. An alternative is the use of re-engineered proteins, in which a single function is eliminated or enhanced. The use of mono-functional elements of a multi-functional protein can also yield cleaner answers. This approach requires detailed knowledge of the structural basis of each function of the protein in question. Thus, a lot of preliminary structure-function work is necessary to make it possible. However, when this information is available, replacing the protein of interest with a mutant in which individual functions are modified can shed light on the biological role of those particular functions. Here, we illustrate this point using the example of protein kinases, most of which have additional non-enzymatic functions, as well as arrestins, known multi-functional signaling regulators in the cell.

  18. Split green fluorescent protein as a modular binding partner for protein crystallization.

    PubMed

    Nguyen, Hau B; Hung, Li-Wei; Yeates, Todd O; Terwilliger, Thomas C; Waldo, Geoffrey S

    2013-12-01

    A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was tested by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10-11) hairpin in complex with GFP(1-9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10-11) hairpin with a variety of GFP(1-9) mutants engineered for favorable crystallization.

  19. NMR analysis of the architecture and functional remodeling of a modular multidomain protein, RPA.

    PubMed

    Brosey, Chris A; Chagot, Marie-Eve; Ehrhardt, Mark; Pretto, Dalyir I; Weiner, Brian E; Chazin, Walter J

    2009-05-13

    Modular proteins with multiple domains tethered by flexible linkers have variable global architectures. Using the eukaryotic ssDNA binding protein, Replication Protein A (RPA), we demonstrate that NMR spectroscopy is a powerful tool to characterize the remodeling of architecture in different functional states. The first direct evidence is obtained for the remodeling of RPA upon binding ssDNA, including an alteration in the availability of the RPA32N domain that may help explain its damage-dependent phosphorylation.

  20. De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity

    PubMed Central

    Boyken, Scott E.; Chen, Zibo; Groves, Benjamin; Langan, Robert A.; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H.; Baker, David

    2017-01-01

    In nature, structural specificity in DNA and proteins is encoded quite differently: in DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen bond networks with atomic accuracy is a milestone for protein design and enables the programming of protein interaction specificity for a broad range of synthetic biology applications. PMID:27151862

  1. Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks

    PubMed Central

    Pritykin, Yuri; Singh, Mona

    2013-01-01

    The availability of large-scale protein-protein interaction networks for numerous organisms provides an opportunity to comprehensively analyze whether simple properties of proteins are predictive of the roles they play in the functional organization of the cell. We begin by re-examining an influential but controversial characterization of the dynamic modularity of the S. cerevisiae interactome that incorporated gene expression data into network analysis. We analyse the protein-protein interaction networks of five organisms, S. cerevisiae, H. sapiens, D. melanogaster, A. thaliana, and E. coli, and confirm significant and consistent functional and structural differences between hub proteins that are co-expressed with their interacting partners and those that are not, and support the view that the former tend to be intramodular whereas the latter tend to be intermodular. However, we also demonstrate that in each of these organisms, simple topological measures are significantly correlated with the average co-expression of a hub with its partners, independent of any classification, and therefore also reflect protein intra- and inter- modularity. Further, cross-interactomic analysis demonstrates that these simple topological characteristics of hub proteins tend to be conserved across organisms. Overall, we give evidence that purely topological features of static interaction networks reflect aspects of the dynamics and modularity of interactomes as well as previous measures incorporating expression data, and are a powerful means for understanding the dynamic roles of hubs in interactomes. PMID:24130468

  2. E2 protein cage as a multifunctional nanoplatform

    NASA Astrophysics Data System (ADS)

    Dalmau Mallorqui, Merce

    Caged protein systems such as viral capsids, heat shock proteins, and ferritin are spherical structures that occur naturally in living organisms and are a growing class of biomimetic templates used to create new materials in nanotechnology. Such systems have been proposed as general drug carriers since they form highly symmetric nanoscale architectures that offer the potential to be tailored according to the desired application. Within this framework, this dissertation focuses on the design and development of a new drug delivery nanoplatform based on the E2 subunit of the pyruvate dehydrogenase protein from Bacillus stearothermophilus. This scaffold forms a 25-nm nanocapsule structure with a hollow cavity. We produced a variant of this protein consisting only of the structural core, and found the thermostability of this self-assembled scaffold to be unusually high, with an onset unfolding temperature of 81.1 +/- 0.9°C and an apparent midpoint unfolding temperature of 91.4 +/- 1.4°C. To evaluate the potential of this scaffold for encapsulation of guest molecules in the internal cavity, we made variants which altered the physicochemical properties of the hollow internal surface. These mutants, yielding up to 240 mutations within this cavity, assembled into correct architectures and exhibited high thermostability that was also comparable to the wild-type scaffold. To show the applicability of this scaffold we coupled two drug-like small molecules to the internal cavity. We also developed a new strategy for encapsulation of small hydrophobic drug molecules. This method is based on hydrophobic differences between the interior cavity and the external buffer to nucleate drug-like agents inside the protein cage. We demonstrate that internal mutations can introduce non-native functionality and enable molecular encapsulation within the cavity while still retaining the dodecahedral structure. Another surface amenable to modifications is the interface between subunits. Such

  3. Engineering modular protein interaction switches by sequence overlap.

    PubMed

    Sallee, Nathan A; Yeh, Brian J; Lim, Wendell A

    2007-04-18

    Many cellular signaling pathways contain proteins whose interactions change in response to upstream inputs, allowing for conditional activation or repression of the interaction based on the presence of the input molecule. The ability to engineer similar regulation into protein interaction elements would provide us with powerful tools for controlling cell signaling. Here we describe an approach for engineering diverse synthetic protein interaction switches. Specifically, by overlapping the sequences of pairs of protein interaction domains and peptides, we have been able to generate mutually exclusive regulation over their interactions. Thus, the hybrid protein (which is composed of the two overlapped interaction modules) can bind to either of the two respective ligands for those modules, but not to both simultaneously. We show that these synthetic switch proteins can be used to regulate specific protein-protein interactions in vivo. These switches allow us to disrupt an interaction with the addition or activation of a protein input that has no natural connection to the interaction in question. Therefore, they give us the ability to make novel connections between normally unrelated signaling pathways and to rewire the input/output relationships of cellular behaviors. Our experiments also suggest a possible mechanism by which complex regulatory proteins might have evolved from simpler components.

  4. Modularity in Protein Complex and Drug Interactions Reveals New Polypharmacological Properties

    PubMed Central

    Nacher, Jose C.; Schwartz, Jean-Marc

    2012-01-01

    Recent studies have highlighted the importance of interconnectivity in a large range of molecular and human disease-related systems. Network medicine has emerged as a new paradigm to deal with complex diseases. Connections between protein complexes and key diseases have been suggested for decades. However, it was not until recently that protein complexes were identified and classified in sufficient amounts to carry out a large-scale analysis of the human protein complex system. We here present the first systematic and comprehensive set of relationships between protein complexes and associated drugs and analyzed their topological features. The network structure is characterized by a high modularity, both in the bipartite graph and in its projections, indicating that its topology is highly distinct from a random network and that it contains a rich and heterogeneous internal modular structure. To unravel the relationships between modules of protein complexes, drugs and diseases, we investigated in depth the origins of this modular structure in examples of particular diseases. This analysis unveils new associations between diseases and protein complexes and highlights the potential role of polypharmacological drugs, which target multiple cellular functions to combat complex diseases driven by gain-of-function mutations. PMID:22279562

  5. Emerging Multifunctional Roles of Claudin Tight Junction Proteins in Bone

    PubMed Central

    Alshbool, Fatima. Z.

    2014-01-01

    The imbalance between bone formation and resorption during bone remodeling has been documented to be a major factor in the pathogenesis of osteoporosis. Recent evidence suggests a significant role for the tight junction proteins, Claudins (Cldns), in the regulation of bone remodeling processes. In terms of function, whereas Cldns act “canonically” as key determinants of paracellular permeability, there is considerable recent evidence to suggest that Cldns also participate in cell signaling, ie, a “noncanonical function”. To this end, Cldns have been shown to regulate cell proliferation, differentiation, and gene expression in a variety of cell types. The present review will discuss Cldns' structure, their expression profile, regulation of expression, and their canonical and non- canonical functions in general with special emphasis on bone cells. In order to shed light on the noncanonical functions of Cldns in bone, we will highlight the role of Cldn-18 in regulating bone resorption and osteoclast differentiation. Collectively, we hope to provide a framework for guiding future research on understanding how Cldns modulate osteoblast and osteoclast function and overall bone homeostasis. Such studies should provide valuable insights into the pathogenesis of osteoporosis, and may highlight Cldns as novel targets for the diagnosis and therapeutic management of osteoporosis. PMID:24758302

  6. Emerging multifunctional roles of Claudin tight junction proteins in bone.

    PubMed

    Alshbool, Fatima Z; Mohan, Subburaman

    2014-07-01

    The imbalance between bone formation and resorption during bone remodeling has been documented to be a major factor in the pathogenesis of osteoporosis. Recent evidence suggests a significant role for the tight junction proteins, Claudins (Cldns), in the regulation of bone remodeling processes. In terms of function, whereas Cldns act "canonically" as key determinants of paracellular permeability, there is considerable recent evidence to suggest that Cldns also participate in cell signaling, ie, a "noncanonical function". To this end, Cldns have been shown to regulate cell proliferation, differentiation, and gene expression in a variety of cell types. The present review will discuss Cldns' structure, their expression profile, regulation of expression, and their canonical and non- canonical functions in general with special emphasis on bone cells. In order to shed light on the noncanonical functions of Cldns in bone, we will highlight the role of Cldn-18 in regulating bone resorption and osteoclast differentiation. Collectively, we hope to provide a framework for guiding future research on understanding how Cldns modulate osteoblast and osteoclast function and overall bone homeostasis. Such studies should provide valuable insights into the pathogenesis of osteoporosis, and may highlight Cldns as novel targets for the diagnosis and therapeutic management of osteoporosis.

  7. Multifunctional Electrospun Nanofibers Incorporated with an Anti-infection Drug and Immobilized with Proteins

    NASA Astrophysics Data System (ADS)

    Zhou, Shufei

    Electrospinning has been used to fabricate ultrafine fibers with sizes ranging from nano to micrometers. Nanofibers electrospun from biocompatible and biodegradable polymers have been extensively investigated for their potential applications in wound healing and tissue regeneration. These nanofiber materials can be modified to incorporate bioactive molecules, such as antibacterial agents that provide infection control, or functional proteins which promote cell proliferation and tissue reconstruction. Despite the numerous studies on the development and design of nanofibers for biomedical applications, there has been little research on multifunctional nanofibers that are incorporated with both antibacterial drug(s) and bioactive proteins. The objective of the current study is, therefore, to develop nanofibers that are functionalized by several bioactive molecules. In this study, electrospinning was utilized to fabricate nanofibers from biodegradable polymers PLLA (Poly-L-lactide) and the copolymer PLLA-PEG (Polyethylene glycol)-NH2.A water soluble antibiotic drug, Tetracycline Hydrochloride (TCH), was incorporated into the electrospun nanofibers via emulsion electrospinning. The TCH-loaded nanofibers were surface modified to produce functional groups that can be further conjugated with a model protein, Bovine Serum Albumin (BSA).Drug releasing profiles of the medicated nanofibers were monitored and their antimicrobial properties were evaluated. Proteins (BSAs) immobilized on the fiber surface were verified by ATR-FTIR. The number of immobilized BSAs was determined using a UV-Vis spectrophotometer. The results of the study suggested that this multifunctional nanofibrous material could be a promising material for wound dressing or scaffolds for tissue engineering.

  8. Simultaneous detection of the tumor suppressor FHIT gene and protein using the multi-functional biochip.

    PubMed

    Askari, Minoo D F; Miller, Gordon H; Vo-Dinh, Tuan

    2002-01-01

    The tumor suppressor gene, fragile histidine triad (FHIT), encompasses the most common human chromosomal fragile site, at 3pl4.2. Detection of FHIT gene is important in cancer diagnostics since its alterations have been associated with several human cancers. A unique multi-functional biochip for simultaneous detection of FHIT DNA and FHIT protein on the same platform was applied. The design of the biochip is based on miniaturization of photodiodes, where functioning of multiple optical sensing elements, amplifiers, discriminators, and logic circuitry are integrated on a single IC board. Performance of biochip is based on biomolecular recognition processes using both DNA and protein bioreceptors, Cy5-labeled probes and laser excitation. Application of biochip for concurrent detection of various immobilized target DNA and protein molecules and multiplex of DNA and protein on the same microarray was accomplished. Linearity of biochip for quantitative measurements was demonstrated. Results demonstrated utility of this multi-functional biochip as a useful detection technology with applications in biological and clinical laboratories.

  9. Cross-Linked Protein Nanofilter with Antibacterial Properties for Multifunctional Air Filtration.

    PubMed

    Souzandeh, Hamid; Molki, Banafsheh; Zheng, Min; Beyenal, Haluk; Scudiero, Louis; Wang, Yu; Zhong, Wei-Hong

    2017-07-12

    Development of high-performance nanomaterials with not only strong ability to trap the pollutants but also good structure stability under varying environmental conditions is a critical need for air-filtration applications. However, it has been very challenging for a filtering material to simultaneously realize multifunctional air filtration and good environmental stability. Here, based on our previous studies on protein-based nanofilters, we report a cross-linked protein nanofabric to address this challenging issue. It is found that cross-linked protein nanofabrics can significantly improve the structure stability against different moisture levels and temperatures, while maintaining the multifunctional filtration performance. Moreover, it is demonstrated that the cross-linked protein nanomaterials also possess antibacterial properties, such as Shewanella oneidensis bacteria, further improving the environmental stability. The effects of cross-linking with different loadings of cross-linking agent on the structure stability and filtration performance are further investigated at different humidity levels and temperatures. This study provides a cost-effective solution for advanced "green" nanomaterials with excellent performance in both filtration functions and structure stability under varying environment.

  10. Computer-aided design of modular protein devices: Boolean AND gene activation

    NASA Astrophysics Data System (ADS)

    Salis, H.; Kaznessis, Y. N.

    2006-12-01

    Many potentially useful synthetic gene networks require the expression of an engineered gene if and only if two different DNA-binding proteins exist in sufficient concentration. While some natural and engineered systems activate gene expression according to a logical AND-like behavior, they often utilize allosteric or cooperative protein-protein interactions, rendering their components unsuitable for a toolbox of modular parts for use in multiple applications. Here, we develop a quantitative model to demonstrate that a small system of interacting fusion proteins, called a protein device, can activate an engineered gene according to the Boolean AND behavior while using only modular protein domains and DNA sites. The fusion proteins are created from transactivating, DNA-binding, non-DNA binding, and protein-protein interaction domains along with the corresponding peptide ligands. Using a combined kinetic and thermodynamic model, we identify the characteristics of the molecular components and their rates of constitutive production that maximize the fidelity of AND behavior. These AND protein devices facilitate the creation of complex genetic programs and may be used to create gene therapies, biosensors and other biomedical and biotechnological applications that turn on gene expression only when multiple DNA-binding proteins are simultaneously present.

  11. Characterization and production of multifunctional cationic peptides derived from rice proteins.

    PubMed

    Taniguchi, Masayuki; Ochiai, Akihito

    2017-04-01

    Food proteins have been identified as a source of bioactive peptides. These peptides are inactive within the sequence of the parent protein and must be released during gastrointestinal digestion, fermentation, or food processing. Of bioactive peptides, multifunctional cationic peptides are more useful than other peptides that have specific activity in promotion of health and/or the treatment of diseases. We have identified and characterized cationic peptides from rice enzymes and proteins that possess multiple functions, including antimicrobial, endotoxin-neutralizing, arginine gingipain-inhibitory, and/or angiogenic activities. In particular, we have elucidated the contribution of cationic amino acids (arginine and lysine) in the peptides to their bioactivities. Further, we have discussed the critical parameters, particularly proteinase preparations and fractionation or purification, in the enzymatic hydrolysis process for producing bioactive peptides from food proteins. Using an ampholyte-free isoelectric focusing (autofocusing) technique as a tool for fractionation, we successfully prepared fractions containing cationic peptides with multiple functions.

  12. Delineation of modular proteins: domain boundary prediction from sequence information.

    PubMed

    Kong, Lesheng; Ranganathan, Shoba

    2004-06-01

    The delineation of domain boundaries of a given sequence in the absence of known 3D structures or detectable sequence homology to known domains benefits many areas in protein science, such as protein engineering, protein 3D structure determination and protein structure prediction. With the exponential growth of newly determined sequences, our ability to predict domain boundaries rapidly and accurately from sequence information alone is both essential and critical from the viewpoint of gene function annotation. Anyone attempting to predict domain boundaries for a single protein sequence is invariably confronted with a plethora of databases that contain boundary information available from the internet and a variety of methods for domain boundary prediction. How are these derived and how well do they work? What definition of 'domain' do they use? We will first clarify the different definitions of protein domains, and then describe the available public databases with domain boundary information. Finally, we will review existing domain boundary prediction methods and discuss their strengths and weaknesses.

  13. Molecular evolution of viral multifunctional proteins: the case of potyvirus HC-Pro.

    PubMed

    Hasiów-Jaroszewska, Beata; Fares, Mario A; Elena, Santiago F

    2014-01-01

    Our knowledge on the mode of evolution of the multifunctional viral proteins remains incomplete. To tackle this problem, here, we have investigated the evolutionary dynamics of the potyvirus multifunctional protein HC-Pro, with particular focus on its functional domains. The protein was partitioned into the three previously described functional domains, and each domain was analyzed separately and assembled. We searched for signatures of adaptive evolution and evolutionary dependencies of amino acid sites within and between the three domains using the entire set of available potyvirus sequences in GenBank. Interestingly, we identified strongly significant patterns of co-occurrence of adaptive events along the phylogenetic tree in the three domains. These patterns suggest that Domain I, whose main function is to mediate aphid transmission, has likely been coevolving with the other two domains, which are involved in different functions but all requiring the capacity to bind RNA. By contrast, episodes of positive selection on Domains II and III did not correlate, reflecting a trade-off between their evolvability and their evolutionary dependency likely resulting from their functional overlap. Covariation analyses have identified several groups of amino acids with evidence of concerted variation within each domain, but interdomain significant covariations were only found for Domains II and III, further reflecting their functional overlapping.

  14. Infectious Bursal Disease Virus-Host Interactions: Multifunctional Viral Proteins that Perform Multiple and Differing Jobs.

    PubMed

    Qin, Yao; Zheng, Shijun J

    2017-01-14

    Infectious bursal disease (IBD) is an acute, highly contagious and immunosuppressive poultry disease caused by IBD virus (IBDV). The consequent immunosuppression increases susceptibility to other infectious diseases and the risk of subsequent vaccination failure as well. Since the genome of IBDV is relatively small, it has a limited number of proteins inhibiting the cellular antiviral responses and acting as destroyers to the host defense system. Thus, these virulence factors must be multifunctional in order to complete the viral replication cycle in a host cell. Insights into the roles of these viral proteins along with their multiple cellular targets in different pathways will give rise to a rational design for safer and effective vaccines. Here we summarize the recent findings that focus on the virus-cell interactions during IBDV infection at the protein level.

  15. BV/ODV-E26: a palmitoylated, multifunctional structural protein of Autographa californica nucleopolyhedrovirus.

    PubMed

    Burks, Jared K; Summers, Max D; Braunagel, Sharon C

    2007-04-25

    Autographa californica nucleopolyhedrovirus Ac16 is 1 of 17 genes conserved within Type 1 nucleopolyhedroviruses. This report demonstrates that multiple isoforms of the protein encoded by Ac16, BV/ODV-E26 (E26), are present in the infected cell. One form of E26 associates with viral DNA or DNA-binding proteins, while a second form associates with intracellular membranes and this is likely due to palmitoylation. The different forms of E26 present unique epitopes that can be discriminated by antiserum produced to bacterially or virally produced antigen. A summation of the data now available on E26 suggests that it is a multifunctional protein and the functional states assume unique conformations that can be discriminated by differing antisera.

  16. Infectious Bursal Disease Virus-Host Interactions: Multifunctional Viral Proteins that Perform Multiple and Differing Jobs

    PubMed Central

    Qin, Yao; Zheng, Shijun J.

    2017-01-01

    Infectious bursal disease (IBD) is an acute, highly contagious and immunosuppressive poultry disease caused by IBD virus (IBDV). The consequent immunosuppression increases susceptibility to other infectious diseases and the risk of subsequent vaccination failure as well. Since the genome of IBDV is relatively small, it has a limited number of proteins inhibiting the cellular antiviral responses and acting as destroyers to the host defense system. Thus, these virulence factors must be multifunctional in order to complete the viral replication cycle in a host cell. Insights into the roles of these viral proteins along with their multiple cellular targets in different pathways will give rise to a rational design for safer and effective vaccines. Here we summarize the recent findings that focus on the virus–cell interactions during IBDV infection at the protein level. PMID:28098808

  17. A small multifunctional pentatricopeptide repeat protein in the chloroplast of Chlamydomonas reinhardtii.

    PubMed

    Jalal, Abdullah; Schwarz, Christian; Schmitz-Linneweber, Christian; Vallon, Olivier; Nickelsen, Jörg; Bohne, Alexandra-Viola

    2015-03-01

    Organellar biogenesis is mainly regulated by nucleus-encoded factors, which act on various steps of gene expression including RNA editing, processing, splicing, stabilization, and translation initiation. Among these regulatory factors, pentatricopeptide repeat (PPR) proteins form the largest family of RNA binding proteins, with hundreds of members in flowering plants. In striking contrast, the genome of the unicellular green alga Chlamydomonas reinhardtii encodes only 14 such proteins. In this study, we analyzed PPR7, the smallest and most highly expressed PPR protein in C. reinhardtii. Green fluorescent protein-based localization and gel-filtration analysis revealed that PPR7 forms a part of a high-molecular-weight ribonucleoprotein complex in the chloroplast stroma. RIP-chip analysis of PPR7-bound RNAs demonstrated that the protein associates with a diverse set of chloroplast transcripts in vivo, i.e. rrnS, psbH, rpoC2, rbcL, atpA, cemA-atpH, tscA, and atpI-psaJ. Furthermore, the investigation of PPR7 RNAi strains revealed that depletion of PPR7 results in a light-sensitive phenotype, accompanied by altered levels of its target RNAs that are compatible with the defects in their maturation or stabilization. PPR7 is thus an unusual type of small multifunctional PPR protein, which interacts, probably in conjunction with other RNA binding proteins, with numerous target RNAs to promote a variety of post-transcriptional events.

  18. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN

    SciTech Connect

    Rangaraj, K.; Cooper, P.K.; Trego, K.S.

    2009-01-01

    The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of

  19. The ZIC gene family encodes multi-functional proteins essential for patterning and morphogenesis.

    PubMed

    Houtmeyers, Rob; Souopgui, Jacob; Tejpar, Sabine; Arkell, Ruth

    2013-10-01

    The zinc finger of the cerebellum gene (ZIC) discovered in Drosophila melanogaster (odd-paired) has five homologs in Xenopus, chicken, mice, and humans, and seven in zebrafish. This pattern of gene copy expansion is accompanied by a divergence in gene and protein structure, suggesting that Zic family members share some, but not all, functions. ZIC genes are implicated in neuroectodermal development and neural crest cell induction. All share conserved regions encoding zinc finger domains, however their heterogeneity and specification remain unexplained. In this review, the evolution, structure, and expression patterns of the ZIC homologs are described; specific functions attributable to individual family members are supported. A review of data from functional studies in Xenopus and murine models suggest that ZIC genes encode multifunctional proteins operating in a context-specific manner to drive critical events during embryogenesis. The identification of ZIC mutations in congenital syndromes highlights the relevance of these genes in human development.

  20. Modular Mass Spectrometric Tool for Analysis of Composition and Phosphorylation of Protein Complexes

    PubMed Central

    Blethrow, Justin D.; Tang, Chao; Deng, Changhui; Krutchinsky, Andrew N.

    2007-01-01

    The combination of high accuracy, sensitivity and speed of single and multiple-stage mass spectrometric analyses enables the collection of comprehensive sets of data containing detailed information about complex biological samples. To achieve these properties, we combined two high-performance matrix-assisted laser desorption ionization mass analyzers in one modular mass spectrometric tool, and applied this tool for dissecting the composition and post-translational modifications of protein complexes. As an example of this approach, we here present studies of the Saccharomyces cerevisiae anaphase-promoting complexes (APC) and elucidation of phosphorylation sites on its components. In general, the modular concept we describe could be useful for assembling mass spectrometers operating with both matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) ion sources into powerful mass spectrometric tools for the comprehensive analysis of complex biological samples. PMID:17406682

  1. Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter

    PubMed Central

    Svendsen, Soshana; Zimprich, Chad; McDougall, Mark G; Klaubert, Dieter H; Los, Georgyi V

    2008-01-01

    Background The ability to specifically label proteins within living cells can provide information about their dynamics and function. To study a membrane protein, we fused a multi-functional reporter protein, HaloTag®, to the extracellular domain of a truncated integrin. Results Using the HaloTag technology, we could study the localization, trafficking and processing of an integrin-HaloTag fusion, which we showed had cellular dynamics consistent with native integrins. By labeling live cells with different fluorescent impermeable and permeable ligands, we showed spatial separation of plasma membrane and internal pools of the integrin-HaloTag fusion, and followed these protein pools over time to study bi-directional trafficking. In addition to combining the HaloTag reporter protein with different fluorophores, we also employed an affinity tag to achieve cell capture. Conclusion The HaloTag technology was used successfully to study expression, trafficking, spatial separation and real-time translocation of an integrin-HaloTag fusion, thereby demonstrating that this technology can be a powerful tool to investigate membrane protein biology in live cells. PMID:18384686

  2. Repeat protein engineering: creating functional nanostructures/biomaterials from modular building blocks.

    PubMed

    Main, Ewan R G; Phillips, Jonathan J; Millership, Charlotte

    2013-10-01

    There is enormous interest in molecular self-assembly and the development of biological systems to form smart nanostructures for biotechnology (so-called 'bottom-up fabrications'). Repeat proteins are ideal choices for development of such systems as they: (i) possess a relatively simple relationship between sequence, structure and function; (ii) are modular and non-globular in structure; (iii) act as diverse scaffolds for the mediation of a diverse range of protein-protein interactions; and (iv) have been extensively studied and successfully engineered and designed. In the present review, we summarize recent advances in the use of engineered repeat proteins in the self-assembly of novel materials, nanostructures and biosensors. In particular, we show that repeat proteins are excellent monomeric programmable building blocks that can be triggered to associate into a range of morphologies and can readily be engineered as stimuli-responsive biofunctional materials.

  3. Modular mutagenesis of human placental ribonuclease inhibitor, a protein with leucine-rich repeats.

    PubMed Central

    Lee, F S; Vallee, B L

    1990-01-01

    Human placental ribonuclease inhibitor (PRI) is a potent protein inhibitor of pancreatic ribonucleases and the homologous blood vessel-inducing protein angiogenin. Although inhibition by PRI occurs with a 1:1 stoichiometry, its primary structure is composed predominantly of seven internal leucine-rich repeats. These internal repeats were systematically deleted either singly or in combination by "modular" mutagenesis. Deletion of repeat units 3 plus 4 or repeat unit 6 results in mutants that both bind to and inhibit ribonuclease A. Therefore, the angiogenin/ribonuclease binding site in PRI must reside primarily or entirely in repeats 1, 2, 5, or 7, the short N- or C-terminal segments, or a combination of these. Deletion of repeat units 3-5, 5-6, or 5 alone results in mutants that exhibit only binding activity. Hence, the binding site cannot reside exclusively in repeat 5. Other internal deletions or N- or C-terminal deletions of 6-86% of the protein all abolish activity. These results suggest that PRI has a modular structure, with one primary structural repeat constituting one module. The approach taken may be applicable to other proteins with repeat structures. Images PMID:2408043

  4. Structure-function analysis of SAP97, a modular scaffolding protein that drives dendrite growth.

    PubMed

    Zhang, L; Hsu, F-C; Mojsilovic-Petrovic, J; Jablonski, A M; Zhai, J; Coulter, D A; Kalb, R G

    2015-03-01

    Activation of AMPA receptors assembled with the GluA1 subunit can promote dendrite growth in a manner that depends on its direct binding partner, SAP97. SAP97 is a modular scaffolding protein that has at least seven recognizable protein-protein interaction domains. Several complementary approaches were employed to show that the dendrite branching promoting action of full length SAP97 depends on ligand(s) that bind to the PDZ3 domain. Ligand(s) to PDZ1, PDZ2 and I3 domains also contribute to dendrite growth. The ability of PDZ3 ligand(s) to promote dendrite growth depends on localization at the plasma membrane along with GluA1 and SAP97. These results suggest that the assembly of a multi-protein complex at or near synapses is vital for the translation of AMPA-R activity into dendrite growth.

  5. Tandem repeating modular proteins avoid aggregation in single molecule force spectroscopy experiments.

    PubMed

    Dougan, Lorna; Fernandez, Julio M

    2007-12-13

    We have used single molecule force spectroscopy to explore the unfolding and refolding behavior of the immunoglobulin-like I27 protein in aqueous 2,2,2-trifluoroethanol (TFE). In bulk solution experiments, a 28% v/v TFE solution has previously been observed to enhance intermolecular attractions and lead to misfolding and aggregation of tandem modular proteins of high sequence identity. In our single molecule experiments, however, we measure successful refolding of the polyprotein I27(8) in all TFE solutions up to 35% v/v. Using a single molecule micromanipulation technique, we have shown that refolding of a polyprotein with identical repeats is not hindered by the presence of this cosolvent. These experimental results provide new insight into the properties of tandem repeating proteins and raise interesting questions as to the evolutionary success of such proteins in avoiding misfolding and aggregation.

  6. Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification

    PubMed Central

    Baker, Christopher R.; Booth, Lauren N.; Sorrells, Trevor R.; Johnson, Alexander D.

    2012-01-01

    Summary We examine how different transcriptional network structures can evolve from an ancestral network. By characterizing how the ancestral mode of gene regulation for genes specific to a-type cells in yeast species evolved from an activating paradigm to a repressing one, we show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel regulatory mode. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species. PMID:23021217

  7. Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification.

    PubMed

    Baker, Christopher R; Booth, Lauren N; Sorrells, Trevor R; Johnson, Alexander D

    2012-09-28

    We examine how different transcriptional network structures can evolve from an ancestral network. By characterizing how the ancestral mode of gene regulation for genes specific to a-type cells in yeast species evolved from an activating paradigm to a repressing one, we show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel regulatory mode. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

  8. Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2.

    PubMed

    Berntsson, Ronnie P-A; Odegrip, Richard; Sehlén, Wilhelmina; Skaar, Karin; Svensson, Linda M; Massad, Tariq; Högbom, Martin; Haggård-Ljungquist, Elisabeth; Stenmark, Pål

    2014-02-01

    The Cox protein from bacteriophage P2 is a small multifunctional DNA-binding protein. It is involved in site-specific recombination leading to P2 prophage excision and functions as a transcriptional repressor of the P2 Pc promoter. Furthermore, it transcriptionally activates the unrelated, defective prophage P4 that depends on phage P2 late gene products for lytic growth. In this article, we have investigated the structural determinants to understand how P2 Cox performs these different functions. We have solved the structure of P2 Cox to 2.4 Å resolution. Interestingly, P2 Cox crystallized in a continuous oligomeric spiral with its DNA-binding helix and wing positioned outwards. The extended C-terminal part of P2 Cox is largely responsible for the oligomerization in the structure. The spacing between the repeating DNA-binding elements along the helical P2 Cox filament is consistent with DNA binding along the filament. Functional analyses of alanine mutants in P2 Cox argue for the importance of key residues for protein function. We here present the first structure from the Cox protein family and, together with previous biochemical observations, propose that P2 Cox achieves its various functions by specific binding of DNA while wrapping the DNA around its helical oligomer.

  9. BurrH: a new modular DNA binding protein for genome engineering

    PubMed Central

    Juillerat, Alexandre; Bertonati, Claudia; Dubois, Gwendoline; Guyot, Valérie; Thomas, Séverine; Valton, Julien; Beurdeley, Marine; Silva, George H.; Daboussi, Fayza; Duchateau, Philippe

    2014-01-01

    The last few years have seen the increasing development of new DNA targeting molecular tools and strategies for precise genome editing. However, opportunities subsist to either improve or expand the current toolbox and further broaden the scope of possible biotechnological applications. Here we report the discovery and the characterization of BurrH, a new modular DNA binding protein from Burkholderia rhizoxinica that is composed of highly polymorphic DNA targeting modules. We also engineered this scaffold to create a new class of designer nucleases that can be used to efficiently induce in vivo targeted mutagenesis and targeted gene insertion at a desired locus. PMID:24452192

  10. Mem-ADSVM: A two-layer multi-label predictor for identifying multi-functional types of membrane proteins.

    PubMed

    Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

    2016-06-07

    Identifying membrane proteins and their multi-functional types is an indispensable yet challenging topic in proteomics and bioinformatics. However, most of the existing membrane-protein predictors have the following problems: (1) they do not predict whether a given protein is a membrane protein or not; (2) they are limited to predicting membrane proteins with single-label functional types but ignore those with multi-functional types; and (3) there is still much room for improvement for their performance. To address these problems, this paper proposes a two-layer multi-label predictor, namely Mem-ADSVM, which can identify membrane proteins (Layer I) and their multi-functional types (Layer II). Specifically, given a query protein, its associated gene ontology (GO) information is retrieved by searching a compact GO-term database with its homologous accession number. Subsequently, the GO information is classified by a binary support vector machine (SVM) classifier to determine whether it is a membrane protein or not. If yes, it will be further classified by a multi-label multi-class SVM classifier equipped with an adaptive-decision (AD) scheme to determine to which functional type(s) it belongs. Experimental results show that Mem-ADSVM significantly outperforms state-of-the-art predictors in terms of identifying both membrane proteins and their multi-functional types. This paper also suggests that the two-layer prediction architecture is better than the one-layer for prediction performance. For reader׳s convenience, the Mem-ADSVM server is available online at http://bioinfo.eie.polyu.edu.hk/MemADSVMServer/. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Structural basis for the modular recognition of single-stranded RNA by PPR proteins

    NASA Astrophysics Data System (ADS)

    Yin, Ping; Li, Quanxiu; Yan, Chuangye; Liu, Ying; Liu, Junjie; Yu, Feng; Wang, Zheng; Long, Jiafu; He, Jianhua; Wang, Hong-Wei; Wang, Jiawei; Zhu, Jian-Kang; Shi, Yigong; Yan, Nieng

    2013-12-01

    Pentatricopeptide repeat (PPR) proteins represent a large family of sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism. PPR proteins, which are found in exceptionally large numbers in the mitochondria and chloroplasts of terrestrial plants, recognize single-stranded RNA (ssRNA) in a modular fashion. The maize chloroplast protein PPR10 binds to two similar RNA sequences from the ATPI-ATPH and PSAJ-RPL33 intergenic regions, referred to as ATPH and PSAJ, respectively. By protecting the target RNA elements from 5' or 3' exonucleases, PPR10 defines the corresponding 5' and 3' messenger RNA termini. Despite rigorous functional characterizations, the structural basis of sequence-specific ssRNA recognition by PPR proteins remains to be elucidated. Here we report the crystal structures of PPR10 in RNA-free and RNA-bound states at resolutions of 2.85 and 2.45Å, respectively. In the absence of RNA binding, the nineteen repeats of PPR10 are assembled into a right-handed superhelical spiral. PPR10 forms an antiparallel, intertwined homodimer and exhibits considerable conformational changes upon binding to its target ssRNA, an 18-nucleotide PSAJ element. Six nucleotides of PSAJ are specifically recognized by six corresponding PPR10 repeats following the predicted code. The molecular basis for the specific and modular recognition of RNA bases A, G and U is revealed. The structural elucidation of RNA recognition by PPR proteins provides an important framework for potential biotechnological applications of PPR proteins in RNA-related research areas.

  12. Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells.

    PubMed

    Qudrat, Anam; Truong, Kevin

    2016-12-09

    To achieve synthetic control over how a cell responds to other cells or the extracellular environment, it is important to reliably engineer proteins that can traffic and span the plasma membrane. Using a modular approach to assemble proteins, we identified the minimum necessary components required to engineer such membrane-spanning proteins with predictable orientation in mammalian cells. While a transmembrane domain (TM) fused to the N-terminus of a protein is sufficient to traffic it to the endoplasmic reticulum (ER), an additional signal peptidase cleavage site downstream of this TM enhanced sorting out of the ER. Next, a second TM in the synthetic protein helped anchor and accumulate the membrane-spanning protein on the plasma membrane. The orientation of the components of the synthetic protein were determined through measuring intracellular Ca(2+) signaling using the R-GECO biosensor and through measuring extracellular quenching of yellow fluorescent protein variants by saturating acidic and salt conditions. This work forms the basis of engineering novel proteins that span the plasma membrane to potentially control intracellular responses to extracellular conditions.

  13. Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling.

    PubMed

    Pan, Catherine Qiurong; Sudol, Marius; Sheetz, Michael; Low, Boon Chuan

    2012-11-01

    Cells coordinate and integrate various functional modules that control their dynamics, intracellular trafficking, metabolism and gene expression. Such capacity is mediated by specific scaffold proteins that tether multiple components of signaling pathways at plasma membrane, Golgi apparatus, mitochondria, endoplasmic reticulum, nucleus and in more specialized subcellular structures such as focal adhesions, cell-cell junctions, endosomes, vesicles and synapses. Scaffold proteins act as "pacemakers" as well as "placemakers" that regulate the temporal, spatial and kinetic aspects of protein complex assembly by modulating the local concentrations, proximity, subcellular dispositions and biochemical properties of the target proteins through the intricate use of their modular protein domains. These regulatory mechanisms allow them to gate the specificity, integration and crosstalk of different signaling modules. In addition to acting as physical platforms for protein assembly, many professional scaffold proteins can also directly modify the properties of their targets while they themselves can be regulated by post-translational modifications and/or mechanical forces. Furthermore, multiple scaffold proteins can form alliances of higher-order regulatory networks. Here, we highlight the emerging themes of scaffold proteins by analyzing their common and distinctive mechanisms of action and regulation, which underlie their functional plasticity in cell signaling. Understanding these mechanisms in the context of space, time and force should have ramifications for human physiology and for developing new therapeutic approaches to control pathological states and diseases.

  14. Potential clinical applications of multi-functional milk proteins and peptides in cancer management.

    PubMed

    Chen, H Y F; Mollstedt, O; Tsai, Men-Hwei; Kreider, R B

    2014-01-01

    The progression of cancer involves multiple changes that alter intracellular signaling to promote cell proliferation. Subsequent remodeling of the tumor microenvironment enhances metastasis by manipulating the immune system. Research in the past decade has shown that milk proteins and peptides are often multi-functional, exerting activities such as anti-microbial, immunomodulatory, cancer cell apoptosis, anti-metastasis, and antioxidant effects. Several milk-derived biologics, such as HAMLET (human α-lactalbumin made lethal to tumor cells) and the human recombinant form of lactoferrin, already demonstrated promising results in clinical trials. Lactoferricin peptide analogs are in early clinical development as antimicrobial agents and cancer immunotherapies. In addition, milk proteins and peptides are well tolerated and many exhibit oral bioavailability; thus they may complement standard therapies to boost overall success in cancer treatments. Lactoferrin, colostrum, and specific milk-derived peptide fractions are currently being developed as clinical nutrition for cancer prevention and chemotherapy protection. This review highlights the potential applications of milk proteins and peptides as pharmaceutical drug candidates and clinical nutrition in the overall management of cancer.

  15. Single Adhesive Nanofibers from a Live Diatom Have the Signature Fingerprint of Modular Proteins

    PubMed Central

    Dugdale, T. M.; Dagastine, R.; Chiovitti, A.; Mulvaney, P.; Wetherbee, R.

    2005-01-01

    The adhesive and mechanical properties of a cell-substratum adhesive secreted by live diatom cells were examined in situ using atomic force microscopy. The resulting force curves have a regular saw-tooth pattern, the characteristic fingerprint of modular proteins, and when bridged between tip and surface can repeatedly be stretched and relaxed resulting in precisely overlaying saw-tooth curves (up to ∼600 successive cycles). The average rupture force of the peaks is 0.794 ± 0.007 (mean ± SE) nN at a loading rate of 0.8 μm/s and the average persistence length is 0.026 ± <0.001 (mean ± SE) nm (fit using the worm-like chain model). We propose that we are pulling on single adhesive nanofibers, each a cohesive unit composed of a set number of modular proteins aligned in register. Furthermore, we can observe and differentiate when up to three adhesive nanofibers are pulled based upon multimodal distributions of force and persistence length. The high force required for bond rupture, high extensibility (∼1.2 μm), and the accurate and rapid refolding upon relaxation, together provide strong and flexible properties ideally suited for the cell-substratum adhesion of this fouling diatom and allow us to understand the mechanism responsible for the strength of adhesion. PMID:16169972

  16. RNA-Binding Proteins in Trichomonas vaginalis: Atypical Multifunctional Proteins Involved in a Posttranscriptional Iron Regulatory Mechanism

    PubMed Central

    Figueroa-Angulo, Elisa E.; Calla-Choque, Jaeson S.; Mancilla-Olea, Maria Inocente; Arroyo, Rossana

    2015-01-01

    Iron homeostasis is highly regulated in vertebrates through a regulatory system mediated by RNA-protein interactions between the iron regulatory proteins (IRPs) that interact with an iron responsive element (IRE) located in certain mRNAs, dubbed the IRE-IRP regulatory system. Trichomonas vaginalis, the causal agent of trichomoniasis, presents high iron dependency to regulate its growth, metabolism, and virulence properties. Although T. vaginalis lacks IRPs or proteins with aconitase activity, possesses gene expression mechanisms of iron regulation at the transcriptional and posttranscriptional levels. However, only one gene with iron regulation at the transcriptional level has been described. Recently, our research group described an iron posttranscriptional regulatory mechanism in the T. vaginalis tvcp4 and tvcp12 cysteine proteinase mRNAs. The tvcp4 and tvcp12 mRNAs have a stem-loop structure in the 5'-coding region or in the 3'-UTR, respectively that interacts with T. vaginalis multifunctional proteins HSP70, α-Actinin, and Actin under iron starvation condition, causing translation inhibition or mRNA stabilization similar to the previously characterized IRE-IRP system in eukaryotes. Herein, we summarize recent progress and shed some light on atypical RNA-binding proteins that may participate in the iron posttranscriptional regulation in T. vaginalis. PMID:26703754

  17. Induction of Multifunctional Broadly Reactive T Cell Responses by a Plasmodium vivax Circumsporozoite Protein Recombinant Chimera.

    PubMed

    Cabrera-Mora, Monica; Fonseca, Jairo Andres; Singh, Balwan; Oliveira-Ferreira, Joseli; Lima-Junior, Josué da Costa; Calvo-Calle, J Mauricio; Moreno, Alberto

    2015-09-01

    Plasmodium vivax is the most widespread species of Plasmodium, causing up to 50% of the malaria cases occurring outside sub-Saharan Africa. An effective vaccine is essential for successful control and potential eradication. A well-characterized vaccine candidate is the circumsporozoite protein (CSP). Preclinical and clinical trials have shown that both antibodies and cellular immune responses have been correlated with protection induced by immunization with CSP. On the basis of our reported approach of developing chimeric Plasmodium yoelii proteins to enhance protective efficacy, we designed PvRMC-CSP, a recombinant chimeric protein based on the P. vivax CSP (PvCSP). In this engineered protein, regions of the PvCSP predicted to contain human T cell epitopes were genetically fused to an immunodominant B cell epitope derived from the N-terminal region I and to repeat sequences representing the two types of PvCSP repeats. The chimeric protein was expressed in soluble form with high yield. As the immune response to PvCSP has been reported to be genetically restricted in the murine model, we tested the immunogenicity of PvRMC-CSP in groups of six inbred strains of mice. PvRMC-CSP was able to induce robust antibody responses in all the mouse strains tested. Synthetic peptides representing the allelic forms of the P. vivax CSP were also recognized to a similar extent regardless of the mouse strain. Furthermore, the immunization regimen induced high frequencies of multifunctional CD4(+) and CD8(+) PvRMC-CSP-specific T cells. The depth and breadth of the immune responses elicited suggest that immunization with PvRMC-CSP can circumvent the genetic restriction of the immune response to P. vivax CSP. Interestingly, PvRMC-CSP was also recognized by naturally acquired antibodies from individuals living in areas where malaria is endemic. These features make PvRMC-CSP a promising vaccine candidate for further development.

  18. Effect of inserted spacer in hepatic cell-penetrating multifunctional peptide component on the DNA intracellular delivery of quaternary complexes based on modular design

    PubMed Central

    Zhang, Luchen; Li, Zhenbo; Sun, Fangli; Xu, Yuhong; Du, Zixiu

    2016-01-01

    A safe and efficient quaternary gene delivery system (named Q-complexes) was constructed based on self-assembly of molecules through noncovalent bonds. This system was formulated through the cooperation and competing interactions of cationic liposomes, multifunctional peptides, and DNA, followed by coating hyaluronic acid on the surface of the ternary complexes. The multifunctional peptide was composed of two functional domains: penetrating hepatic tumor-targeted cell moiety (KRPTMRFRYTWNPMK) and a wrapping gene sequence (polyarginine 16). The effect of spacer insertion between the two domains of multifunctional peptide on the intracellular transfection of Q-complexes was further studied. Experimental results showed that the formulations assembled with various peptides in the spacer elements possessed different intercellular pathways and transfection efficiencies. The Q-complexes containing peptide in the absence of spacer element (Pa) showed the highest gene expression among all samples. The Q-complexes containing peptides with a noncleavable spacer GA (Pc) had no ability of intracellular nucleic acid delivery, whereas those with a cleavable spacer RVRR (Pd) showed moderate transfection activity. These results demonstrated that the different spacers inserted in the multifunctional peptide played an important role in in vitro DNA transfection efficiency. Atomic force microscopy images showed that the morphologies of ternary complexes (LPcD) and Q-complexes (HLcPD) were crystal lamellas, whereas those of other nanocomplexes were spheres. Circular dichroism showed the changed configuration of peptide with spacer GA in nanocomplexes compared with that of its free state, whereas the Pa configuration without spacer in nanocomplexes was consistent with that of its free state. The present study contributed to the structural understanding of Q-complexes, and further effective modification is in progress. PMID:27920533

  19. Phosphorylation of multifunctional galectins by protein kinases CK1, CK2, and PKA.

    PubMed

    Kübler, Dieter; Seidler, Jörg; André, Sabine; Kumar, Sonu; Schwartz-Albiez, Reinhard; Lehmann, Wolf-Dieter; Gabius, Hans-Joachim

    2014-03-15

    Phosphorylation is known to have a strong impact on protein functions. We analyzed members of the lectin family of multifunctional galectins as targets of the protein kinases CK1, CK2, and PKA. Galectins are potent growth regulators able to bind both glycan and peptide motifs at intra- and extracellular sites. Performing in vitro kinase assays, galectin phosphorylation was detected by phosphoprotein staining and autoradiography. The insertion of phosphoryl groups varied to a large extent depending on the type of kinase applied and the respective galectin substrate. Sites of phosphorylation observed in the recombinant galectins were determined by a strategic combination of phosphopeptide enrichment and nano-ultra-performance liquid chromatography tandem mass spectrometry (nanoUPLC-MS/MS). By in silico modeling, phosphorylation sites were visualized three-dimensionally. Our results reveal galectin-type-specific Ser-/Thr-dependent phosphorylation beyond the known example of galectin-3. These data are the basis for functional studies and also illustrate the analytical sensitivity of the applied methods for further work on human lectins.

  20. CotG-Like Modular Proteins Are Common among Spore-Forming Bacilli

    PubMed Central

    Saggese, Anella; Isticato, Rachele; Cangiano, Giuseppina; Ricca, Ezio

    2016-01-01

    ABSTRACT CotG is an abundant protein initially identified as an outer component of the Bacillus subtilis spore coat. It has an unusual structure characterized by several repeats of positively charged amino acids that are probably the outcome of multiple rounds of gene elongation events in an ancestral minigene. CotG is not highly conserved, and its orthologues are present in only two Bacillus and two Geobacillus species. In B. subtilis, CotG is the target of extensive phosphorylation by a still unidentified enzyme and has a role in the assembly of some outer coat proteins. We report now that most spore-forming bacilli contain a protein not homologous to CotG of B. subtilis but sharing a central “modular” region defined by a pronounced positive charge and randomly coiled tandem repeats. Conservation of the structural features in most spore-forming bacilli suggests a relevant role for the CotG-like protein family in the structure and function of the bacterial endospore. To expand our knowledge on the role of CotG, we dissected the B. subtilis protein by constructing deletion mutants that express specific regions of the protein and observed that they have different roles in the assembly of other coat proteins and in spore germination. IMPORTANCE CotG of B. subtilis is not highly conserved in the Bacillus genus; however, a CotG-like protein with a modular structure and chemical features similar to those of CotG is common in spore-forming bacilli, at least when CotH is also present. The conservation of CotG-like features when CotH is present suggests that the two proteins act together and may have a relevant role in the structure and function of the bacterial endospore. Dissection of the modular composition of CotG of B. subtilis by constructing mutants that express only some of the modules has allowed a first characterization of CotG modules and will be the basis for a more detailed functional analysis. PMID:26953338

  1. Modular architecture of protein binding units for designing properties of cellulose nanomaterials.

    PubMed

    Malho, Jani-Markus; Arola, Suvi; Laaksonen, Päivi; Szilvay, Géza R; Ikkala, Olli; Linder, Markus B

    2015-10-05

    Molecular biomimetic models suggest that proteins in the soft matrix of nanocomposites have a multimodular architecture. Engineered proteins were used together with nanofibrillated cellulose (NFC) to show how this type of architecture leads to function. The proteins consist of two cellulose-binding modules (CBM) separated by 12-, 24-, or 48-mer linkers. Engineering the linkers has a considerable effects on the interaction between protein and NFC in both wet colloidal state and a dry film. The protein optionally incorporates a multimerizing hydrophobin (HFB) domain connected by another linker. The modular structure explains effects in the hydrated gel state, as well as the deformation of composite materials through stress distribution and crosslinking. Based on this work, strategies can be suggested for tuning the mechanical properties of materials through the coupling of protein modules and their interlinking architectures. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

  2. Non-Carrier Nanoparticles Adjuvant Modular Protein Vaccine in a Particle-Dependent Manner

    PubMed Central

    Seth, Arjun; Ritchie, Fiona K.; Wibowo, Nani; Lua, Linda H. L.; Middelberg, Anton P. J.

    2015-01-01

    Nanoparticles are increasingly used to adjuvant vaccine formulations due to their biocompatibility, ease of manufacture and the opportunity to tailor their size, shape, and physicochemical properties. The efficacy of similarly-sized silica (Si-OH), poly (D,L-lactic-co-glycolic acid) (PLGA) and poly caprolactone (PCL) nanoparticles (nps) to adjuvant recombinant capsomere presenting antigenic M2e modular peptide from Influenza A virus (CapM2e) was investigated in vivo. Formulation of CapM2e with Si-OH or PLGA nps significantly boosted the immunogenicity of modular capsomeres, even though CapM2e was not actively attached to the nanoparticles prior to injection (i.e., formulation was by simple mixing). In contrast, PCL nps showed no significant adjuvant effect using this simple-mixing approach. The immune response induced by CapM2e alone or formulated with nps was antibody-biased with very high antigen-specific antibody titer and less than 20 cells per million splenocytes secreting interferon gamma. Modification of silica nanoparticle surface properties through amine functionalization and pegylation did not lead to significant changes in immune response. This study confirms that simple mixing-based formulation can lead to effective adjuvanting of antigenic protein, though with antibody titer dependent on nanoparticle physicochemical properties. PMID:25756283

  3. Multifunctionality of the linker histones: an emerging role for protein-protein interactions.

    PubMed

    McBryant, Steven J; Lu, Xu; Hansen, Jeffrey C

    2010-05-01

    Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators have reported specific interactions between linker histones and proteins involved in important cellular processes. The purpose of this review is to highlight evidence indicating an important alternative mode of action for H1, namely protein-protein interactions. We first review key aspects of the traditional view of linker histone action, including the importance of the H1 C-terminal domain. We then discuss the current state of knowledge of linker histone interactions with other proteins, and, where possible, highlight the mechanism of linker histone-mediated protein-protein interactions. Taken together, the data suggest a combinatorial role for the linker histones, functioning both as primary chromatin architectural proteins and simultaneously as recruitment hubs for proteins involved in accessing and modifying the chromatin fiber.

  4. Multifunctionality of the linker histones: an emerging role for protein-protein interactions

    PubMed Central

    McBryant, Steven J; Lu, Xu; Hansen, Jeffrey C

    2010-01-01

    Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators have reported specific interactions between linker histones and proteins involved in important cellular processes. The purpose of this review is to highlight evidence indicating an important alternative mode of action for H1, namely protein-protein interactions. We first review key aspects of the traditional view of linker histone action, including the importance of the H1 C-terminal domain. We then discuss the current state of knowledge of linker histone interactions with other proteins, and, where possible, highlight the mechanism of linker histone-mediated protein-protein interactions. Taken together, the data suggest a combinatorial role for the linker histones, functioning both as primary chromatin architectural proteins and simultaneously as recruitment hubs for proteins involved in accessing and modifying the chromatin fiber. PMID:20309017

  5. Organization and evolution of multifunctional Ca(2+)/CaM-dependent protein kinase genes.

    PubMed

    Tombes, Robert M; Faison, M Omar; Turbeville, J M

    2003-12-11

    The "multi-functional" Ca(2+) and calmodulin-dependent protein kinase, type II (CaMK-II) is an evolutionarily conserved protein. It has been found as a single gene in the horseshoe crab, marine sponge, sea urchin, nematode, and fruit fly, whereas most vertebrates possess four genes (alpha, beta, gamma, and delta). Species from fruit flies to humans encode alternative splice variants which are differentially targeted to phosphorylate diverse downstream targets of Ca(2+) signaling. By comparing known CaMK-II protein and nucleotide sequences, we have now provided evidence for the evolutionary relatedness of CaMK-IIs. Parsimony analyses unambiguously indicate that the four vertebrate CaMK-II genes arose via repeated duplications. Nucleotide phylogenies show consistent but moderate support for the placement of the vertebrate delta CaMK-II as the earliest diverging vertebrate gene. delta CaMK-II is the only gene with both central and C-terminal variable domains and has three to four times more intronic sequence than the other three genes. beta and gamma CaMK-II genes show strong sequence similarity and have comparable exon and intron organization and utilization. alpha CaMK-II is absent from amphibians (Xenopus laevis) and has the most restricted tissue specificity in mammals, whereas beta, gamma, and delta CaMK-IIs are expressed in most tissues. All 38 known mammalian CaMK-II splice variants were compiled with their tissue specificity and exon usage. Some of these variants use alternative 5' and 3' donors within a single exon as well as alternative promoters. These findings serve as an important benchmark for future phylogenetic, developmental, or biochemical studies on this important, conserved, and highly regulated gene family.

  6. Purification of Regucalcin from the Seminal Vesicular Fluid: A Calcium Binding Multi-Functional Protein.

    PubMed

    Harikrishna, P; Shende, A M; Reena, K K; Thomas, Jobin; Bhure, S K

    2016-08-01

    Regucalcin is a multi-functional protein having roles in calcium homeostasis as well as in anti-apoptotic, anti-prolific and anti-oxidative functions. Recently, it has been reported from the male reproductive tract, but its role in male reproduction needs further investigation; for which the native regucalcin of reproductive origin will be more appropriate. The gel exclusion chromatography followed by diethyl aminoethane cellulose chromatography and two-dimentional cellulose acetate membrane electrophoresis used for its purification are time consuming and less specific. Here, the regucalcin gene from buffalo testis has been cloned, expressed and purified in recombinant form, and subsequently used for raising hyper-immune serum. The Western blot of seminal vesicular fluid probed with anti-regucalcin polyclonal and monoclonal antibodies showed the presence of 28 and 34 kDa bands specific to regucalcin. Further, an affinity matrix has been prepared using anti-regucalcin polyclonal antibodies. An immuno-affinity chromatography method has been standardized to isolate regucalcin from seminal vesicular fluid. The initial complexity of the protein mixture in the seminal vesicular fluid has been reduced by a heat coagulation step. The purified protein on sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a single band at 68 kDa that has been further confirmed as regucalcin by Liquid chromatography-mass spectrometry/mass spectrometry. The RGN purified from seminal vesicular fluid will be more appropriate for studying its possible role in male reproduction, especially sperm cell capacitation, hyperactivation, acrosome reaction and cryopreservation. The study can be applied in purifying regucalcin from different tissues or species with minor modifications in the methodology.

  7. Programmable RNA-binding protein composed of repeats of a single modular unit

    PubMed Central

    Adamala, Katarzyna P.; Martin-Alarcon, Daniel A.; Boyden, Edward S.

    2016-01-01

    The ability to monitor and perturb RNAs in living cells would benefit greatly from a modular protein architecture that targets unmodified RNA sequences in a programmable way. We report that the RNA-binding protein PumHD (Pumilio homology domain), which has been widely used in native and modified form for targeting RNA, can be engineered to yield a set of four canonical protein modules, each of which targets one RNA base. These modules (which we call Pumby, for Pumilio-based assembly) can be concatenated in chains of varying composition and length, to bind desired target RNAs. The specificity of such Pumby–RNA interactions was high, with undetectable binding of a Pumby chain to RNA sequences that bear three or more mismatches from the target sequence. We validate that the Pumby architecture can perform RNA-directed protein assembly and enhancement of translation of RNAs. We further demonstrate a new use of such RNA-binding proteins, measurement of RNA translation in living cells. Pumby may prove useful for many applications in the measurement, manipulation, and biotechnological utilization of unmodified RNAs in intact cells and systems. PMID:27118836

  8. Proteolytic activity of Plasmodium falciparum subtilisin-like protease 3 on parasite profilin, a multifunctional protein.

    PubMed

    Alam, Asrar; Bhatnagar, Raj K; Relan, Udbhav; Mukherjee, Paushali; Chauhan, Virander S

    2013-10-01

    Subtilisin-like proteases of malaria parasite Plasmodium falciparum (PfSUB1, 2 and 3) are expressed at late asexual blood stages. PfSUB1 and 2 are considered important drug targets due to their essentiality for parasite blood stages and role in merozoite egress and invasion of erythrocytes. We have earlier shown the in vitro serine protease activity of PfSUB3 and its localization at asexual blood stages. In this study, we attempted to identify the biological substrate(s) of PfSUB3 and found parasite profilin (PfPRF) as a substrate of the protease. Eukaryotic profilins are multifunctional proteins with primary role in regulation of actin filament assembly. PfPRF possesses biochemical features of eukaryotic profilins and its rodent ortholog is essential in blood stages. Profilin from related apicomplexan parasite Toxoplasma gondii (TgPRF) is known to be involved in parasite motility, host cell invasion, active egress from host cell, immune evasion and virulence in mice. In this study, mature PfSUB3 proteolysed recombinant PfPRF in a dose-dependent manner in in vitro assays. Recombinant PfPRF was assessed for its proinflammatory activity and found to induce high level of TNF-α and low but significant level of IL-12 from mouse bone marrow-derived dendritic cells. Proteolysis of PfPRF by PfSUB3 is suggestive of the probable role of the protease in the processes of motility, virulence and immune evasion.

  9. α-Enolase, a Multifunctional Protein: Its Role on Pathophysiological Situations

    PubMed Central

    Díaz-Ramos, Àngels; Roig-Borrellas, Anna; García-Melero, Ana; López-Alemany, Roser

    2012-01-01

    α-Enolase is a key glycolytic enzyme in the cytoplasm of prokaryotic and eukaryotic cells and is considered a multifunctional protein. α-enolase is expressed on the surface of several cell types, where it acts as a plasminogen receptor, concentrating proteolytic plasmin activity on the cell surface. In addition to glycolytic enzyme and plasminogen receptor functions, α-Enolase appears to have other cellular functions and subcellular localizations that are distinct from its well-established function in glycolysis. Furthermore, differential expression of α-enolase has been related to several pathologies, such as cancer, Alzheimer's disease, and rheumatoid arthritis, among others. We have identified α-enolase as a plasminogen receptor in several cell types. In particular, we have analyzed its role in myogenesis, as an example of extracellular remodelling process. We have shown that α-enolase is expressed on the cell surface of differentiating myocytes, and that inhibitors of α-enolase/plasminogen binding block myogenic fusion in vitro and skeletal muscle regeneration in mice. α-Enolase could be considered as a marker of pathological stress in a high number of diseases, performing several of its multiple functions, mainly as plasminogen receptor. This paper is focused on the multiple roles of the α-enolase/plasminogen axis, related to several pathologies. PMID:23118496

  10. Structural Insight into the Core of CAD, the Multifunctional Protein Leading De Novo Pyrimidine Biosynthesis.

    PubMed

    Moreno-Morcillo, María; Grande-García, Araceli; Ruiz-Ramos, Alba; Del Caño-Ochoa, Francisco; Boskovic, Jasminka; Ramón-Maiques, Santiago

    2017-06-06

    CAD, the multifunctional protein initiating and controlling de novo biosynthesis of pyrimidines in animals, self-assembles into ∼1.5 MDa hexamers. The structures of the dihydroorotase (DHO) and aspartate transcarbamoylase (ATC) domains of human CAD have been previously determined, but we lack information on how these domains associate and interact with the rest of CAD forming a multienzymatic unit. Here, we prove that a construct covering human DHO and ATC oligomerizes as a dimer of trimers and that this arrangement is conserved in CAD-like from fungi, which holds an inactive DHO-like domain. The crystal structures of the ATC trimer and DHO-like dimer from the fungus Chaetomium thermophilum confirm the similarity with the human CAD homologs. These results demonstrate that, despite being inactive, the fungal DHO-like domain has a conserved structural function. We propose a model that sets the DHO and ATC complex as the central element in the architecture of CAD. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Theory of force-extension curves for modular proteins and DNA hairpins

    NASA Astrophysics Data System (ADS)

    Bonilla, L. L.; Carpio, A.; Prados, A.

    2015-05-01

    We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest-neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices.

  12. Regulated unfolding: a basic principle of intraprotein signaling in modular proteins.

    PubMed

    Schultz, Joachim E; Natarajan, Janani

    2013-11-01

    Modular proteins possess N-terminal sensor domains connected with different C-terminal output domains. Different output domains, for example, phosphodiesterases adenylyl cyclases, are regulated by identical N-terminal domains. Therefore, the mechanisms of intraprotein signaling share properties suitable to regulation of disparate output enzymes, which see the same signal but react differently. The common denominator is a reversible switch of folding/unfolding that connects sensor and output domains. In the inhibited state, output domains are restrained, whereas in the activated state domains are released to assemble according to intrinsic domain properties. We review recent work investigating the mechanism of intraprotein signaling and discuss how this signaling mechanism may have contributed to the evolutionary diversity of specific small molecule-binding domains without loss of regulatory properties.

  13. Identification and characterization of multifunctional cationic and amphipathic peptides from soybean proteins.

    PubMed

    Taniguchi, Masayuki; Saito, Kengo; Nomoto, Takafumi; Namae, Toshiki; Ochiai, Akihito; Saitoh, Eiichi; Tanaka, Takaaki

    2017-07-01

    In this study, we identified and chemically synthesized three cationic and amphipathic peptides (Glycinin-17, BCAS-16, and BCBS-11) from soybean proteins. These peptides had high isoelectric points, high positive net charges, and included multiple hydrophobic amino acids. Subsequently, we identified multiple functions of these peptides, including antimicrobial, lipopolysaccharide-neutralizing, and angiogenic activities, and examined their cytotoxic activities against mammalian red blood cells. Glycinin-17, BCAS-16, and BCBS-11 exhibited antimicrobial activity against Porphyromonas gingivalis and Candida albicans whereas Glycinin-17 did not possess antimicrobial effects on Propionibacterium acnes and Streptococcus mutans. Membrane-depolarization assays and flow cytometric analyses showed that the antimicrobial properties of Glycinin-17, BCAS-16, and BCBS-11 against P. gingivalis, P. acnes, and S. mutans were dependent on membrane-disrupting potential. In contrast, major antimicrobial activities of these peptides against C. albicans were dependent on interactions with targets other than cell membranes. Furthermore, chromogenic Limulus amebocyte lysate assays showed that 50% effective concentrations (EC50 , 0.12-0.31 μM) of these three peptides neutralize LPS with similar potency (EC50 : 0.11 μM) to that of polymyxin B. Moreover, tube-formation assays in human umbilical vein endothelial cells showed similar angiogenic activities of the three peptides as that following treatment with LL-37. Although BCAS-16 exhibited hemolytic activity, the rate of hemolysis for Glycinin-17 and BCBS-11 in the presence of 500-μM Glycinin-17 and BCBS-11 was less than 2%. These results demonstrate that cationic and amphipathic peptides from soybean proteins, particularly Glycinin-17 and BCBS-11, have potential as multifunctional ingredients for healthcare applications. © 2017 Wiley Periodicals, Inc.

  14. Multifunctional reagents for quantitative proteome-wide analysis of protein modification in human cells and dynamic profiling of protein lipidation during vertebrate development.

    PubMed

    Broncel, Malgorzata; Serwa, Remigiusz A; Ciepla, Paulina; Krause, Eberhard; Dallman, Margaret J; Magee, Anthony I; Tate, Edward W

    2015-05-11

    Novel multifunctional reagents were applied in combination with a lipid probe for affinity enrichment of myristoylated proteins and direct detection of lipid-modified tryptic peptides by mass spectrometry. This method enables high-confidence identification of the myristoylated proteome on an unprecedented scale in cell culture, and allowed the first quantitative analysis of dynamic changes in protein lipidation during vertebrate embryonic development. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Comparative analysis of lentiviral vectors and modular protein nanovectors for traumatic brain injury gene therapy

    PubMed Central

    Negro-Demontel, María Luciana; Saccardo, Paolo; Giacomini, Cecilia; Yáñez-Muñoz, Rafael Joaquín; Ferrer-Miralles, Neus; Vazquez, Esther; Villaverde, Antonio; Peluffo, Hugo

    2014-01-01

    Traumatic brain injury (TBI) remains as one of the leading causes of mortality and morbidity worldwide and there are no effective treatments currently available. Gene therapy applications have emerged as important alternatives for the treatment of diverse nervous system injuries. New strategies are evolving with the notion that each particular pathological condition may require a specific vector. Moreover, the lack of detailed comparative studies between different vectors under similar conditions hampers the selection of an ideal vector for a given pathological condition. The potential use of lentiviral vectors versus several modular protein-based nanovectors was compared using a controlled cortical impact model of TBI under the same gene therapy conditions. We show that variables such as protein/DNA ratio, incubation volume, and presence of serum or chloroquine in the transfection medium impact on both nanovector formation and transfection efficiency in vitro. While lentiviral vectors showed GFP protein 1 day after TBI and increased expression at 14 days, nanovectors showed stable and lower GFP transgene expression from 1 to 14 days. No toxicity after TBI by any of the vectors was observed as determined by resulting levels of IL-1β or using neurological sticky tape test. In fact, both vector types induced functional improvement per se. PMID:26015985

  16. Novel modular domain PB1 recognizes PC motif to mediate functional protein–protein interactions

    PubMed Central

    Ito, Takashi; Matsui, Yasushi; Ago, Tetsuro; Ota, Kazuhisa; Sumimoto, Hideki

    2001-01-01

    Modular domains mediating specific protein–protein interactions play central roles in the formation of complex regulatory networks to execute various cellular activities. Here we identify a novel domain PB1 in the budding yeast protein Bem1p, which functions in polarity establishment, and mammalian p67phox, which activates the microbicidal phagocyte NADPH oxidase. Each of these specifically recognizes an evolutionarily conserved PC motif to interact directly with Cdc24p (an essential protein for cell polarization) and p40phox (a component of the signaling complex for the oxidase), respectively. Swapping the PB1 domain of Bem1p with that of p67phox, which abolishes its interaction with Cdc24p, confers on cells temperature- sensitive growth and a bilateral mating defect. These phenotypes are suppressed by a mutant Cdc24p harboring the PC motif-containing region of p40phox, which restores the interaction with the altered Bem1p. This domain-swapping experiment demonstrates that Bem1p function requires interaction with Cdc24p, in which the PB1 domain and the PC motif participate as responsible modules. PMID:11483497

  17. Modularity analysis based on predicted protein-protein interactions provides new insights into pathogenicity and cellular process of Escherichia coli O157:H7

    PubMed Central

    2011-01-01

    Background With the development of experimental techniques and bioinformatics, the quantity of data available from protein-protein interactions (PPIs) is increasing exponentially. Functional modules can be identified from protein interaction networks. It follows that the investigation of functional modules will generate a better understanding of cellular organization, processes, and functions. However, experimental PPI data are still limited, and no modularity analysis of PPIs in pathogens has been published to date. Results In this study, we predict and analyze the functional modules of E. coli O157:H7 systemically by integrating several bioinformatics methods. After evaluation, most of the predicted modules are found to be biologically significant and functionally homogeneous. Six pathogenicity-related modules were discovered and analyzed, including novel modules. These modules provided new information on the pathogenicity of O157:H7. The modularity of cellular function and cooperativity between modules are also discussed. Moreover, modularity analysis of O157:H7 can provide possible candidates for biological pathway extension and clues for discovering new pathways of cross-talk. Conclusions This article provides the first modularity analysis of a pathogen and sheds new light on the study of pathogens and cellular processes. Our study also provides a strategy for applying modularity analysis to any sequenced organism. PMID:22188601

  18. Multifunctional nanocrystals

    DOEpatents

    Klimov, Victor I.; Hollingsworth, Jennifer A.; Crooker, Scott A.; Kim, Hyungrak

    2010-06-22

    Multifunctional nanocomposites are provided including a core of either a magnetic material or an inorganic semiconductor, and, a shell of either a magnetic material or an inorganic semiconductor, wherein the core and the shell are of differing materials, such multifunctional nanocomposites having multifunctional properties including magnetic properties from the magnetic material and optical properties from the inorganic semiconductor material. Various applications of such multifunctional nanocomposites are also provided.

  19. Multifunctional nanocrystals

    DOEpatents

    Klimov, Victor I.; Hollingsworth, Jennifer A.; Crooker, Scott A.; Kim, Hyungrak

    2007-08-28

    Multifunctional nanocomposites are provided including a core of either a magnetic material or an inorganic semiconductor, and, a shell of either a magnetic material or an inorganic semiconductor, wherein the core and the shell are of differing materials, such multifunctional nanocomposites having multifunctional properties including magnetic properties from the magnetic material and optical properties from the inorganic semiconductor material. Various applications of such multifunctional nanocomposites are also provided.

  20. Self-assembly and modular functionalization of three-dimensional crystals from oppositely charged proteins

    PubMed Central

    Liljeström, Ville; Mikkilä, Joona; Kostiainen, Mauri A.

    2014-01-01

    Multicomponent crystals and nanoparticle superlattices are a powerful approach to integrate different materials into ordered nanostructures. Well-developed, especially DNA-based, methods for their preparation exist, yet most techniques concentrate on molecular and synthetic nanoparticle systems in non-biocompatible environment. Here we describe the self-assembly and characterization of binary solids that consist of crystalline arrays of native biomacromolecules. We electrostatically assembled cowpea chlorotic mottle virus particles and avidin proteins into heterogeneous crystals, where the virus particles adopt a non-close-packed body-centred cubic arrangement held together by avidin. Importantly, the whole preparation process takes place at room temperature in a mild aqueous medium allowing the processing of delicate biological building blocks into ordered structures with lattice constants in the nanometre range. Furthermore, the use of avidin–biotin interaction allows highly selective pre- or post-functionalization of the protein crystals in a modular way with different types of functional units, such as fluorescent dyes, enzymes and plasmonic nanoparticles. PMID:25033911

  1. A modular approach to the design of protein-based smart gels.

    PubMed

    Grove, Tijana Z; Forster, Jason; Pimienta, Genaro; Dufresne, Eric; Regan, Lynne

    2012-07-01

    The modular nature of repeat proteins makes them a versatile platform for the design of smart materials with predetermined properties. Here, we present a general strategy for combining protein modules with specified stability and function into arrays for the assembly of stimuli-responsive gels. We have designed tetratricopeptide repeat (TPR) arrays which contain peptide-binding modules that specify the strength and reversibility of network crosslinking in combination with spacer modules that specify crosslinking geometry and overall stability of the array. By combining such arrays with multivalent peptide ligands, self-supporting stimuli-responsive gels are formed. Using microrheology, we characterized the kinetics of gelation as a function of concentration and stoichiometry of the components. We also show that such gels are effective in encapsulating and releasing small molecules. Moreover, TPR gels alone are fully compatible with cell growth, whereas gels loaded with an anticancer compound release the compound, resulting in cell death. Thus, we have demonstrated that this new class of tunable biomaterials is ripe for further development as tissue engineering and drug delivery platform.

  2. Modular control of glutamatergic neuronal identity in C.elegans by distinct homeodomain proteins

    PubMed Central

    Serrano-Saiz, Esther; Poole, Richard J.; Felton, Terry; Zhang, Feifan; De La Cruz, Estanisla Daniel; Hobert, Oliver

    2013-01-01

    The choice of using one of many possible neurotransmitter systems is a critical step in defining the identity of an individual neuron type. We show here that the key defining feature of glutamatergic neurons, the vesicular glutamate transporter EAT-4/VGLUT is expressed in 38 of the 118 anatomically defined neuron classes of the C.elegans nervous system. We show that eat-4/VGLUT expression is controlled in a modular manner, with distinct cis-regulatory modules driving expression in distinct glutamatergic neuron classes. We identify 13 different transcription factors, 11 of them homeodomain proteins, that act in specific combinations in 25 different glutamatergic neuron classes to initiate and maintain eat-4/VGLUT expression. We show that the adoption of a glutamatergic phenotype is linked to the adoption of other terminal identity features of a neuron, including cotransmitter phenotypes. Examination of mouse orthologs of these homeodomain proteins resulted in the identification of mouse LHX1 as a regulator of glutamatergic neurons in the brainstem. PMID:24243022

  3. A modular toolkit to inhibit proline-rich motif–mediated protein–protein interactions

    PubMed Central

    Opitz, Robert; Müller, Matthias; Reuter, Cédric; Barone, Matthias; Soicke, Arne; Roske, Yvette; Piotukh, Kirill; Huy, Peter; Beerbaum, Monika; Wiesner, Burkhard; Beyermann, Michael; Schmieder, Peter; Freund, Christian; Volkmer, Rudolf; Oschkinat, Hartmut; Schmalz, Hans-Günther; Kühne, Ronald

    2015-01-01

    Small-molecule competitors of protein–protein interactions are urgently needed for functional analysis of large-scale genomics and proteomics data. Particularly abundant, yet so far undruggable, targets include domains specialized in recognizing proline-rich segments, including Src-homology 3 (SH3), WW, GYF, and Drosophila enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains. Here, we present a modular strategy to obtain an extendable toolkit of chemical fragments (ProMs) designed to replace pairs of conserved prolines in recognition motifs. As proof-of-principle, we developed a small, selective, peptidomimetic inhibitor of Ena/VASP EVH1 domain interactions. Highly invasive MDA MB 231 breast-cancer cells treated with this ligand showed displacement of VASP from focal adhesions, as well as from the front of lamellipodia, and strongly reduced cell invasion. General applicability of our strategy is illustrated by the design of an ErbB4-derived ligand containing two ProM-1 fragments, targeting the yes-associated protein 1 (YAP1)-WW domain with a fivefold higher affinity. PMID:25848013

  4. Self-assembly and modular functionalization of three-dimensional crystals from oppositely charged proteins

    NASA Astrophysics Data System (ADS)

    Liljeström, Ville; Mikkilä, Joona; Kostiainen, Mauri A.

    2014-07-01

    Multicomponent crystals and nanoparticle superlattices are a powerful approach to integrate different materials into ordered nanostructures. Well-developed, especially DNA-based, methods for their preparation exist, yet most techniques concentrate on molecular and synthetic nanoparticle systems in non-biocompatible environment. Here we describe the self-assembly and characterization of binary solids that consist of crystalline arrays of native biomacromolecules. We electrostatically assembled cowpea chlorotic mottle virus particles and avidin proteins into heterogeneous crystals, where the virus particles adopt a non-close-packed body-centred cubic arrangement held together by avidin. Importantly, the whole preparation process takes place at room temperature in a mild aqueous medium allowing the processing of delicate biological building blocks into ordered structures with lattice constants in the nanometre range. Furthermore, the use of avidin-biotin interaction allows highly selective pre- or post-functionalization of the protein crystals in a modular way with different types of functional units, such as fluorescent dyes, enzymes and plasmonic nanoparticles.

  5. Construction of multifunctional proteins for tissue engineering: epidermal growth factor with collagen binding and cell adhesive activities.

    PubMed

    Hannachi Imen, Elloumi; Nakamura, Makiko; Mie, Masayasu; Kobatake, Eiry

    2009-01-01

    The development of different techniques based on natural and polymeric scaffolds are useful for the design of different biomimetic materials. These approaches, however, require supplementary steps for the chemical or physical modification of the biomaterial. To avoid such steps, in the present study, we constructed a new multifunctional protein that can be easily immobilized onto hydrophobic surfaces, and at the same time helps enhance specific cell adhesion and proliferation onto collagen substrates. A collagen binding domain was fused to a previously constructed protein, which had an epidermal growth factor fused to a hydrophobic peptide that allows for cell adhesion. The new fusion protein, designated fnCBD-ERE-EGF is produced in Escherichia coli, and its abilities to bind to collagen and promote cell proliferation were investigated. fnCBD-ERE-EGF was shown to keep both collagen binding and cell growth-promoting activities comparable to those of the corresponding unfused proteins. The results obtained in this study also suggest the use of a fnCBD-ERE-EGF as an alternative for the design of multifunctional ECM-bound growth factor based materials.

  6. Evolution of a multifunctional gene: The warm temperature acclimation protein Wap65 in the European seabass Dicentrarchus labrax.

    PubMed

    Sarropoulou, Elena; Fernandes, Jorge M O; Mitter, Karin; Magoulas, Antonios; Mulero, Victoriano; Sepulcre, Maria P; Figueras, Antonio; Novoa, Beatriz; Kotoulas, Georgios

    2010-05-01

    The warm temperature acclimation protein Wap65 has been shown to be involved in temperature acclimation, in immune response as well as in development. In teleosts, two types of Wap65 proteins, Wap65-1 and Wap65-2 are found, both acting as a multifunctional agent in several biological processes. In the present study we identified both transcripts Wap65-1 and Wap65-2 for the European seabass (Dicentrarchus labrax), examined their evolutionary rate and performed selection tests. The two paralogues were shown to be under moderate positive selection indicating their evolutionary adaptation. This functional diversification was further explored through expression studies. Both transcripts were differentially expressed during development as well as in various tissues and pathogen challenges, showing that Wap65-1 and Wap65-2 have evolved diverse functions. These results direct to the hypothesis that Wap65 proteins may, similarly to heat-shock proteins, have a general role in cell physiology.

  7. [The multifunctional RNA polymerase L protein of non-segmented negative strand RNA viruses catalyzes unique mRNA capping].

    PubMed

    Ogino, Tomoaki

    2014-01-01

    Non-segmented negative strand RNA viruses belonging to the Mononegavirales order possess RNA-dependent RNA polymerase L proteins within viral particles. The L protein is a multifunctional enzyme catalyzing viral RNA synthesis and processing (i.e., mRNA capping, cap methylation, and polyadenylation). Using vesicular stomatitis virus (VSV) as a prototypic model virus, we have shown that the L protein catalyzes the unconventional mRNA capping reaction, which is strikingly different from the eukaryotic reaction. Furthermore, co-transcriptional pre-mRNA capping with the VSV L protein was found to be required for accurate stop?start transcription to synthesize full-length mRNAs in vitro and virus propagation in host cells. This article provides a review of historical and present studies leading to the elucidation of the molecular mechanism of VSV mRNA capping.

  8. Savinase, the most suitable enzyme for releasing peptides from lentil (Lens culinaris var. Castellana) protein concentrates with multifunctional properties.

    PubMed

    Garcia-Mora, Patricia; Peñas, Elena; Frias, Juana; Martínez-Villaluenga, Cristina

    2014-05-07

    The aim of this study was to produce multifunctional hydrolysates from lentil protein concentrates. Four different proteases (Alcalase, Savinase, Protamex, and Corolase 7089) and different hydrolysis times were evaluated for their degree and pattern of proteolysis and their angiotensin I-converting enzyme (ACE) inhibitory and antioxidant activities. Alcalase and Savinase showed the highest proteolytic effectiveness (P ≤ 0.05), which resulted in higher yield of peptides. The hydrolysate produced by Savinase after 2 h of hydrolysis (S2) displayed the highest ACE-inhibitory (IC50 = 0.18 mg/mL) and antioxidant activity (1.22 μmol of Trolox equiv/mg of protein). Subsequent reverse-phase HPLC-tandem mass spectrometric analysis of 3 kDa permeates of S2 showed 32 peptides, mainly derived from convicilin, vicilin, and legumin containing bioactive amino acid sequences, which makes them potential contributors to ACE-inhibitory and antioxidant activities detected. The ACE-inhibitory and antioxidant activities of S2 were significantly improved after in vitro gastrointestinal digestion (P ≤ 0.05). Multifunctional hydrolysates could encourage value-added utilization of lentil proteins for the formulation of functional foods and nutraceuticals.

  9. Multifunctional cellulase and hemicellulase

    DOEpatents

    Fox, Brian G.; Takasuka, Taichi; Bianchetti, Christopher M.

    2015-09-29

    A multifunctional polypeptide capable of hydrolyzing cellulosic materials, xylan, and mannan is disclosed. The polypeptide includes the catalytic core (cc) of Clostridium thermocellum Cthe_0797 (CelE), the cellulose-specific carbohydrate-binding module CBM3 of the cellulosome anchoring protein cohesion region (CipA) of Clostridium thermocellum (CBM3a), and a linker region interposed between the catalytic core and the cellulose-specific carbohydrate binding module. Methods of using the multifunctional polypeptide are also disclosed.

  10. A Modular Method for the High-Yield Synthesis of Site-Specific Protein-Polymer Therapeutics.

    PubMed

    Pang, Yan; Liu, Jinyao; Qi, Yizhi; Li, Xinghai; Chilkoti, Ashutosh

    2016-08-22

    A versatile method is described to engineer precisely defined protein/peptide-polymer therapeutics by a modular approach that consists of three steps: 1) fusion of a protein/peptide of interest with an elastin-like polypeptide that enables facile purification and high yields; 2) installation of a clickable group at the C terminus of the recombinant protein/peptide with almost complete conversion by enzyme-mediated ligation; and 3) attachment of a polymer by a click reaction with near-quantitative conversion. We demonstrate that this modular approach is applicable to various protein/peptide drugs and used it to conjugate them to structurally diverse water-soluble polymers that prolong the plasma circulation duration of these proteins. The protein/peptide-polymer conjugates exhibited significantly improved pharmacokinetics and therapeutic effects over the native protein/peptide upon administration to mice. The studies reported here provide a facile method for the synthesis of protein/peptide-polymer conjugates for therapeutic use and other applications.

  11. One-step affinity purification of recombinant TATA binding proteins utilizing a modular protein interaction partner.

    PubMed

    Shooltz, Dean D; Alberts, Glen L; Triezenberg, Steven J

    2008-06-01

    We describe a rapid and effective procedure for purifying recombinant eukaryotic TATA binding protein (TBP) from Escherichia coli. The method employs an affinity ligand comprising glutathione-S-transferase fused to the carboxyl-terminal activation domain of the transcriptional activator VP16 and an amino-terminal domain (TAND2) of the yeast TBP-associated factor TAF1. TBP can be purified without the need for extrinsic affinity tags, subsequent proteolysis, or downstream clean-up steps. This TBP purification process is rapid (requiring about 4h after bacterial harvest) and does not require sophisticated chromatographic equipment. The resulting material is monodisperse, structured, and functionally active. We demonstrate the efficacy of this method for purifying recombinant full-length or TBP core fragments encoded by yeast, humans and Arabidopsis.

  12. Multifunctional pattern-generating circuits.

    PubMed

    Briggman, K L; Kristan, W B

    2008-01-01

    The ability of distinct anatomical circuits to generate multiple behavioral patterns is widespread among vertebrate and invertebrate species. These multifunctional neuronal circuits are the result of multistable neural dynamics and modular organization. The evidence suggests multifunctional circuits can be classified by distinct architectures, yet the activity patterns of individual neurons involved in more than one behavior can vary dramatically. Several mechanisms, including sensory input, the parallel activity of projection neurons, neuromodulation, and biomechanics, are responsible for the switching between patterns. Recent advances in both analytical and experimental tools have aided the study of these complex circuits.

  13. Chapter 3.03 - Multifunctional Enzyme Systems for Plant Cell Wall Degradation

    SciTech Connect

    Xu, Qi; Luo, Yonghua; Ding, Shi-You; Himmel, Michael E.; Bu, Lintao; Lamed, Raphael; Bayer, Edward A.

    2011-10-14

    Multifunctional enzymes refer to proteins that consist of two or more catalytic modules. Many microorganisms use multifunctional enzymes to efficiently break down the recalcitrant polymeric networks that constitute plant cell walls. Future applications of multifunctional enzymes may represent a potential solution to the problem of high enzyme cost for processing lignocellulosic biomass into fermentable sugars. Currently, commercial enzyme mixtures used in simultaneous saccharification fermentation process for biofuel production are derived primarily from free enzyme systems produced by fungi. In this context, we have analyzed the modular structures of 16 937 genes corresponding to 34 glycoside hydrolase families putatively related to the degradation of lignocellulose in the Carbohydrate Active enZyme (CAZy) database. Among these genes, 64 gene sequences have been identified to putatively encode multifunctional enzymes, and up to five catalytic modules have been found in a single polypeptide. Based on their deduced polypeptide sequences, they can be classified into four types, that is, cellulase-cellulase, cellulase-hemicellulase, hemicellulase-hemicellulase, and hemicellulase-carbohydrate esterase. The compositional modules and architectural structures of these enzymes are analyzed here, and their putative activities on breaking down cell walls are discussed. We further discuss the predicted intramolecular synergistic mechanisms between the catalytic modules, including substrate channeling, which is a mechanism often proposed for carbohydrate-binding modules residing in multifunctional enzymes. Furthermore, the potential applications of native and engineered multifunctional enzymes for biomass conversion technology are also reviewed.

  14. The adenovirus L4-22K protein is multifunctional and is an integral component of crucial aspects of infection.

    PubMed

    Wu, Kai; Orozco, Diana; Hearing, Patrick

    2012-10-01

    A variety of cellular and viral processes are coordinately regulated during adenovirus (Ad) infection to achieve optimal virus production. The Ad late gene product L4-22K has been associated with disparate activities during infection, including the regulation of late gene expression, viral DNA packaging, and infectious virus production. We generated and characterized two L4-22K mutant viruses to further explore L4-22K functions during viral infection. Our results show that L4-22K is indeed important for temporal control of viral gene expression not only because it activates late gene expression but also because it suppresses early gene expression. We also show that the L4-22K protein binds to viral packaging sequences in vivo and is essential to recruit two other packaging proteins, IVa2 and L1-52/55K, to this region. The elimination of L4-22K gave rise to the production of only empty virus capsids and not mature virions, which confirms that the L4-22K protein is required for Ad genome packaging. Finally, L4-22K contributes to adenovirus-induced cell death by regulating the expression of the adenovirus death protein. Thus, the adenovirus L4-22K protein is multifunctional and an integral component of crucial aspects of infection.

  15. The Adenovirus L4-22K Protein Is Multifunctional and Is an Integral Component of Crucial Aspects of Infection

    PubMed Central

    Wu, Kai; Orozco, Diana

    2012-01-01

    A variety of cellular and viral processes are coordinately regulated during adenovirus (Ad) infection to achieve optimal virus production. The Ad late gene product L4-22K has been associated with disparate activities during infection, including the regulation of late gene expression, viral DNA packaging, and infectious virus production. We generated and characterized two L4-22K mutant viruses to further explore L4-22K functions during viral infection. Our results show that L4-22K is indeed important for temporal control of viral gene expression not only because it activates late gene expression but also because it suppresses early gene expression. We also show that the L4-22K protein binds to viral packaging sequences in vivo and is essential to recruit two other packaging proteins, IVa2 and L1-52/55K, to this region. The elimination of L4-22K gave rise to the production of only empty virus capsids and not mature virions, which confirms that the L4-22K protein is required for Ad genome packaging. Finally, L4-22K contributes to adenovirus-induced cell death by regulating the expression of the adenovirus death protein. Thus, the adenovirus L4-22K protein is multifunctional and an integral component of crucial aspects of infection. PMID:22811519

  16. New insight into multifunctional role of peroxiredoxin family protein: Determination of DNA protection properties of bacterioferritin comigratory protein under hyperthermal and oxidative stresses

    SciTech Connect

    Lee, Sangmin; Chung, Jeong Min; Yun, Hyung Joong; Won, Jonghan; Jung, Hyun Suk

    2016-01-22

    Bacterioferritin comigratory protein (BCP) is a monomeric conformer acting as a putative thiol-dependent bacterial peroxidase, however molecular basis of DNA-protection via DNA-binding has not been clearly understood. In this study, we characterized the DNA binding properties of BCP using various lengths and differently shaped architectures of DNA. An electrophoretic mobility shift assay and electron microscopy analysis showed that recombinant TkBCP bound to DNA of a circular shape (double-stranded DNA and single-stranded DNA) and a linear shape (16–1000 bp) as well as various architectures of DNA. In addition, DNA protection experiments indicated that TkBCP can protect DNA against hyperthermal and oxidative stress by removing highly reactive oxygen species (ROS) or by protecting DNA from thermal degradation. Based on these results, we suggest that TkBCP is a multi-functional DNA-binding protein which has DNA chaperon and antioxidant functions. - Highlights: • Bacterioferritin comigratory protein (BCP) protects DNA from oxidative stress by reducing ROS. • TkBCP does not only scavenge ROS, but also protect DNA from hyperthermal stress. • BCP potentially adopts the multi-functional role in DNA binding activities and anti-oxidant functions.

  17. Multifunctional Thioredoxin-Like Protein from the Gastrointestinal Parasitic Nematodes Strongyloides ratti and Trichuris suis Affects Mucosal Homeostasis

    PubMed Central

    Hansmann, Jan; Winter, Dominic; Schramm, Guido; Erttmann, Klaus D.; Liebau, Eva

    2016-01-01

    The cellular redox state is important for the regulation of multiple functions and is essential for the maintenance of cellular homeostasis and antioxidant defense. In the excretory/secretory (E/S) products of Strongyloides ratti and Trichuris suis sequences for thioredoxin (Trx) and Trx-like protein (Trx-lp) were identified. To characterize the antioxidant Trx-lp and its interaction with the parasite's mucosal habitat, S. ratti and T. suis Trx-lps were cloned and recombinantly expressed. The primary antioxidative activity was assured by reduction of insulin and IgM. Further analysis applying an in vitro mucosal 3D-cell culture model revealed that the secreted Trx-lps were able to bind to monocytic and intestinal epithelial cells and induce the time-dependent release of cytokines such as TNF-α, IL-22, and TSLP. In addition, the redox proteins also possessed chemotactic activity for monocytic THP-1 cells and fostered epithelial wound healing activity. These results confirm that the parasite-secreted Trx-lps are multifunctional proteins that can affect the host intestinal mucosa. PMID:27872753

  18. Multi-functional roles for the polypeptide transport associated domains of Toc75 in chloroplast protein import

    PubMed Central

    Paila, Yamuna D; Richardson, Lynn GL; Inoue, Hitoshi; Parks, Elizabeth S; McMahon, James; Inoue, Kentaro; Schnell, Danny J

    2016-01-01

    Toc75 plays a central role in chloroplast biogenesis in plants as the membrane channel of the protein import translocon at the outer envelope of chloroplasts (TOC). Toc75 is a member of the Omp85 family of bacterial and organellar membrane insertases, characterized by N-terminal POTRA (polypeptide-transport associated) domains and C-terminal membrane-integrated β-barrels. We demonstrate that the Toc75 POTRA domains are essential for protein import and contribute to interactions with TOC receptors, thereby coupling preprotein recognition at the chloroplast surface with membrane translocation. The POTRA domains also interact with preproteins and mediate the recruitment of molecular chaperones in the intermembrane space to facilitate membrane transport. Our studies are consistent with the multi-functional roles of POTRA domains observed in other Omp85 family members and demonstrate that the domains of Toc75 have evolved unique properties specific to the acquisition of protein import during endosymbiotic evolution of the TOC system in plastids. DOI: http://dx.doi.org/10.7554/eLife.12631.001 PMID:26999824

  19. Multifunctional epoxy supports: a new tool to improve the covalent immobilization of proteins. The promotion of physical adsorptions of proteins on the supports before their covalent linkage.

    PubMed

    Mateo, C; Fernández-Lorente, G; Abian, O; Fernández-Lafuente, R; Guisán, J M

    2000-01-01

    Multifunctional supports containing epoxy groups are here proposed as a second generation of activated supports for covalent immobilization of enzymes following the epoxy chemistry on any type of support (hydrophobic or hydrophilic ones) under very mild experimental conditions (e.g., low ionic strength, neutral pH values, and low temperatures). These multifunctional supports have been easily prepared by modifying a small fraction (10-20%) of the epoxy groups contained in commercial epoxy supports. In this way, additional groups that were able to physically adsorb proteins (e.g., cationic or anionic groups, metal chelate, phenyl boronate) are generated on the support surface. The covalent immobilization of proteins on these supports proceeds via their initial physical adsorption on the supports (via different structural features). Then, "intramolecular" covalent linkages between some nucleophilic groups of the adsorbed enzyme (e.g., amino, thiol, or hydroxy groups) and the dense layer of nearby epoxy groups on the support are established. This two-step covalent immobilization dramatically improves the very low reactivity of epoxy groups toward nonadsorbed proteins. In this way, all other relevant practical advantages of epoxy groups for protein immobilization (their high stability and their ability to form very strong linkages with several nucleophilic enzyme residues with minimal chemical modification) can be an object of universal exploitation. The use of these new multifunctional supports exhibits important advantages regarding immobilization of enzymes previously adsorbed on hydrophobic homofunctional epoxy supports: (i) hydrophilic supports can also be used for immobilization of industrial enzymes; (ii) immobilization can also be carried out at low ionic strength; (iii) every protein contained in crude extracts from Escherichia coli and Acetobacter turbidans can be immobilized by sequentially using a set of different supports; (iv) in most cases, each enzyme

  20. Mouse Spam1 (PH-20) is a multifunctional protein: evidence for its expression in the female reproductive tract.

    PubMed

    Zhang, Hong; Martin-DeLeon, Patricia A

    2003-08-01

    Sperm adhesion molecule 1 (Spam1) is a widely conserved sperm surface protein with multiple roles in mammalian fertilization. Although the gene for this protein has been thought to be testis specific based on Northern blot analysis, there is evidence for nontesticular expression when transcripts are analyzed by more sensitive techniques. In the present investigation, results of a reverse transcription polymerase chain reaction assay, an RNase-protection assay (RPA), and an in situ transcript hybridization assay revealed that the murine Spam1 gene is transcribed in the female genital tract. RPA revealed that Spam1 transcripts are synthesized in a region-dependent manner, with the oviduct having lower transcript levels than the uterus and vagina. The transcripts levels were 3- to 10-fold lower in the female genital tract than in the testis. In situ transcript hybridization assay revealed RNA in the luminal epithelium in all three regions of the genital tract and in the uterine myometrium and the oviductal mesothelium. Western blot analysis and immunohistochemistry demonstrated that the protein concentration is 1.5- to 3-fold lower in female tissues than in sperm, and localization is similar to that of the transcripts. The protein has hyaluronidase activity at neutral pH, which is unique for sperm hyaluronidase, but not at acidic pH. In the uterus, Spam1 expression fluctuated during the estrous cycle. Its localization suggests that in addition to functioning as a secretory protein, it may be involved in hyaluronic acid metabolism or turnover in the female genital tract. Our results provide further evidence that Spam1 is a multifunctional protein and that it is less restricted in its expression than previously reported.

  1. Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase

    PubMed Central

    Jacobs, Dave; Glossip, Danielle; Xing, Heming; Muslin, Anthony J.; Kornfeld, Kerry

    1999-01-01

    MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, form a modular recognition system, as they can function independently or in combination. FXFP is specific for ERK, whereas the D box mediates binding to ERK and JNK MAP kinase, suggesting that the partially overlapping substrate specificities of ERK and JNK result from recognition of shared and unique docking sites. These findings enabled us to predict new ERK substrates and design peptide inhibitors of ERK that functioned in vitro and in vivo. PMID:9925641

  2. A Compact, Multifunctional Fusion Module Directs Cholesterol-Dependent Homomultimerization and Syncytiogenic Efficiency of Reovirus p10 FAST Proteins

    PubMed Central

    Key, Tim; Duncan, Roy

    2014-01-01

    The homologous p10 fusion-associated small transmembrane (FAST) proteins of the avian (ARV) and Nelson Bay (NBV) reoviruses are the smallest known viral membrane fusion proteins, and are virulence determinants of the fusogenic reoviruses. The small size of FAST proteins is incompatible with the paradigmatic membrane fusion pathway proposed for enveloped viral fusion proteins. Understanding how these diminutive viral fusogens mediate the complex process of membrane fusion is therefore of considerable interest, from both the pathogenesis and mechanism-of-action perspectives. Using chimeric ARV/NBV p10 constructs, the 36–40-residue ectodomain was identified as the major determinant of the differing fusion efficiencies of these homologous p10 proteins. Extensive mutagenic analysis determined the ectodomain comprises two distinct, essential functional motifs. Syncytiogenesis assays, thiol-specific surface biotinylation, and liposome lipid mixing assays identified an ∼25-residue, N-terminal motif that dictates formation of a cystine loop fusion peptide in both ARV and NBV p10. Surface immunofluorescence staining, FRET analysis and cholesterol depletion/repletion studies determined the cystine loop motif is connected through a two-residue linker to a 13-residue membrane-proximal ectodomain region (MPER). The MPER constitutes a second, independent motif governing reversible, cholesterol-dependent assembly of p10 multimers in the plasma membrane. Results further indicate that: (1) ARV and NBV homomultimers segregate to distinct, cholesterol-dependent microdomains in the plasma membrane; (2) p10 homomultimerization and cholesterol-dependent microdomain localization are co-dependent; and (3) the four juxtamembrane MPER residues present in the multimerization motif dictate species-specific microdomain association and homomultimerization. The p10 ectodomain therefore constitutes a remarkably compact, multifunctional fusion module that directs syncytiogenic efficiency and

  3. BAG3 Is a Modular, Scaffolding Protein that physically Links Heat Shock Protein 70 (Hsp70) to the Small Heat Shock Proteins.

    PubMed

    Rauch, Jennifer N; Tse, Eric; Freilich, Rebecca; Mok, Sue-Ann; Makley, Leah N; Southworth, Daniel R; Gestwicki, Jason E

    2017-01-06

    Small heat shock proteins (sHsps) are a family of ATP-independent molecular chaperones that are important for binding and stabilizing unfolded proteins. In this task, the sHsps have been proposed to coordinate with ATP-dependent chaperones, including heat shock protein 70 (Hsp70). However, it is not yet clear how these two important components of the chaperone network are linked. We report that the Hsp70 co-chaperone, BAG3, is a modular, scaffolding factor to bring together sHsps and Hsp70s. Using domain deletions and point mutations, we found that BAG3 uses both of its IPV motifs to interact with sHsps, including Hsp27 (HspB1), αB-crystallin (HspB5), Hsp22 (HspB8), and Hsp20 (HspB6). BAG3 does not appear to be a passive scaffolding factor; rather, its binding promoted de-oligomerization of Hsp27, likely by competing for the self-interactions that normally stabilize large oligomers. BAG3 bound to Hsp70 at the same time as Hsp22, Hsp27, or αB-crystallin, suggesting that it might physically bring the chaperone families together into a complex. Indeed, addition of BAG3 coordinated the ability of Hsp22 and Hsp70 to refold denatured luciferase in vitro. Together, these results suggest that BAG3 physically and functionally links Hsp70 and sHsps.

  4. Scalable Production of a Multifunctional Protein (TSG-6) That Aggregates with Itself and the CHO Cells That Synthesize It

    PubMed Central

    Kim, Dong-Ki; Choi, Hosoon; Nishida, Hidetaka; Oh, Joo Youn; Gregory, Carl; Lee, Ryang Hwa; Yu, Ji Min; Watanabe, Jun; An, Su Yeon; Bartosh, Thomas J.; Prockop, Darwin J.

    2016-01-01

    TNF-α stimulated gene/protein 6 (TNFAIP6/TSG-6) is a multifunctional protein that has a number of potential therapeutic applications. Experiments and clinical trials with TSG-6, however, have been limited by the technical difficulties of producing the recombinant protein. We prepared stable clones of CHO cells that expressed recombinant human TSG-6 (rhTSG-6) as a secreted glycoprotein. Paradoxically, both cell number and protein production decreased dramatically when the clones were expanded. The decreases occurred because the protein aggregated the synthesizing CHO cells by binding to the brush border of hyaluronan that is found around many cultured cells. In addition, the rhTSG-6 readily self-aggregated. To address these problems, we added to the medium an inhibitor of hyaluronan synthesis and heparin to compete with the binding of TSG-6 to hyaluronan. Also, we optimized the composition of the culture medium, and transferred the CHO cells from a spinner culture system to a bioreactor that controlled pH and thereby decreased pH-dependent binding properties of the protein. With these and other improvements in the culture conditions, we obtained 57.0 mg ± 9.16 S.D. of rhTSG-6 in 5 or 6 liter of medium. The rhTSG-6 accounted for 18.0% ± 3.76 S.D. of the total protein in the medium. We then purified the protein with a Ni-chelate column that bound the His tag engineered into the C-terminus of the protein followed by an anion exchange column. The yield of the purified monomeric rhTSG-6 was 4.1 mg to 5.6 mg per liter of culture medium. After intravenous injection into mice, the protein had a longer plasma half-life than commercially available rhTSG-6 isolated from a mammalian cell lysate, apparently because it was recovered as a secreted glycoprotein. The bioactivity of the rhTSG-6 in suppressing inflammation was demonstrated in a murine model. PMID:26793973

  5. The YopD translocator of Yersinia pseudotuberculosis is a multifunctional protein comprised of discrete domains.

    PubMed

    Olsson, Jan; Edqvist, Petra J; Bröms, Jeanette E; Forsberg, Ake; Wolf-Watz, Hans; Francis, Matthew S

    2004-07-01

    To establish an infection, Yersinia pseudotuberculosis utilizes a plasmid-encoded type III translocon to microinject several anti-host Yop effectors into the cytosol of target eukaryotic cells. YopD has been implicated in several key steps during Yop effector translocation, including maintenance of yop regulatory control and pore formation in the target cell membrane through which effectors traverse. These functions are mediated, in part, by an interaction with the cognate chaperone, LcrH. To gain insight into the complex molecular mechanisms of YopD function, we performed a systematic mutagenesis study to search for discrete functional domains. We highlighted amino acids beyond the first three N-terminal residues that are dispensable for YopD secretion and confirmed that an interaction between YopD and LcrH is essential for maintenance of yop regulatory control. In addition, discrete domains within YopD that are essential for both pore formation and translocation of Yop effectors were identified. Significantly, other domains were found to be important for effector microinjection but not for pore formation. Therefore, YopD is clearly essential for several discrete steps during efficient Yop effector translocation. Recognition of this modular YopD domain structure provides important insights into the function of YopD.

  6. Initiating protease with modular domains interacts with β-glucan recognition protein to trigger innate immune response in insects.

    PubMed

    Takahashi, Daisuke; Garcia, Brandon L; Kanost, Michael R

    2015-11-10

    The autoactivation of an initiating serine protease upon binding of pattern recognition proteins to pathogen surfaces is a crucial step in eliciting insect immune responses such as the activation of Toll and prophenoloxidase pathways. However, the molecular mechanisms responsible for autoactivation of the initiating protease remains poorly understood. Here, we investigated the molecular basis for the autoactivation of hemolymph protease 14 (HP14), an initiating protease in hemolymph of Manduca sexta, upon the binding of β-1,3-glucan by its recognition protein, βGRP2. Biochemical analysis using HP14 zymogen (proHP14), βGRP2, and the recombinant proteins as truncated forms showed that the amino-terminal modular low-density lipoprotein receptor class A (LA) domains within HP14 are required for proHP14 autoactivation that is stimulated by its interaction with βGRP2. Consistent with this result, recombinant LA domains inhibit the activation of proHP14 and prophenoloxidase, likely by competing with the interaction between βGRP2 and LA domains within proHP14. Using surface plasmon resonance, we demonstrated that immobilized LA domains directly interact with βGRP2 in a calcium-dependent manner and that high-affinity interaction requires the C-terminal glucanase-like domain of βGRP2. Importantly, the affinity of LA domains for βGRP2 increases nearly 100-fold in the presence of β-1,3-glucan. Taken together, these results present the first experimental evidence to our knowledge that LA domains of an insect modular protease and glucanase-like domains of a βGRP mediate their interaction, and that this binding is essential for the protease autoactivation. Thus, our study provides important insight into the molecular basis underlying the initiation of protease cascade in insect immune responses.

  7. Initiating protease with modular domains interacts with β-glucan recognition protein to trigger innate immune response in insects

    PubMed Central

    Takahashi, Daisuke; Garcia, Brandon L.; Kanost, Michael R.

    2015-01-01

    The autoactivation of an initiating serine protease upon binding of pattern recognition proteins to pathogen surfaces is a crucial step in eliciting insect immune responses such as the activation of Toll and prophenoloxidase pathways. However, the molecular mechanisms responsible for autoactivation of the initiating protease remains poorly understood. Here, we investigated the molecular basis for the autoactivation of hemolymph protease 14 (HP14), an initiating protease in hemolymph of Manduca sexta, upon the binding of β-1,3-glucan by its recognition protein, βGRP2. Biochemical analysis using HP14 zymogen (proHP14), βGRP2, and the recombinant proteins as truncated forms showed that the amino-terminal modular low-density lipoprotein receptor class A (LA) domains within HP14 are required for proHP14 autoactivation that is stimulated by its interaction with βGRP2. Consistent with this result, recombinant LA domains inhibit the activation of proHP14 and prophenoloxidase, likely by competing with the interaction between βGRP2 and LA domains within proHP14. Using surface plasmon resonance, we demonstrated that immobilized LA domains directly interact with βGRP2 in a calcium-dependent manner and that high-affinity interaction requires the C-terminal glucanase-like domain of βGRP2. Importantly, the affinity of LA domains for βGRP2 increases nearly 100-fold in the presence of β-1,3-glucan. Taken together, these results present the first experimental evidence to our knowledge that LA domains of an insect modular protease and glucanase-like domains of a βGRP mediate their interaction, and that this binding is essential for the protease autoactivation. Thus, our study provides important insight into the molecular basis underlying the initiation of protease cascade in insect immune responses. PMID:26504233

  8. Multifunctional and Redundant Roles of Leptospira interrogans Proteins in Bacterial-Adhesion and fibrin clotting inhibition.

    PubMed

    Pereira, Priscila R M; Fernandes, Luis G V; de Souza, Gisele O; Vasconcellos, Silvio A; Heinemann, Marcos B; Romero, Eliete C; Nascimento, Ana L T O

    2017-09-01

    Pathogenic Leptopira is the etiological agent of leptospirosis, the most widespread zoonotic infection in the world. The disease represents a major public health problem, especially in tropical countries. The present work focused on two hypothetical proteins of unknown function, encoded by the genes LIC13059 and LIC10879, and predicted to be surface-exposed proteins. The genes were cloned and the proteins expressed using E. coli as a host system. We report that the recombinant proteins interacted with extracellular matrix (ECM) laminin, in a dose-dependent fashion and are novel potential adhesins. The recombinant proteins were called Lsa25.6 (rLIC13059) and Lsa16 (rLIC10879), for Leptospiral surface adhesins, followed by the respective molecular masses. The proteins attached to plasminogen (PLG), generating plasmin, in the presence of PLG-activator uPA. Both proteins bind to fibrinogen (Fg), but only Lsa25.6 inhibited fibrin clotting by thrombin-catalyzed reaction. Moreover, Lsa16 interacts with the mammalian cell receptor E-cadherin, and could contribute to bacterial attachment to epithelial cells. The proteins were recognized by confirmed leptospirosis serum samples, suggesting that they are expressed during infection. The corresponding leptospiral proteins are surface exposed based on proteinase K accessibility assay, being LIC10879 most probably exposed in its dimer form. The data of this study extend the spectrum of surface-exposed proteins of L. interrogans and indicate a possible role of the originally annotated hypothetical proteins in infection processes. Copyright © 2017 Elsevier GmbH. All rights reserved.

  9. A modular DNA carrier protein based on the structure of diphtheria toxin mediates target cell-specific gene delivery.

    PubMed

    Uherek, C; Fominaya, J; Wels, W

    1998-04-10

    Modular fusion proteins that combine distinct functions required for cell type-specific uptake and intracellular delivery of DNA present an attractive approach for the development of self-assembling vectors for targeted gene delivery. Here, we describe a novel DNA carrier protein termed GD5 that mimics the structure of the bacterial diphtheria toxin (DT) and facilitates target cell-specific gene transfer via receptor-mediated endocytosis. GD5 carries at the N terminus the DNA-binding domain of the yeast transcription factor Gal4, which is connected to a C-terminal antibody fragment specific for the tumor-associated ErbB2 antigen via an internal DT translocation domain as an endosome escape activity. Bacterially expressed GD5 protein specifically bound to ErbB2-expressing cells and formed protein-DNA complexes with a luciferase reporter gene construct. These complexes, after compensation of excess negative charge with poly-L-lysine, served as a specific transfection vector for ErbB2-expressing cells. Inhibitors of endosomal acidification drastically reduced GD5-mediated transfection, indicating that the DT translocation domain of GD5, similar to the parental toxin, is strictly dependent on the transit through an acidic environment. Our results suggest that fusion proteins that employ the natural endosome escape mechanism of bacterial toxins might aid in the development of efficient nonviral vectors for applications in gene therapy.

  10. Protein kinase CK2 phosphorylation regulates the interaction of Kaposi's sarcoma-associated herpesvirus regulatory protein ORF57 with its multifunctional partner hnRNP K

    PubMed Central

    Malik, Poonam; Clements, J. Barklie

    2004-01-01

    ORF57 protein of Kaposi's sarcoma-associated herpesvirus has a counterpart in all herpesvirus of mammals and birds and regulates gene expression at transcriptional and post-transcriptional levels. ORF57 was capable of self-interaction and bound a rapidly migrating form of heterogeneous nuclear ribonucleoprotein K (hnRNP K), a multifunctional cellular protein involved in gene expression. In virus infected cell extracts, ORF57 was present in a complex with hnRNP K that had protein kinase CK2 activity, and was phosphorylated by CK2. Different regions of ORF57 bound both catalytic α/α′ and regulatory β subunits of CK2. CK2 modification enhanced the ORF57–hnRNP K interaction, and may regulate the presence and activities of components in the complex. We suggest that ORF57 and hnRNP K interaction may modulate ORF57-mediated regulation of viral gene expression. Herpesviral ORF57 (Rhadinovirus) and ICP27 (Simplexvirus) proteins both interact with hnRNP K and CK2 implying that adaptation of the ancestral hnRNP K and CK2 to associate with viral regulatory ancestor protein likely pre-dates divergence of these Herpesviridae genera that occurred 200 million years ago. PMID:15486205

  11. Thermochemical nanolithography of multi-functional templates for selective assembly of bioactive proteins

    NASA Astrophysics Data System (ADS)

    Wang, Debin; Kodali, Vamsi; Underwood, William; Jarvholm, Jonas; Okada, Takashi; Jones, Simon; Rumi, Mariacristina; Dai, Zhenting; King, William; Marder, Seth; Curtis, Jennifer; Riedo, Elisa

    2009-03-01

    Atomic force microscopy based techniques have been successful in generating protein nano-arrays on various substrates. However, several challenges still exist in terms of resolution, writing speed, cost, substrate choice, protein bioactivity, multi-component patterning, and surface passivation. Recently, we have developed the use of thermochemical nanolithography combined with post covalent functionalization and molecular recognition on a polymer surface of a single chip to produce multiplexed nanopatterns at speeds of mm/s. These patterns can then be functionalized under native conditions to create tailored nano-assemblies of two different species of proteins coexisting on the same surface. The proteins attach selectively and strongly to the nanopatterns via covalent and/or specific interactions, while retaining their ability to interact specifically with other proteins in buffered solution. At present, this method has produced nanopatterns of bio-active proteins with features as small as 40 nm on polymer films. This technique opens up new possibilities in nanoscale manipulation of biological macromolecules as well as many molecular biophysics studies such as inter-protein interactions.

  12. Highly selective isolation and purification of heme proteins in biological samples using multifunctional magnetic nanospheres.

    PubMed

    Liu, Yating; Li, Yan; Wei, Yun

    2014-12-01

    Magnetic particles with suitable surface modification are capable of binding proteins selectively, and magnetic separations have advantages of rapidity, convenience, and high selectivity. In this paper, new magnetic nanoparticles modified with imidazolium ionic liquid (Fe3O4 @SiO2 @ILs) were successfully fabricated. N-Methylimidazolium was immobilized onto silica-coated magnetic nanoparticles via γ-chloropropyl modification as a magnetic nanoadsorbent for heme protein separation. The particle size was about 90 nm without significant aggregation during the preparation process. Hemoglobin as one of heme proteins used in this experiment was compared with other nonheme proteins. It has been found that the magnetic nanoparticles can be used for more rapid, efficient, and specific adsorption of hemoglobin with a binding capacity as high as 5.78 mg/mg. In comparison with other adsorption materials of proteins in the previous reports, Fe3 O4 @SiO2 @ILs magnetic nanoparticles exhibit the excellent performance in isolation of heme proteins with higher binding capacity and selectivity. In addition, a short separation time makes the functionalized nanoparticles suitable for purifying unstable proteins, as well as having other potential applications in a variety of biomedical fields.

  13. Expression of the multifunctional Y-box protein, YB-1, in myofibroblasts of the infarcted rat heart

    SciTech Connect

    Kamalov, German; Varma, Balwantkumar R.; Lu Li; Sun Yao; Weber, Karl T.; Guntaka, Ramareddy V. . E-mail: rguntaka@utmem.edu

    2005-08-19

    Intracellular signaling mechanisms regulating the turnover of {alpha}-SMA-positive myofibroblasts (myoFbs) at the site of myocardial infarction (MI) are poorly understood. Y-Box (YB)-1, a multifunctional protein, may be involved in regulation of proliferation, migration and apoptosis of myoFbs. Our objective was to study the expression of YB-1 in the infarcted rat heart and its localization in myoFbs. On days 3-28 following MI, we monitored YB-1 expression and its colocalization with {alpha}-SMA, and proliferation markers PCNA and Ki-67 in infarcted tissue by Western blot, immunohistochemistry, and immunofluorescent double-labeling. YB-1 is barely detectable in normal myocardium. At the infarct site, however, YB-1 is markedly elevated from day 3 post-MI concomitant with the induction of cell proliferation. MyoFbs are the major source of YB-1 and retain it up to day 28 post-MI. We suggest early expression of YB-1 promotes proliferation and migration of myoFbs, whereas prolonged expression may be responsible for scar formation.

  14. Polyelectrolyte/silver nanocomposite multilayer films as multifunctional thin film platforms for remote activated protein and drug delivery.

    PubMed

    Anandhakumar, S; Raichur, Ashok M

    2013-11-01

    We demonstrate a nanoparticle loading protocol to develop a transparent, multifunctional polyelectrolyte multilayer film for externally activated drug and protein delivery. The composite film was designed by alternate adsorption of poly(allylamine hydrochloride) (PAH) and dextran sulfate (DS) on a glass substrate followed by nanoparticle synthesis through a polyol reduction method. The films showed a uniform distribution of spherical silver nanoparticles with an average diameter of 50±20 nm, which increased to 80±20 nm when the AgNO3 concentration was increased from 25 to 50 mM. The porous and supramolecular structure of the polyelectrolyte multilayer film was used to immobilize ciprofloxacin hydrochloride (CH) and bovine serum albumin (BSA) within the polymeric network of the film. When exposed to external triggers such as ultrasonication and laser light the loaded films were ruptured and released the loaded BSA and CH. The release of CH is faster than that of BSA due to a higher diffusion rate. Circular dichroism measurements confirmed that there was no significant change in the conformation of released BSA in comparison with native BSA. The fabricated films showed significant antibacterial activity against the bacterial pathogen Staphylococcus aureus. Applications envisioned for such drug-loaded films include drug and vaccine delivery through the transdermal route, antimicrobial or anti-inflammatory coatings on implants and drug-releasing coatings for stents. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  15. Multifunctional Delivery Systems for Advanced oral Uptake of Peptide/Protein Drugs.

    PubMed

    Park, Jin Woo; Kim, Sun Jin; Kwag, Dong Sup; Kim, Sol; Park, Jeyoung; Youn, Yu Seok; Bae, You Han; Lee, Eun Seong

    2015-01-01

    In recent years, advances in biotechnology and protein engineering have enabled the production of large quantities of proteins and peptides as important therapeutic agents. Various researchers have used biocompatible functional polymers to prepare oral dosage forms of proteins and peptides for chronic use and for easier administration to enhance patient compliance. However, there is a need to enhance their safety and effectiveness further. Most macromolecules undergo severe denaturation at low pH and enzymatic degradation in the gastrointestinal tract. The macromolecules' large molecular size and low lipophilicity cause low permeation through the intestinal membrane. The major strategies that have been used to overcome these challenges (in oral drug carrier systems) can be classified as follows: enteric coating or encapsulation with pH-sensitive polymers or mucoadhesive polymers, co-administration of protease inhibitors, incorporation of absorption enhancers, modification of the physicochemical properties of the macromolecules, and site-specific delivery to the colon. This review attempts to summarize the various advanced oral delivery carriers, including nanoparticles, lipid carriers, such as liposomes, nano-aggregates using amphiphilic polymers, complex coacervation of oppositely charged polyelectrolytes, and inorganic porous particles. The particles were formulated and/or surface modified with functional polysaccharides or synthetic polymers to improve oral bioavailability of proteins and peptides. We also discuss formulation strategies to overcome barriers, therapeutic efficacies in vivo, and potential benefits and issues for successful oral dosage forms of the proteins and peptides.

  16. Harpins, multifunctional proteins secreted by gram-negative plant-pathogenic bacteria.

    PubMed

    Choi, Min-Seon; Kim, Wooki; Lee, Chanhui; Oh, Chang-Sik

    2013-10-01

    Harpins are glycine-rich and heat-stable proteins that are secreted through type III secretion system in gram-negative plant-pathogenic bacteria. Many studies show that these proteins are mostly targeted to the extracellular space of plant tissues, unlike bacterial effector proteins that act inside the plant cells. Over the two decades since the first harpin of pathogen origin, HrpN of Erwinia amylovora, was reported in 1992 as a cell-free elicitor of hypersensitive response (HR), diverse functional aspects of harpins have been determined. Some harpins were shown to have virulence activity, probably because of their involvement in the translocation of effector proteins into plant cytoplasm. Based on this function, harpins are now considered to be translocators. Their abilities of pore formation in the artificial membrane, binding to lipid components, and oligomerization are consistent with this idea. When harpins are applied to plants directly or expressed in plant cells, these proteins trigger diverse beneficial responses such as induction of defense responses against diverse pathogens and insects and enhancement of plant growth. Therefore, in this review, we will summarize the functions of harpins as virulence factors (or translocators) of bacterial pathogens, elicitors of HR and immune responses, and plant growth enhancers.

  17. Multifunctionality and mechanism of ligand binding in a mosquito antiinflammatory protein

    SciTech Connect

    Calvo, Eric; Mans, Ben J.; Ribeiro, José M.C.; Andersen, John F.

    2009-04-07

    The mosquito D7 salivary proteins are encoded by a multigene family related to the arthropod odorant-binding protein (OBP) superfamily. Forms having either one or two OBP domains are found in mosquito saliva. Four single-domain and one two-domain D7 proteins from Anopheles gambiae and Aedes aegypti (AeD7), respectively, were shown to bind biogenic amines with high affinity and with a stoichiometry of one ligand per protein molecule. Sequence comparisons indicated that only the C-terminal domain of AeD7 is homologous to the single-domain proteins from A. gambiae, suggesting that the N-terminal domain may bind a different class of ligands. Here, we describe the 3D structure of AeD7 and examine the ligand-binding characteristics of the N- and C-terminal domains. Isothermal titration calorimetry and ligand complex crystal structures show that the N-terminal domain binds cysteinyl leukotrienes (cysLTs) with high affinities (50-60 nM) whereas the C-terminal domain binds biogenic amines. The lipid chain of the cysLT binds in a hydrophobic pocket of the N-terminal domain, whereas binding of norepinephrine leads to an ordering of the C-terminal portion of the C-terminal domain into an alpha-helix that, along with rotations of Arg-176 and Glu-268 side chains, acts to bury the bound ligand.

  18. [Modular enteral nutrition in pediatrics].

    PubMed

    Murillo Sanchís, S; Prenafeta Ferré, M T; Sempere Luque, M D

    1991-01-01

    Modular Enteral Nutrition may be a substitute for Parenteral Nutrition in children with different pathologies. Study of 4 children with different pathologies selected from a group of 40 admitted to the Maternal-Childrens Hospital "Valle de Hebrón" in Barcelona, who received modular enteral nutrition. They were monitored on a daily basis by the Dietician Service. Modular enteral nutrition consists of modules of proteins, peptides, lipids, glucids and mineral salts-vitamins. 1.--Craneo-encephalic traumatisms with loss of consciousness, Feeding with a combination of parenteral nutrition and modular enteral nutrition for 7 days. In view of the tolerance and good results of the modular enteral nutrition, the parenteral nutrition was suspended and modular enteral nutrition alone used up to a total of 43 days. 2.--55% burns with 36 days of hyperproteic modular enteral nutrition together with normal feeding. A more rapid recovery was achieved with an increase in total proteins and albumin. 3.--Persistent diarrhoea with 31 days of modular enteral nutrition, 5 days on parenteral nutrition alone and 8 days on combined parenteral nutrition and modular enteral nutrition. In view of the tolerance and good results of the modular enteral nutrition, the parenteral nutrition was suspended. 4.--Mucoviscidosis with a total of 19 days on modular enteral nutrition, 12 of which were exclusively on modular enteral nutrition and 7 as a night supplement to normal feeding. We administered proteic intakes of up to 20% of the total calorific intake and in concentrations of up to 1.2 calories/ml of the final preparation, always with a good tolerance. Modular enteral nutrition can and should be used as a substitute for parenteral nutrition in children with different pathologies, thus preventing the complications inherent in parenteral nutrition.

  19. phiX174 cistron A protein is a multifunctional enzyme in DNA replication.

    PubMed

    Eisenberg, S; Griffith, J; Kornberg, A

    1977-08-01

    The cistron A protein induced by phage varphiX174 nicks (produces a single-strand break in) the viral strand of the superhelical varphiX duplex DNA, thereby forming a complex with the DNA. The protein, seen bound to the DNA in the electron microscope, was located in the restriction endonuclease fragment between nucleotides 4290 and 4330 on the varphiX map [Sanger, F., Air, G. M., Barrel, B. G., Brown, N. L., Coulson, A. R., Fiddes, J. C., Hutchison, C. A., III, Slocomb, P. M. Y. & Smith, M. (1977) Nature 265, 687-695]. Replication also was initiated at this point, thus identifying the site of cistron A protein nicking and binding as the origin of replication. The cisA-DNA complex (separated from free cistron A protein), upon the addition of Escherichia coli rep protein, ATP, and DNA binding protein, is unwound to generate a single-stranded linear [presumably the nicked (+) strand] and a circular [presumably the (-) strand] molecule. The cisA-DNA complex, upon the further addition of DNA polymerase III holoenzyme and deoxynucleoside triphosphates, supports replication to generate viral, single-stranded circles, as many as 15 circles per cisA-DNA complex. The replicating intermediates seen in the electron microscope are a novel form of "rolling circle" [Gilbert, W. & Dressler, D. H. (1969) Cold Spring Harbor Symp. Quant. Biol. 33, 473-485]. The 5' end (presumably with the cistron A protein bound to it) is locked in the replication fork and loops back to accompany the strand-separation and replication fork around the template [(-) strand] circle. Thus, the multiple functions of cistron A protein include: (i) nicking the viral strand at the origin of replication to initiate a round of replication, (ii) participating in a complex which supports fork movement in strand separation and replication, (iii) nicking again at the regenerated origin to produce a unit-length DNA, and (iv) ligating the newly generated 3'-OH end to the 5'-phosphate-complexed end to form a circular

  20. The Sbi protein is a multifunctional immune evasion factor of Staphylococcus aureus.

    PubMed

    Smith, Emma Jane; Visai, Livia; Kerrigan, Steven W; Speziale, Pietro; Foster, Timothy J

    2011-09-01

    The second immunoglobulin-binding protein (Sbi) of Staphylococcus aureus has two N-terminal domains that bind the Fc region of IgG in a fashion similar to that of protein A and two domains that can bind to the complement protein C3 and promote its futile consumption in the fluid phase. It has been proposed that Sbi helps bacteria to avoid innate immune defenses. By comparing a mutant defective in Sbi with mutants defective in protein A, clumping factor A, iron-regulated surface determinant H, and capsular polysaccharide, it was shown that Sbi is indeed an immune evasion factor that promotes bacterial survival in whole human blood and the avoidance of neutrophil-mediated opsonophagocytosis. Sbi is present in the culture supernatant and is also associated with the cell envelope. S. aureus strains that expressed truncates of Sbi lacking N-terminal domains D1 and D2 (D1D2) or D3 and D4 (D3D4) or a C-terminal truncate that was no longer retained in the cell envelope were analyzed. Both the secreted and envelope-associated forms of Sbi contributed to immune evasion. The IgG-binding domains contributed only when Sbi was attached to the cell, while only the secreted C3-binding domains were biologically active.

  1. Involvement of Novel Multifunction Steroid Hormone Receptor Coactivator, E6-Associated Protein, in Prostate Gland Tumorigenesis

    DTIC Science & Technology

    2009-01-01

    8. 25. Nawaz Z, Lonard DM, Smith CL, Lev-Lehman E, Tsai SY, Tsai MJ, O’Malley BW 1999 The Angelman syndrome-associated protein, E6-AP, is a...CM, Noebels JL, Eichele G, Sweatt JD, Beaudet AL 1998 Mutation of the Angelman ubiquitin ligase in mice causes increased 12 cytoplasmic p53 and

  2. Involvement of Novel Multifunctional Steroid Hormone Receptor Coactivator, E6-Associated Protein, in Prostate Gland Tumorigenesis

    DTIC Science & Technology

    2008-01-01

    Angelman syndrome-associated protein, E6-AP, is a coactivator for the nuclear hormone receptor superfamily. Mol Cell Biol 19:1182-9. 26. Hsiao PW, Chang C...Albrecht U, Atkins CM, Noebels JL, Eichele G, Sweatt JD, Beaudet AL 1998 Mutation of the Angelman ubiquitin ligase in mice causes increased cytoplasmic

  3. Multifunctional RNA Processing Protein SRm160 Induces Apoptosis and Regulates Eye and Genital Development in Drosophila

    PubMed Central

    Fan, Yu-Jie; Gittis, Aryn H.; Juge, François; Qiu, Chen; Xu, Yong-Zhen; Rabinow, Leonard

    2014-01-01

    SRm160 is an SR-like protein implicated in multiple steps of RNA processing and nucleocytoplasmic export. Although its biochemical functions have been extensively described, its genetic interactions and potential participation in signaling pathways remain largely unknown, despite the fact that it is highly phosphorylated in both mammalian cells and Drosophila. To begin elucidating the functions of the protein in signaling and its potential role in developmental processes, we characterized mutant and overexpression SRm160 phenotypes in Drosophila and their interactions with the locus encoding the LAMMER protein kinase, Doa. SRm160 mutations are recessive lethal, while its overexpression generates phenotypes including roughened eyes and highly disorganized internal eye structure, which are due at least in part to aberrantly high levels of apoptosis. SRm160 is required for normal somatic sex determination, since its alleles strongly enhance a subtle sex transformation phenotype induced by Doa kinase alleles. Moreover, modification of SRm160 by DOA kinase appears to be necessary for its activity, since Doa alleles suppress phenotypes induced by SRm160 overexpression in the eye and enhance those in genital discs. Modification of SRm160 may occur through direct interaction because DOA kinase phosphorylates it in vitro. Remarkably, SRm160 protein was concentrated in the nuclei of precellular embryos but was very rapidly excluded from nuclei or degraded coincident with cellularization. Also of interest, transcripts are restricted almost exclusively to the developing nervous system in mature embryos. PMID:24907259

  4. Basigin: a multifunctional membrane protein with an emerging role in infections by malaria parasites.

    PubMed

    Muramatsu, Takashi

    2012-10-01

    Malaria is one of the most serious infectious diseases at the beginning of the twenty-first century. Various membrane proteins are present in Plasmodium falciparum, the principal malaria pathogen. Among them, P. falciparum reticulocyte-binding protein homolog 5 (PfRh5) is indispensable for erythrocyte invasion, and has become a promising vaccine target. Basigin (CD147, EMMPRIN) has been identified as the erythrocyte receptor of PfRh5, and shown to be essential for the invasion of multiple strains of the pathogen. Fundamental information on basigin is fully described, including structure as a member of the immunoglobulin superfamily and function based on its interactions with external molecules and with proteins within the same membrane. The involvement of basigin in many diseases such as cancer and inflammatory diseases is also described, the implication being that anti-basigin therapy might be helpful to treat certain illnesses. Finally, PfRh5 as a vaccine candidate is covered, and its interaction with basigin is evaluated. The identification of basigin, a well-characterized membrane protein, as a receptor essential for malaria infection will contribute significantly to prevention and treatment of malaria. As an example, anti-basigin therapy can be considered an alternative approach to the treatment of drug-resistant malaria.

  5. The antagonistic effect of Banana bunchy top virus multifunctional protein B4 against Fusarium oxysporum.

    PubMed

    Zhuang, Jun; Coates, Christopher J; Mao, Qianzhuo; Wu, Zujian; Xie, Lianhui

    2016-06-01

    The viral-induced banana bunchy top disease and the fungal-induced banana blight are two major causes of concern for industrial scale production of bananas. Banana blight is particularly troublesome, affecting ∼80% of crops worldwide. Strict guidelines and protocols are in place in order to ameliorate the effects of this devastating disease, yet little success has been achieved. From the data presented here, we have found that Banana bunchy top virus (BBTV)-infected bananas are more resistant to Fusarium oxysporum f. sp. cubense (Foc). BBTV appears to be antagonistic towards Foc, thus improving the survivability of plants against blight. The BBTV suppressor of RNA silencing, namely protein B4, displays fungicidal properties in vitro. Furthermore, transgenic tomatoes expressing green fluorescent protein (GFP)-tagged protein B4 demonstrate enhanced resistance to F. oxysporum f. sp. lycopersici (Fol). Differential gene expression analysis indicates that increased numbers of photogenesis-related gene transcripts are present in dark-green leaves of B4-GFP-modified tomato plants relative to those found in WT plants. Conversely, the transcript abundance of immunity-related genes is substantially lower in transgenic tomatoes compared with WT plants, suggesting that plant defences may be influenced by protein B4. This viral-fungal interaction provides new insights into microbial community dynamics within a single host and has potential commercial value for the breeding of transgenic resistance to Fusarium-related blight/wilt. © 2016 BSPP AND JOHN WILEY & SONS LTD.

  6. A Multi-Functional Imaging Approach to High-Content Protein Interaction Screening

    PubMed Central

    Matthews, Daniel R.; Fruhwirth, Gilbert O.; Weitsman, Gregory; Carlin, Leo M.; Ofo, Enyinnaya; Keppler, Melanie; Barber, Paul R.; Tullis, Iain D. C.; Vojnovic, Borivoj; Ng, Tony; Ameer-Beg, Simon M.

    2012-01-01

    Functional imaging can provide a level of quantification that is not possible in what might be termed traditional high-content screening. This is due to the fact that the current state-of-the-art high-content screening systems take the approach of scaling-up single cell assays, and are therefore based on essentially pictorial measures as assay indicators. Such phenotypic analyses have become extremely sophisticated, advancing screening enormously, but this approach can still be somewhat subjective. We describe the development, and validation, of a prototype high-content screening platform that combines steady-state fluorescence anisotropy imaging with fluorescence lifetime imaging (FLIM). This functional approach allows objective, quantitative screening of small molecule libraries in protein-protein interaction assays. We discuss the development of the instrumentation, the process by which information on fluorescence resonance energy transfer (FRET) can be extracted from wide-field, acceptor fluorescence anisotropy imaging and cross-checking of this modality using lifetime imaging by time-correlated single-photon counting. Imaging of cells expressing protein constructs where eGFP and mRFP1 are linked with amino-acid chains of various lengths (7, 19 and 32 amino acids) shows the two methodologies to be highly correlated. We validate our approach using a small-scale inhibitor screen of a Cdc42 FRET biosensor probe expressed in epidermoid cancer cells (A431) in a 96 microwell-plate format. We also show that acceptor fluorescence anisotropy can be used to measure variations in hetero-FRET in protein-protein interactions. We demonstrate this using a screen of inhibitors of internalization of the transmembrane receptor, CXCR4. These assays enable us to demonstrate all the capabilities of the instrument, image processing and analytical techniques that have been developed. Direct correlation between acceptor anisotropy and donor FLIM is observed for FRET assays, providing

  7. Multifunctional nanoparticle-protein conjugates with controllable bioactivity and pH responsiveness

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Xue, Lulu; Yuan, Yuqi; Pan, Jingjing; Zhang, Chenjie; Wang, Hongwei; Brash, John L.; Yuan, Lin; Chen, Hong

    2016-02-01

    The modulation of protein activity is of significance for disease therapy, molecular diagnostics, and tissue engineering. Nanoparticles offer a new platform for the preparation of protein conjugates with improved protein properties. In the present work, Escherichia coli (E. coli) inorganic pyrophosphatase (PPase) and poly(methacrylic acid) (PMAA) were attached together to gold nanoparticles (AuNPs), forming AuNP-PPase-PMAA conjugates having controllable multi-biofunctionalities and responsiveness to pH. By treating with poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) and regulating the pH, the bioactivity of the conjugate becomes ``on/off''-switchable. In addition, by taking advantage of the ability of AuNPs to undergo reversible aggregation/dispersion, the conjugates can be recycled and reused multiple times; and due to the shielding effect of the PMAA, the conjugated enzyme has high resistance to protease digestion. This approach has considerable potential in areas such as controlled delivery and release of drugs, biosensing, and biocatalysis.The modulation of protein activity is of significance for disease therapy, molecular diagnostics, and tissue engineering. Nanoparticles offer a new platform for the preparation of protein conjugates with improved protein properties. In the present work, Escherichia coli (E. coli) inorganic pyrophosphatase (PPase) and poly(methacrylic acid) (PMAA) were attached together to gold nanoparticles (AuNPs), forming AuNP-PPase-PMAA conjugates having controllable multi-biofunctionalities and responsiveness to pH. By treating with poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) and regulating the pH, the bioactivity of the conjugate becomes ``on/off''-switchable. In addition, by taking advantage of the ability of AuNPs to undergo reversible aggregation/dispersion, the conjugates can be recycled and reused multiple times; and due to the shielding effect of the PMAA, the conjugated enzyme has high resistance to protease digestion

  8. Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation.

    PubMed

    Huang, Ying; Bayfield, Mark A; Intine, Robert V; Maraia, Richard J

    2006-07-01

    By sequence-specific binding to 3' UUU-OH, the La protein shields precursor (pre)-RNAs from 3' end digestion and is required to protect defective pre-transfer RNAs from decay. Although La is comprised of a La motif and an RNA-recognition motif (RRM), a recent structure indicates that the RRM beta-sheet surface is not involved in UUU-OH recognition, raising questions as to its function. Progressively defective suppressor tRNAs in Schizosaccharomyces pombe reveal differential sensitivities to La and Rrp6p, a 3' exonuclease component of pre-tRNA decay. 3' end protection is compromised by mutations to the La motif but not the RRM surface. The most defective pre-tRNAs require a second activity of La, in addition to 3' protection, that requires an intact RRM surface. The two activities of La in tRNA maturation map to its two conserved RNA-binding surfaces and suggest a modular model that has implications for its other ligands.

  9. Spider wrapping silk fibre architecture arising from its modular soluble protein precursor

    PubMed Central

    Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E.; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K.

    2015-01-01

    Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable “beads-on-a-string” concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability. PMID:26112753

  10. Spider wrapping silk fibre architecture arising from its modular soluble protein precursor.

    PubMed

    Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K

    2015-06-26

    Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable "beads-on-a-string" concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability.

  11. Spider wrapping silk fibre architecture arising from its modular soluble protein precursor

    NASA Astrophysics Data System (ADS)

    Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E.; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K.

    2015-06-01

    Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable “beads-on-a-string” concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability.

  12. Tat is a multifunctional viral protein that modulates cellular gene expression and functions.

    PubMed

    Clark, Evan; Nava, Brenda; Caputi, Massimo

    2017-02-07

    The human immunodeficiency virus type I (HIV-1) has developed several strategies to condition the host environment to promote viral replication and spread. Viral proteins have evolved to perform multiple functions, aiding in the replication of the viral genome and modulating the cellular response to the infection. Tat is a small, versatile, viral protein that controls transcription of the HIV genome, regulates cellular gene expression and generates a permissive environment for viral replication by altering the immune response and facilitating viral spread to multiple tissues. Studies carried out utilizing biochemical, cellular, and genomic approaches show that the expression and activity of hundreds of genes and multiple molecular networks are modulated by Tat via multiple mechanisms.

  13. HIV-1 p6 - a structured to flexible multifunctional membrane-interacting protein.

    PubMed

    Solbak, Sara Marie Øie; Reksten, Tove Ragna; Hahn, Friedrich; Wray, Victor; Henklein, Petra; Henklein, Peter; Halskau, Øyvind; Schubert, Ulrich; Fossen, Torgils

    2013-02-01

    The human immunodeficiency virus type 1 (HIV-1) p6 protein has recently been recognized as a docking site for several cellular and viral binding partners and is important for the formation of infectious viruses. Most of its known functions are suggested to occur under hydrophobic conditions near the cytoplasmic membrane, where the protein is presumed to exist in its most structured state. Although p6 is involved in manifold specific interactions, the protein has previously been considered to possess a random structure in aqueous solution. We show that p6 exhibits a defined structure with N- and C-terminal helical domains, connected by a flexible hinge region in 100mM dodecylphosphocholine micelle solution at pH 7 devoid of any organic co-solvents, indicating that this is a genuine limiting structural feature of the molecule in a hydrophobic environment. Furthermore, we show that p6 directly interacts with a cytoplasmic model membrane through both N-terminal and C-terminal regions by use of surface plasmon resonance (SPR) spectroscopy. Phosphorylation of Ser-40 located in the center of the C-terminal α-helix does not alter the secondary structure of the protein but amplifies the interaction with membranes significantly, indicating that p6 binds to the polar head groups at the surface of the cytoplasmic membrane. The increased hydrophobic membrane interaction of p6(23-52) S40F correlated with the observed increased amount of the polyprotein Gag in the RIPA insoluble fraction when Ser40 of p6 was mutated with Phe indicating that p6 modulates the membrane interactions of HIV-1 Gag.

  14. CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline.

    PubMed

    Fischer, Axel W; Heinze, Sten; Putnam, Daniel K; Li, Bian; Pino, James C; Xia, Yan; Lopez, Carlos F; Meiler, Jens

    2016-01-01

    In silico prediction of a protein's tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure prediction algorithms. We developed a protein structure prediction pipeline employing a three-stage approach, consisting of low-resolution topology search, high-resolution refinement, and molecular dynamics simulation to predict the tertiary structure of proteins from the primary structure alone or including distance restraints either from predicted residue-residue contacts, nuclear magnetic resonance (NMR) nuclear overhauser effect (NOE) experiments, or mass spectroscopy (MS) cross-linking (XL) data. The protein structure prediction pipeline was evaluated in the CASP11 experiment on twenty regular protein targets as well as thirty-three 'assisted' protein targets, which also had distance restraints available. Although the low-resolution topology search module was able to sample models with a global distance test total score (GDT_TS) value greater than 30% for twelve out of twenty proteins, frequently it was not possible to select the most accurate models for refinement, resulting in a general decay of model quality over the course of the prediction pipeline. In this study, we provide a detailed overall analysis, study one target protein in more detail as it travels through the protein structure prediction pipeline, and evaluate the impact of limited experimental data.

  15. Modular entanglement.

    PubMed

    Gualdi, Giulia; Giampaolo, Salvatore M; Illuminati, Fabrizio

    2011-02-04

    We introduce and discuss the concept of modular entanglement. This is the entanglement that is established between the end points of modular systems composed by sets of interacting moduli of arbitrarily fixed size. We show that end-to-end modular entanglement scales in the thermodynamic limit and rapidly saturates with the number of constituent moduli. We clarify the mechanisms underlying the onset of entanglement between distant and noninteracting quantum systems and its optimization for applications to quantum repeaters and entanglement distribution and sharing.

  16. Direct stimulation of translation by the multifunctional herpesvirus ICP27 protein.

    PubMed

    Larralde, Osmany; Smith, Richard W P; Wilkie, Gavin S; Malik, Poonam; Gray, Nicola K; Clements, J Barklie

    2006-02-01

    Herpes simplex virus type 1 (HSV-1) ICP27 protein is an essential regulator of viral gene expression with roles at various levels of RNA metabolism in the nucleus. Using the tethered function assay, we showed a cytoplasmic activity for ICP27 in directly enhancing mRNA translation in vivo in the absence of other viral factors. The region of ICP27 required for translational stimulation maps to the C terminus. Furthermore, in infected cells, ICP27 is associated with polyribosomes, indicating a function in translation during the lytic cycle.

  17. Involvement of Novel Multifunction Steroid Hormone Receptor Coactivator, E6-Associated Protein, in Prostate Gland Tumorigenesis

    DTIC Science & Technology

    2010-01-01

    synthesized RhoA G14V protein in NETN buffer (100 mM NaCl, 1 mM EDTA, 20 mM Tris (pH 8.0), and 0.5% Nonidet P - 40 ) for 2–3 hours at room...to test the effects of loss E6- AP on the normal development of the prostate gland ( 40 , 41). We have also generated E6-AP transgenic mouse line that...expression of p -Akt in all the lobes compared to the wild- type, there was no significant differences between the extents of p -Akt over expression between

  18. Evolution of sparsity and modularity in a model of protein allostery

    NASA Astrophysics Data System (ADS)

    Hemery, Mathieu; Rivoire, Olivier

    2015-04-01

    The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary constraints may take is important to interpret the information in protein sequences. To study this problem, we introduce a simple but physical model of protein evolution where selection targets allostery, the functional coupling of distal sites on protein surfaces. This model shows how the geometrical organization of couplings between amino acids within a protein structure can depend crucially on its evolutionary history. In particular, two scenarios are found to generate a spatial concentration of functional constraints: high mutation rates and fluctuating selective pressures. This second scenario offers a plausible explanation for the high tolerance of natural proteins to mutations and for the spatial organization of their least tolerant amino acids, as revealed by sequence analysis and mutagenesis experiments. It also implies a faculty to adapt to new selective pressures that is consistent with observations. The model illustrates how several independent functional modules may emerge within the same protein structure, depending on the nature of past environmental fluctuations. Our model thus relates the evolutionary history of proteins to the geometry of their functional constraints, with implications for decoding and engineering protein sequences.

  19. A multifunctional protein EWS regulates the expression of Drosha and microRNAs.

    PubMed

    Kim, K Y; Hwang, Y J; Jung, M-K; Choe, J; Kim, Y; Kim, S; Lee, C-J; Ahn, H; Lee, J; Kowall, N W; Kim, Y K; Kim, J-I; Lee, S B; Ryu, H

    2014-01-01

    EWS (Ewing's Sarcoma) gene encodes an RNA/DNA-binding protein that is ubiquitously expressed and involved in various cellular processes. EWS deficiency leads to impaired development and early senescence through unknown mechanisms. We found that EWS regulates the expression of Drosha and microRNAs (miRNAs). EWS deficiency resulted in increased expression of Drosha, a well-known microprocessor, and increased levels of miR-29b and miR-18b. Importantly, miR-29b and miR-18b were directly involved in the post-transcriptional regulation of collagen IV alpha 1 (Col4a1) and connective tissue growth factor (CTGF) in EWS knock-out (KO) mouse embryonic fibroblast cells. The upregulation of Drosha, miR-29b and miR-18b and the sequential downregulation of Col4a1 and CTGF contributed to the deregulation of dermal development in EWS KO mice. Otherwise, knockdown of Drosha rescued miRNA-dependent downregulation of Col4a1 and CTGF proteins. Taken together, our data indicate that EWS is involved in post-transcriptional regulation of Col4a1 and CTGF via a Drosha-miRNA-dependent pathway. This finding suggests that EWS has a novel role in dermal morphogenesis through the modulation of miRNA biogenesis.

  20. The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication.

    PubMed

    Portela, Agustín; Digard, Paul

    2002-04-01

    All viruses with negative-sense RNA genomes encode a single-strand RNA-binding nucleoprotein (NP). The primary function of NP is to encapsidate the virus genome for the purposes of RNA transcription, replication and packaging. The purpose of this review is to illustrate using the influenza virus NP as a well-studied example that the molecule is much more than a structural RNA-binding protein, but also functions as a key adapter molecule between virus and host cell processes. It does so through the ability to interact with a wide variety of viral and cellular macromolecules, including RNA, itself, two subunits of the viral RNA-dependent RNA polymerase and the viral matrix protein. NP also interacts with cellular polypeptides, including actin, components of the nuclear import and export apparatus and a nuclear RNA helicase. The evidence for the existence of each of these activities and their possible roles in transcription, replication and intracellular trafficking of the virus genome is considered.

  1. Multifunctional Ebselen drug functions through the activation of DNA damage response and alterations in nuclear proteins.

    PubMed

    Azad, Gajendra K; Balkrishna, Shah Jaimin; Sathish, Narayanan; Kumar, Sangit; Tomar, Raghuvir S

    2012-01-15

    Several studies have demonstrated that Ebselen is an anti-inflammatory and anti-oxidative agent. Contrary to this, studies have also shown a high degree of cellular toxicity associated with Ebselen usage, the underlying mechanism of which remains less understood. In this study we have attempted to identify a possible molecular mechanism behind the above by investigating the effects of Ebselen on Saccharomyces cerevisiae. Significant growth arrest was documented in yeast cells exposed to Ebselen similar to that seen in presence of DNA damaging agents (including methyl methane sulfonate [MMS] and hydroxy urea [HU]). Furthermore, mutations in specific lysine residues in the histone H3 tail (H3 K56R) resulted in increased sensitivity of yeast cells to Ebselen presumably due to alterations in post-translational modifications of histone proteins towards regulating replication and DNA damage repair. Our findings suggest that Ebselen functions through activation of DNA damage response, alterations in histone modifications, activation of checkpoint kinase pathway and derepression of ribonucleotide reductases (DNA repair genes) which to the best of our knowledge is being reported for the first time. Interestingly subsequent to Ebselen exposure there were changes in global yeast protein expression and specific histone modifications, identification of which is expected to reveal a fundamental cellular mechanism underlying the action of Ebselen. Taken together these observations will help to redesign Ebselen-based therapy in clinical trials. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. WSTF does it all: a multifunctional protein in transcription, repair and replication

    PubMed Central

    Barnett, Chris; Krebs, Jocelyn E.

    2011-01-01

    Williams Syndrome Transcription Factor (WSTF) has emerged as an incredibly versatile nuclear protein. WSTF and the ATP-dependent chromatin remodeling complexes in which it exists, WINAC, WICH and B-WICH have been studied in a variety of organisms. This research has revealed roles for WSTF in a number of diverse molecular events. WSTF function includes chromatin assembly, Pol I and III gene regulation, vitamin D metabolism and DNA repair. In addition to functioning as a subunit of several ATP-dependent chromatin remodeling complexes, WSTF binds specifically to acetylated histones and is itself a histone kinase, as well as a target of phosphorylation. This review will describe the three known WSTF-containing complexes and discuss their various roles as well as mechanisms of regulating WSTF activity. PMID:21326359

  3. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle.

    PubMed

    Hergeth, Sonja P; Schneider, Robert

    2015-11-01

    The linker histone H1 family members are a key component of chromatin and bind to the nucleosomal core particle around the DNA entry and exit sites. H1 can stabilize both nucleosome structure and higher-order chromatin architecture. In general, H1 molecules consist of a central globular domain with more flexible tail regions at both their N- and C-terminal ends. The existence of multiple H1 subtypes and a large variety of posttranslational modifications brings about a considerable degree of complexity and makes studying this protein family challenging. Here, we review recent progress in understanding the function of linker histones and their subtypes beyond their role as merely structural chromatin components. We summarize current findings on the role of H1 in heterochromatin formation, transcriptional regulation and embryogenesis with a focus on H1 subtypes and their specific modifications.

  4. Multifunctional roles of insulin-like growth factor binding protein 5 in breast cancer

    PubMed Central

    Akkiprik, Mustafa; Feng, Yumei; Wang, Huamin; Chen, Kexin; Hu, Limei; Sahin, Aysegul; Krishnamurthy, Savitri; Ozer, Ayse; Hao, Xishan; Zhang, Wei

    2008-01-01

    The insulin-like growth factor axis, which has been shown to protect cells from apoptosis, plays an essential role in normal cell physiology and in cancer development. The family of insulin-like growth factor binding proteins (IGFBPs) has been shown to have a diverse spectrum of functions in cell growth, death, motility, and tissue remodeling. Among the six IGFBP family members, IGFBP-5 has recently been shown to play an important role in the biology of breast cancer, especially in breast cancer metastasis; however, the exact mechanisms of action remain obscure and sometimes paradoxical. An in-depth understanding of IGFBP-5 would shed light on its potential role as a target for breast cancer therapeutics. PMID:18710598

  5. WSTF does it all: a multifunctional protein in transcription, repair, and replication.

    PubMed

    Barnett, Chris; Krebs, Jocelyn E

    2011-02-01

    Williams syndrome transcription factor (WSTF) has emerged as an incredibly versatile nuclear protein. WSTF and the ATP-dependent chromatin remodeling complexes in which it exists, WINAC, WICH, and B-WICH, have been studied in a variety of organisms. This research has revealed roles for WSTF in a number of diverse molecular events. WSTF function includes chromatin assembly, RNA polymerase I and III gene regulation, vitamin D metabolism, and DNA repair. In addition to functioning as a subunit of several ATP-dependent chromatin remodeling complexes, WSTF binds specifically to acetylated histones and is itself a histone kinase as well as a target of phosphorylation. This review will describe the three known WSTF-containing complexes and discuss their various roles as well as mechanisms of regulating WSTF activity.

  6. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle

    PubMed Central

    Hergeth, Sonja P; Schneider, Robert

    2015-01-01

    The linker histone H1 family members are a key component of chromatin and bind to the nucleosomal core particle around the DNA entry and exit sites. H1 can stabilize both nucleosome structure and higher-order chromatin architecture. In general, H1 molecules consist of a central globular domain with more flexible tail regions at both their N- and C-terminal ends. The existence of multiple H1 subtypes and a large variety of posttranslational modifications brings about a considerable degree of complexity and makes studying this protein family challenging. Here, we review recent progress in understanding the function of linker histones and their subtypes beyond their role as merely structural chromatin components. We summarize current findings on the role of H1 in heterochromatin formation, transcriptional regulation and embryogenesis with a focus on H1 subtypes and their specific modifications. PMID:26474902

  7. Analysis of the Linker Region Joining the Adenylation and Carrier Protein Domains of the Modular Non-Ribosomal Peptide Synthetases

    PubMed Central

    Miller, Bradley R.; Sundlov, Jesse A.; Drake, Eric J.; Makin, Thomas A.; Gulick, Andrew M.

    2014-01-01

    Non-Ribosomal Peptide Synthetases (NRPSs) are multi-modular proteins capable of producing important peptide natural products. Using an assembly-line process the amino acid substrate and peptide intermediates are passed between the active sites of different catalytic domains of the NRPS while bound covalently to a peptidyl carrier protein (PCP) domain. Examination of the linker sequences that join the NRPS adenylation and PCP domains identified several conserved proline residues that are not found in standalone adenylation domains. We examined the roles of these proline residues and neighboring conserved sequences through mutagenesis and biochemical analysis of the reaction catalyzed by the adenylation domain and the fully reconstituted NRPS pathway. In particular, we identified a conserved LPxP motif at the start of the adenylation-PCP linker. The LPxP motif interacts with a region on the adenylation domain to stabilize a critical catalytic lysine residue belonging to the A10 motif that immediately precedes the linker. Further, this interaction with the C-terminal sub-domain of the adenylation domain may coordinate movement of the PCP with the conformational change of the adenylation domain. Through this work, we extend the conserved A10 motif of the adenylation domain and identify residues that enable proper adenylation domain function. PMID:24975514

  8. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family.

    PubMed

    Ferreiro, Diego U; Cho, Samuel S; Komives, Elizabeth A; Wolynes, Peter G

    2005-12-02

    Proteins consisting of repeating amino acid motifs are abundant in all kingdoms of life, especially in higher eukaryotes. Repeat-containing proteins self-organize into elongated non-globular structures. Do the same general underlying principles that dictate the folding of globular domains apply also to these extended topologies? Using a simplified structure-based model capturing a perfectly funneled energy landscape, we surveyed the predicted mechanism of folding for ankyrin repeat containing proteins. The ankyrin family is one of the most extensively studied classes of non-globular folds. The model based only on native contacts reproduces most of the experimental observations on the folding of these proteins, including a folding mechanism that is reminiscent of a nucleation propagation growth. The confluence of simulation and experimental results suggests that the folding of non-globular proteins is accurately described by a funneled energy landscape, in which topology plays a determinant role in the folding mechanism.

  9. Modular Integrated Secretory System Engineering in Pichia pastoris To Enhance G-Protein Coupled Receptor Expression.

    PubMed

    Claes, Katrien; Vandewalle, Kristof; Laukens, Bram; Laeremans, Toon; Vosters, Olivier; Langer, Ingrid; Parmentier, Marc; Steyaert, Jan; Callewaert, Nico

    2016-10-21

    Membrane protein research is still hampered by the generally very low levels at which these proteins are naturally expressed, necessitating heterologous expression. Protein degradation, folding problems, and undesired post-translational modifications often occur, together resulting in low expression levels of heterogeneous protein products that are unsuitable for structural studies. We here demonstrate how the integration of multiple engineering modules in Pichia pastoris can be used to increase both the quality and the quantity of overexpressed integral membrane proteins, with the human CXCR4 G-protein coupled receptor as an example. The combination of reduced proteolysis, enhanced ER folding capacity, GlycoDelete-based N-Glycan trimming, and nanobody-based fold stabilization improved the expression of this GPCR in P. pastoris from a low expression level of a heterogeneously glycosylated, proteolyzed product to substantial quantities (2-3 mg/L shake flask culture) of a nonproteolyzed, homogeneously glycosylated proteoform. We expect that this set of tools will contribute to successful expression of more membrane proteins in a quantity and quality suitable for functional and structural studies.

  10. Multifunctional peptides derived from an egg yolk protein hydrolysate: isolation and characterization.

    PubMed

    Zambrowicz, Aleksandra; Pokora, Marta; Setner, Bartosz; Dąbrowska, Anna; Szołtysik, Marek; Babij, Konrad; Szewczuk, Zbigniew; Trziszka, Tadeusz; Lubec, Gert; Chrzanowska, Józefa

    2015-02-01

    An egg yolk protein by-product following ethanol extraction of phospholipids (YP) was hydrolyzed with pepsin to produce and identify novel peptides that revealed antioxidant, ACE inhibitory and antidiabetic (α-glucosidase and DPP-IV inhibitory) activities. The peptic hydrolysate of YP was fractionated by ion-exchange chromatography and reversed-phase high-pressure liquid chromatography. Isolated peptides were identified using mass spectrometry (MALDI-ToF) and the Mascot Search Results database. Four peptides of MW ranging from 1,210.62 to 1,677.88 Da corresponded to the fragments of Apolipoprotein B (YINQMPQKSRE; YINQMPQKSREA), Vitellogenin-2 (VTGRFAGHPAAQ) and Apovitellenin-1 (YIEAVNKVSPRAGQF). These peptides were chemically synthesized and showed antioxidant, ACE inhibitory or/and antidiabetic activities. Peptide YIEAVNKVSPRAGQF exerted the strongest ACE inhibitory activity, with IC50 = 9.4 µg/mL. The peptide YINQMPQKSRE showed the strongest DPPH free radical scavenging and DPP-IV inhibitory activities and its ACE inhibitory activity (IC50) reached 10.1 µg/mL. The peptide VTGRFAGHPAAQ revealed the highest α-glucosidase inhibitory activity (IC50 = 365.4 µg/mL). A novel nutraceutical effect for peptides from an egg yolk hydrolysate was shown.

  11. A Modular Approach To Study Protein Adsorption on Surface Modified Hydroxyapatite.

    PubMed

    Ozhukil Kollath, Vinayaraj; Van den Broeck, Freya; Fehér, Krisztina; Martins, José C; Luyten, Jan; Traina, Karl; Mullens, Steven; Cloots, Rudi

    2015-07-13

    Biocompatible inorganic nano- and microcarriers can be suitable candidates for protein delivery. This study demonstrates facile methods of functionalization by using nanoscale linker molecules to change the protein adsorption capacity of hydroxyapatite (HA) powder. The adsorption capacity of bovine serum albumin as a model protein has been studied with respect to the surface modifications. The selected linker molecules (lysine, arginine, and phosphoserine) can influence the adsorption capacity by changing the electrostatic nature of the HA surface. Qualitative and quantitative analyses of linker-molecule interactions with the HA surface have been performed by using NMR spectroscopy, zeta-potential measurements, X-ray photoelectron spectroscopy, and thermogravimetric analyses. Additionally, correlations to theoretical isotherm models have been calculated with respect to Langmuir and Freundlich isotherms. Lysine and arginine increased the protein adsorption, whereas phosphoserine reduced the protein adsorption. The results show that the adsorption capacity can be controlled with different functionalization, depending on the protein-carrier selections under consideration. The scientific knowledge acquired from this study can be applied in various biotechnological applications that involve biomolecule-inorganic material interfaces.

  12. The barley stripe mosaic virus 58-kilodalton beta(b) protein is a multifunctional RNA binding protein.

    PubMed Central

    Donald, R G; Lawrence, D M; Jackson, A O

    1997-01-01

    The barley stripe mosaic virus (BSMV) beta(b) gene product is the major viral nonstructural protein synthesized during early stages of the infection cycle and is required for systemic movement of the virus. To examine the biochemical properties of beta(b), a histidine tag was engineered at the amino terminus and the protein was purified from BSMV-infected barley tissue by metal affinity chromatography. The beta(b) protein bound ATPs in vitro, with a preference for ATP over dATP, and also exhibited ATPase activity. In addition, beta(b) bound RNA without detectable sequence specificity. However, binding was selective, as the beta(b) protein had a strong affinity for both single-stranded (ss) and double-stranded (ds) RNAs but not for tRNA or DNA substrates. Mutational analyses of beta(b) purified from Escherichia coli indicated that the protein has multiple RNA binding sites. These sites appear to contribute differently, because mutants that were altered in their binding affinities for ss and ds RNA substrates were recovered. PMID:8995680

  13. Modular Peptides Promote Human Mesenchymal Stem Cell Differentiation on Biomaterial Surfaces

    PubMed Central

    Lee, Jae Sam; Lee, Jae Sung; Murphy, William L.

    2009-01-01

    Summary Molecular design strategies in biomedical applications often involve creating modular “fusion” proteins, in which distinct domains within a single molecule can perform multiple functions. We have synthesized a new class of modular peptides that include a biologically active sequence derived from the growth factor BMP-2 and a series of hydroxyapatite-binding sequences inspired by the N-terminal α-helix of osteocalcin. These modular peptides can bind in a sequence-dependent manner to the surface of “bone-like” hydroxyapatite coatings, which are nucleated and grown on a biodegradable polymer surface via a biomimetic process. The BMP2-derived sequence of the modular peptides is biologically active, as measured by its ability to promote osteogenic differentiation of human mesenchymal stem cells. Our study indicates that the modular peptides described here are multifunctional, and the characteristics of this approach suggest that it can potentially be applied to a range of biomaterials for regenerative medicine applications. PMID:19665062

  14. Large-scale modelling of the divergent spectrin repeats in nesprins: giant modular proteins.

    PubMed

    Autore, Flavia; Pfuhl, Mark; Quan, Xueping; Williams, Aisling; Roberts, Roland G; Shanahan, Catherine M; Fraternali, Franca

    2013-01-01

    Nesprin-1 and nesprin-2 are nuclear envelope (NE) proteins characterized by a common structure of an SR (spectrin repeat) rod domain and a C-terminal transmembrane KASH [Klarsicht-ANC-Syne-homology] domain and display N-terminal actin-binding CH (calponin homology) domains. Mutations in these proteins have been described in Emery-Dreifuss muscular dystrophy and attributed to disruptions of interactions at the NE with nesprins binding partners, lamin A/C and emerin. Evolutionary analysis of the rod domains of the nesprins has shown that they are almost entirely composed of unbroken SR-like structures. We present a bioinformatical approach to accurate definition of the boundaries of each SR by comparison with canonical SR structures, allowing for a large-scale homology modelling of the 74 nesprin-1 and 56 nesprin-2 SRs. The exposed and evolutionary conserved residues identify important pbs for protein-protein interactions that can guide tailored binding experiments. Most importantly, the bioinformatics analyses and the 3D models have been central to the design of selected constructs for protein expression. 1D NMR and CD spectra have been performed of the expressed SRs, showing a folded, stable, high content α-helical structure, typical of SRs. Molecular Dynamics simulations have been performed to study the structural and elastic properties of consecutive SRs, revealing insights in the mechanical properties adopted by these modules in the cell.

  15. Large-Scale Modelling of the Divergent Spectrin Repeats in Nesprins: Giant Modular Proteins

    PubMed Central

    Autore, Flavia; Pfuhl, Mark; Quan, Xueping; Williams, Aisling; Roberts, Roland G.; Shanahan, Catherine M.; Fraternali, Franca

    2013-01-01

    Nesprin-1 and nesprin-2 are nuclear envelope (NE) proteins characterized by a common structure of an SR (spectrin repeat) rod domain and a C-terminal transmembrane KASH [Klarsicht–ANC–Syne-homology] domain and display N-terminal actin-binding CH (calponin homology) domains. Mutations in these proteins have been described in Emery-Dreifuss muscular dystrophy and attributed to disruptions of interactions at the NE with nesprins binding partners, lamin A/C and emerin. Evolutionary analysis of the rod domains of the nesprins has shown that they are almost entirely composed of unbroken SR-like structures. We present a bioinformatical approach to accurate definition of the boundaries of each SR by comparison with canonical SR structures, allowing for a large-scale homology modelling of the 74 nesprin-1 and 56 nesprin-2 SRs. The exposed and evolutionary conserved residues identify important pbs for protein-protein interactions that can guide tailored binding experiments. Most importantly, the bioinformatics analyses and the 3D models have been central to the design of selected constructs for protein expression. 1D NMR and CD spectra have been performed of the expressed SRs, showing a folded, stable, high content α-helical structure, typical of SRs. Molecular Dynamics simulations have been performed to study the structural and elastic properties of consecutive SRs, revealing insights in the mechanical properties adopted by these modules in the cell. PMID:23671687

  16. Rosetta:MSF: a modular framework for multi-state computational protein design

    PubMed Central

    Hupfeld, Enrico; Sterner, Reinhard

    2017-01-01

    Computational protein design (CPD) is a powerful technique to engineer existing proteins or to design novel ones that display desired properties. Rosetta is a software suite including algorithms for computational modeling and analysis of protein structures and offers many elaborate protocols created to solve highly specific tasks of protein engineering. Most of Rosetta’s protocols optimize sequences based on a single conformation (i. e. design state). However, challenging CPD objectives like multi-specificity design or the concurrent consideration of positive and negative design goals demand the simultaneous assessment of multiple states. This is why we have developed the multi-state framework MSF that facilitates the implementation of Rosetta’s single-state protocols in a multi-state environment and made available two frequently used protocols. Utilizing MSF, we demonstrated for one of these protocols that multi-state design yields a 15% higher performance than single-state design on a ligand-binding benchmark consisting of structural conformations. With this protocol, we designed de novo nine retro-aldolases on a conformational ensemble deduced from a (βα)8-barrel protein. All variants displayed measurable catalytic activity, testifying to a high success rate for this concept of multi-state enzyme design. PMID:28604768

  17. Modular Protein Expression Toolbox (MoPET), a standardized assembly system for defined expression constructs and expression optimization libraries

    PubMed Central

    Birkenfeld, Jörg; Franz, Jürgen; Gritzan, Uwe; Linden, Lars; Trautwein, Mark

    2017-01-01

    The design and generation of an optimal expression construct is the first and essential step in in the characterization of a protein of interest. Besides evaluation and optimization of process parameters (e.g. selection of the best expression host or cell line and optimal induction conditions and time points), the design of the expression construct itself has a major impact. However, the path to this final expression construct is often not straight forward and includes multiple learning cycles accompanied by design variations and retesting of construct variants, since multiple, functional DNA sequences of the expression vector backbone, either coding or non-coding, can have a major impact on expression yields. To streamline the generation of defined expression constructs of otherwise difficult to express proteins, the Modular Protein Expression Toolbox (MoPET) has been developed. This cloning platform allows highly efficient DNA assembly of pre-defined, standardized functional DNA modules with a minimal cloning burden. Combining these features with a standardized cloning strategy facilitates the identification of optimized DNA expression constructs in shorter time. The MoPET system currently consists of 53 defined DNA modules divided into eight functional classes and can be flexibly expanded. However, already with the initial set of modules, 792,000 different constructs can be rationally designed and assembled. Furthermore, this starting set was used to generate small and mid-sized combinatorial expression optimization libraries. Applying this screening approach, variants with up to 60-fold expression improvement have been identified by MoPET variant library screening. PMID:28520717

  18. A modular perspective of protein structures: application to fragment based loop modeling.

    PubMed

    Fernandez-Fuentes, Narcis; Fiser, Andras

    2013-01-01

    Proteins can be decomposed into supersecondary structure modules. We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular secondary structures connected by a loop, to explore the evolution and current variety of structure building blocks. Here, we discuss recent observations about the saturation of Smotif geometries in protein structures and how it opens new avenues in protein structure modeling and design. As a first application of these observations we describe our loop conformation modeling algorithm, ArchPred that takes advantage of Smotifs classification. In this application, instead of focusing on specific loop properties the method narrows down possible template conformations in other, often not homologous structures, by identifying the most likely supersecondary structure environment that cradles the loop. Beyond identifying the correct starting supersecondary structure geometry, it takes into account information of fit of anchor residues, sterical clashes, match of predicted and observed dihedral angle preferences, and local sequence signal.

  19. The aryl hydrocarbon receptor nuclear translocator (ARNT) family of proteins: transcriptional modifiers with multi-functional protein interfaces.

    PubMed

    Labrecque, M P; Prefontaine, G G; Beischlag, T V

    2013-08-01

    The basic Helix-Loop-Helix/PER-ARNT-SIM (bHLH-PAS) domain family of transcription factors mediates cellular responses to a variety of internal and external stimuli. As functional transcription factors, these proteins act as bHLH-PAS heterodimers and can be further sub-classified into sensory/activated subunits and regulatory or ARNT-like proteins. This class of proteins act as master regulators of the bHLH-PAS superfamily of transcription factors that mediate circadian rhythm gene programs, innate and adaptive immune responses, oxygen-sensing mechanisms and compensate for deleterious environmental exposures. Some contribute to the etiology of human pathologies including cancer because of their effects on cell growth and metabolism. We will review the canonical roles of ARNT and ARNT-like proteins with an emphasis on coactivator selectivity and recruitment. We will also discuss recent advances in our understanding of noncanonical DNA-binding independent or off-target roles of ARNT that are uncoupled from its classic heterodimeric bHLH-PAS binding partners. Understanding the DNA binding-independent functions of ARNT may identify novel therapeutic options for the treatment of a large spectrum of disease states.

  20. The Conserved Modular Elements of the Acyl Carrier Proteins of Lipid Synthesis Are Only Partially Interchangeable*

    PubMed Central

    Zhu, Lei; Cronan, John E.

    2015-01-01

    Prior work showed that expression of acyl carrier proteins (ACPs) of a diverse set of bacteria replaced the function of Escherichia coli ACP in lipid biosynthesis. However, the AcpAs of Lactococcus lactis and Enterococcus faecalis were inactive. Both failed to support growth of an E. coli acpP mutant strain. This defect seemed likely because of the helix II sequences of the two AcpAs, which differed markedly from those of the proteins that supported growth. To test this premise, chimeric ACPs were constructed in which L. lactis helix II replaced helix II of E. coli AcpP and vice versa. Expression of the AcpP protein L. lactis AcpA helix II allowed weak growth, whereas the L. lactis AcpA-derived protein that contained E. coli AcpP helix II failed to support growth of the E. coli mutant strain. Replacement of the L. lactis AcpA helix II residues in this protein showed that substitution of valine for the phenylalanine residue four residues downstream of the phosphopanthetheine-modified serine gave robust growth and allowed modification by the endogenous AcpS phosphopantetheinyl transferase (rather than the promiscuous Sfp transferase required to modify the L. lactis AcpA and the chimera of L. lactis AcpA helix II in AcpP). Further chimera constructs showed that the lack of function of the L. lactis AcpA-derived protein containing E. coli AcpP helix II was due to incompatibility of L. lactis AcpA helix I with the downstream elements of AcpP. Therefore, the origins of ACP incompatibility can reside in either helix I or in helix II. PMID:25861991

  1. Molecular Architecture and Evolution of a Modular Spider Silk Protein Gene

    NASA Astrophysics Data System (ADS)

    Hayashi, Cheryl Y.; Lewis, Randolph V.

    2000-02-01

    Spider flagelliform silk is one of the most elastic natural materials known. Extensive sequencing of spider silk genes has shown that the exons and introns of the flagelliform gene underwent intragenic concerted evolution. The intron sequences are more homogenized within a species than are the exons. This pattern can be explained by extreme mutation and recombination pressures on the internally repetitive exons. The iterated sequences within exons encode protein structures that are critical to the function of silks. Therefore, attributes that make silks exceptional biomaterials may also hinder the fixation of optimally adapted protein sequences.

  2. Molecular architecture and evolution of a modular spider silk protein gene.

    PubMed

    Hayashi, C Y; Lewis, R V

    2000-02-25

    Spider flagelliform silk is one of the most elastic natural materials known. Extensive sequencing of spider silk genes has shown that the exons and introns of the flagelliform gene underwent intragenic concerted evolution. The intron sequences are more homogenized within a species than are the exons. This pattern can be explained by extreme mutation and recombination pressures on the internally repetitive exons. The iterated sequences within exons encode protein structures that are critical to the function of silks. Therefore, attributes that make silks exceptional biomaterials may also hinder the fixation of optimally adapted protein sequences.

  3. The elastic free energy of a tandem modular protein under force.

    PubMed

    Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

    2015-05-01

    Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins.

  4. The DNA-dependent protein kinase: A multifunctional protein kinase with roles in DNA double strand break repair and mitosis.

    PubMed

    Jette, Nicholas; Lees-Miller, Susan P

    2015-03-01

    The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemistry, structure and function of DNA-PK, its roles in DNA double strand break repair and its newly described roles in mitosis and other cellular processes.

  5. The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis

    PubMed Central

    Jette, Nicholas; Lees-Miller, Susan P.

    2015-01-01

    The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemistry, structure and function of DNA-PK, its roles in DNA double strand break repair and its newly described roles in mitosis and other cellular processes. PMID:25550082

  6. Peroxisomal ATP-Binding Cassette Transporter COMATOSE and the Multifunctional Protein ABNORMAL INFLORESCENCE MERISTEM Are Required for the Production of Benzoylated Metabolites in Arabidopsis Seeds1[W

    PubMed Central

    Bussell, John D.; Reichelt, Michael; Wiszniewski, Andrew A.G.; Gershenzon, Jonathan; Smith, Steven M.

    2014-01-01

    Secondary metabolites derived from benzoic acid (BA) are of central importance in the interactions of plants with pests, pathogens, and symbionts and are potentially important in plant development. Peroxisomal β-oxidation has recently been shown to contribute to BA biosynthesis in plants, but not all of the enzymes involved have been defined. In this report, we demonstrate that the peroxisomal ATP-binding cassette transporter COMATOSE is required for the accumulation of benzoylated secondary metabolites in Arabidopsis (Arabidopsis thaliana) seeds, including benzoylated glucosinolates and substituted hydroxybenzoylcholines. The ABNORMAL INFLORESCENCE MERISTEM protein, one of two multifunctional proteins encoded by Arabidopsis, is essential for the accumulation of these compounds, and MULTIFUNCTIONAL PROTEIN2 contributes to the synthesis of substituted hydroxybenzoylcholines. Of the two major 3-ketoacyl coenzyme A thiolases, KAT2 plays the primary role in BA synthesis. Thus, BA biosynthesis in Arabidopsis employs the same core set of β-oxidation enzymes as in the synthesis of indole-3-acetic acid from indole-3-butyric acid. PMID:24254312

  7. Modular organization of residue-level contacts shape the selection pressure on individual amino acid sites of ribosomal proteins.

    PubMed

    Mallik, Saurav; Kundu, Sudip

    2017-02-22

    Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly and stability is of central importance. Here we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid-nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, inter-nucleotide contacts are disregarded). Contact number is defined as the number of nucleotides contacted. Involvement of individual amino acids in OaantCs with smaller contact numbers is more random, while only a few amino acids significantly contribute to OaantCs with higher contact numbers. An investigation of structure, stability and assembly of bacterial ribosome depicts the involvement of these OaantCs in diverse biophysical interactions stabilizing the complex, including high-affinity protein-RNA contacts, inter-protein cooperativity, inter-subunit bridge, packing of multiple ribosomal RNA domains etc. Amino acid-nucleotide constituents of OaantCs with higher contact numbers are generally associated with significantly slower substitution rates compared to that of OaantCs with smaller contact numbers. This evolutionary rate heterogeneity emerges from the strong purifying selection pressure that conserves the respective amino acid physicochemical properties relevant to the stabilizing interaction with OaantC nucleotides. An analysis of relative molecular orientations of OaantC residues and their interaction energetics provides the biophysical ground of purifying selection conserving OaantC amino acid physicochemical properties.

  8. Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis

    PubMed Central

    2010-01-01

    Background sRNAs, which belong to the non-coding RNA family and range from approximately 50 to 400 nucleotides, serve various important gene regulatory roles. Most are believed to be trans-regulating and function by being complementary to their target mRNAs in order to inhibiting translation by ribosome occlusion. Despite this understanding of their functionality, the global properties associated with regulation by sRNAs are not yet understood. Here we use topological analysis of sRNA targets in terms of protein-protein interaction and transcription-regulatory networks in Escherichia coli to shed light on the global correlation between sRNA regulation and cellular control networks. Results The analysis of sRNA targets in terms of their networks showed that some specific network properties could be identified. In protein-protein interaction network, sRNA targets tend to occupy more central positions (higher closeness centrality, p-val = 0.022) and more cliquish (larger clustering coefficient, p-val = 0.037). The targets of the same sRNA tend to form a network module (shorter characteristic path length, p-val = 0.015; larger density, p-val = 0.019; higher in-degree ratio, p-val = 0.009). Using the transcription-regulatory network, sRNA targets tend to be under multiple regulation (higher indegree, p-val = 0.013) and the targets usually are important to the transfer of regulatory signals (higher betweenness, p-val = 0.012). As was found for the protein-protein interaction network, the targets that are regulated by the same sRNA also tend to be closely knit within the transcription-regulatory network (larger density, p-val = 0.036), and inward interactions between them are greater than the outward interactions (higher in-degree ratio, p-val = 0.023). However, after incorporating information on predicted sRNAs and down-stream targets, the results are not as clear-cut, but the overall network modularity is still evident. Conclusions Our results indicate that s

  9. Modular evolution of glutathione peroxidase genes in association with different biochemical properties of their encoded proteins in invertebrate animals

    PubMed Central

    Bae, Young-An; Cai, Guo-Bin; Kim, Seon-Hee; Zo, Young-Gun; Kong, Yoon

    2009-01-01

    Background Phospholipid hydroperoxide glutathione peroxidases (PHGPx), the most abundant isoforms of GPx families, interfere directly with hydroperoxidation of lipids. Biochemical properties of these proteins vary along with their donor organisms, which has complicated the phylogenetic classification of diverse PHGPx-like proteins. Despite efforts for comprehensive analyses, the evolutionary aspects of GPx genes in invertebrates remain largely unknown. Results We isolated GPx homologs via in silico screening of genomic and/or expressed sequence tag databases of eukaryotic organisms including protostomian species. Genes showing strong similarity to the mammalian PHGPx genes were commonly found in all genomes examined. GPx3- and GPx7-like genes were additionally detected from nematodes and platyhelminths, respectively. The overall distribution of the PHGPx-like proteins with different biochemical properties was biased across taxa; selenium- and glutathione (GSH)-dependent proteins were exclusively detected in platyhelminth and deuterostomian species, whereas selenium-independent and thioredoxin (Trx)-dependent enzymes were isolated in the other taxa. In comparison of genomic organization, the GSH-dependent PHGPx genes showed a conserved architectural pattern, while their Trx-dependent counterparts displayed complex exon-intron structures. A codon for the resolving Cys engaged in reductant binding was found to be substituted in a series of genes. Selection pressure to maintain the selenocysteine codon in GSH-dependent genes also appeared to be relaxed during their evolution. With the dichotomized fashion in genomic organizations, a highly polytomic topology of their phylogenetic trees implied that the GPx genes have multiple evolutionary intermediate forms. Conclusion Comparative analysis of invertebrate GPx genes provides informative evidence to support the modular pathways of GPx evolution, which have been accompanied with sporadic expansion/deletion and exon

  10. Design of a Modular Protein-Based MRI Contrast Agent for Targeted Application

    PubMed Central

    Kraff, Oliver; Heider, Dominik; Schramm, Alexander; Hoffmann, Daniel; Bayer, Peter

    2013-01-01

    Magnetic resonance imaging (MRI) offers a non-radioactive alternative for the non-invasive detection of tumours. Low molecular weight MRI contrast agents currently in clinical use suffer either from a lack of specificity for tumour tissue or from low relaxivity and thus low contrast amplification. In this study, we present the newly designed two domain fusion protein Zarvin, which is able to bind to therapeutic IgG antibodies suitable for targeting, while facilitating contrast enhancement through high affinity binding sites for Gd3+. We show that the Zarvin fold is stable under serum conditions, specifically targets a cancer cell-line when bound to the Cetuximab IgG, and allows for imaging with high relaxivity, a property that would be advantageous for the detection of small tumours and metastases at 1.5 or 3 T. PMID:23762349

  11. A modular and adaptive mass spectrometry-based platform for support of bioprocess development toward optimal host cell protein clearance.

    PubMed

    Walker, Donald E; Yang, Feng; Carver, Joseph; Joe, Koman; Michels, David A; Yu, X Christopher

    2017-03-27

    A modular and adaptive mass spectrometry (MS)-based platform was developed to provide fast, robust and sensitive host cell protein (HCP) analytics to support process development. This platform relies on one-dimensional ultra-high performance liquid chromatography (1D UHPLC) combined with several different MS data acquisition strategies to meet the needs of purification process development. The workflow was designed to allow HCP composition and quantitation for up to 20 samples per day, a throughput considered essential for real time bioprocess development support. With data-dependent acquisition (DDA), the 1D UHPLC-MS/MS method had excellent speed and demonstrated robustness in detecting unknown HCPs at ≥ 50 ng/mg (ppm) level. Combining 1D UHPLC with sequential window acquisition of all theoretical spectra (SWATH) MS enabled simultaneous detection and quantitation of all HCPs in single-digit ng/mg range within 1 hour, demonstrating for the first time the benefit of SWATH MS as a technique for HCP analysis. As another alternative, a targeted MS approach can be used to track the clearance of specific known HCP under various process conditions. This study highlights the importance of designing a robust LC-MS/MS workflow that not only allows HCP discovery, but also affords greatly improved process knowledge and capability in HCP removal. As an orthogonal and complementary detection approach to traditional HCP analysis by enzyme-linked immunosorbent assay, the reported LC-MS/MS workflow supports the development of bioprocesses with optimal HCP clearance and the production of safe and high quality therapeutic biopharmaceuticals.

  12. Association of CAD, a multifunctional protein involved in pyrimidine synthesis, with mLST8, a component of the mTOR complexes

    PubMed Central

    2013-01-01

    Background mTOR is a genetically conserved serine/threonine protein kinase, which controls cell growth, proliferation, and survival. A multifunctional protein CAD, catalyzing the initial three steps in de novo pyrimidine synthesis, is regulated by the phosphorylation reaction with different protein kinases, but the relationship with mTOR protein kinase has not been known. Results CAD was recovered as a binding protein with mLST8, a component of the mTOR complexes, from HEK293 cells transfected with the FLAG-mLST8 vector. Association of these two proteins was confirmed by the co-immuoprecipitaiton followed by immunoblot analysis of transfected myc-CAD and FLAG-mLST8 as well as that of the endogenous proteins in the cells. Analysis using mutant constructs suggested that CAD has more than one region for the binding with mLST8, and that mLST8 recognizes CAD and mTOR in distinct ways. The CAD enzymatic activity decreased in the cells depleted of amino acids and serum, in which the mTOR activity is suppressed. Conclusion The results obtained indicate that mLST8 bridges between CAD and mTOR, and plays a role in the signaling mechanism where CAD is regulated in the mTOR pathway through the association with mLST8. PMID:23594158

  13. Theory for the Emergence of Modularity in Complex Systems

    NASA Astrophysics Data System (ADS)

    Deem, Michael; Park, Jeong-Man

    2013-03-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a theory for the dynamics of modularity in these systems. We find a principle of least action for the evolved modularity at long times. In addition, we find a fluctuation dissipation relation for the rate of change of modularity at short times. We discuss a number of biological and social systems that can be understood with this framework. The modularity of the protein-protein interaction network increases when yeast are exposed to heat shock, and the modularity of the protein-protein networks in both yeast and E. coli appears to have increased over evolutionary time. Food webs in low-energy, stressful environments are more modular than those in plentiful environments, arid ecologies are more modular during droughts, and foraging of sea otters is more modular when food is limiting. The modularity of social networks changes over time: stock brokers instant messaging networks are more modular under stressful market conditions, criminal networks are more modular under increased police pressure, and world trade network modularity has decreased

  14. Limits of cooperativity in a structurally modular protein: response of the Notch ankyrin domain to analogous alanine substitutions in each repeat.

    PubMed

    Bradley, Christina Marchetti; Barrick, Doug

    2002-11-22

    To determine the limits of cooperativity in a structurally modular protein, we characterized the structure and stability of glycine variants of the ankyrin repeat domain from the Drosophila melangaster Notch receptor. The substitutions are of analogous alanine residues to glycine in each repeat, and allow the same perturbation to be examined at different positions in the protein. The ankyrin domain is insensitive to substitution in repeat one, suggesting that the first repeat is not fully-folded. Glycine substitutions in repeat two through seven are strongly destabilizing, but the variants retain their overall secondary and tertiary structures. Spectroscopic and calorimetric data are consistent with two-state unfolding transitions for the repeat-two through repeat-five glycine variants, and for the wild-type protein. These data indicate that, despite its modular structure, the Notch ankyrin domain unfolds as a cooperative unit consisting of the six C-terminal repeats, and that this cooperativity is maintained in the presence of severely destabilizing substitutions in the N-terminal and central repeats. In contrast, glycine substitution in repeat six leads to a multi-state unfolding transition, suggesting that the coupling that gives rise to long-range cooperativity in the wild-type protein may have a weak link in the C-terminal region. Such behavior is captured by a simple statistical thermodynamic model in which an unstable C-terminal region is coupled to a stable N-terminal region through a strongly stabilizing interface.

  15. Quasispecies theory for evolution of modularity

    NASA Astrophysics Data System (ADS)

    Park, Jeong-Man; Niestemski, Liang Ren; Deem, Michael W.

    2015-01-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent.

  16. Quasispecies Theory for Evolution of Modularity

    PubMed Central

    Park, Jeong-Man; Niestemski, Liang Ren; Deem, Michael W.

    2015-01-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent. PMID:25679649

  17. Quasispecies theory for evolution of modularity.

    PubMed

    Park, Jeong-Man; Niestemski, Liang Ren; Deem, Michael W

    2015-01-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent.

  18. Single Cell Microgel Based Modular Bioinks for Uncoupled Cellular Micro- and Macroenvironments.

    PubMed

    Kamperman, Tom; Henke, Sieger; van den Berg, Albert; Shin, Su Ryon; Tamayol, Ali; Khademhosseini, Ali; Karperien, Marcel; Leijten, Jeroen

    2017-02-01

    Modular bioinks based on single cell microgels within distinct injectable prepolymers enable uncoupling of biomaterials' micro- and macroenvironments. These inks allow biofabrication of 3D constructs that recapitulate the multiscale modular design of native tissues with a single cell resolution. This approach represents a major step forward in endowing engineered constructs with the multifunctionality that underlies the behavior of native tissues.

  19. Modular shield

    DOEpatents

    Snyder, Keith W.

    2002-01-01

    A modular system for containing projectiles has a sheet of material including at least a polycarbonate layer held by a metal frame having a straight frame member corresponding to each straight edge of the sheet. Each frame member has a U-shaped shield channel covering and holding a straight edge of the sheet and an adjacent U-shaped clamp channel rigidly held against the shield channel. A flexible gasket separates each sheet edge from its respective shield channel; and each frame member is fastened to each adjacent frame member only by clamps extending between adjacent clamp channels.

  20. Helix-Destabilizing, β-Branched, and Polar Residues in the Baboon Reovirus p15 Transmembrane Domain Influence the Modularity of FAST Proteins

    PubMed Central

    Clancy, Eileen K.; Duncan, Roy

    2011-01-01

    The fusogenic reoviruses induce syncytium formation using the fusion-associated small transmembrane (FAST) proteins. A recent study indicated the p14 FAST protein transmembrane domain (TMD) can be functionally replaced by the TMDs of the other FAST proteins but not by heterologous TMDs, suggesting that the FAST protein TMDs are modular fusion units. We now show that the p15 FAST protein is also a modular fusogen, as indicated by the functional replacement of the p15 ectodomain with the corresponding domain from the p14 FAST protein. Paradoxically, the p15 TMD is not interchangeable with the TMDs of the other FAST proteins, implying that unique attributes of the p15 TMD are required when this fusion module is functioning in the context of the p15 ecto- and/or endodomain. A series of point substitutions, truncations, and reextensions were created in the p15 TMD to define features that are specific to the functioning of the p15 TMD. Removal of only one or two residues from the N terminus or four residues from the C terminus of the p15 TMD eliminated membrane fusion activity, and there was a direct correlation between the fusion-promoting function of the p15 TMD and the presence of N-terminal, hydrophobic β-branched residues. Substitution of the glycine residues and triserine motif present in the p15 TMD also impaired or eliminated the fusion-promoting activity of the p15 TMD. The ability of the p15 TMD to function in an ecto- and endodomain-specific context is therefore influenced by stringent sequence requirements that reflect the importance of TMD polar residues and helix-destabilizing residues. PMID:21367887

  1. Modular Certification

    NASA Technical Reports Server (NTRS)

    Rushby, John; Miner, Paul S. (Technical Monitor)

    2002-01-01

    Airplanes are certified as a whole: there is no established basis for separately certifying some components, particularly software-intensive ones, independently of their specific application in a given airplane. The absence of separate certification inhibits the development of modular components that could be largely "precertified" and used in several different contexts within a single airplane, or across many different airplanes. In this report, we examine the issues in modular certification of software components and propose an approach based on assume-guarantee reasoning. We extend the method from verification to certification by considering behavior in the presence of failures. This exposes the need for partitioning, and separation of assumptions and guarantees into normal and abnormal cases. We then identify three classes of property that must be verified within this framework: safe function, true guarantees, and controlled failure. We identify a particular assume-guarantee proof rule (due to McMillan) that is appropriate to the applications considered, and formally verify its soundness in PVS.

  2. Local modularity for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Tao; Zhang, Yan; Hu, Ke; Li, Jian-Ming; Xu, Xiao-Ke; Liu, Cui-Cui; Chen, Shi

    2016-02-01

    Community detection is a topic of interest in the study of complex networks such as the protein-protein interaction networks and metabolic networks. In recent years, various methods were proposed to detect community structures of the networks. Here, a kind of local modularity with tunable parameter is derived from the Newman-Girvan modularity by a special self-loop strategy that depends on the community division of the networks. By the self-loop strategy, one can easily control the definition of modularity, and the resulting modularity can be optimized by using the existing modularity optimization algorithms. The local modularity is used as the target function for community detection, and a self-consistent method is proposed for the optimization of the local modularity. We analyze the behaviors of the local modularity and show the validity of the local modularity in detecting community structures on various networks.

  3. Thick-walled carbon composite multifunctional structures

    NASA Astrophysics Data System (ADS)

    Haake, John M.; Jacobs, Jack H.; McIlroy, Bruce E.

    1997-06-01

    Satellite programs are moving in the direction of smaller and lighter structures. Technological advances have permitted more sophisticated equipment to be consolidated into compact spaces. Micro-satellites, between 10 and 100 kg, will incorporate micro-electric devices into the lay-up of the satellite structure. These structures will be designed to carry load, provide thermal control, enhance damping, and include integrated passive electronics. These multifunctional structures offer lighter weight, reduced volume, and a 'smarter' overall package for incorporation of sensors, electronics, fiber optics, powered appendages or active components. McDonnell Douglas Corporation (MDC) has applied technology from the synthesis and processing of intelligent cost effective structures (SPICES) and independent research and development (IRAD) programs to the modular instrument support system (MISS) for multifunctional space structures and micro-satellites. The SPICES program was funded by the Defense Advanced Research Projects Agency (DARPA) to develop affordable manufacturing processes for smart materials to be used in vibration control, and the MISS program was funded by NASA-Langley. The MISS program was conceived to develop concepts and techniques to make connections between different multifunctional structures. MDA fabricated a trapezoidal carbon composite structure out of IM7/977-3 tape prepreg. Flex circuits, thermal and optical conduits were embedded to realize a utility modular connector. These provide electrical, thermal, optical and mechanical connections between micro- satellite components. A quick disconnect mount was also developed to accommodate a variety of devices such as solar arrays, power sources, thermal transfer and vibration control modules.

  4. Evolution of Efficient Modular Polyketide Synthases by Homologous Recombination

    PubMed Central

    Chemler, Joseph A.; Tripathi, Ashootosh; Hansen, Douglas A.; O'Neil-Johnson, Mark; Williams, Russell B.; Starks, Courtney; Park, Sung Ryeol; Sherman, David H.

    2015-01-01

    The structural scaffolds of many complex natural products are produced by multifunctional type I polyketide synthase (PKS) enzymes that operate as bio-synthetic assembly lines. The modular nature of these megaenzymes presents an opportunity to construct custom biocatalysts built in a lego-like fashion by inserting, deleting, or exchanging native or foreign domains to produce targeted variants of natural polyketides. However, previously engineered PKS enzymes are often impaired resulting in limited production compared to native systems. Here, we show a versatile method for generating and identifying functional chimeric PKS enzymes for synthesizing custom macrolactones and macrolides. PKS genes from the pikromycin and erythromycin pathways were hybridized in Saccharomyces cerevisiae to generate hybrid libraries. We used a 96-well plate format for plasmid purification, transformations, sequencing, protein expression, in vitro reactions and analysis of metabolite formation. Active chimeric enzymes were identified with new functionality. Streptomyces venezuelae strains that expressed these PKS chimeras were capable of producing engineered macrolactones. Furthermore, a macrolactone generated from selected PKS chimeras was fully functionalized into a novel macrolide analogue. This method permits the engineering of PKS pathways as modular building blocks for the production of new antibiotic-like molecules. PMID:26230368

  5. Protein-Assisted Assembly of Modular 3D Plasmonic Raspberry-like Core/Satellite Nanoclusters: Correlation of Structure and Optical Properties.

    PubMed

    Höller, Roland P M; Dulle, Martin; Thomä, Sabrina; Mayer, Martin; Steiner, Anja Maria; Förster, Stephan; Fery, Andreas; Kuttner, Christian; Chanana, Munish

    2016-06-28

    We present a bottom-up assembly route for a large-scale organization of plasmonic nanoparticles (NPs) into three-dimensional (3D) modular assemblies with core/satellite structure. The protein-assisted assembly of small spherical gold or silver NPs with a hydrophilic protein shell (as satellites) onto larger metal NPs (as cores) offers high modularity in sizes and composition at high satellite coverage (close to the jamming limit). The resulting dispersions of metal/metal nanoclusters exhibit high colloidal stability and therefore allow for high concentrations and a precise characterization of the nanocluster architecture in dispersion by small-angle X-ray scattering (SAXS). Strong near-field coupling between the building blocks results in distinct regimes of dominant satellite-to-satellite and core-to-satellite coupling. High robustness against satellite disorder was proved by UV/vis diffuse reflectance (integrating sphere) measurements. Generalized multiparticle Mie theory (GMMT) simulations were employed to describe the electromagnetic coupling within the nanoclusters. The close correlation of structure and optical property allows for the rational design of core/satellite nanoclusters with tailored plasmonics and well-defined near-field enhancement, with perspectives for applications such as surface-enhanced spectroscopies.

  6. Protein-Assisted Assembly of Modular 3D Plasmonic Raspberry-like Core/Satellite Nanoclusters: Correlation of Structure and Optical Properties

    PubMed Central

    Höller, Roland P. M.; Dulle, Martin; Thomä, Sabrina; Mayer, Martin; Steiner, Anja Maria; Förster, Stephan; Fery, Andreas

    2016-01-01

    We present a bottom-up assembly route for a large-scale organization of plasmonic nanoparticles (NPs) into three-dimensional (3D) modular assemblies with core/satellite structure. The protein-assisted assembly of small spherical gold or silver NPs with a hydrophilic protein shell (as satellites) onto larger metal NPs (as cores) offers high modularity in sizes and composition at high satellite coverage (close to the jamming limit). The resulting dispersions of metal/metal nanoclusters exhibit high colloidal stability and therefore allow for high concentrations and a precise characterization of the nanocluster architecture in dispersion by small-angle X-ray scattering (SAXS). Strong near-field coupling between the building blocks results in distinct regimes of dominant satellite-to-satellite and core-to-satellite coupling. High robustness against satellite disorder was proved by UV/vis diffuse reflectance (integrating sphere) measurements. Generalized multiparticle Mie theory (GMMT) simulations were employed to describe the electromagnetic coupling within the nanoclusters. The close correlation of structure and optical property allows for the rational design of core/satellite nanoclusters with tailored plasmonics and well-defined near-field enhancement, with perspectives for applications such as surface-enhanced spectroscopies. PMID:26982386

  7. Regulation of the multifunctional Ca2+/calmodulin-dependent protein kinase II by the PP2C phosphatase PPM1F in fibroblasts.

    PubMed

    Harvey, Bohdan P; Banga, Satnam S; Ozer, Harvey L

    2004-06-04

    The regulation of the multifunctional calcium/calmodulin dependent protein kinase II (CaMKII) by serine/threonine protein phosphatases has been extensively studied in neuronal cells; however, this regulation has not been investigated previously in fibroblasts. We cloned a cDNA from SV40-transformed human fibroblasts that shares 80% homology to a rat calcium/calmodulin-dependent protein kinase phosphatase that encodes a PPM1F protein. By using extracts from transfected cells, PPM1F, but not a mutant (R326A) in the conserved catalytic domain, was found to dephosphorylate in vitro a peptide corresponding to the auto-inhibitory region of CaMKII. Further analyses demonstrated that PPM1F specifically dephosphorylates the phospho-Thr-286 in autophosphorylated CaMKII substrate and thus deactivates the CaMKII in vitro. Coimmunoprecipitation of CaMKII with PPM1F indicates that the two proteins can interact intracellularly. Binding of PPM1F to CaMKII involves multiple regions and is not dependent on intact phosphatase activity. Furthermore, overexpression of PPM1F in fibroblasts caused a reduction in the CaMKII-specific phosphorylation of the known substrate vimentin(Ser-82) following induction of the endogenous CaM kinase. These results identify PPM1F as a CaM kinase phosphatase within fibroblasts, although it may have additional functions intracellularly since it has been presented elsewhere as POPX2 and hFEM-2. We conclude that PPM1F, possibly together with the other previously described protein phosphatases PP1 and PP2A, can regulate the activity of CaMKII. Moreover, because PPM1F dephosphorylates the critical autophosphorylation site of CaMKII, we propose that this phosphatase plays a key role in the regulation of the kinase intracellularly.

  8. Protein-mediated synthesis of nanosized Mn-doped ZnS: a multifunctional, UV-durable bio-nanocomposite.

    PubMed

    Makhal, Abhinandan; Sarkar, Soumik; Pal, Samir Kumar

    2012-10-01

    The design of synthetic nanoparticles (NPs) capable of recognizing given chemical entities in a specific and predictable manner is of great fundamental and practical importance. Herein, we report a simple, fast, water-soluble, and green phosphine free colloidal synthesis route for the preparation of multifunctional enzyme-capped ZnS bionanocomposites (BNCs) with/without transitional metal-ion doping. The enzymes α-Chymotrypsin (CHT), associated with the NPs, are demonstrated as an effectual host for organic dye Methylene Blue (MB) revealing the molecular recognition of such dye molecules by the BNCs. An effective hosting of MB in the close proximity of ZnS NPs (with ~3 nm size) leads to photocatalysis of the dyes which has further been investigated with doped-semiconductors. The NP-associated enzyme α-CHT is found to be active toward a substrate (Ala-Ala-Phe-7-amido-4-methyl-coumarin), hence leads to significant enzyme catalysis. Irradiation induced luminescence enhancement (IILE) measurements on the BNCs clearly interpret the role of surface capping agents which protect against deep UV damaging of ZnS NPs.

  9. The emergence of modularity in biological systems

    NASA Astrophysics Data System (ADS)

    Lorenz, Dirk M.; Jeng, Alice; Deem, Michael W.

    2011-06-01

    In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks.

  10. Emerging Multifunctional Metal-Organic Framework Materials.

    PubMed

    Li, Bin; Wen, Hui-Min; Cui, Yuanjing; Zhou, Wei; Qian, Guodong; Chen, Banglin

    2016-10-01

    Metal-organic frameworks (MOFs), also known as coordination polymers, represent an interesting type of solid crystalline materials that can be straightforwardly self-assembled through the coordination of metal ions/clusters with organic linkers. Owing to the modular nature and mild conditions of MOF synthesis, the porosities of MOF materials can be systematically tuned by judicious selection of molecular building blocks, and a variety of functional sites/groups can be introduced into metal ions/clusters, organic linkers, or pore spaces through pre-designing or post-synthetic approaches. These unique advantages enable MOFs to be used as a highly versatile and tunable platform for exploring multifunctional MOF materials. Here, the bright potential of MOF materials as emerging multifunctional materials is highlighted in some of the most important applications for gas storage and separation, optical, electric and magnetic materials, chemical sensing, catalysis, and biomedicine.

  11. Aminoacyl-tRNA synthetase-interacting multifunctional protein 1 suppresses tumor growth in breast cancer-bearing mice by negatively regulating myeloid-derived suppressor cell functions.

    PubMed

    Hong, Hye-Jin; Lim, Hui Xuan; Song, Ju Han; Lee, Arim; Kim, Eugene; Cho, Daeho; Cohen, Edward P; Kim, Tae Sung

    2016-01-01

    Myeloid-derived suppressor cells (MDSCs) are one of the most important cell types that contribute to negative regulation of immune responses in the tumor microenvironment. Recently, aminoacyl-tRNA synthetase-interacting multifunctional protein 1 (AIMP1), a novel pleiotropic cytokine, was identified as an antitumor protein that inhibits angiogenesis and induces antitumor responses. However, the effect of AIMP1 on MDSCs in the tumor environment remains unclear. In the present study, we demonstrated that AIMP1 significantly inhibited tumor growth in 4T1 breast cancer-bearing mice and reduced MDSCs population of tumor sites and spleens of tumor-bearing mice. AIMP1 reduced expansion of MDSCs from bone marrow-derived cells in the tumor-conditioned media. AIMP1 also negatively regulated suppressive activities of MDSCs by inhibiting IL-6 and NO production, and Arg-1 expression. Furthermore, treatment of breast cancer-bearing mice with AIMP1 decreased the capacity of MDSCs to suppress T cell proliferation and Treg cell induction. Western blot and inhibition experiments showed that downregulation of MDSCs functions by AIMP1 may result from attenuated activation of STATs, Akt, and ERK. These findings indicate that AIMP1 plays an essential role in negative regulation of suppressive functions of MDSCs. Therefore, it has a significant potential as a therapeutic agent for cancer treatment.

  12. Modular protein expression by RNA trans-splicing enables flexible expression of antibody formats in mammalian cells from a dual-host phage display vector.

    PubMed

    Shang, Yonglei; Tesar, Devin; Hötzel, Isidro

    2015-10-01

    A recently described dual-host phage display vector that allows expression of immunoglobulin G (IgG) in mammalian cells bypasses the need for subcloning of phage display clone inserts to mammalian vectors for IgG expression in large antibody discovery and optimization campaigns. However, antibody discovery and optimization campaigns usually need different antibody formats for screening, requiring reformatting of the clones in the dual-host phage display vector to an alternative vector. We developed a modular protein expression system mediated by RNA trans-splicing to enable the expression of different antibody formats from the same phage display vector. The heavy-chain region encoded by the phage display vector is directly and precisely fused to different downstream heavy-chain sequences encoded by complementing plasmids simply by joining exons in different pre-mRNAs by trans-splicing. The modular expression system can be used to efficiently express structurally correct IgG and Fab fragments or other antibody formats from the same phage display clone in mammalian cells without clone reformatting.

  13. Multifunctional Mitochondrial AAA Proteases

    PubMed Central

    Glynn, Steven E.

    2017-01-01

    Mitochondria perform numerous functions necessary for the survival of eukaryotic cells. These activities are coordinated by a diverse complement of proteins encoded in both the nuclear and mitochondrial genomes that must be properly organized and maintained. Misregulation of mitochondrial proteostasis impairs organellar function and can result in the development of severe human diseases. ATP-driven AAA+ proteins play crucial roles in preserving mitochondrial activity by removing and remodeling protein molecules in accordance with the needs of the cell. Two mitochondrial AAA proteases, i-AAA and m-AAA, are anchored to either face of the mitochondrial inner membrane, where they engage and process an array of substrates to impact protein biogenesis, quality control, and the regulation of key metabolic pathways. The functionality of these proteases is extended through multiple substrate-dependent modes of action, including complete degradation, partial processing, or dislocation from the membrane without proteolysis. This review discusses recent advances made toward elucidating the mechanisms of substrate recognition, handling, and degradation that allow these versatile proteases to control diverse activities in this multifunctional organelle. PMID:28589125

  14. Modular robot

    DOEpatents

    Ferrante, Todd A.

    1997-01-01

    A modular robot may comprise a main body having a structure defined by a plurality of stackable modules. The stackable modules may comprise a manifold, a valve module, and a control module. The manifold may comprise a top surface and a bottom surface having a plurality of fluid passages contained therein, at least one of the plurality of fluid passages terminating in a valve port located on the bottom surface of the manifold. The valve module is removably connected to the manifold and selectively fluidically connects the plurality of fluid passages contained in the manifold to a supply of pressurized fluid and to a vent. The control module is removably connected to the valve module and actuates the valve module to selectively control a flow of pressurized fluid through different ones of the plurality of fluid passages in the manifold. The manifold, valve module, and control module are mounted together in a sandwich-like manner and comprise a main body. A plurality of leg assemblies are removably connected to the main body and are removably fluidically connected to the fluid passages in the manifold so that each of the leg assemblies can be selectively actuated by the flow of pressurized fluid in different ones of the plurality of fluid passages in the manifold.

  15. Modular robot

    DOEpatents

    Ferrante, T.A.

    1997-11-11

    A modular robot may comprise a main body having a structure defined by a plurality of stackable modules. The stackable modules may comprise a manifold, a valve module, and a control module. The manifold may comprise a top surface and a bottom surface having a plurality of fluid passages contained therein, at least one of the plurality of fluid passages terminating in a valve port located on the bottom surface of the manifold. The valve module is removably connected to the manifold and selectively fluidically connects the plurality of fluid passages contained in the manifold to a supply of pressurized fluid and to a vent. The control module is removably connected to the valve module and actuates the valve module to selectively control a flow of pressurized fluid through different ones of the plurality of fluid passages in the manifold. The manifold, valve module, and control module are mounted together in a sandwich-like manner and comprise a main body. A plurality of leg assemblies are removably connected to the main body and are removably fluidically connected to the fluid passages in the manifold so that each of the leg assemblies can be selectively actuated by the flow of pressurized fluid in different ones of the plurality of fluid passages in the manifold. 12 figs.

  16. The Modular Adaptive Ribosome.

    PubMed

    Yadav, Anupama; Radhakrishnan, Aparna; Panda, Anshuman; Singh, Amartya; Sinha, Himanshu; Bhanot, Gyan

    2016-01-01

    The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5'UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.

  17. The Modular Adaptive Ribosome

    PubMed Central

    Yadav, Anupama; Radhakrishnan, Aparna; Panda, Anshuman; Singh, Amartya; Sinha, Himanshu; Bhanot, Gyan

    2016-01-01

    The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5’UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments. PMID:27812193

  18. SdrI of Staphylococcus saprophyticus is a multifunctional protein: localization of the fibronectin-binding site.

    PubMed

    Sakinç, Türkân; Kleine, Britta; Michalski, Nadine; Kaase, Martin; Gatermann, Sören G

    2009-11-01

    Staphylococcus saprophyticus, an important cause of urinary tract infections in young women, expresses the surface protein SdrI, a member of the serine-aspartate repeat (SD) protein family. Here we analyse the fibronectin-binding ability of SdrI, as S. saprophyticus is known to bind fibronectin and there is no known SD protein with this function. This protein does not contain the binding motif typical for fibronectin-binding proteins. Using recombinant fragments of SdrI, we localized the binding domain in the A region and show that SdrI bound to the N-terminal 30-kDa fragment of fibronectin. The fibronectin-binding function was shown in the natural host using an SdrI knockout mutant that showed decreased binding to fibronectin compared with wild-type strain 7108.

  19. Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p

    PubMed Central

    Spingola, Marc; Armisen, Javier; Ares, Manuel

    2004-01-01

    Mer1p activates the splicing of at least three pre-mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from Mer1p splicing activation. The C-terminal KH-type RNA-binding domain of Mer1p recognizes introns that contain the Mer1p splicing enhancer, while the N-terminal domain interacts with the spliceosome and activates splicing. Prior studies have implicated the U1 snRNP and recognition of the 5′ splice site as key elements in Mer1p-activated splicing. We provide new evidence that Mer1p may also function at later steps of spliceosome assembly. First, Mer1p can activate splicing of introns that have mutated branch point sequences. Secondly, Mer1p fails to activate splicing in the absence of the non-essential U2 snRNP protein Snu17p. Thirdly, Mer1p interacts with the branch point binding proteins Mud2p and Bbp1p and the U2 snRNP protein Prp11p by two-hybrid assays. We conclude that Mer1p is a modular splicing regulator that can activate splicing at several early steps of spliceosome assembly and depends on the activities of both U1 and U2 snRNP proteins to activate splicing. PMID:14973223

  20. Multifunctional roles for the N-terminal basic motif of Alfalfa mosaic virus coat protein: nucleolar/cytoplasmic shuttling, modulation of RNA-binding activity, and virion formation.

    PubMed

    Herranz, Mari Carmen; Pallas, Vicente; Aparicio, Frederic

    2012-08-01

    In addition to virion formation, the coat protein (CP) of Alfalfa mosaic virus (AMV) is involved in the regulation of replication and translation of viral RNAs, and in cell-to-cell and systemic movement of the virus. An intriguing feature of the AMV CP is its nuclear and nucleolar accumulation. Here, we identify an N-terminal lysine-rich nucleolar localization signal (NoLS) in the AMV CP required to both enter the nucleus and accumulate in the nucleolus of infected cells, and a C-terminal leucine-rich domain which might function as a nuclear export signal. Moreover, we demonstrate that AMV CP interacts with importin-α, a component of the classical nuclear import pathway. A mutant AMV RNA 3 unable to target the nucleolus exhibited reduced plus-strand RNA synthesis and cell-to-cell spread. Moreover, virion formation and systemic movement were completely abolished in plants infected with this mutant. In vitro analysis demonstrated that specific lysine residues within the NoLS are also involved in modulating CP-RNA binding and CP dimerization, suggesting that the NoLS represents a multifunctional domain within the AMV CP. The observation that nuclear and nucleolar import signals mask RNA-binding properties of AMV CP, essential for viral replication and translation, supports a model in which viral expression is carefully modulated by a cytoplasmic/nuclear balance of CP accumulation.

  1. Integration of binding peptide selection and multifunctional particles as tool-box for capture of soluble proteins in serum

    PubMed Central

    Cusano, Angela Maria; Causa, Filippo; Moglie, Raffaella Della; Falco, Nunzia; Scognamiglio, Pasqualina Liana; Aliberti, Anna; Vecchione, Raffaele; Battista, Edmondo; Marasco, Daniela; Savarese, Marika; Raucci, Umberto; Rega, Nadia; Netti, Paolo Antonio

    2014-01-01

    In this paper, we report on a general approach for the detection of a specific tumoural biomarker directly in serum. Such detection is made possible using a protein-binding peptide selected through an improved phage display technique and then conjugated to engineered microparticles (MPs). Protein biomarkers represent an unlimited source of information for non-invasive diagnostic and prognostic tests; MP-based assays are becoming largely used in manipulation of soluble biomarkers, but their direct use in serum is hampered by the complex biomolecular environment. Our technique overcomes the current limitations as it produces a selective MP—engineered with an antifouling layer—that ‘captures’ the relevant protein staying impervious to the background. Our system succeeds in fishing-out the human tumour necrosis factor alpha directly in serum with a high selectivity degree. Our method could have great impact in soluble protein manipulation and detection for a wide variety of diagnostic applications. PMID:25100324

  2. Integration of binding peptide selection and multifunctional particles as tool-box for capture of soluble proteins in serum.

    PubMed

    Cusano, Angela Maria; Causa, Filippo; Moglie, Raffaella Della; Falco, Nunzia; Scognamiglio, Pasqualina Liana; Aliberti, Anna; Vecchione, Raffaele; Battista, Edmondo; Marasco, Daniela; Savarese, Marika; Raucci, Umberto; Rega, Nadia; Netti, Paolo Antonio

    2014-10-06

    In this paper, we report on a general approach for the detection of a specific tumoural biomarker directly in serum. Such detection is made possible using a protein-binding peptide selected through an improved phage display technique and then conjugated to engineered microparticles (MPs). Protein biomarkers represent an unlimited source of information for non-invasive diagnostic and prognostic tests; MP-based assays are becoming largely used in manipulation of soluble biomarkers, but their direct use in serum is hampered by the complex biomolecular environment. Our technique overcomes the current limitations as it produces a selective MP--engineered with an antifouling layer--that 'captures' the relevant protein staying impervious to the background. Our system succeeds in fishing-out the human tumour necrosis factor alpha directly in serum with a high selectivity degree. Our method could have great impact in soluble protein manipulation and detection for a wide variety of diagnostic applications.

  3. Recovery of paramyxovirus simian virus 5 with a V protein lacking the conserved cysteine-rich domain: the multifunctional V protein blocks both interferon-beta induction and interferon signaling.

    PubMed

    He, Biao; Paterson, Reay G; Stock, Nicola; Durbin, Joan E; Durbin, Russell K; Goodbourn, Stephen; Randall, Richard E; Lamb, Robert A

    2002-11-10

    The V protein of the Paramyxovirus simian virus 5 (SV5) is a multifunctional protein containing an N-terminal 164 residue domain that is shared with the P protein and a distinct C-terminal domain that is cysteine-rich and which is highly conserved among Paramyxoviruses. We report the recovery from Vero cells [interferon (IFN) nonproducing cells] of a recombinant SV5 (rSV5) that lacks the V protein C-terminal specific domain (rSV5VDeltaC). In Vero cells rSV5VDeltaC forms large plaques and grows at a rate and titer similar to those of rSV5. In BHK or CV-1 cells rSV5VDeltaC forms small plaques and grows poorly. However, even when grown in Vero cells rSV5VDeltaC reverts to pseudo-wild-type virus in four to five passages, indicating the importance of the V protein for successful replication of SV5. Whereas rSV5 grows in many cell types with minimal cytopathic effect (CPE), rSV5VDeltaC causes extensive CPE in the same cell types. To overcome the antiviral state induced by IFN, many viruses have evolved mechanisms to counteract the effects of IFN by blocking the production of IFN and abrogating IFN signaling. Whereas rSV5 blocks IFN signaling by mediating the degradation of STAT1, rSV5VDeltaC does not cause the degradation of STAT1 and IFN signaling occurs through formation of the ISGF3 transcription complex. Furthermore, we find that rSV5 infection of cells prevents production of IFN-beta. The transcription factor IRF-3 which is required for transcription of the IFN-beta gene is not translocated from the cytoplasm to the nucleus in rSV5-infected cells. In contrast, in rSV5VDeltaC-infected cells IRF-3 is localized predominantly in the nucleus and IFN-beta is produced. By using ectopic expression of IRF-3, it was shown that after dsRNA treatment and expression of the V protein IRF-3 remained in the cytoplasm, whereas after dsRNA treatment and expression of the P protein (which lacks the C-terminal cysteine-rich domain) IRF-3 was localized predominantly in the nucleus. Thus

  4. Lightweight composites for modular panelized construction

    NASA Astrophysics Data System (ADS)

    Vaidya, Amol S.

    Rapid advances in construction materials technology have enabled civil engineers to achieve impressive gains in the safety, economy, and functionality of structures built to serve the common needs of society. Modular building systems is a fast-growing modern, form of construction gaining recognition for its increased efficiency and ability to apply modern technology to the needs of the market place. In the modular construction technique, a single structural panel can perform a number of functions such as providing thermal insulation, vibration damping, and structural strength. These multifunctional panels can be prefabricated in a manufacturing facility and then transferred to the construction site. A system that uses prefabricated panels for construction is called a "panelized construction system". This study focuses on the development of pre-cast, lightweight, multifunctional sandwich composite panels to be used for panelized construction. Two thermoplastic composite panels are proposed in this study, namely Composite Structural Insulated Panels (CSIPs) for exterior walls, floors and roofs, and Open Core Sandwich composite for multifunctional interior walls of a structure. Special manufacturing techniques are developed for manufacturing these panels. The structural behavior of these panels is analyzed based on various building design codes. Detailed descriptions of the design, cost analysis, manufacturing, finite element modeling and structural testing of these proposed panels are included in this study in the of form five peer-reviewed journal articles. The structural testing of the proposed panels involved in this study included flexural testing, axial compression testing, and low and high velocity impact testing. Based on the current study, the proposed CSIP wall and floor panels were found satisfactory, based on building design codes ASCE-7-05 and ACI-318-05. Joining techniques are proposed in this study for connecting the precast panels on the construction

  5. RBP16 is a multifunctional gene regulatory protein involved in editing and stabilization of specific mitochondrial mRNAs in Trypanosoma brucei

    PubMed Central

    PELLETIER, MICHEL; READ, LAURIE K.

    2003-01-01

    RBP16 is a Trypanosoma brucei mitochondrial RNA-binding protein that associates with guide RNAs (gRNAs), mRNAs, and ribosomal RNAs. Based on its inclusion in the multifunctional Y-box protein family and its ability to bind multiple RNA classes, we hypothesized that RBP16 plays a role in diverse aspects of mitochondrial gene regulation. To gain insight into RBP16 function, we generated cells expressing less than 10% of wild-type RBP16 levels by tetracycline-regulated RNA interference (RNAi). Poisoned primer extension analyses revealed that edited, but not unedited, CYb mRNA is reduced by ∼98% in tetracycline-induced RBP16 RNAi cells, suggesting that RBP16 is critical for CYb RNA editing. The down-regulation of CYb editing in RBP16 RNAi transfectants apparently entails a defect in gRNA utilization, as gCYb[560] abundance is similar in uninduced and induced cells. We observed a surprising degree of specificity regarding the ability of RBP16 to modulate editing, as editing of mRNAs other than CYb is not significantly affected upon RBP16 disruption. However, the abundance of the never edited mitochondrial RNAs COI and ND4 is reduced by 70%–80% in RBP16 RNAi transfectants, indicating an additional role for RBP16 in the stabilization of these mRNAs. Analysis of RNAs bound to RBP16 immunoprecipitated from wild-type cells reveals that RBP16 is associated with multiple gRNA sequence classes in vivo, including those whose abundance and usage appear unaffected by RBP16 disruption. Overall, our results indicate that RBP16 is an accessory factor that regulates the editing and stability of specific populations of mitochondrial mRNAs. PMID:12649497

  6. Sustained tumor regression of human colorectal cancer xenografts using a multifunctional mannosylated fusion protein in antibody-directed enzyme prodrug therapy.

    PubMed

    Sharma, Surinder K; Pedley, R Barbara; Bhatia, Jeetendra; Boxer, Geoffrey M; El-Emir, Ethaar; Qureshi, Uzma; Tolner, Berend; Lowe, Helen; Michael, N Paul; Minton, Nigel; Begent, Richard H J; Chester, Kerry A

    2005-01-15

    Antibody-directed enzyme prodrug therapy (ADEPT) requires highly selective antibody-mediated delivery of enzyme to tumor. MFE-CP, a multifunctional genetic fusion protein of antibody and enzyme, was designed to achieve this by two mechanisms. First by using a high affinity and high specificity single chain Fv antibody directed to carcinoembryonic antigen. Second by rapid removal of antibody-enzyme from normal tissues by virtue of post-translational mannosylation. The purpose of this paper is to investigate these dual functions in an animal model of pharmacokinetics, pharmacodynamics, toxicity, and efficacy. MFE-CP was expressed in the yeast Pichia pastoris and purified via an engineered hexahistidine tag. Biodistribution and therapeutic effect of a single ADEPT cycle (1,000 units/kg MFE-CP followed by 70 mg/kg ZD2767P prodrug at 6, 7, and 8 hours) and multiple ADEPT cycles (9-10 cycles within 21-24 days) was studied in established human colon carcinoma xenografts, LS174T, and SW1222. Selective localization of functional enzyme in tumors and rapid clearance from plasma was observed within 6 hours, resulting in tumor to plasma ratios of 1,400:1 and 339:1, respectively for the LS174T and SW1222 models. A single ADEPT cycle produced reproducible tumor growth delay in both models. Multiple ADEPT cycles significantly enhanced the therapeutic effect of a single cycle in the LS174T xenografts (P = 0.001) and produced regressions in the SW1222 xenografts (P = 0.0001), with minimal toxicity. MFE-CP fusion protein, in combination with ZD2767P, provides a new and successful ADEPT system, which offers the potential for multiple cycles and antitumor efficacy. These results provide a basis for the next stage in clinical development of ADEPT.

  7. Kiwellin, a modular protein from green and gold kiwi fruits: evidence of in vivo and in vitro processing and IgE binding.

    PubMed

    Tuppo, Lisa; Giangrieco, Ivana; Palazzo, Paola; Bernardi, Maria Livia; Scala, Enrico; Carratore, Vito; Tamburrini, Maurizio; Mari, Adriano; Ciardiello, M Antonietta

    2008-05-28

    Kiwellin, an allergenic protein formerly isolated from green kiwi fruit, has been identified as the most abundant component of the gold kiwi species. A protein named KiTH, showing a 20 kDa band on reducing SDS-PAGE and 100% identity with the C-terminal region of kiwellin, has been identified in the extract of the ripe green species. In vitro treatment of purified kiwellin with the protease actinidin from green kiwi fruit originated KiTH and kissper, a recently described pore-forming peptide. Primary structure analysis and experimental evidence suggest that kiwellin is a modular protein with two domains. It may undergo in vivo proteolytic processing by actinidin, thus producing KiTH and kissper. When probed with sera recognizing kiwellin from green kiwi fruit, KiTH showed IgE binding, with reactivity levels sometimes different from those of kiwellin. The IgE-binding capacity of kiwellin from gold kiwi fruit appears to be similar to that of the green species.

  8. SH2B1 (SH2-B) and JAK2: a multifunctional adaptor protein and kinase made for each other.

    PubMed

    Maures, Travis J; Kurzer, Jason H; Carter-Su, Christin

    2007-01-01

    Src homology 2 (SH2) B adaptor protein 1 (SH2B1; originally named SH2-B) is a member of a family of adaptor proteins that influences a variety of signaling pathways mediated by Janus kinase (JAK) and receptor tyrosine kinases. Although SH2B1 performs classical adaptor functions, such as recruitment of specific proteins to activated receptors, it also demonstrates a unique ability to enhance the kinase activity of the cytokine receptor-associated tyrosine kinase JAK2, as well as that of several receptor tyrosine kinases. SH2B1 is also among a small number of adaptor proteins shown to undergo nucleocytoplasmic shuttling, although its exact role within the nucleus is not yet clear. Deletion of the SH2B1 gene results in severe obesity and both leptin and insulin resistance, as well as infertility, which might be a consequence of resistance to insulin-like growth factor I. Thus, knockout mice support a role for SH2B1 as a positive regulator of JAK2 signaling pathways initiated by leptin, as well as of pathways initiated by insulin and, potentially, by insulin-like growth factor I.

  9. Modular Fixturing System

    NASA Technical Reports Server (NTRS)

    Littell, Justin Anderson (Inventor); Street, Jon P. (Inventor)

    2017-01-01

    The modular fixturing system of the present invention is modular, reusable and capable of significant customization, both in terms of system radius and system height, allowing it to be arranged and rearranged in numerous unique configurations. The system includes multiple modular stanchions having stanchion shafts and stanchion feet that removably attach to apertures in a table. Angle brackets attached to the modular stanchions support shelves. These shelves in turn provide support to work pieces during fabrication processes such as welding.

  10. Portable modular detection system

    DOEpatents

    Brennan, James S.; Singh, Anup; Throckmorton, Daniel J.; Stamps, James F.

    2009-10-13

    Disclosed herein are portable and modular detection devices and systems for detecting electromagnetic radiation, such as fluorescence, from an analyte which comprises at least one optical element removably attached to at least one alignment rail. Also disclosed are modular detection devices and systems having an integrated lock-in amplifier and spatial filter and assay methods using the portable and modular detection devices.

  11. Novel multifunctional dopamine D2/D3 receptors agonists with potential neuroprotection and anti-alpha synuclein protein aggregation properties.

    PubMed

    Luo, Dan; Sharma, Horrick; Yedlapudi, Deepthi; Antonio, Tamara; Reith, Maarten E A; Dutta, Aloke K

    2016-11-01

    Our ongoing drug development endeavor to design compounds for symptomatic and neuroprotective treatment of Parkinson's disease (PD) led us to carry out a structure activity relationship study based on dopamine agonists pramipexole and 5-OHDPAT. Our goal was to incorporate structural elements in these agonists in a way to preserve their agonist activity while producing inhibitory activity against aggregation of α-synuclein protein. In our design we appended various catechol and related phenol derivatives to the parent agonists via different linker lengths. Structural optimization led to development of several potent agonists among which (-)-8a, (-)-14 and (-)-20 exhibited potent neuroprotective properties in a cellular PD model involving neurotoxin 6-OHDA. The lead compounds (-)-8a and (-)-14 were able to modulate aggregation of α-synuclein protein efficiently. Finally, in an in vivo PD animal model, compound (-)-8a exhibited efficacious anti-parkinsonian effect. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. β-Catenin–related protein WRM-1 is a multifunctional regulatory subunit of the LIT-1 MAPK complex

    PubMed Central

    Yang, Xiao-Dong; Karhadkar, Tejas R.; Medina, Jessica; Robertson, Scott M.; Lin, Rueyling

    2015-01-01

    Vertebrate β-catenin has two functions, as a structural component of the adherens junction in cell adhesion and as the T-cell factor (TCF) transcriptional coactivator in canonical Wnt (wingless-related integration site) signaling. These two functions are split between three of the four β-catenin–related proteins present in the round worm Caenorhabditis elegans. The fourth β-catenin–related protein, WRM-1, exhibits neither of these functions. Instead, WRM-1 binds the MAPK loss of intestine 1 (LIT-1), and these two proteins have been shown to be essential for the transcription of Wnt target genes by phosphorylating and regulating the nuclear level of the sole worm TCF protein. We showed previously that WRM-1 binds to worm TCF and functions as the substrate-binding subunit for LIT-1. In this study, we show that phosphorylation of T220 in the activation loop is essential for LIT-1 kinase activity in vivo and in vitro. T220 can be phosphorylated either through LIT-1 autophosphorylation or directly by the upstream MAP3K MOM-4. Our data support a model in which WRM-1, which can undergo homotypic interaction, binds LIT-1 and thereby generates a kinase complex in which LIT-1 molecules are situated in a conformation enabling autophosphorylation as well as promoting phosphorylation of the T220 residue by MOM-4. In addition, we show that WRM-1 is essential for the translocation of the LIT-1 kinase complex to the nucleus, the site of its TCF substrate. To our knowledge, this is the first report of a MAP3K directly activating a MAPK by phosphorylation within the activation loop. This study should help uncover novel and as yet underappreciated functions of vertebrate β-catenin. PMID:25548171

  13. Multifunctional roles of leader protein of foot-and-mouth disease viruses in suppressing host antiviral responses.

    PubMed

    Liu, Yingqi; Zhu, Zixiang; Zhang, Miaotao; Zheng, Haixue

    2015-10-28

    Foot-and-mouth disease virus (FMDV) leader protein (L(pro)) is a papain-like proteinase, which plays an important role in FMDV pathogenesis. L(pro) exists as two forms, Lab and Lb, due to translation being initiated from two different start codons separated by 84 nucleotides. L(pro) self-cleaves from the nascent viral polyprotein precursor as the first mature viral protein. In addition to its role as a viral proteinase, L(pro) also has the ability to antagonize host antiviral effects. To promote FMDV replication, L(pro) can suppress host antiviral responses by three different mechanisms: (1) cleavage of eukaryotic translation initiation factor 4 γ (eIF4G) to shut off host protein synthesis; (2) inhibition of host innate immune responses through restriction of interferon-α/β production; and (3) L(pro) can also act as a deubiquitinase and catalyze deubiquitination of innate immune signaling molecules. In the light of recent functional and biochemical findings regarding L(pro), this review introduces the basic properties of L(pro) and the mechanisms by which it antagonizes host antiviral responses.

  14. Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

    PubMed Central

    Mallik, Saurav

    2017-01-01

    Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly, and stability is of central importance. Here, we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid–nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, internucleotide contacts are disregarded). Contact number is defined as the number of nucleotides contacted. Involvement of individual amino acids in OaantCs with smaller contact numbers is more random, whereas only a few amino acids significantly contribute to OaantCs with higher contact numbers. An investigation of structure, stability, and assembly of bacterial ribosome depicts the involvement of these OaantCs in diverse biophysical interactions stabilizing the complex, including high-affinity protein–RNA contacts, interprotein cooperativity, intersubunit bridge, packing of multiple ribosomal RNA domains, etc. Amino acid–nucleotide constituents of OaantCs with higher contact numbers are generally associated with significantly slower substitution rates compared with that of OaantCs with smaller contact numbers. This evolutionary rate heterogeneity emerges from the strong purifying selection pressure that conserves the respective amino acid physicochemical properties relevant to the stabilizing interaction with OaantC nucleotides. An analysis of relative molecular orientations of OaantC residues and their interaction energetics provides the biophysical ground of purifying selection conserving OaantC amino acid physicochemical properties. PMID:28338825

  15. The complex subcellular distribution of satellite panicum mosaic virus capsid protein reflects its multifunctional role during infection.

    PubMed

    Qi, Dong; Omarov, Rustem T; Scholthof, Karen-Beth G

    2008-06-20

    Satellite panicum mosaic virus (SPMV) depends on its helper Panicum mosaic virus for replication and movement in host plants. The positive-sense single-stranded genomic RNA of SPMV encodes a 17-kDa capsid protein (CP) to form 16-nm virions. We determined that SPMV CP accumulates in both cytosolic and non-cytosolic fractions, but cytosolic accumulation of SPMV CP is exclusively associated with virions. An N-terminal arginine-rich motif (N-ARM) on SPMV CP is used to bind its cognate RNA and to form virus particles. Intriguingly, virion formation is dispensable for successful systemic SPMV RNA accumulation, yet this process still depends on an intact N-ARM. In addition, a C-terminal domain on the SPMV CP is necessary for self-interaction. Biochemical fractionation and fluorescent microscopy of green fluorescent protein-tagged SPMV CP demonstrated that the non-cytosolic SPMV CP is associated with the cell wall, the nucleus and other membranous organelles. To our knowledge, this is the first report that a satellite virus CP not only accumulates exclusively as virions in the cytosol but also is directed to the nucleolus and membranes. That SPMV CP is found both in the nucleus and the cell wall suggests its involvement in viral nuclear import and cell-to-cell transport.

  16. Generation of multiple bioactive macrolides by hybrid modular polyketide synthases in Streptomyces venezuelae.

    PubMed

    Yoon, Yeo Joon; Beck, Brian J; Kim, Beom Seok; Kang, Han Young; Reynolds, Kevin A; Sherman, David H

    2002-02-01

    The plasmid-based replacement of the multifunctional protein subunits of the pikromycin PKS in S. venezuelae by the corresponding subunits from heterologous modular PKSs resulted in recombinant strains that produce both 12- and 14-membered ring macrolactones with predicted structural alterations. In all cases, novel macrolactones were produced and further modified by the DesVII glycosyltransferase and PikC hydroxylase, leading to biologically active macrolide structures. These results demonstrate that hybrid PKSs in S. venezuelae can produce a multiplicity of new macrolactones that are modified further by the highly flexible DesVII glycosyltransferase and PikC hydroxylase tailoring enzymes. This work demonstrates the unique capacity of the S. venezuelae pikromycin pathway to expand the toolbox of combinatorial biosynthesis and to accelerate the creation of novel biologically active natural products.

  17. CML9, a multifunctional Arabidopsis thaliana calmodulin-like protein involved in stress responses and plant growth?

    PubMed Central

    Leba, Louis-Jérôme; Perochon, Alexandre; Cheval, Cécilia; Ranty, Benoit; Galaud, Jean-Philippe; Aldon, Didier

    2012-01-01

    Plants have evolved complex signaling networks to respond to their fluctuating environment and adapt their growth and development. Calcium-dependent signaling pathways play key role in the onset of these adaptive responses. In plant cells, the intracellular calcium transients are triggered by numerous stimuli and it is supposed that the large repertory of calcium sensors present in higher plants could contribute to integrate these signals in physiological responses. Here, we present data on CML9, a calmodulin-like protein that appears to be involved in plant responses to both biotic and abiotic stress. Using a reverse genetic approach based on gain and loss of function mutants, we present here data indicating that this CML might also be involved in root growth control in response to the flagellin, a pathogen-associated molecular pattern (PAMP) also involved in plant immunity. PMID:22899061

  18. The Multifunctional RNA-Binding Protein La Is Required for Mouse Development and for the Establishment of Embryonic Stem Cells

    PubMed Central

    Park, Jung-Min; Kohn, Matthew J.; Bruinsma, Monique W.; Vech, Claire; Intine, Robert V.; Fuhrmann, Stacy; Grinberg, Alex; Mukherjee, Ipsita; Love, Paul E.; Ko, Minoru S.; DePamphilis, Melvin L.; Maraia, Richard J.

    2006-01-01

    The La protein is a target of autoantibodies in patients suffering from Sjögren's syndrome, systemic lupus erythematosus, and neonatal lupus. Ubiquitous in eukaryotes, La functions as a RNA-binding protein that promotes the maturation of tRNA precursors and other nascent transcripts synthesized by RNA polymerase III as well as other noncoding RNAs. La also associates with a class of mRNAs that encode ribosome subunits and precursors to snoRNAs involved in ribosome biogenesis. Thus, it was surprising that La is dispensable in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the organisms from which it has been characterized most extensively. To determine whether La is essential in mammals and if so, at which developmental stage it is required, mice were created with a disrupted La gene, and the offspring from La+/−intercrosses were analyzed. La−/− offspring were detected at the expected frequency among blastocysts prior to implantation, whereas no nullizygotes were detected after implantation, indicating that La is required early in development. Blastocysts derived from La+/− intercrosses yielded 38 La+/+ and La+/− embryonic stem (ES) cell lines but no La−/− ES cell lines, suggesting that La contributes a critical function toward the establishment or survival of ES cells. Consistent with this, La−/− blastocyst outgrowths revealed loss of the inner cell mass (ICM). The results indicate that in contrast to the situation in yeasts, La is essential in mammals and is one of a limited number of genes required as early as the development of the ICM. PMID:16449655

  19. Multifunctionality in molecular magnetism.

    PubMed

    Pinkowicz, Dawid; Czarnecki, Bernard; Reczyński, Mateusz; Arczyński, Mirosław

    2015-01-01

    Molecular magnetism draws from the fundamental ideas of structural chemistry and combines them with experimental physics resulting in one of the highest profile current topics, namely molecular materials that exhibit multifunctionality. Recent advances in the design of new generations of multifunctional molecular magnets that retain the functions of the building blocks and exhibit non-trivial magnetic properties at higher temperatures provide promising evidence that they may be useful for the future construction of nanoscale devices. This article is not a complete review but is rather an introduction into thefascinating world of multifunctional solids with magnetism as the leitmotif. We provide a subjective selection and discussion of the most inspiring examples of multifunctional molecular magnets: magnetic sponges, guest-responsive magnets, molecular magnets with ionic conductivity, photomagnets and non-centrosymmetric and chiral magnets.

  20. Multifunctional thin film surface

    DOEpatents

    Brozik, Susan M.; Harper, Jason C.; Polsky, Ronen; Wheeler, David R.; Arango, Dulce C.; Dirk, Shawn M.

    2015-10-13

    A thin film with multiple binding functionality can be prepared on an electrode surface via consecutive electroreduction of two or more aryl-onium salts with different functional groups. This versatile and simple method for forming multifunctional surfaces provides an effective means for immobilization of diverse molecules at close proximities. The multifunctional thin film has applications in bioelectronics, molecular electronics, clinical diagnostics, and chemical and biological sensing.

  1. Identification of calcium-dependent protein kinase (CDPK): A multi-functional gene family in Rafflesia cantleyi

    NASA Astrophysics Data System (ADS)

    Amini, Safoora; Goh, Hoe-Han; Wan, Kiew-Lian

    2016-11-01

    Rafflesia, a parasitic plant that belongs to the Rafflesiaceae family, is notable for producing the largest flowers in the world. This study focused on identification of Calcium-dependent protein kinases (CDPKs) due to their vital roles in plant growth and development, biotic and abiotic stress responses, and hormone signaling. RNA-seq data generated from three bud stages of Rafflesia cantleyi ie BS1, BS2, and BS3 and were assembled. Based on the BLAST searches of Rafflesia unique transcripts (UTs) to Arabidopsis TAIR database, a total of 14 unique transcripts (UTs) were identified as CDPK1 to CDPK5, CDPK7 to CDPK11, CDPK16, CDPK18, CDPK19, and CDPK28. These genes are expressed at all three bud stages of R. cantleyi with up-regulation pattern at BS1 vs. BS2 and BS2 vs. BS3. This result shows that the expression of CDPK gene family increases by developmental progress in Rafflesia in order to regulate biochemical and molecular changes at the cellular level in response to exposure to environmental changes. However, CDPKs functions in plants growth and defense process still need more experimental evidence to deeply understand their biological roles in R. cantleyi.

  2. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

    PubMed

    Pal, Lipika R; Guda, Chittibabu

    2006-11-07

    The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.

  3. All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.

    PubMed Central

    Bergdoll, M.; Eltis, L. D.; Cameron, A. D.; Dumas, P.; Bolin, J. T.

    1998-01-01

    The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modern family of proteins represented by these structures arose through a rich evolutionary history that includes multiple gene duplication and fusion events. These events appear to be historically shared in some cases, but parallel and historically independent in others. A significant early event is proposed to be the establishment of metal-binding in an oligomeric ancestor prior to the first gene fusion. Variations in the spatial arrangements of homologous modules are observed that are consistent with the structural principles of three-dimensional domain swapping, but in the unusual context of the formation of larger monomers from smaller dimers or tetramers. The comparisons support a general mechanism for metalloprotein evolution that exploits the symmetry of a homooligomeric protein to originate a metal binding site and relies upon the relaxation of symmetry, as enabled by gene duplication, to establish and refine specific functions. PMID:10082363

  4. Multifunctional Modular Common Compact Components of Lasers (SYSTEM 2350)

    DTIC Science & Technology

    2007-11-02

    pumping geometry transverse to the cavity axis. In this arrangement the individual laser diode emitters are not required to be coherent with each other...rangefinding, and target profiling, and adding optical augmentation and MILES as required. A diode pumped ND:YAG Laser Engine and switchable OPO wavelength...augmentation and MILES as required. A diode pumped ND:YAG Laser Engine and switchable OPO wavelength conversion satisfied the high end designation requirement

  5. The SPARC-related modular calcium binding protein 2 (SMOC2) gene polymorphism in primary glaucoma: a case-control study

    PubMed Central

    Al-Dabbagh, Najwa; Al-Shahrani, Hamoud; Al-Dohayan, Nourah; Mustafa, Md; Arfin, Misbahul; Al-Asmari, Abdulrahman K

    2017-01-01

    Primary glaucomas are among the most common eye diseases that may potentially result in bilateral blindness. Both genetics and environmental factors are reported to be involved in the etiology of primary glaucomas. Secreted protein acidic and rich in cysteine (SPARC)-related modular calcium binding protein 2 (SMOC2) is a matricellular glycoprotein encoded by the SMOC2 gene and known to regulate the expression of extracellular matrix (ECM) proteins and matrix metalloproteinases (MMPs), which play an important role in the pathogenesis of primary glaucomas. The frequencies of alleles and genotypes of SMOC2 variants were examined in 406 Saudi subjects, including primary open angle glaucoma (POAG, n=140) and primary angle closure glaucoma (PACG, n=64) patients and 202 matched healthy controls using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Genotyping of SMOC2 polymorphism (rs13208776) revealed a significantly higher frequency of the heterozygous genotype GA (P<0.01) and a lower frequency of wild type GG genotype (P=0.05) in glaucoma patients compared to the controls. Upon stratification of the patients on the basis of types of glaucoma, PACG patients had a significantly higher frequency of GA genotype as compared to the controls (P<0.01), whereas there was no significant difference between the POAG patient and control groups in frequencies of SMOC2 alleles and genotypes. Further, there was no significant difference in frequency distribution of alleles and genotypes between male and female patients. This study indicates that the GA genotype of SMOC2 (G>A) polymorphism is significantly associated with PACG and may be a risk factor. However, further large-scale studies in the Saudi population as well as in other ethnic populations are needed to confirm this association. PMID:28356709

  6. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level

    PubMed Central

    Pal, Lipika R; Guda, Chittibabu

    2006-01-01

    Background The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. Results This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. Conclusion This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome. PMID:17090320

  7. Disorder in Milk Proteins: α-Lactalbumin. Part B. A Multifunctional Whey Protein Acting as an Oligomeric Molten Globular "Oil Container" in the Anti-Tumorigenic Drugs, Liprotides.

    PubMed

    Uversky, Vladimir N; Permyakov, Serge E; Breydo, Leonid; Redwan, Elrashdy M; Almehdar, Hussein A; Permyakov, Eugene A

    2016-07-15

    This is a second part of the three-part article from a series of reviews on the abundance and roles of intrinsic disorder in milk proteins. We continue to describe α-lactalbumin, a small globular Ca2+-binding protein, which besides being one of the two components of lactose synthase that catalyzes the final step of the lactose biosynthesis in the lactating mammary gland, possesses a multitude of other functions. In fact, recent studies indicated that some partially folded forms of this protein possess noticeable bactericidal activity and other forms might be related to induction of the apoptosis of tumor cells. In its anti-tumorigenic function, oligomeric α-lactalbumin serves as a founding member of a new family of anticancer drugs termed liprotides (for lipids and partially denatured proteins), where an oligomeric molten globular protein acts as an "oil container" or cargo for the delivery of oleic acid to the cell membranes.

  8. Modular design of a novel chimeric protein with combined thrombin inhibitory activity and plasminogen-activating potential.

    PubMed

    Wirsching, Frank; Luge, Cornelia; Schwienhorst, Andreas

    2002-03-01

    In order to design plasminogen activators with improved thrombolytic properties we sought to construct the bifunctional protein HLS-2 which combines both a plasminogen-activating and an anticoagulative activity. The chimeric protein comprises four elements: a derivative of thrombin inhibitor hirudin, a 6-amino acid spacer, the sequence of plasminogen-activator staphylokinase (Sak), and a 13-amino acid expression tag at the C-terminus. The gene of the fusion protein was obtained by SOE-PCR, cloned into pCANTAB5E, and expressed in E. coli BL21. HLS-2 was purified from periplasmatic extracts and characterized by Western blotting. Plasminogen-activation of HLS-2 and of Sak in equimolar mixtures with plasminogen showed near equivalence as measured by plasmin-mediated cleavage of chromogenic substrate S-2403. For catalytic amounts of plasminogen-activator, however, HLS-2 was less effective by a factor of 1.7. HLS-2 also inhibited both the amidolytic and the fibrinolytic activities of thrombin. Similar concentrations of either commercial HV1 (42 pmol/L) or HLS-2 (250 pmol/L) were required to halve the initial rate of thrombin reaction with fluorogenic substrate Tos-Gly-Pro-Arg-AMC, suggesting the retention of high-affinity inhibition of thrombin by the fusion protein sufficiently strong to substitute anticoagulative comedication during fibrinolytic treatment. The results provide a rationale for further testing the efficacy of HLS-2 for the lysis of platelet-rich arterial blood clots and for the prevention of reocclusion after thrombolysis.

  9. A Prototype for Modular Cell Engineering.

    PubMed

    Wilbanks, Brandon; Layton, Donovan; Garcia, Sergio; Trinh, Cong

    2017-10-10

    When aiming to produce a target chemical at high yield, titer, and productivity, various combinations of genetic parts available to build the target pathway can generate a large number of strains for characterization. This engineering approach will become increasingly laborious and expensive when seeking to develop desirable strains for optimal production of a large space of biochemicals due to extensive screening. Our recent theoretical development of modular cell (MODCELL) design principles can offer a promising solution for rapid generation of optimal strains by coupling a modular cell and exchangeable production modules in a plug-and-play fashion. In this study, we experimentally validated some designed properties of MODCELL by demonstrating: i) a modular (chassis) cell is required to couple with a production module, a heterologous ethanol pathway, as a testbed, ii) degree of coupling between the modular cell and production modules can be modulated to enhance growth and product synthesis, iii) a modular cell can be used as a host to select an optimal pyruvate decarboxylase (PDC) of the ethanol production module and to help identify a hypothetical PDC protein, and iv) adaptive laboratory evolution based on growth selection of the modular cell can enhance growth and product synthesis rates. We envision that the MODCELL design provides a powerful prototype for modular cell engineering to rapidly create optimal strains for synthesis of a large space of biochemicals.

  10. Development of an antibody-based, modular biosensor for 129Xe NMR molecular imaging of cells at nanomolar concentrations

    PubMed Central

    Rose, Honor M.; Witte, Christopher; Rossella, Federica; Klippel, Stefan; Freund, Christian; Schröder, Leif

    2014-01-01

    Magnetic resonance imaging (MRI) is seriously limited when aiming for visualization of targeted contrast agents. Images are reconstructed from the weak diamagnetic properties of the sample and require an abundant molecule like water as the reporter. Micromolar to millimolar concentrations of conventional contrast agents are needed to generate image contrast, thus excluding many molecular markers as potential targets. To address this limitation, we developed and characterized a functional xenon NMR biosensor that can identify a specific cell surface marker by targeted 129Xe MRI. Cells expressing the cell surface protein CD14 can be spatially distinguished from control cells with incorporation of as little as 20 nM of the xenon MRI readout unit, cryptophane-A. Cryptophane-A serves as a chemical host for hyperpolarized nuclei and facilitates the sensitivity enhancement achieved by xenon MRI. Although this paper describes the application of a CD14-specific biosensor, the construct has been designed in a versatile, modular fashion. This allows for quick and easy adaptation of the biosensor to any cell surface target for which there is a specific antibody. In addition, the modular design facilitates the creation of a multifunctional probe that incorporates readout modules for different detection methods, such as fluorescence, to complement the primary MRI readout. This modular antibody-based approach not only offers a practical technique with which to screen targets, but one which can be readily applied as the xenon MRI field moves closer to molecular imaging applications in vivo. PMID:25071165

  11. A novel multi-functional chloroplast protein: identification of a 40 kDa immunophilin-like protein located in the thylakoid lumen.

    PubMed Central

    Fulgosi, H; Vener, A V; Altschmied, L; Herrmann, R G; Andersson, B

    1998-01-01

    We describe the identification of the first immunophilin associated with the photosynthetic membrane of chloroplasts. This complex 40 kDa immunophilin, designated TLP40 (thylakoid lumen PPIase), located in the lumen of the thylakoids, was found to play a dual role in photosynthesis involving both biogenesis and intraorganelle signalling. It originates in a single-copy nuclear gene, is made as a precursor of 49.2 kDa with a bipartite lumenal targeting transit peptide, and is characterized by a structure including a cyclophilin-like C-terminal segment of 20 kDa, a predicted N-terminal leucine zipper and a potential phosphatase-binding domain. It can exist in different oligomeric conformations and attach to the inner membrane surface. It is confined predominantly to the non-appressed thylakoid regions, the site of protein integration into the photosynthetic membrane. The isolated protein possesses peptidyl-prolyl cis-trans isomerase protein folding activity characteristic of immunophilins, but is not inhibited by cyclosporin A. TLP40 also exerts an effect on dephosphorylation of several key proteins of photosystem II, probably as a constituent of a transmembrane signal transduction chain. This first evidence for a direct role of immunophilins in a photoautotrophic process suggests that light-mediated protein phosphorylation in photosynthetic membranes and the role of the thylakoid lumen are substantially more complex than anticipated. PMID:9501079

  12. Multifunctional nanoparticles: analytical prospects.

    PubMed

    de Dios, Alejandro Simón; Díaz-García, Marta Elena

    2010-05-07

    Multifunctional nanoparticles are among the most exciting nanomaterials with promising applications in analytical chemistry. These applications include (bio)sensing, (bio)assays, catalysis and separations. Although most of these applications are based on the magnetic, optical and electrochemical properties of multifunctional nanoparticles, other aspects such as the synergistic effect of the functional groups and the amplification effect associated with the nanoscale dimension have also been observed. Considering not only the nature of the raw material but also the shape, there is a huge variety of nanoparticles. In this review only magnetic, quantum dots, gold nanoparticles, carbon and inorganic nanotubes as well as silica, titania and gadolinium oxide nanoparticles are addressed. This review presents a narrative summary on the use of multifunctional nanoparticles for analytical applications, along with a discussion on some critical challenges existing in the field and possible solutions that have been or are being developed to overcome these challenges.

  13. Mechanics of Multifunctional Materials & Microsystems

    DTIC Science & Technology

    2012-03-09

    Mechanics of Materials; Life Prediction (Materials & Micro-devices); Sensing, Precognition & Diagnosis; Multifunctional Design of Autonomic...Life Prediction (Materials & Micro-devices); Sensing, Precognition & Diagnosis; Multifunctional Design of Autonomic Systems; Multifunctional...release; distribution is unlimited. 7 VISION: EXPANDED • site specific • autonomic AUTONOMIC AEROSPACE STRUCTURES • Sensing & Precognition • Self

  14. EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.

    PubMed

    Moore, Simon J; Lai, Hung-En; Kelwick, Richard J R; Chee, Soo Mei; Bell, David J; Polizzi, Karen Marie; Freemont, Paul S

    2016-10-21

    Golden Gate cloning is a prominent DNA assembly tool in synthetic biology for the assembly of plasmid constructs often used in combinatorial pathway optimization, with a number of assembly kits developed specifically for yeast and plant-based expression. However, its use for synthetic biology in commonly used bacterial systems such as Escherichia coli has surprisingly been overlooked. Here, we introduce EcoFlex a simplified modular package of DNA parts for a variety of applications in E. coli, cell-free protein synthesis, protein purification and hierarchical assembly of transcription units based on the MoClo assembly standard. The kit features a library of constitutive promoters, T7 expression, RBS strength variants, synthetic terminators, protein purification tags and fluorescence proteins. We validate EcoFlex by assembling a 68-part containing (20 genes) plasmid (31 kb), characterize in vivo and in vitro library parts, and perform combinatorial pathway assembly, using pooled libraries of either fluorescent proteins or the biosynthetic genes for the antimicrobial pigment violacein as a proof-of-concept. To minimize pathway screening, we also introduce a secondary module design site to simplify MoClo pathway optimization. In summary, EcoFlex provides a standardized and multifunctional kit for a variety of applications in E. coli synthetic biology.

  15. Implementing Modular A Levels.

    ERIC Educational Resources Information Center

    Holding, Gordon

    This document, which is designed for curriculum managers at British further education (FE) colleges, presents basic information on the implementation and perceived benefits of the General Certificate of Education (GCE) modular A (Advanced) levels. The information was synthesized from a survey of 12 FE colleges that introduced the modular A levels…

  16. Modular tokamak configuration

    SciTech Connect

    Thomson, S.L.

    1985-01-01

    This report is concerned with the modular tokamak configuration, and presents information on the following topics: modularity; external vacuum boundary; vertical maintenance; combined reactor building/biological shield with totally remote maintenance; independent TF coils; minimum TF coil bore; saddle PF coils; and heat transport system in bore.

  17. Modular Buildings Buying Guide.

    ERIC Educational Resources Information Center

    Morris, Susan

    1991-01-01

    Suggests that child care program directors who are expanding their programs or opening new child care centers investigate the possibility of renting, leasing, or purchasing a modular building. Discusses the advantages of modular buildings over conventional building construction or rented space in an occupied building. Provides information about…

  18. Transcriptional activation by the sexual pheromone and wounding: a new gene family from Volvox encoding modular proteins with (hydroxy)proline-rich and metalloproteinase homology domains.

    PubMed

    Hallmann, A; Amon, P; Godl, K; Heitzer, M; Sumper, M

    2001-06-01

    The green alga Volvox represents the simplest kind of multicellular organism: it is composed of only two cell types, somatic and reproductive, making it suitable as a model system. The sexual development of males and females of Volvox carteri is triggered by a sex-inducing pheromone at a concentration of < 10-16 M. Early biochemical responses to the pheromone involve structural modifications within the extracellular matrix (ECM). By differential screenings of cDNA libraries made from mRNAs of pheromone-treated Volvox, four novel genes were identified that encode four closely related Volvox metalloproteinases that we use to define a new protein family, the VMPs. The existence of several features common to matrix glycoproteins, such as signal peptides, a (hydroxy)proline content of 12-25%, and Ser(Pro)2-4 repeats, suggest an extracellular localization of the VMPs within the ECM. Synthesis of VMP cDNAs is triggered not only by the sex-inducing pheromone, but also by wounding, and is restricted to the somatic cell type. Sequence comparisons suggest that the VMPs are members of the MB clan of zinc-dependent matrix metalloproteinases, although the putative zinc binding site of all VMPs is QEXXHXXGXXH rather than HEXXHXXGXXH. The presence of glutamine instead of histidine in the zinc binding motif suggests a novel family, or even clan, of peptidases. Like the matrixin family of human collagenases, Volvox VMPs exhibit a modular structure: they possess a metalloproteinase homology domain and a (hydroxy)proline-rich domain, and one of them, VMP4, also has two additional domains. Metalloproteinases seem to be crucial for biochemical modifications of the ECM during development or after wounding in the lower eukaryote Volvox with only two cell types, just as in higher organisms.

  19. Multifunctional Tanks for Spacecraft

    NASA Technical Reports Server (NTRS)

    Collins, David H.; Lewis, Joseph C.; MacNeal, Paul D.

    2006-01-01

    A document discusses multifunctional tanks as means to integrate additional structural and functional efficiencies into designs of spacecraft. Whereas spacecraft tanks are traditionally designed primarily to store fluids and only secondarily to provide other benefits, multifunctional tanks are designed to simultaneously provide multiple primary benefits. In addition to one or more chamber(s) for storage of fluids, a multifunctional tank could provide any or all of the following: a) Passageways for transferring the fluids; b) Part or all of the primary structure of a spacecraft; c) All or part of an enclosure; d) Mechanical interfaces to components, subsystems, and/or systems; e) Paths and surfaces for transferring heat; f)Shielding against space radiation; j) Shielding against electromagnetic interference; h) Electrically conductive paths and surfaces; and i) Shades and baffles to protect against sunlight and/or other undesired light. Many different multifunctional-tank designs are conceivable. The design of a particular tank can be tailored to the requirements for the spacecraft in which the tank is to be installed. For example, the walls of the tank can be flat or curved or have more complicated shapes, and the tank can include an internal structure for strengthening the tank and/or other uses.

  20. Cyclic modular beta-sheets.

    PubMed

    Woods, R Jeremy; Brower, Justin O; Castellanos, Elena; Hashemzadeh, Mehrnoosh; Khakshoor, Omid; Russu, Wade A; Nowick, James S

    2007-03-07

    The development of peptide beta-hairpins is problematic, because folding depends on the amino acid sequence and changes to the sequence can significantly decrease folding. Robust beta-hairpins that can tolerate such changes are attractive tools for studying interactions involving protein beta-sheets and developing inhibitors of these interactions. This paper introduces a new class of peptide models of protein beta-sheets that addresses the problem of separating folding from the sequence. These model beta-sheets are macrocyclic peptides that fold in water to present a pentapeptide beta-strand along one edge; the other edge contains the tripeptide beta-strand mimic Hao [JACS 2000, 122, 7654] and two additional amino acids. The pentapeptide and Hao-containing peptide strands are connected by two delta-linked ornithine (deltaOrn) turns [JACS 2003, 125, 876]. Each deltaOrn turn contains a free alpha-amino group that permits the linking of individual modules to form divalent beta-sheets. These "cyclic modular beta-sheets" are synthesized by standard solid-phase peptide synthesis of a linear precursor followed by solution-phase cyclization. Eight cyclic modular beta-sheets 1a-1h containing sequences based on beta-amyloid and macrophage inflammatory protein 2 were synthesized and characterized by 1H NMR. Linked cyclic modular beta-sheet 2, which contains two modules of 1b, was also synthesized and characterized. 1H NMR studies show downfield alpha-proton chemical shifts, deltaOrn delta-proton magnetic anisotropy, and NOE cross-peaks that establish all compounds but 1c and 1g to be moderately or well folded into a conformation that resembles a beta-sheet. Pulsed-field gradient NMR diffusion experiments show little or no self-association at low (

  1. Evolution of Complex Modular Biological Networks

    PubMed Central

    Hintze, Arend; Adami, Christoph

    2008-01-01

    Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their modularity of function, with modules defined as sets of genes that are strongly interconnected but whose function is separable from those of other modules. Here, we investigate the in silico evolution of modularity and robustness in complex artificial metabolic networks that encode an increasing amount of information about their environment while acquiring ubiquitous features of biological, social, and engineering networks, such as scale-free edge distribution, small-world property, and fault-tolerance. These networks evolve in environments that differ in their predictability, and allow us to study modularity from topological, information-theoretic, and gene-epistatic points of view using new tools that do not depend on any preconceived notion of modularity. We find that for our evolved complex networks as well as for the yeast protein–protein interaction network, synthetic lethal gene pairs consist mostly of redundant genes that lie close to each other and therefore within modules, while knockdown suppressor gene pairs are farther apart and often straddle modules, suggesting that knockdown rescue is mediated by alternative pathways or modules. The combination of network modularity tools together with genetic interaction data constitutes a powerful approach to study and dissect the role of modularity in the evolution and function of biological networks. PMID:18266463

  2. Modular kinetic analysis.

    PubMed

    Krab, Klaas

    2011-01-01

    Modularization is an important strategy to tackle the study of complex biological systems. Modular kinetic analysis (MKA) is a quantitative method to extract kinetic information from such a modularized system that can be used to determine the control and regulatory structure of the system, and to pinpoint and quantify the interaction of effectors with the system. The principles of the method are described, and the relation with metabolic control analysis is discussed. Examples of application of MKA are given. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Modular tokamak magnetic system

    DOEpatents

    Yang, Tien-Fang

    1988-01-01

    A modular tokamak system comprised of a plurality of interlocking moldules. Each module is comprised of a vacuum vessel section, a toroidal field coil, moldular saddle coils which generate a poloidal magnetic field and ohmic heating coils.

  4. Successful modular cosmology

    NASA Astrophysics Data System (ADS)

    Kadota, Kenji; Stewart, Ewan D.

    2003-07-01

    We present a modular cosmology scenario where the difficulties encountered in conventional modular cosmology are solved in a self-consistent manner, with definite predictions to be tested by observation. Notably, the difficulty of the dilaton finding its way to a precarious weak coupling minimum is made irrelevant by having eternal modular inflation at the vacuum supersymmetry breaking scale after the dilaton is stabilised. Neither this eternal inflation nor the subsequent non-slow-roll modular inflation destabilise the dilaton from its precarious minimum due to the low energy scale of the inflation and consequent small back reaction on the dilaton potential. The observed flat CMB spectrum is obtained from fluctuations in the angular component of a modulus near a symmetric point, which are hugely magnified by the roll down of the modulus to Planckian values, allowing them to dominate the final curvature perturbation. We also give precise calculations of the spectral index and its running.

  5. Alternative splice variants in TIM barrel proteins from human genome correlate with the structural and evolutionary modularity of this versatile protein fold.

    PubMed

    Ochoa-Leyva, Adrián; Montero-Morán, Gabriela; Saab-Rincón, Gloria; Brieba, Luis G; Soberón, Xavier

    2013-01-01

    After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the

  6. Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

    PubMed Central

    Ochoa-Leyva, Adrián; Montero-Morán, Gabriela; Saab-Rincón, Gloria; Brieba, Luis G.; Soberón, Xavier

    2013-01-01

    After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the

  7. A Modular Robotic Architecture

    DTIC Science & Technology

    1990-11-01

    DATES COVERED AD-A232 007 Januar 1991 professional paper5 FUNOING NUMBERS A MODULAR ROBOTIC ARCHITECTURE PR: ZE92 WU: DN300029 PE: 0602936N - S. AUTHOR...mobile robots will help alleviate these problems, and, if made widely available, will promote standardization and compatibility among systems throughout...the industry. The Modular Robotic Architecture (MRA) is a generic control system that meets the above needs by providing developers with a standard set

  8. Multifunctional nanoparticles composite for MALDI-MS: Cd2+-doped carbon nanotubes with CdS nanoparticles as the matrix, preconcentrating and accelerating probes of microwave enzymatic digestion of peptides and proteins for direct MALDI-MS analysis.

    PubMed

    Shrivas, Kamlesh; Wu, Hui-Fen

    2010-12-01

    For the first time, we utilized multifunctional nanoparticles composite (NPs composite) for matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis of peptides and proteins. Multiwalled carbon nanotubes doped with Cd(2+) ions and modified with cadmium sulfide NPs were synthesized by a chemical reduction method at room temperature. The multifunctional NPs composite applied for the analysis of peptides and microwave-digested proteins in the atmospheric pressure matrix-assisted laser desorption/ionization ion-trap and MALDI time-of-flight (TOF) mass spectrometry (MS) was successfully demonstrated. The maximum detection sensitivity for peptides in MALDI-MS was achieved by the adsorption of negatively charged peptides onto the surfaces of NP composite through electrostatic interactions. The optimal conditions of peptide mixtures were obtained at 20 min of incubation time using 1 mg of NPs composite when the pH of the sample solution was kept higher than the pI values of peptides. The potentiality of the NP composite in the preconcentration of peptides was compared with that of the individual NP by calculating the preconcentration factors (PF) and found that the NPs composite showed a 4-6 times of PF than the other NPs. In addition, the NPs composite was also applied as heat-absorbing materials for efficient microwave tryptic digestion of cytochrome c and lysozyme from milk protein in MALDI-TOF-MS analysis. We believe that the use of NPs composite technique would be an efficient and powerful preconcentrating tool for MALDI-MS for the study of proteome research. Copyright © 2010 John Wiley & Sons, Ltd.

  9. Modularity and mental architecture.

    PubMed

    Robbins, Philip

    2013-11-01

    Debates about the modularity of cognitive architecture have been ongoing for at least the past three decades, since the publication of Fodor's landmark book The Modularity of Mind. According to Fodor, modularity is essentially tied to informational encapsulation, and as such is only found in the relatively low-level cognitive systems responsible for perception and language. According to Fodor's critics in the evolutionary psychology camp, modularity simply reflects the fine-grained functional specialization dictated by natural selection, and it characterizes virtually all aspects of cognitive architecture, including high-level systems for judgment, decision making, and reasoning. Though both of these perspectives on modularity have garnered support, the current state of evidence and argument suggests that a broader skepticism about modularity may be warranted. WIREs Cogn Sci 2013, 4:641-649. doi: 10.1002/wcs.1255 CONFLICT OF INTEREST: The author has declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.

  10. Multifunctional Antenna Techniques

    DTIC Science & Technology

    2015-11-25

    Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Multifunctional antennas, reconfigurable antennas, electromagnetics REPORT... Electromagnetic Analysis and Applications, (06 2013): 223. doi: 10.4236/jemaa.2013.55036 Teng-Kai Chen, Gregory H. Huff. Transmission line analysis...of the Archimedean spiral antenna in free space, Journal of Electromagnetic Waves and Applications, (04 2014): 1175. doi: 10.1080/09205071

  11. Multifunctional Materials and Structures

    DTIC Science & Technology

    2003-07-01

    searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments...Power F Affordability Ø Proposed Solution – “ LIVE ” Ship Concept F Lightweight, High Performance Multifunctional Composite Structure F Desired...www.onr.navy.mil/sci_tech/grandc.htm F Navy DD(X) Program 1 July 2003© 2003 University of Delaware All rights reservedYarlagadda ONR Review - 4 “ LIVE ” Ship

  12. Adaptive multifunctional composites

    NASA Astrophysics Data System (ADS)

    Wang, Ya; Inman, Daniel J.

    2013-05-01

    The adaptive multifunctional composite structure studied here is to address two issues remaining in lightweight structural composites required by many engineering applications. The first is to add additional functionality to multifunctional composites and the second is to provide adaptive damping in structures that cover a wide range of frequencies and temperatures. Because of its potential for practical payoffs, passive structural damping can find wide application through the use of high-damping viscoelastic polymers or elastomers. However, all passive damping using these damping materials suffer from failing at certain temperatures and in certain frequency ranges. The extreme environments often seen by engineering systems provide high temperature, which is exactly where damping levels in structures reduce causing unacceptable vibrations. In addition, as loading frequencies reduce damping levels also fall off, and many loads experienced by large structures are low frequency. The proposed research addresses increasing the range of effectiveness of damping by addressing the temperature and frequency dependence of material damping by using a multifunctional composite system containing an active element. Previous research has yielded a finite element model of linear viscoelastic material and structural behavior that captures characteristic frequency-dependent behavior, continuing research has addressed the accommodation of temperature dependence, and the examination of the new concept of `electronic damping' or `e-damping'. The resulting modeling approach is validated through experimental validation.

  13. The Rocketdyne Multifunction Tester. Part 1: Test Method

    NASA Technical Reports Server (NTRS)

    Murphy, Brian T.; Scharrer, Joseph K.; Sutton, Robert F.

    1991-01-01

    The Rocketdyne Multifunction Tester is a general purpose test apparatus which utilizes axial and radial magnetic bearings as shaft excitation devices. The tester is modular in design so that different seal and bearing packages can be tested on the same test stand. The tester will be used for rotordynamic coefficient extraction, as well as life and fluid/material compatibility evaluations. Use of a magnetic bearing as a shaft excitation device opens up many possibilities for shaft excitation and rotordynamic coefficient extraction. In addition to describing the basic apparatus, some of the excitation and extraction methods are described. Some of the excitation methods to be discussed include random, aperiodic, harmonic, impulse and chirp.

  14. Genome-Wide Detection and Analysis of Multifunctional Genes

    PubMed Central

    Pritykin, Yuri; Ghersi, Dario; Singh, Mona

    2015-01-01

    Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. However, to date, genome-wide analysis of multifunctional genes (and the proteins they encode) has been limited. Here we introduce a computational approach that uses known functional annotations to extract genes playing a role in at least two distinct biological processes. We leverage functional genomics data sets for three organisms—H. sapiens, D. melanogaster, and S. cerevisiae—and show that, as compared to other annotated genes, genes involved in multiple biological processes possess distinct physicochemical properties, are more broadly expressed, tend to be more central in protein interaction networks, tend to be more evolutionarily conserved, and are more likely to be essential. We also find that multifunctional genes are significantly more likely to be involved in human disorders. These same features also hold when multifunctionality is defined with respect to molecular functions instead of biological processes. Our analysis uncovers key features about multifunctional genes, and is a step towards a better genome-wide understanding of gene multifunctionality. PMID:26436655

  15. On particle ionization/enrichment of multifunctional nanoprobes: washing/separation-free, acceleration and enrichment of microwave-assisted tryptic digestion of proteins via bare TiO2 nanoparticles in ESI-MS and comparing to MALDI-MS.

    PubMed

    Wu, Hui-Fen; Agrawal, Kavita; Shrivas, Kamlesh; Lee, Yi-Hsien

    2010-12-01

    A simple, rapid, straightforward and washing/separation free of in-solution digestion method for microwave-assisted tryptic digestion of proteins (cytochrome c, lysozyme and myoglobin) using bare TiO(2) nanoparticles (NPs) prepared in aqueous solution to serve as multifunctional nanoprobes in electrospray ionization mass spectrometry (ESI-MS) was demonstrated. The current approach is termed as 'on particle ionization/enrichment (OPIE)' and it can be applied in ESI-MS, atmospheric pressure-matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The bare TiO(2) NPs can assist, accelerate and effectively enhance the digestion efficiency, sequence coverage and detection sensitivity of peptides for the microwave-assisted tryptic digestion of proteins in ESI-MS. The reason is attributed to the fact that proteins or partially digested proteins are easily attracted or concentrated onto the surface of TiO(2) NPs, resulting in higher efficiency of digestion reactions in the microwave experiments. Besides, the TiO(2) NPs could act as a microwave absorber to accelerate and enrich the protein fragments in a short period of time (40-60 s) from the microwave experiments in ESI-MS. Furthermore, the bare TiO(2) NPs prepared in aqueous solution exhibit high adsorption capability toward the protein fragments (peptides); thus, the OPIE approach for detecting the digested protein fragments via ESI and MALDI ionization could be achieved. The current technique is also a washing and separation-free technique for accelerating and enriching microwave-assisted tryptic digestion of proteins in the ESI-MS and MALDI-MS. It exhibits potential to be widely applied to biotechnology and proteome research in the near future.

  16. Symmetric modular torsatron

    DOEpatents

    Rome, J.A.; Harris, J.H.

    1984-01-01

    A fusion reactor device is provided in which the magnetic fields for plasma confinement in a toroidal configuration is produced by a plurality of symmetrical modular coils arranged to form a symmetric modular torsatron referred to as a symmotron. Each of the identical modular coils is helically deformed and comprise one field period of the torsatron. Helical segments of each coil are connected by means of toroidally directed windbacks which may also provide part of the vertical field required for positioning the plasma. The stray fields of the windback segments may be compensated by toroidal coils. A variety of magnetic confinement flux surface configurations may be produced by proper modulation of the winding pitch of the helical segments of the coils, as in a conventional torsatron, winding the helix on a noncircular cross section and varying the poloidal and radial location of the windbacks and the compensating toroidal ring coils.

  17. Self Evolving Modular Network

    NASA Astrophysics Data System (ADS)

    Tokunaga, Kazuhiro; Kawabata, Nobuyuki; Furukawa, Tetsuo

    We propose a novel modular network called the Self-Evolving Modular Network (SEEM). The SEEM has a modular network architecture with a graph structure and these following advantages: (1) new modules are added incrementally to allow the network to adapt in a self-organizing manner, and (2) graph's paths are formed based on the relationships between the models represented by modules. The SEEM is expected to be applicable to evolving functions of an autonomous robot in a self-organizing manner through interaction with the robot's environment and categorizing large-scale information. This paper presents the architecture and an algorithm for the SEEM. Moreover, performance characteristic and effectiveness of the network are shown by simulations using cubic functions and a set of 3D-objects.

  18. Modular optical detector system

    DOEpatents

    Horn, Brent A.; Renzi, Ronald F.

    2006-02-14

    A modular optical detector system. The detector system is designed to detect the presence of molecules or molecular species by inducing fluorescence with exciting radiation and detecting the emitted fluorescence. Because the system is capable of accurately detecting and measuring picomolar concentrations it is ideally suited for use with microchemical analysis systems generally and capillary chromatographic systems in particular. By employing a modular design, the detector system provides both the ability to replace various elements of the detector system without requiring extensive realignment or recalibration of the components as well as minimal user interaction with the system. In addition, the modular concept provides for the use and addition of a wide variety of components, including optical elements (lenses and filters), light sources, and detection means, to fit particular needs.

  19. Multifunctional materials and composites

    DOEpatents

    Seo, Dong-Kyun; Jeon, Ki-Wan

    2017-08-22

    Forming multifunctional materials and composites thereof includes contacting a first material having a plurality of oxygen-containing functional groups with a chalcogenide compound, and initiating a chemical reaction between the first material and the chalcogenide compound, thereby replacing oxygen in some of the oxygen-containing functional groups with chalcogen from the chalcogen-containing compound to yield a second material having chalcogen-containing functional groups and oxygen-containing functional groups. The first material is a carbonaceous material or a macromolecular material. A product including the second material is collected and may be processed further to yield a modified product or a composite.

  20. Templated biomimetic multifunctional coatings

    NASA Astrophysics Data System (ADS)

    Sun, Chih-Hung; Gonzalez, Adriel; Linn, Nicholas C.; Jiang, Peng; Jiang, Bin

    2008-02-01

    We report a bioinspired templating technique for fabricating multifunctional optical coatings that mimic both unique functionalities of antireflective moth eyes and superhydrophobic cicada wings. Subwavelength-structured fluoropolymer nipple arrays are created by a soft-lithography-like process. The utilization of fluoropolymers simultaneously enhances the antireflective performance and the hydrophobicity of the replicated films. The specular reflectivity matches the optical simulation using a thin-film multilayer model. The dependence of the size and the crystalline ordering of the replicated nipples on the resulting antireflective properties have also been investigated by experiment and modeling. These biomimetic materials may find important technological application in self-cleaning antireflection coatings.

  1. Multifunctional reference electrode

    DOEpatents

    Redey, L.; Vissers, D.R.

    1981-12-30

    A multifunctional, low mass reference electrode of a nickel tube, thermocouple means inside the nickel tube electrically insulated therefrom for measuring the temperature thereof, a housing surrounding the nickel tube, an electrolyte having a fixed sulfide ion activity between the housing and the outer surface of the nickel tube forming the nickel/nickel sulfide/sulfide half-cell are described. An ion diffusion barrier is associated with the housing in contact with the electrolyte. Also disclosed is a cell using the reference electrode to measure characteristics of a working electrode.

  2. Multifunctional reference electrode

    DOEpatents

    Redey, Laszlo; Vissers, Donald R.

    1983-01-01

    A multifunctional, low mass reference electrode of a nickel tube, thermocouple means inside the nickel tube electrically insulated therefrom for measuring the temperature thereof, a housing surrounding the nickel tube, an electrolyte having a fixed sulfide ion activity between the housing and the outer surface of the nickel tube forming the nickel/nickel sulfide/sulfide half-cell. An ion diffusion barrier is associated with the housing in contact with the electrolyte. Also disclosed is a cell using the reference electrode to measure characteristics of a working electrode.

  3. Modular biowaste monitoring system

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.

    1975-01-01

    The objective of the Modular Biowaste Monitoring System Program was to generate and evaluate hardware for supporting shuttle life science experimental and diagnostic programs. An initial conceptual design effort established requirements and defined an overall modular system for the collection, measurement, sampling and storage of urine and feces biowastes. This conceptual design effort was followed by the design, fabrication and performance evaluation of a flight prototype model urine collection, volume measurement and sampling capability. No operational or performance deficiencies were uncovered as a result of the performance evaluation tests.

  4. Modular Optofluidic Systems (MOPS)

    NASA Astrophysics Data System (ADS)

    Ackermann, Tobias N.; Dietvorst, Jiri; Sanchis, Ana; Salvador, Juan P.; Munoz-Berbel, Xavier; Alvarez-Conde, Erica; Kopp, Daniel; Zappe, Hans; Marco, M.-Pilar; Llobera, Andreu

    2016-12-01

    Elementary PDMS-based building blocks of fluidic, optical and optofluidic components for Lab on a chip (LOC) platforms has here been developed. All individual modules are compatible and can be anchored and released with the help of puzzle-type connectors This approach is a powerful toolbox to create modular optofluidic systems (MOPS), which can be modified/upgraded to user needs and in-situ reconfigurable. In addition, the PDMS can locally be functionalized, defining a modular biosensor. Measurements in absorbance and fluorescence have been pursued as demonstrator.

  5. Modular total absorption spectrometer

    NASA Astrophysics Data System (ADS)

    Karny, M.; Rykaczewski, K. P.; Fijałkowska, A.; Rasco, B. C.; Wolińska-Cichocka, M.; Grzywacz, R. K.; Goetz, K. C.; Miller, D.; Zganjar, E. F.

    2016-11-01

    The design and performance of the Modular Total Absorption Spectrometer built and commissioned at the Oak Ridge National Laboratory is presented. The active volume of the detector is approximately one ton of NaI(Tl), which results in very high full γ energy peak efficiency of 71% at 6 MeV and nearly flat efficiency of around 81.5% for low energy γ-rays between 300 keV and 1 MeV. In addition to the high peak efficiency, the modular construction of the detector permits the use of a γ-coincidence technique in data analysis as well as β-delayed neutron observation.

  6. Voluntary initiation of movement: multifunctional integration of subjective agency.

    PubMed

    Grüneberg, Patrick; Kadone, Hideki; Suzuki, Kenji

    2015-01-01

    This paper investigates subjective agency (SA) as a special type of efficacious action consciousness. Our central claims are, firstly, that SA is a conscious act of voluntarily initiating bodily motion. Secondly, we argue that SA is a case of multifunctional integration of behavioral functions being analogous to multisensory integration of sensory modalities. This is based on new perspectives on the initiation of action opened up by recent advancements in robot assisted neuro-rehabilitation which depends on the active participation of the patient and yields experimental evidence that there is SA in terms of a conscious act of voluntarily initiating bodily motion (phenomenal performance). Conventionally, action consciousness has been considered as a sense of agency (SoA). According to this view, the conscious subject merely echoes motor performance and does not cause bodily motion. Depending on sensory input, SoA is implemented by means of unifunctional integration (binding) and inevitably results in non-efficacious action consciousness. In contrast, SA comes as a phenomenal performance which causes motion and builds on multifunctional integration. Therefore, the common conception of the brain should be shifted toward multifunctional integration in order to allow for efficacious action consciousness. For this purpose, we suggest the heterarchic principle of asymmetric reciprocity and neural operators underlying SA. The general idea is that multifunctional integration allows conscious acts to be simultaneously implemented with motor behavior so that the resulting behavior (SA) comes as efficacious action consciousness. Regarding the neural implementation, multifunctional integration rather relies on operators than on modular functions. A robotic case study and possible experimental setups with testable hypotheses building on SA are presented.

  7. Voluntary initiation of movement: multifunctional integration of subjective agency

    PubMed Central

    Grüneberg, Patrick; Kadone, Hideki; Suzuki, Kenji

    2015-01-01

    This paper investigates subjective agency (SA) as a special type of efficacious action consciousness. Our central claims are, firstly, that SA is a conscious act of voluntarily initiating bodily motion. Secondly, we argue that SA is a case of multifunctional integration of behavioral functions being analogous to multisensory integration of sensory modalities. This is based on new perspectives on the initiation of action opened up by recent advancements in robot assisted neuro-rehabilitation which depends on the active participation of the patient and yields experimental evidence that there is SA in terms of a conscious act of voluntarily initiating bodily motion (phenomenal performance). Conventionally, action consciousness has been considered as a sense of agency (SoA). According to this view, the conscious subject merely echoes motor performance and does not cause bodily motion. Depending on sensory input, SoA is implemented by means of unifunctional integration (binding) and inevitably results in non-efficacious action consciousness. In contrast, SA comes as a phenomenal performance which causes motion and builds on multifunctional integration. Therefore, the common conception of the brain should be shifted toward multifunctional integration in order to allow for efficacious action consciousness. For this purpose, we suggest the heterarchic principle of asymmetric reciprocity and neural operators underlying SA. The general idea is that multifunctional integration allows conscious acts to be simultaneously implemented with motor behavior so that the resulting behavior (SA) comes as efficacious action consciousness. Regarding the neural implementation, multifunctional integration rather relies on operators than on modular functions. A robotic case study and possible experimental setups with testable hypotheses building on SA are presented. PMID:26052308

  8. Multifunctional sandwich composites

    NASA Astrophysics Data System (ADS)

    Vaidya, Uday K.

    2003-10-01

    Sandwich composites find increasing use as flexural load bearing lightweight sub-elements in air/space vehicles, rail/ground transportation, marine and sporting goods. The core in these applications is usually balsa wood, foam or honeycomb with laminated carbon or glass facesheets. A limitation of traditional sandwich onfigurations is that the space in the core becomes inaccessible once the facesheets are bonded in place. Significant multi-functional benefits can be obtained by making either the facesheets or the core, space accessible. Multi-functionality is generally referred to as value added to the structure that enhances functions beyond traditional load bearing. Such functions may include sound/vibration damping, ability to route wires or embed sensors. The present work reviews recent work done in enhancing the functionality of the core by use of the space in the core. The damage created by impact to sandwich constructions is always a limiting issue in design. In the present work, low velocity impact (LVI) response of newer/multi-functional sandwich constructions has been studied. Concepts of increasing sandwich core functionality have been reported.

  9. Functional group diversity increases with modularity in complex food webs.

    PubMed

    Montoya, D; Yallop, M L; Memmott, J

    2015-06-10

    Biodiversity increases the ability of ecosystems to provide multiple functions. Most studies report a positive relationship between species richness and the number of ecosystem functions. However, it is not known whether the number of functional groups is related to the structure of the underlying species interaction network. Here we present food web data from 115 salt marsh islands and show that network structure is associated with the number of functional groups present. Functional group diversity is heterogeneously distributed across spatial scales, with some islands hosting more functional groups than others. Functional groups form modules within the community so that food webs with more modular architectures have more functional group diversity. Further, in communities with different interaction types, modularity can be seen as the multifunctional equivalent of trophic complementarity. Collectively, these findings reveal spatial heterogeneity in the number of functional groups that emerges from patterns in the structure of the food web.

  10. Functional group diversity increases with modularity in complex food webs

    PubMed Central

    Montoya, D.; Yallop, M.L.; Memmott, J.

    2015-01-01

    Biodiversity increases the ability of ecosystems to provide multiple functions. Most studies report a positive relationship between species richness and the number of ecosystem functions. However, it is not known whether the number of functional groups is related to the structure of the underlying species interaction network. Here we present food web data from 115 salt marsh islands and show that network structure is associated with the number of functional groups present. Functional group diversity is heterogeneously distributed across spatial scales, with some islands hosting more functional groups than others. Functional groups form modules within the community so that food webs with more modular architectures have more functional group diversity. Further, in communities with different interaction types, modularity can be seen as the multifunctional equivalent of trophic complementarity. Collectively, these findings reveal spatial heterogeneity in the number of functional groups that emerges from patterns in the structure of the food web. PMID:26059871

  11. Modular invariant inflation

    SciTech Connect

    Kobayashi, Tatsuo; Nitta, Daisuke; Urakawa, Yuko

    2016-08-08

    Modular invariance is a striking symmetry in string theory, which may keep stringy corrections under control. In this paper, we investigate a phenomenological consequence of the modular invariance, assuming that this symmetry is preserved as well as in a four dimensional (4D) low energy effective field theory. As a concrete setup, we consider a modulus field T whose contribution in the 4D effective field theory remains invariant under the modular transformation and study inflation drived by T. The modular invariance restricts a possible form of the scalar potenntial. As a result, large field models of inflation are hardly realized. Meanwhile, a small field model of inflation can be still accomodated in this restricted setup. The scalar potential traced during the slow-roll inflation mimics the hilltop potential V{sub ht}, but it also has a non-negligible deviation from V{sub ht}. Detecting the primordial gravitational waves predicted in this model is rather challenging. Yet, we argue that it may be still possible to falsify this model by combining the information in the reheating process which can be determined self-completely in this setup.

  12. Modular invariant gaugino condensation

    SciTech Connect

    Gaillard, M.K.

    1991-05-09

    The construction of effective supergravity lagrangians for gaugino condensation is reviewed and recent results are presented that are consistent with modular invariance and yield a positive definite potential of the noscale type. Possible implications for phenomenology are briefly discussed. 29 refs.

  13. Modular invariant inflation

    NASA Astrophysics Data System (ADS)

    Kobayashi, Tatsuo; Nitta, Daisuke; Urakawa, Yuko

    2016-08-01

    Modular invariance is a striking symmetry in string theory, which may keep stringy corrections under control. In this paper, we investigate a phenomenological consequence of the modular invariance, assuming that this symmetry is preserved as well as in a four dimensional (4D) low energy effective field theory. As a concrete setup, we consider a modulus field T whose contribution in the 4D effective field theory remains invariant under the modular transformation and study inflation drived by T. The modular invariance restricts a possible form of the scalar potenntial. As a result, large field models of inflation are hardly realized. Meanwhile, a small field model of inflation can be still accomodated in this restricted setup. The scalar potential traced during the slow-roll inflation mimics the hilltop potential Vht, but it also has a non-negligible deviation from Vht. Detecting the primordial gravitational waves predicted in this model is rather challenging. Yet, we argue that it may be still possible to falsify this model by combining the information in the reheating process which can be determined self-completely in this setup.

  14. A Modular CAI System.

    ERIC Educational Resources Information Center

    Van Der Mast, Charles

    The experimental CAI system which is being tested at Delft University of Technology is structured in a modular manner to account for high changeability. The concept formulated for this project was the outcome of research into technological, organizational, and educational developments in CAI, and the enumeration of the common aspects of the…

  15. Modular core holder

    SciTech Connect

    Mueller, J.; Cole, C.W.; Hamid, S.; Lucas, J.K.

    1991-03-05

    This patent describes a modular core holder. It comprises: a sleeve, forming an internal cavity for receiving a core. The sleeve including segments; support means, overlying the sleeve, for supporting the sleeve; and access means, positioned between at least two of the segments of the sleeve, for allowing measurement of conditions within the internal cavity.

  16. MRV - Modular Robotic Vehicle

    NASA Technical Reports Server (NTRS)

    Ridley, Justin; Bluethmann, Bill

    2015-01-01

    The Modular Robotic Vehicle, or MRV, completed in 2013, was developed at the Johnson Space Center in order to advance technologies which have applications for future vehicles both in space and on Earth. With seating for two people, MRV is a fully electric vehicle modeled as a "city car", suited for busy urban environments.

  17. Modular Perspectives on Bilingualism.

    ERIC Educational Resources Information Center

    Francis, Norbert

    2002-01-01

    This research review traces the current discussion on models of bilingualism to the contributions of Vygotsky and Luria. Proposes that a modular approach to studying the different aspects of bilingual development promises to chart a course toward finding a broader common ground around research findings and interpretations that appear to be…

  18. Modularity in robotic systems

    NASA Technical Reports Server (NTRS)

    Tesar, Delbert; Butler, Michael S.

    1989-01-01

    Most robotic systems today are designed one at a time, at a high cost of time and money. This wasteful approach has been necessary because the industry has not established a foundation for the continued evolution of intelligent machines. The next generation of robots will have to be generic, versatile machines capable of absorbing new technology rapidly and economically. This approach is demonstrated in the success of the personal computer, which can be upgraded or expanded with new software and hardware at virtually every level. Modularity is perceived as a major opportunity to reduce the 6 to 7 year design cycle time now required for new robotic manipulators, greatly increasing the breadth and speed of diffusion of robotic systems in manufacturing. Modularity and its crucial role in the next generation of intelligent machines are the focus of interest. The main advantages that modularity provides are examined; types of modules needed to create a generic robot are discussed. Structural modules designed by the robotics group at the University of Texas at Austin are examined to demonstrate the advantages of modular design.

  19. Modular, Multilayer Perceptron

    NASA Technical Reports Server (NTRS)

    Cheng, Li-Jen; Liu, Tsuen-Hsi

    1991-01-01

    Combination of proposed modular, multilayer perceptron and algorithm for its operation recognizes new objects after relatively brief retraining sessions. (Perceptron is multilayer, feedforward artificial neural network fully connected and trained via back-propagation learning algorithm.) Knowledge pertaining to each object to be recognized resides in subnetwork of full network, therefore not necessary to retrain full network to recognize each new object.

  20. Two Functionally Identical Modular Enhancers in Drosophila Troponin T Gene Establish the Correct Protein Levels in Different Muscle TypesD⃞

    PubMed Central

    Mas, José-Antonio; García-Zaragoza, Elena; Cervera, Margarita

    2004-01-01

    The control of muscle-specific expression is one of the principal mechanisms by which diversity is generated among muscle types. In an attempt to elucidate the regulatory mechanisms that control fiber diversity in any given muscle, we have focused our attention on the transcriptional regulation of the Drosophila Troponin T gene. Two, nonredundant, functionally identical, enhancer-like elements activate Troponin T transcription independently in all major muscles of the embryo and larvae as well as in adult somatic and visceral muscles. Here, we propose that the differential but concerted interaction of these two elements underlies the mechanism by which a particular muscle-type establish the correct levels of Troponin T expression, adapting these levels to their specific needs. This mechanism is not exclusive to the Troponin T gene, but is also relevant to the muscle-specific Troponin I gene. In conjunction with in vivo transgenic studies, an in silico analysis of the Troponin T enhancer-like sequences revealed that both these elements are organized in a modular manner. Extending this analysis to the Troponin I and Tropomyosin regulatory elements, the two other components of the muscle-regulatory complex, we have discovered a similar modular organization of phylogenetically conserved domains. PMID:14718560

  1. Hierarchical multifunctional nanocomposites

    NASA Astrophysics Data System (ADS)

    Ghasemi-Nejhad, Mehrdad N.

    2014-03-01

    Nanocomposites; including nano-materials such as nano-particles, nanoclays, nanofibers, nanotubes, and nanosheets; are of significant importance in the rapidly developing field of nanotechnology. Due to the nanometer size of these inclusions, their physicochemical characteristics differ significantly from those of micron size and bulk materials. The field of nanocomposites involves the study of multiphase materials where at least one of the constituent phases has one dimension less than 100 nm. This is the range where the phenomena associated with the atomic and molecular interaction strongly influence the macroscopic properties of materials. Since the building blocks of nanocomposites are at nanoscale, they have an enormous surface area with numerous interfaces between the two intermix phases. The special properties of the nano-composite arise from the interaction of its phases at the interface and/or interphase regions. By contrast, in a conventional composite based on micrometer sized filler such as carbon fibers, the interfaces between the filler and matrix constitutes have a much smaller surface-to-volume fraction of the bulk materials, and hence influence the properties of the host structure to a much smaller extent. The optimum amount of nanomaterials in the nanocomposites depends on the filler size, shape, homogeneity of particles distribution, and the interfacial bonding properties between the fillers and matrix. The promise of nanocomposites lies in their multifunctionality, i.e., the possibility of realizing unique combination of properties unachievable with traditional materials. The challenges in reaching this promise are tremendous. They include control over the distribution in size and dispersion of the nanosize constituents, and tailoring and understanding the role of interfaces between structurally or chemically dissimilar phases on bulk properties. While the properties of the matrix can be improved by the inclusions of nanomaterials, the

  2. The multifunctional protein AtMFP2 is co-ordinately expressed with other genes of fatty acid beta-oxidation during seed germination in Arabidopsis thaliana (L.) Heynh.

    PubMed

    Eastmond, P J; Graham, I A

    2000-02-01

    In germinating oilseeds peroxisomal fatty acid beta-oxidation is responsible for the mobilization of storage lipids. This pathway also occurs in other tissues where it has a variety of additional physiological functions. The central enzymatic steps of peroxisomal beta-oxidation are performed by acyl-CoA oxidase (ACOX), the multifunctional protein (MFP) and 3-ketoacyl-CoA thiolase (thiolase). In order to investigate the function and regulation of beta-oxidation in plants it is first necessary to identify and characterize genes encoding the relevant enzymes in a single model species. Recently we and others have reported on the cloning and characterization of genes encoding four ACOXs and a thiolase from the oilseed Arabidopsis thaliana. Here we identify a gene encoding an Arabidopsis MFP (AtMFP2) that is induced transiently during germination. The pattern of AtMFP2 expression closely reflects changes in the activities of 2-trans-enoyl-CoA hydratase and L-3-hydroxyacyl-CoA dehydrogenase. Similar patterns of expression have previously been reported for ACOX and thiolase genes. We conclude that genes encoding the three main proteins responsible for beta-oxidation are co-ordinately expressed during oilseed germination and may share a common mechanism of regulation.

  3. Multi-functional windows

    NASA Astrophysics Data System (ADS)

    Nag, Nagendra; Goldman, Lee M.; Balasubramanian, Sreeram; Sastri, Suri

    2013-06-01

    The requirements for modern aircraft are driving the need for conformal windows for future sensor systems. However, limitations on optical systems and the physical properties of optically transparent materials currently limit the geometry of existing windows and window assemblies to faceted assemblies of flat windows held in weight bearing frames. Novel material systems will have to be developed which combine different materials (e.g. ductile metals with transparent ceramics) into structures that combine transparency with structural integrity. Surmet's demonstrated ability to produce novel transparent ceramic/metal structures will allow us to produce such structures in the types of conformal shapes required for future aircraft applications. Furthermore, the ability to incorporate transparencies into such structures also holds out the promise of creating multi-functional windows which provide a broad range of capabilities that might include RF antennas and de-icing in addition to transparency. Recent results in this area will be presented.

  4. Designing ECM-mimetic materials using protein engineering.

    PubMed

    Cai, Lei; Heilshorn, Sarah C

    2014-04-01

    The natural extracellular matrix (ECM), with its multitude of evolved cell-instructive and cell-responsive properties, provides inspiration and guidelines for the design of engineered biomaterials. One strategy to create ECM-mimetic materials is the modular design of protein-based engineered ECM (eECM) scaffolds. This modular design strategy involves combining multiple protein domains with different functionalities into a single, modular polymer sequence, resulting in a multifunctional matrix with independent tunability of the individual domain functions. These eECMs often enable decoupled control over multiple material properties for fundamental studies of cell-matrix interactions. In addition, since the eECMs are frequently composed entirely of bioresorbable amino acids, these matrices have immense clinical potential for a variety of regenerative medicine applications. This brief review demonstrates how fundamental knowledge gained from structure-function studies of native proteins can be exploited in the design of novel protein-engineered biomaterials. While the field of protein-engineered biomaterials has existed for over 20years, the community is only now beginning to fully explore the diversity of functional peptide modules that can be incorporated into these materials. We have chosen to highlight recent examples that either (i) demonstrate exemplary use as matrices with cell-instructive and cell-responsive properties or (ii) demonstrate outstanding creativity in terms of novel molecular-level design and macro-level functionality. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  5. Extracellular Self-Assembly of Functional and Tunable Protein Conjugates from Bacillus subtilis.

    PubMed

    Gilbert, Charlie; Howarth, Mark; Harwood, Colin R; Ellis, Tom

    2017-03-07

    The ability to stably and specifically conjugate recombinant proteins to one another is a powerful approach for engineering multifunctional enzymes, protein therapeutics, and novel biological materials. While many of these applications have been illustrated through in vitro and in vivo intracellular protein conjugation methods, extracellular self-assembly of protein conjugates offers unique advantages: simplifying purification, reducing toxicity and burden, and enabling tunability. Exploiting the recently described SpyTag-SpyCatcher system, we describe here how enzymes and structural proteins can be genetically encoded to covalently conjugate in culture media following programmable secretion from Bacillus subtilis. Using this approach, we demonstrate how self-conjugation of a secreted industrial enzyme, XynA, dramatically increases its resilience to boiling, and we show that cellular consortia can be engineered to self-assemble functional protein-protein conjugates with tunable composition. This novel genetically encoded modular system provides a flexible strategy for protein conjugation harnessing the substantial advantages of extracellular self-assembly.

  6. Poly(I:C) is an effective adjuvant for antibody and multi-functional CD4+ T cell responses to Plasmodium falciparum circumsporozoite protein (CSP) and αDEC-CSP in Non Human Primates

    PubMed Central

    Tewari, Kavita; Flynn, Barbara J.; Boscardin, Silvia B.; Kastenmueller, Kathrin; Salazar, Andres M.; Anderson, Charles A.; Soundarapandian, Velu; Ahumada, Adriana; Keler, Tibor; Hoffman, Stephen L.; Nussenzweig, Michel C.; Steinman, Ralph M.; Seder, Robert A.

    2010-01-01

    Development of a fully effective vaccine against the pre-erythrocytic stage of malaria infection will likely require induction of both humoral and cellular immune responses. Protein based vaccines can elicit such broad-based immunity depending on the adjuvant and how the protein is formulated. Here to assess these variables, non-human primates (NHP) were immunized three times with Plasmodium falciparum (Pf) circumsporozoite protein (CSP) or CSP cloned into MG38, a monoclonal antibody that targets DEC-205 (αDEC-CSP), an endocytic receptor on dendritic cells (DCs). Both vaccines were administered with or without poly(I:C) as adjuvant. Following three immunizations, the magnitude and quality of cytokine secreting CD4+ T cells were comparable between CSP + poly(I:C) and αDEC-CSP + poly(I:C) groups with both regimens eliciting multi-functional cytokine responses. However, NHP immunized with CSP + poly(I:C) had significantly higher serum titers of CSP-specific IgG antibodies and indirect immunofluorescent antibody (IFA) titers against Pf sporozoites. Furthermore, sera from both CSP or αDEC-CSP + poly(I:C) immunized animals limited sporozoite invasion of a hepatocyte cell line (HC04) in vitro. To determine whether CSP-specific responses could be enhanced, all NHP primed with CSP or αDEC-CSP + poly(I:C) were boosted with a single dose of 150,000 irradiated Pf sporozoites (PfSPZ) intravenously. Remarkably, boosting had no effect on the CSP-specific immunity. Finally, immunization with CSP + poly-ICLC reduced malaria parasite burden in the liver in an experimental mouse model. Taken together, these data showing that poly(I:C) is an effective adjuvant for inducing potent antibody and Th1 immunity with CSP based vaccines offers a potential alternative to the existing protein based pre-erythrocytic vaccines. PMID:20846528

  7. Modular reflector concept study

    NASA Astrophysics Data System (ADS)

    Vaughan, D. H.

    1981-02-01

    The feasibility was studied of constructing large space structures, specifically a 100 meter paraboloidal R.F. reflector, by individually deploying a number of relatively small structural modules, and then joining them to form a single large structure in orbit. The advantage of this approach is that feasibility of a large antenna may be demonstrated by ground and flight tests of several smaller and less costly subelements. Thus, initial development costs are substantially reduced and a high degree of reliability can be obtained without commitment to construction of a very large system. The three candidate structural concepts investigated are: (1) the deployable cell module; (2) the paraboloidal extendable truss antenna adapted to modular assembly; and (3) the modular extendable truss antenna (META).

  8. Modular space station

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The modular space station comprising small, shuttle-launched modules, and characterized by low initial cost and incremental manning, is described. The initial space station is designed to be delivered into orbit by three space shuttles and assembled in space. The three sections are the power/subsystems module, the crew/operations module, and the general purpose laboratory module. It provides for a crew of six. Subsequently duplicate/crew/operations and power/subsystems modules will be mated to the original modules, and provide for an additional six crewmen. A total of 17 research and applications modules is planned, three of which will be free-flying modules. Details are given on the program plan, modular characteristics, logistics, experiment support capability and requirements, operations analysis, design support analyses, and shuttle interfaces.

  9. ATIS - A modular approach

    NASA Astrophysics Data System (ADS)

    Kirson, Allan

    The author describes a modular approach to the design of an in-vehicle navigation and route guidance system that supports a phased implementation of the technology, and anticipates expected differences in implementation in different parts of the world and for different makes and models of vehicle. A series of sensors in the vehicle are used to determine the vehicle's position by dead reckoning and map-matching. The system then calculates the best route to the selected destination, taking into account the real-time traffic information received from a traffic management center, and presents route guidance instructions to the user as the route is traversed. Attention is given to modularity considerations, vehicle positioning, driver support, vehicle-to-infrastructure communications, and the role of standards.

  10. Modular reflector concept study

    NASA Technical Reports Server (NTRS)

    Vaughan, D. H.

    1981-01-01

    The feasibility was studied of constructing large space structures, specifically a 100 meter paraboloidal R.F. reflector, by individually deploying a number of relatively small structural modules, and then joining them to form a single large structure in orbit. The advantage of this approach is that feasibility of a large antenna may be demonstrated by ground and flight tests of several smaller and less costly subelements. Thus, initial development costs are substantially reduced and a high degree of reliability can be obtained without commitment to construction of a very large system. The three candidate structural concepts investigated are: (1) the deployable cell module; (2) the paraboloidal extendable truss antenna adapted to modular assembly; and (3) the modular extendable truss antenna (META).

  11. Quantum spaces are modular

    NASA Astrophysics Data System (ADS)

    Freidel, Laurent; Leigh, Robert G.; Minic, Djordje

    2016-11-01

    At present, our notion of space is a classical concept. Taking the point of view that quantum theory is more fundamental than classical physics, and that space should be given a purely quantum definition, we revisit the notion of Euclidean space from the point of view of quantum mechanics. Since space appears in physics in the form of labels on relativistic fields or Schrödinger wave functionals, we propose to define Euclidean quantum space as a choice of polarization for the Heisenberg algebra of quantum theory. We show, following Mackey, that generically, such polarizations contain a fundamental length scale and that contrary to what is implied by the Schrödinger polarization, they possess topologically distinct spectra. These are the modular spaces. We show that they naturally come equipped with additional geometrical structures usually encountered in the context of string theory or generalized geometry. Moreover, we show how modular space reconciles the presence of a fundamental scale with translation and rotation invariance. We also discuss how the usual classical notion of space comes out as a form of thermodynamical limit of modular space while the Schrödinger space is a singular limit.

  12. Multifunctional recombinant phycobiliprotein-based fluorescent constructs and phycobilisome display

    DOEpatents

    Glazer, Alexander N.; Cai, Yuping

    2007-02-13

    The invention provides multifunctional fusion constructs which are rapidly incorporated into a macromolecular structure such as a phycobilisome such that the fusion proteins are separated from one another and unable to self-associate. The invention provides methods and compositions for displaying a functional polypeptide domain on an oligomeric phycobiliprotein. including fusion proteins comprising a functional displayed domain and a functional phycobiliprotein domain incorporated in a functional oligomeric phycobiliprotein. The fusion proteins provide novel specific labeling reagents.

  13. Multifunctional recombinant phycobiliprotein-based fluorescent constructs and phycobilisome display

    DOEpatents

    Glazer, Alexander N.; Cai, Yuping

    2007-01-30

    The invention provides multifunctional fusion constructs which are rapidly incorporated into a macromolecular structure such as a phycobilisome such that the fusion proteins are separated from one another and unable to self-associate. The invention provides methods and compositions for displaying a functional polypeptide domain on an oligomeric phycobiliprotein, including fusion proteins comprising a functional displayed domain and a functional phycobiliprotein domain incorporated in a functional oligomeric phycobiliprotein. The fusion proteins provide novel specific labeling reagents.

  14. Multifunctional recombinant phycobiliprotein-based fluorescent constructs and phycobilisome display

    DOEpatents

    Glazer, Alexander N.; Cai, Yuping

    2003-11-18

    The invention provides multifunctional fusion constructs which are rapidly incorporated into a macromolecular structure such as a phycobilisome such that the fusion proteins are separated from one another and unable to self-associate. The invention provides methods and compositions for displaying a functional polypeptide domain on an oligomeric phycobiliprotein, including fusion proteins comprising a functional displayed domain and a functional phycobiliprotein domain incorporated in a functional oligomeric phycobiliprotein. The fusion proteins provide novel specific labeling reagents.

  15. Workflow and cost analysis on MODULAR ANALYTICS.

    PubMed

    Stolz, Herbert; Dossler, Bettina; Keller, Franz; Steigerwald, Udo

    2003-01-01

    Four stand-alone analyzers in a centralized laboratory were replaced by two modular analytical systems processing 45 methods of the general chemistry and specific protein segment. This consolidation led to a reduction of the daily workflow and operational costs. The cost saving with 1.3 million reported results per year was 53,000 Euro, which can be assessed as an important contribution to cost reduction in the health care system.

  16. Enzyme screening with synthetic multifunctional pores: Focus on biopolymers

    PubMed Central

    Sordé, Nathalie; Das, Gopal; Matile, Stefan

    2003-01-01

    This report demonstrates that a single set of identical synthetic multifunctional pores can detect the activity of many different enzymes. Enzymes catalyzing either synthesis or degradation of DNA (exonuclease III or polymerase I), RNA (RNase A), polysaccharides (heparinase I, hyaluronidase, and galactosyltransferase), and proteins (papain, ficin, elastase, subtilisin, and pronase) are selected to exemplify this key characteristic of synthetic multifunctional pore sensors. Because anionic, cationic, and neutral substrates can gain access to the interior of complementarily functionalized pores, such pores can be the basis for very user-friendly screening of a broad range of enzymes. PMID:14530413

  17. Enzyme screening with synthetic multifunctional pores: focus on biopolymers.

    PubMed

    Sordé, Nathalie; Das, Gopal; Matile, Stefan

    2003-10-14

    This report demonstrates that a single set of identical synthetic multifunctional pores can detect the activity of many different enzymes. Enzymes catalyzing either synthesis or degradation of DNA (exonuclease III or polymerase I), RNA (RNase A), polysaccharides (heparinase I, hyaluronidase, and galactosyltransferase), and proteins (papain, ficin, elastase, subtilisin, and pronase) are selected to exemplify this key characteristic of synthetic multifunctional pore sensors. Because anionic, cationic, and neutral substrates can gain access to the interior of complementarily functionalized pores, such pores can be the basis for very user-friendly screening of a broad range of enzymes.

  18. Modularity enhances the rate of evolution in a rugged fitness landscape.

    PubMed

    Park, Jeong-Man; Chen, Man; Wang, Dong; Deem, Michael W

    2015-03-19

    Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. Approximately 25% of the observed rate of fitness increase of the virus could be ascribed to a modular viral landscape.

  19. Modularity Enhances the Rate of Evolution in a Rugged Fitness Landscape

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Park, Jeong-Man; Chen, Man; Deem, Michael

    Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. A modular model of the fitness landscape of the virus better fits the observed virus evolution data.

  20. Modularity Enhances the Rate of Evolution in a Rugged Fitness Landscape

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Park, Jeong-Man; Chen, Man; Deem, Michael

    2015-03-01

    Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. A modular model of the fitness landscape of the virus better fits the observed virus evolution data. This research was supported by the US National Institutes of Health under Grant 1 R01 GM 100468-01. JMP was also supported by the National Research Foundation of Korea Grant (NRF-2013R1A1A2006983).

  1. Modularity enhances the rate of evolution in a rugged fitness landscape

    NASA Astrophysics Data System (ADS)

    Park, Jeong-Man; Chen, Man; Wang, Dong; Deem, Michael W.

    2015-04-01

    Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. Approximately 25% of the observed rate of fitness increase of the virus could be ascribed to a modular viral landscape.

  2. LMDS Lightweight Modular Display System.

    DTIC Science & Technology

    1982-02-16

    LIGHTWEIGHT MODULAR DISPLAY SYSTEM %C AD Gomez SW Wolfe EW Davenport BD Calder 16 February 1982 * / DTrSJUL 22 3829 Approved for public release...375 4. TITLE (and Subtitle) S. TYPE OF REPORT & PERIOD COVERED Oct 77 to Jan 82 LMDS LIGHTWEIGHT MODULAR DISPLAY SYSTEM S. PERFORMING ORG. REPORT...Processing Power Distribution Modular Display Low Cost Tactical Display Tactical Tablet Lightweight Display General Purpose Dispiay Functional Modules Touch

  3. Multifunctions of bounded variation

    NASA Astrophysics Data System (ADS)

    Vinter, R. B.

    2016-02-01

    Consider control systems described by a differential equation with a control term or, more generally, by a differential inclusion with velocity set F (t , x). Certain properties of state trajectories can be derived when it is assumed that F (t , x) is merely measurable w.r.t. the time variable t. But sometimes a refined analysis requires the imposition of stronger hypotheses regarding the time dependence. Stronger forms of necessary conditions for minimizing state trajectories can be derived, for example, when F (t , x) is Lipschitz continuous w.r.t. time. It has recently become apparent that significant addition properties of state trajectories can still be derived, when the Lipschitz continuity hypothesis is replaced by the weaker requirement that F (t , x) has bounded variation w.r.t. time. This paper introduces a new concept of multifunctions F (t , x) that have bounded variation w.r.t. time near a given state trajectory, of special relevance to control. We provide an application to sensitivity analysis.

  4. Multifunctional periodic cellular metals.

    PubMed

    Wadley, Haydn N G

    2006-01-15

    Periodic cellular metals with honeycomb and corrugated topologies are widely used for the cores of light weight sandwich panel structures. Honeycombs have closed cell pores and are well suited for thermal protection while also providing efficient load support. Corrugated core structures provide less efficient and highly anisotropic load support, but enable cross flow heat exchange opportunities because their pores are continuous in one direction. Recent advances in topology design and fabrication have led to the emergence of lattice truss structures with open cell structures. These three classes of periodic cellular metals can now be fabricated from a wide variety of structural alloys. Many topologies are found to provide adequate stiffness and strength for structural load support when configured as the cores of sandwich panels. Sandwich panels with core relative densities of 2-10% and cell sizes in the millimetre range are being assessed for use as multifunctional structures. The open, three-dimensional interconnected pore networks of lattice truss topologies provide opportunities for simultaneously supporting high stresses while also enabling cross flow heat exchange. These highly compressible structures also provide opportunities for the mitigation of high intensity dynamic loads created by impacts and shock waves in air or water. By filling the voids with polymers and hard ceramics, these structures have also been found to offer significant resistance to penetration by projectiles.

  5. Proteins on the catwalk: modelling the structural domains of the CCN family of proteins.

    PubMed

    Holbourn, Kenneth P; Perbal, Bernard; Ravi Acharya, K

    2009-03-01

    The CCN family of proteins (CCN1, CCN2, CCN3, CCN4, CCN5 and CCN6) are multifunctional mosaic proteins that play keys roles in crucial areas of physiology such as angiogenesis, skeletal development tumourigenesis, cell proliferation, adhesion and survival. This expansive repertoire of functions comes through a modular structure of 4 discrete domains that act both independently and in concert. How these interactions with ligands and with neighbouring domains lead to the biological effects is still to be explored but the molecular structure of the domains is likely to play an important role in this. In this review we have highlighted some of the key features of the individual domains of CCN family of proteins based on their biological effects using a homology modelling approach.

  6. Robotic hand with modular extensions

    DOEpatents

    Salisbury, Curt Michael; Quigley, Morgan

    2015-01-20

    A robotic device is described herein. The robotic device includes a frame that comprises a plurality of receiving regions that are configured to receive a respective plurality of modular robotic extensions. The modular robotic extensions are removably attachable to the frame at the respective receiving regions by way of respective mechanical fuses. Each mechanical fuse is configured to trip when a respective modular robotic extension experiences a predefined load condition, such that the respective modular robotic extension detaches from the frame when the load condition is met.

  7. Modular analysis of biological networks.

    PubMed

    Kaltenbach, Hans-Michael; Stelling, Jörg

    2012-01-01

    The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

  8. Multifunctional silk-tropoelastin biomaterial systems

    PubMed Central

    Ghezzi, Chiara E.; Rnjak-Kovacina, Jelena; Weiss, Anthony S.; Kaplan, David L.

    2015-01-01

    New multifunctional, degradable, polymeric biomaterial systems would provide versatile platforms to address cell and tissue needs in both in vitro and in vivo environments. While protein-based composites or alloys are the building blocks of biological organisms, similar systems have not been largely exploited to dates to generate ad hoc biomaterials able to control and direct biological functions, by recapitulating their inherent structural and mechanical complexities. Therefore, we have recently proposed silk-tropoelastin material platforms able to conjugate a mechanically robust and durable protein, silk, to a highly flexible and biologically active protein, tropoelastin. This review focuses on the elucidation of the interactions between silk and tropoelastin in order to control material structure, properties, and ultimately functions. In addition, an approach is provided for novel material designs to provide tools to control biological outcomes via surface roughness, elasticity, and net charge for neuronal and mesenchymal stem cell-based tissue engineering. PMID:26005219

  9. Modular biometric system

    NASA Astrophysics Data System (ADS)

    Hsu, Charles; Viazanko, Michael; O'Looney, Jimmy; Szu, Harold

    2009-04-01

    Modularity Biometric System (MBS) is an approach to support AiTR of the cooperated and/or non-cooperated standoff biometric in an area persistent surveillance. Advanced active and passive EOIR and RF sensor suite is not considered here. Neither will we consider the ROC, PD vs. FAR, versus the standoff POT in this paper. Our goal is to catch the "most wanted (MW)" two dozens, separately furthermore ad hoc woman MW class from man MW class, given their archrivals sparse front face data basis, by means of various new instantaneous input called probing faces. We present an advanced algorithm: mini-Max classifier, a sparse sample realization of Cramer-Rao Fisher bound of the Maximum Likelihood classifier that minimize the dispersions among the same woman classes and maximize the separation among different man-woman classes, based on the simple feature space of MIT Petland eigen-faces. The original aspect consists of a modular structured design approach at the system-level with multi-level architectures, multiple computing paradigms, and adaptable/evolvable techniques to allow for achieving a scalable structure in terms of biometric algorithms, identification quality, sensors, database complexity, database integration, and component heterogenity. MBS consist of a number of biometric technologies including fingerprints, vein maps, voice and face recognitions with innovative DSP algorithm, and their hardware implementations such as using Field Programmable Gate arrays (FPGAs). Biometric technologies and the composed modularity biometric system are significant for governmental agencies, enterprises, banks and all other organizations to protect people or control access to critical resources.

  10. Modular Biometric Monitoring System

    NASA Technical Reports Server (NTRS)

    Chmiel, Alan J. (Inventor); Humphreys, Bradley T. (Inventor)

    2017-01-01

    A modular system for acquiring biometric data includes a plurality of data acquisition modules configured to sample biometric data from at least one respective input channel at a data acquisition rate. A representation of the sampled biometric data is stored in memory of each of the plurality of data acquisition modules. A central control system is in communication with each of the plurality of data acquisition modules through a bus. The central control system is configured to control communication of data, via the bus, with each of the plurality of data acquisition modules.

  11. Geometric Kac Moody modularity

    NASA Astrophysics Data System (ADS)

    Lynker, Monika; Schimmrigk, Rolf

    2006-05-01

    It is shown how the arithmetic structure of algebraic curves encoded in the Hasse-Weil L-function can be related to affine Kac-Moody algebras. This result is useful in relating the arithmetic geometry of Calabi-Yau varieties to the underlying exactly solvable theory. In the case of the genus three Fermat curve we identify the Hasse-Weil L-function with the Mellin transform of the twist of a number theoretic modular form derived from the string function of a non-twisted affine Lie algebra. The twist character is associated to the number field of quantum dimensions of the conformal field theory.

  12. Modular space station facilities.

    NASA Technical Reports Server (NTRS)

    Parker, P. J.

    1973-01-01

    The modular space station will operate as a general purpose laboratory (GPL). In addition, the space station will be able to support many attached or free-flying research and application modules that would be dedicated to specific projects like astronomy or earth observations. The GPL primary functions have been organized into functional laboratories including an electrical/electronics laboratory, a mechanical sciences laboratory, an experiment and test isolation laboratory, a hard data process facility, a data evaluation facility, an optical sciences laboratory, a biomedical and biosciences laboratory, and an experiment/secondary command and control center.

  13. Modular gear bearings

    NASA Technical Reports Server (NTRS)

    Vranish, John M. (Inventor)

    2009-01-01

    A gearing system using modular gear bearing components. Each component is composed of a core, one or more modules attached to the core and two or more fastening modules rigidly attaching the modules to the core. The modules, which are attached to the core, may consist of gears, rollers or gear bearing components. The core orientation affects the orientation of the modules attached to the core. This is achieved via the keying arrangement of the core and the component modules that attach to the core. Such an arrangement will also facilitate the phase tuning of gear modules with respect to the core and other gear modules attached to the core.

  14. Modularity of music processing.

    PubMed

    Peretz, Isabelle; Coltheart, Max

    2003-07-01

    The music faculty is not a monolithic entity that a person either has or does not. Rather, it comprises a set of neurally isolable processing components, each having the potential to be specialized for music. Here we propose a functional architecture for music processing that captures the typical properties of modular organization. The model rests essentially on the analysis of music-related deficits in neurologically impaired individuals, but provides useful guidelines for exploring the music faculty in normal people, using methods such as neuroimaging.

  15. Modular and Hierarchically Modular Organization of Brain Networks

    PubMed Central

    Meunier, David; Lambiotte, Renaud; Bullmore, Edward T.

    2010-01-01

    Brain networks are increasingly understood as one of a large class of information processing systems that share important organizational principles in common, including the property of a modular community structure. A module is topologically defined as a subset of highly inter-connected nodes which are relatively sparsely connected to nodes in other modules. In brain networks, topological modules are often made up of anatomically neighboring and/or functionally related cortical regions, and inter-modular connections tend to be relatively long distance. Moreover, brain networks and many other complex systems demonstrate the property of hierarchical modularity, or modularity on several topological scales: within each module there will be a set of sub-modules, and within each sub-module a set of sub-sub-modules, etc. There are several general advantages to modular and hierarchically modular network organization, including greater robustness, adaptivity, and evolvability of network function. In this context, we review some of the mathematical concepts available for quantitative analysis of (hierarchical) modularity in brain networks and we summarize some of the recent work investigating modularity of structural and functional brain networks derived from analysis of human neuroimaging data. PMID:21151783

  16. A novel gene therapy strategy using secreted multifunctional anti-HIV proteins to confer protection to gene-modified and unmodified target cells.

    PubMed

    Falkenhagen, A; Ameli, M; Asad, S; Read, S E; Joshi, S

    2014-02-01

    Current human immunodeficiency virus type I (HIV) gene therapy strategies focus on rendering HIV target cells non-permissive to viral replication. However, gene-modified cells fail to accumulate in patients and the virus continues to replicate in the unmodified target cell population. We have designed lentiviral vectors encoding secreted anti-HIV proteins to protect both gene-modified and unmodified cells from infection. Soluble CD4 (sCD4), a secreted single chain variable fragment (sscFv(17b)) and a secreted fusion inhibitor (sFI(T45)) were used to target receptor binding, co-receptor binding and membrane fusion, respectively. Additionally, we designed bi- and tri-functional fusion proteins to exploit the multistep nature of HIV entry. Of the seven antiviral proteins tested, sCD4, sCD4-scFv(17b), sCD4-FI(T45) and sCD4-scFv(17b)-FI(T45) efficiently inhibited HIV entry. The neutralization potency of the bi-functional fusion proteins sCD4-scFv(17b) and sCD4-FI(T45) was superior to that of sCD4 and the Food and Drug Administration-approved fusion inhibitor T-20. In co-culture experiments, sCD4, sCD4-scFv(17b) and sCD4-FI(T45) secreted from gene-modified producer cells conferred substantial protection to unmodified peripheral blood mononuclear cells. In conclusion, continuous delivery of secreted anti-HIV proteins via gene therapy may be a promising strategy to overcome the limitations of the current treatment.

  17. Modular antenna design study

    NASA Technical Reports Server (NTRS)

    Ribble, J. W.

    1981-01-01

    The mechanical design of a modular antenna concept was developed sufficiently to allow manufacture of a working demonstration model of a module, to predict mass properties, and to make performance estimates for antenna reflectors composed of these modules. The primary features of this concept are: (1) each module is an autonomous structural element which can be attached to adjacent modules through a three point connection; (2) the upper surface is a folding hexagonal truss plate mechanism which serves as the supporting structure for a reflective surface; and (3) the entire truss and surface can be folded into a cylindrical envelope in which all truss elements are essentially parallel. The kinematic studies and engineering demonstration model fully verified the deployment kinematics, stowing philosophy, and deployment sequencing for large antenna modules. It was established that such modules can be stowed in packages as small as 25 cm in diameter, using 1.27 cm diameter structural tubes. The development activity indicates that this deployable modular approach towards building large structures in space will support erection of 450 m apertures for operation up to 3 GHz with a single space shuttle flight.

  18. Modular reflector concept study

    NASA Technical Reports Server (NTRS)

    Vaughan, D. H.

    1981-01-01

    A study was conducted to evaluate the feasibility of space erecting a 100 meter paraboloidal radio frequency reflector by joining a number of individually deployed structural modules. Three module design concepts were considered: (1) the deployable cell module (DCM); (2) the modular paraboloidal erectable truss antenna (Mod-PETA); and (3) the modular erectable truss antenna (META). With the space shuttle (STS) as the launch system, the methodology of packaging and stowing in the orbiter, and of dispensing, deploying and joining, in orbit, were studied and the necessary support equipment identified. The structural performance of the completed reflectors was evaluated and their overall operational capability and feasibility were evaluated and compared. The potential of the three concepts to maintain stable shape in the space environment was determined. Their ability to operate at radio frequencies of 1 GHz and higher was assessed assuming the reflector surface to consist of a number of flat, hexagonal facets. A parametric study was performed to determine figure degradation as a function of reflector size, flat facet size, and f/D ratio.

  19. Modular radiochemistry synthesis system

    SciTech Connect

    Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

    2015-12-15

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  20. Modular radiochemistry synthesis system

    DOEpatents

    Satyamurthy, Nagichettiar; Barrio, Jorge R; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark A; Shen, Clifton Kwang-Fu

    2015-02-10

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  1. Preheating after modular inflation

    NASA Astrophysics Data System (ADS)

    Barnaby, Neil; Bond, J. Richard; Huang, Zhiqi; Kofman, Lev

    2009-12-01

    We study (p)reheating in modular (closed string) inflationary scenarios, with a special emphasis on Kähler moduli/Roulette models. It is usually assumed that reheating in such models occurs through perturbative decays. However, we find that there are very strong non-perturbative preheating decay channels related to the particular shape of the inflaton potential (which is highly nonlinear and has a very steep minimum). Preheating after modular inflation, proceeding through a combination of tachyonic instability and broad-band parametric resonance, is perhaps the most violent example of preheating after inflation known in the literature. Further, we consider the subsequent transfer of energy to the standard model sector in scenarios where the standard model particles are confined to a D7-brane wrapping the inflationary blow-up cycle of the compactification manifold or, more interestingly, a non-inflationary blow-up cycle. We explicitly identify the decay channels of the inflaton in these two scenarios. We also consider the case where the inflationary cycle shrinks to the string scale at the end of inflation; here a field theoretical treatment of reheating is insufficient and one must turn instead to a stringy description. We estimate the decay rate of the inflaton and the reheat temperature for various scenarios.

  2. Modular Robotic Vehicle

    NASA Technical Reports Server (NTRS)

    Borroni-Bird, Christopher E. (Inventor); Vitale, Robert L. (Inventor); Lee, Chunhao J. (Inventor); Ambrose, Robert O. (Inventor); Bluethmann, William J. (Inventor); Junkin, Lucien Q. (Inventor); Lutz, Jonathan J. (Inventor); Guo, Raymond (Inventor); Lapp, Anthony Joseph (Inventor); Ridley, Justin S. (Inventor)

    2015-01-01

    A modular robotic vehicle includes a chassis, driver input devices, an energy storage system (ESS), a power electronics module (PEM), modular electronic assemblies (eModules) connected to the ESS via the PEM, one or more master controllers, and various embedded controllers. Each eModule includes a drive wheel containing a propulsion-braking module, and a housing containing propulsion and braking control assemblies with respective embedded propulsion and brake controllers, and a mounting bracket covering a steering control assembly with embedded steering controllers. The master controller, which is in communication with each eModule and with the driver input devices, communicates with and independently controls each eModule, by-wire, via the embedded controllers to establish a desired operating mode. Modes may include a two-wheel, four-wheel, diamond, and omni-directional steering modes as well as a park mode. A bumper may enable docking with another vehicle, with shared control over the eModules of the vehicles.

  3. Modular radiochemistry synthesis system

    SciTech Connect

    Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, Michael R.; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

    2016-11-01

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  4. Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis.

    PubMed

    Cameron, Elizabeth A; Kwiatkowski, Kurt J; Lee, Byung-Hoo; Hamaker, Bruce R; Koropatkin, Nicole M; Martens, Eric C

    2014-09-09

    To compete for the dynamic stream of nutrients flowing into their ecosystem, colonic bacteria must respond rapidly to new resources and then catabolize them efficiently once they are detected. The Bacteroides thetaiotaomicron starch utilization system (Sus) is a model for nutrient acquisition by symbiotic gut bacteria, which harbor thousands of related Sus-like systems. Structural investigation of the four Sus outer membrane proteins (SusD, -E, -F, and -G) revealed that they contain a total of eight starch-binding sites that we demonstrated, using genetic and biochemical approaches, to play distinct roles in starch metabolism in vitro and in vivo in gnotobiotic mice. SusD, whose homologs are abundant in the human microbiome, is critical for the initial sensing of available starch, allowing sus transcriptional activation at much lower concentrations than without this function. In contrast, seven additional binding sites across SusE, -F, and -G are dispensable for sus activation. However, they optimize the rate of growth on starch in a manner dependent on the expression of the bacterial polysaccharide capsule, suggesting that they have evolved to offset the diffusion barrier created by this structure. These findings demonstrate how proteins with similar biochemical behavior can serve orthogonal functions during different stages of cellular adaptation to nutrients. Finally, we demonstrated in gnotobiotic mice fed a starch-rich diet that the Sus binding sites confer a competitive advantage to B. thetaiotaomicron in vivo in a manner that is dependent on other colonizing microbes. This study reveals how numerically dominant families of carbohydrate-binding proteins in the human microbiome fulfill separate and sometimes cooperative roles to optimize gut commensal bacteria for nutrient acquisition. Our intestinal tract harbors trillions of symbiotic microbes. A critical function contributed by this microbial community is the ability to degrade most of the complex

  5. ZmLEA3, a multifunctional group 3 LEA protein from maize (Zea mays L.), is involved in biotic and abiotic stresses.

    PubMed

    Liu, Yang; Wang, Li; Xing, Xin; Sun, Liping; Pan, Jiaowen; Kong, Xiangpei; Zhang, Maoying; Li, Dequan

    2013-06-01

    Late embryogenesis abundant (LEA) proteins accumulate to high levels during the late stage of seed maturation and in response to water deficit, and are involved in protecting higher plants from damage caused by environmental stresses, especially drought. In the present study, a novel maize (Zea mays L.) group 3 LEA gene, ZmLEA3, was identified and later characterized using transgenic tobacco plants to investigate its functions in abiotic and biotic stresses. Transcript accumulation demonstrated that ZmLEA3 was induced in leaves by high salinity, low temperature, osmotic and oxidative stress as well as by signaling molecules such as ABA, salicylic acid (SA) and methyl jasmonate (MeJA). The transcript of ZmLEA3 could also be induced by pathogens [Pseudomonas syringae pv. tomato DC3000 (pst dc3000)]. ZmLEA3 is located in the cytosol and the nucles. Further study indicated that the ZmLEA3 protein could bind Mn(2+), Fe(3+), Cu(2+) and Zn(2+). Overexpression of ZmLEA3 in transgenic tobacco (Nicotiana tabacum) and yeast (GS115) conferred tolerance to osmotic and oxidative stresses. Interestingly, we also found that overexpression of ZmLEA3 in transgenic tobacco increased the hypersensitive cell death triggered by pst dc3000 and enhanced the expression of PR1a, PR2 and PR4 when compared with the wild type. Thus, we proposed that the ZmLEA3 protein plays a role in protecting plants from damage by protecting protein structure and binding metals under osmotic and oxidative stresses. In addition, ZmLEA3 may also enhance transgenic plant tolerance to biotic stress.

  6. Effect of the multifunctional proteins RPA, YB-1, and XPC repair factor on AP site cleavage by DNA glycosylase NEIL1.

    PubMed

    Pestryakov, Pavel; Zharkov, Dmitry O; Grin, Inga; Fomina, Elizaveta E; Kim, Ekaterina R; Hamon, Loïc; Eliseeva, Irina A; Petruseva, Irina O; Curmi, Patrick A; Ovchinnikov, Lev P; Lavrik, Olga I

    2012-04-01

    DNA glycosylases are key enzymes in the first step of base excision DNA repair, recognizing DNA damage and catalyzing the release of damaged nucleobases. Bifunctional DNA glycosylases also possess associated apurinic/apyrimidinic (AP) lyase activity that nick the damaged DNA strand at an abasic (or AP) site, formed either spontaneously or at the first step of repair. NEIL1 is a bifunctional DNA glycosylase capable of processing lesions, including AP sites, not only in double-stranded but also in single-stranded DNA. Here, we show that proteins participating in DNA damage response, YB-1 and RPA, affect AP site cleavage by NEIL1. Stimulation of the AP lyase activity of NEIL1 was observed when an AP site was located in a 60 nt-long double-stranded DNA. Both RPA and YB-1 inhibited AP site cleavage by NEIL1 when the AP site was located in single-stranded DNA. Taking into account a direct interaction of YB-1 with the AP site, located in single-stranded DNA, and the high affinity of both YB-1 and RPA for single-stranded DNA, this behavior is presumably a consequence of a competition with NEIL1 for the DNA substrate. Xeroderma pigmentosum complementation group C protein (XPC), a key protein of another DNA repair pathway, was shown to interact directly with AP sites but had no effect on AP site cleavage by NEIL1.

  7. Quantum modular forms, mock modular forms, and partial theta functions

    NASA Astrophysics Data System (ADS)

    Kimport, Susanna

    Defined by Zagier in 2010, quantum modular forms have been the subject of an explosion of recent research. Many of these results are aimed at discovering examples of these functions, which are defined on the rational numbers and have "nice" modularity properties. Though the subject is in its early stages, numerous results (including Zagier's original examples) show these objects naturally arising from many areas of mathematics as limits of other modular-like functions. One such family of examples is due to Folsom, Ono, and Rhoades, who connected these new objects to partial theta functions (introduced by Rogers in 1917) and mock modular forms (about which there is a rich theory, whose origins date back to Ramanujan in 1920). In this thesis, we build off of the work of Folsom, Ono, and Rhoades by providing an infinite family of quantum modular forms of arbitrary positive half-integral weight. Further, this family of quantum modular forms "glues" mock modular forms to partial theta functions and is constructed from a so-called "universal" mock theta function by extending a method of Eichler and Zagier (originally defined for holomorphic Jacobi forms) into a non-holomorphic setting. In addition to the infinite family, we explore the weight 1/2 and 3/2 functions in more depth. For both of these weights, we are able to explicitly write down the quantum modular form, as well as the corresponding "errors to modularity," which can be shown to be Mordell integrals of specific theta functions and, as a consequence, are real-analytic functions. Finally, we turn our attention to the partial theta functions associated with these low weight examples. Berndt and Kim provide asymptotic expansions for a certain class of partial theta functions as q approaches 1 radially within the unit disk. Here, we extend this work to not only obtain asymptotic expansions for this class of functions as q approaches any root of unity, but also for a certain class of derivatives of these functions

  8. Identification of in vivo HSP90-interacting proteins reveals modularity of HSP90 complexes is dependent on the environment in psychrophilic bacteria

    PubMed Central

    García-Descalzo, Laura; Alcazar, Alberto; Baquero, Fernando

    2010-01-01

    Heat shock protein 90 (HSP90) is a conserved molecular chaperone that functions as part of complexes in which different client proteins target it to diverse sets of substrates. In this paper, HSP90 complexes were investigated in γ-proteobacteria from mild (Shewanella oneidensis) and cold environments (Shewanella frigidimarina and Psychrobacter frigidicola), to determine changes in HSP90 interactions with client proteins in response to the adaptation to cold environments. HSP90 participation in cold adaptation was determined using the specific inhibitor 17-allylamino-geldanamycin. Then, HSP90 was immunoprecipitated from bacterial cultures, and the proteins in HSP90 complexes were analyzed by two-dimensional gel electrophoresis and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. According to HSP90-associated protein analysis, only 15 common proteins were found in both species from the same genus, S. oneidensis and S. frigidimarina, whereas a significant higher number of common proteins were found in both psychrophilic species S. frigidimarina and P. frigidicola 21 (p < 0.001). Only two HSP90-interacting proteins, the chaperone proteins DnaK and GroEL, were common to the three species. Interestingly, some proteins related to energy metabolism (isocitrate lyase, succinyl-CoA synthetase, alcohol dehydrogenase, NAD(+) synthase, and malate dehydrogenase) and some translation factors only interacted with HSP90 in psychrophilic bacteria. We can conclude that HSP90 and HSP90-associated proteins might take part in the mechanism of adaptation to cold environments, and interestingly, organisms living in similar environments conserve similar potential HSP90 interactors in opposition to phylogenetically closely related organisms of the same genus but from different environments. PMID:20890740

  9. Spacecraft Modularity for Serviceable Satellites

    NASA Technical Reports Server (NTRS)

    Rossetti, Dino; Keer, Beth; Panek, John; Ritter, Bob; Reed, Benjamin; Cepollina, Frank

    2015-01-01

    Spacecraft modularity has been a topic of interest at NASA since the 1970s, when the Multi-­-Mission Modular Spacecraft (MMS) was developed at the Goddard Space Flight Center. Since then, modular concepts have been employed for a variety of spacecraft and, as in the case of the Hubble Space Telescope (HST) and the International Space Station (ISS), have been critical to the success of on-­- orbit servicing. Modularity is even more important for future robotic servicing. Robotic satellite servicing technologies under development by NASA can extend mission life and reduce lifecycle cost and risk. These are optimized when the target spacecraft is designed for servicing, including advanced modularity. This paper will explore how spacecraft design, as demonstrated by the Reconfigurable Operational spacecraft for Science and Exploration (ROSE) spacecraft architecture, and servicing technologies can be developed in parallel to fully take advantage of the promise of both.

  10. Spacecraft Modularity for Serviceable Satellites

    NASA Technical Reports Server (NTRS)

    Reed, Benjamin B.; Rossetti, Dino; Keer, Beth; Panek, John; Cepollina, Frank; Ritter, Robert

    2015-01-01

    Spacecraft modularity has been a topic of interest at NASA since the 1970s, when the Multi-Mission Modular Spacecraft (MMS) was developed at the Goddard Space Flight Center. Since then, modular concepts have been employed for a variety of spacecraft and, as in the case of the Hubble Space Telescope (HST) and the International Space Station (ISS), have been critical to the success of on-orbit servicing. Modularity is even more important for future robotic servicing. Robotic satellite servicing technologies under development by NASA can extend mission life and reduce life-cycle cost and risk. These are optimized when the target spacecraft is designed for servicing, including advanced modularity. This paper will explore how spacecraft design, as demonstrated by the Reconfigurable Operational spacecraft for Science and Exploration (ROSE) spacecraft architecture, and servicing technologies can be developed in parallel to fully take advantage of the promise of both.

  11. Enhanced multifunctional paint for detection of radiation

    DOEpatents

    Farmer, Joseph C.; Moses, Edward Ira; Rubenchik, Alexander M.

    2017-03-07

    An enhanced multifunctional paint apparatus, systems, and methods for detecting radiation on a surface include providing scintillation particles; providing an enhance neutron absorptive material; providing a binder; combining the scintillation particles, the enhance neutron absorptive material, and the binder creating a multifunctional paint; applying the multifunctional paint to the surface; and monitoring the surface for detecting radiation.

  12. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    DTIC Science & Technology

    2014-03-28

    Approved for Public Release; Distribution Unlimited Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic...non peer-reviewed journals: Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration" Report Title In... nanoscience of multifunctional materials: atomistic exploration” PI:Inna Ponomareva We have accomplished the following. 1. We have developed a set of

  13. The modular xylanase Xyn10A from Rhodothermus marinus is cell-attached, and its C-terminal domain has several putative homologues among cell-attached proteins within the phylum Bacteroidetes.

    PubMed

    Karlsson, Eva Nordberg; Hachem, Maher Abou; Ramchuran, Santosh; Costa, Hugo; Holst, Olle; Fex Svenningsen, Åsa; Hreggvidsson, Gudmundur O

    2004-12-15

    Until recently, the function of the fifth domain of the thermostable modular xylanase Xyn10A from Rhodothermus marinus was unresolved. A putative homologue to this domain was however identified in a mannanase (Man26A) from the same microorganism which raised questions regarding a common function. An extensive search of all accessible data-bases as well as the partially sequenced genomes of R. marinus and Cytophaga hutchinsonii showed that homologues of this domain were encoded by multiple genes in microorganisms in the phylum Bacteroidetes. Moreover, the domain occurred invariably at the C-termini of proteins that were predominantly extra-cellular/cell attached. A primary structure motif of three conserved regions including structurally important glycines and a proline was also identified suggesting a conserved 3D fold. This bioinformatic evidence suggested a possible role of this domain in mediating cell attachment. To confirm this theory, R. marinus was grown, and activity assays showed that the major part of the xylanase activity was connected to whole cells. Moreover, immunocytochemical detection using a Xyn10A-specific antibody proved presence of Xyn10A on the R. marinus cell surface. In the light of this, a revision of experimental data present on both Xyn10A and Man26A was performed, and the results all indicate a cell-anchoring role of the domain, suggesting that this domain represents a novel type of module that mediates cell attachment in proteins originating from members of the phylum Bacteroidetes.

  14. Multifunctional Nutrient-Binding Proteins Adapt Human Symbiotic Bacteria for Glycan Competition in the Gut by Separately Promoting Enhanced Sensing and Catalysis

    PubMed Central

    Cameron, Elizabeth A.; Kwiatkowski, Kurt J.; Lee, Byung-Hoo; Hamaker, Bruce R.; Koropatkin, Nicole M.

    2014-01-01

    ABSTRACT To compete for the dynamic stream of nutrients flowing into their ecosystem, colonic bacteria must respond rapidly to new resources and then catabolize them efficiently once they are detected. The Bacteroides thetaiotaomicron starch utilization system (Sus) is a model for nutrient acquisition by symbiotic gut bacteria, which harbor thousands of related Sus-like systems. Structural investigation of the four Sus outer membrane proteins (SusD, -E, -F, and -G) revealed that they contain a total of eight starch-binding sites that we demonstrated, using genetic and biochemical approaches, to play distinct roles in starch metabolism in vitro and in vivo in gnotobiotic mice. SusD, whose homologs are abundant in the human microbiome, is critical for the initial sensing of available starch, allowing sus transcriptional activation at much lower concentrations than without this function. In contrast, seven additional binding sites across SusE, -F, and -G are dispensable for sus activation. However, they optimize the rate of growth on starch in a manner dependent on the expression of the bacterial polysaccharide capsule, suggesting that they have evolved to offset the diffusion barrier created by this structure. These findings demonstrate how proteins with similar biochemical behavior can serve orthogonal functions during different stages of cellular adaptation to nutrients. Finally, we demonstrated in gnotobiotic mice fed a starch-rich diet that the Sus binding sites confer a competitive advantage to B. thetaiotaomicron in vivo in a manner that is dependent on other colonizing microbes. This study reveals how numerically dominant families of carbohydrate-binding proteins in the human microbiome fulfill separate and sometimes cooperative roles to optimize gut commensal bacteria for nutrient acquisition. PMID:25205092

  15. Modular Flooring System

    NASA Technical Reports Server (NTRS)

    Thate, Robert

    2012-01-01

    The modular flooring system (MFS) was developed to provide a portable, modular, durable carpeting solution for NASA fs Robotics Alliance Project fs (RAP) outreach efforts. It was also designed to improve and replace a modular flooring system that was too heavy for safe use and transportation. The MFS was developed for use as the flooring for various robotics competitions that RAP utilizes to meet its mission goals. One of these competitions, the FIRST Robotics Competition (FRC), currently uses two massive rolls of broadloom carpet for the foundation of the arena in which the robots are contained during the competition. The area of the arena is approximately 30 by 72 ft (approximately 9 by 22 m). This carpet is very cumbersome and requires large-capacity vehicles, and handling equipment and personnel to transport and deploy. The broadloom carpet sustains severe abuse from the robots during a regular three-day competition, and as a result, the carpet is not used again for competition. Similarly, broadloom carpets used for trade shows at convention centers around the world are typically discarded after only one use. This innovation provides a green solution to this wasteful practice. Each of the flooring modules in the previous system weighed 44 lb (.20 kg). The improvements in the overall design of the system reduce the weight of each module by approximately 22 lb (.10 kg) (50 %), and utilize an improved "module-to-module" connection method that is superior to the previous system. The MFS comprises 4-by-4-ft (.1.2-by- 1.2-m) carpet module assemblies that utilize commercially available carpet tiles that are bonded to a lightweight substrate. The substrate surface opposite from the carpeted surface has a module-to-module connecting interface that allows for the modules to be connected, one to the other, as the modules are constructed. This connection is hidden underneath the modules, creating a smooth, co-planar flooring surface. The modules are stacked and strapped

  16. Multifunction laser source for ground and airborne applications

    NASA Astrophysics Data System (ADS)

    Crépy, Bruno

    2011-06-01

    Multiple ground and airborne vehicles could share common and multifunctional laser modules. The host system constraints and requirements have similarities making a laser modular concept interesting. Among the desired functions, the core ones are the designation and the rangefinding capabilities. A diode pumped laser source at 1μm with a switchable OPO stage for wavelength conversion fully satisfies the designation and rangefinding tasks. Over the last years, CILAS has developed the key technologies for the improvement of the main system parameters with the imperative constraints to be International Traffic in Arm Regulations Free (ITAR Free). Particularly, this novel architecture avoids thermo electric cooler (TEC) generally used to stabilise the wavelength of the laser diode pump source within the entire operational thermal range.

  17. The multifunctional peptide synthetase performing the first step of penicillin biosynthesis in Penicillium chrysogenum is a 421,073 dalton protein similar to Bacillus brevis peptide antibiotic synthetases.

    PubMed Central

    Smith, D J; Earl, A J; Turner, G

    1990-01-01

    The nucleotide sequence of the Penicillium chrysogenum Oli13 acvA gene encoding delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase, which performs the first step in penicillin biosynthesis, has been determined. The acvA gene contains an open reading frame of 11,238 bp encoding a protein of 3746 amino acids with a predicted mol. wt of 421,073 dalton. Three domains within the protein of approximately 570 amino acids have between 38% and 43% identity with each other and share similarity with two antibiotic peptide synthetases from Bacillus brevis as well as two other enzymes capable of performing ATP-pyrophosphate exchange reactions. The acvA gene is located close to the pcbC gene encoding isopenicillin N synthetase, the enzyme for the second step of beta-lactam biosynthesis, and is transcribed in the opposite orientation to it. The intergenic region of 1107 bp from which the acvA and pcbC genes are divergently transcribed has also been sequenced. PMID:2118102

  18. The Emergence of Modularity in Biological Systems

    PubMed Central

    Lorenz, Dirk M.; Jeng, Alice; Deem, Michael W.

    2015-01-01

    In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks. There once were two watchmakers, named Hora and Tempus, who manufactured very fine watches. Both of them were highly regarded, and the phones in their workshops rang frequently — new customers were constantly calling them. However, Hora prospered, while Tempus became poorer and poorer and finally lost his shop. What was the reason? The watches the men made consisted of about 1,000 parts each. Tempus had so constructed his that if he had one partly assembled and had to put it down — to answer the phone say— it immediately fell to pieces and had to be reassembled from the elements. The better the customers liked his watches, the more they phoned him, the more difficult it became for him to find enough uninterrupted time to finish a watch. The watches that Hora made were no less complex than those of Tempus. But he had designed them so that he could put together subassemblies of about ten elements each. Ten of these subassemblies, again, could be put together into a larger subassembly; and a system of ten of the latter sub

  19. Modular arctic structures system

    SciTech Connect

    Reusswig, G. H.

    1984-12-04

    A modular and floatable offshore exploration and production platform system for use in shallow arctic waters is disclosed. A concrete base member is floated to the exploration or production site, and ballated into a predredged cavity. The cavity and base are sized to provide a stable horizontal base 30 feet below the mean water/ice plane. An exploration or production platform having a massive steel base is floated to the site and ballasted into position on the base. Together, the platform, base and ballast provide a massive gravity structure that is capable of resisting large ice and wave forces that impinge on the structure. The steel platform has a sloping hourglass profile to deflect horizontal ice loads vertically, and convert the horizontal load to a vertical tensile stress, which assists in breaking the ice as it advances toward the structure.

  20. Modular small hydro configuration

    NASA Astrophysics Data System (ADS)

    1981-09-01

    Smaller sites (those under 750 kilowatts) which previously were not attractive to develop using equipment intended for application at larger scale sites, were the focal point in the conception of a system which utilizes standard industrial components which are generally available within short procurement times. Such components were integrated into a development scheme for sites having 20 feet to 150 feet of head. The modular small hydro configuration maximizes the use of available components and minimizes modification of existing civil works. A key aspect of the development concept is the use of a vertical turbine multistage pump, used in the reverse mode as a hydraulic turbine. The configuration allows for automated operation and control of the hydroelectric facilities with sufficient flexibility for inclusion of potential hydroelectric sites into dispersed storage and generation (DSG) utility grid systems.

  1. Modular error embedding

    DOEpatents

    Sandford, II, Maxwell T.; Handel, Theodore G.; Ettinger, J. Mark

    1999-01-01

    A method of embedding auxiliary information into the digital representation of host data containing noise in the low-order bits. The method applies to digital data representing analog signals, for example digital images. The method reduces the error introduced by other methods that replace the low-order bits with auxiliary information. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user through use of a digital key. The modular error embedding method includes a process to permute the order in which the host data values are processed. The method doubles the amount of auxiliary information that can be added to host data values, in comparison with bit-replacement methods for high bit-rate coding. The invention preserves human perception of the meaning and content of the host data, permitting the addition of auxiliary data in the amount of 50% or greater of the original host data.

  2. Modular Optical PDV System

    SciTech Connect

    Araceli Rutkowski, David Esquibel

    2008-12-11

    A modular optical photon Doppler velocimetry (PDV) detector system has been developed by using readily available optical components with a 20-GHz Miteq optical detector into eight channels of single-wide modules integrated into a 3U rack unit (1U = 1.75 inches) with a common power supply. Optical fibers were precisely trimmed, welded, and timed within each unit. This system has been used to collect dynamic velocity data on various physics experiments. An optical power meter displays the laser input power to the module and optical power at the detector. An adjustable micro-electromechanical system (MEMS) optical attenuator is used to adjust the amount of unshifted light entering the detector. Front panel LEDs show the presence of power to the module. A fully loaded chassis with eight channels consumes 45 watts of power. Each chassis requires 1U spacing above and below for heat management. Modules can be easily replaced.

  3. Modular weapon control unit

    SciTech Connect

    Boccabella, M.F.; McGovney, G.N.

    1997-01-01

    The goal of the Modular Weapon Control Unit (MWCU) program was to design and develop a reconfigurable weapon controller (programmer/sequencer) that can be adapted to different weapon systems based on the particular requirements for that system. Programmers from previous systems are conceptually the same and perform similar tasks. Because of this commonality and the amount of re-engineering necessary with the advent of every new design, the idea of a modular, adaptable system has emerged. Also, the controller can be used in more than one application for a specific weapon system. Functionality has been divided into a Processor Module (PM) and an Input/Output Module (IOM). The PM will handle all operations that require calculations, memory, and timing. The IOM will handle interfaces to the rest of the system, input level shifting, output drive capability, and detection of interrupt conditions. Configuration flexibility is achieved in two ways. First, the operation of the PM is determined by a surface mount Read-Only Memory (ROM). Other surface-mount components can be added or neglected as necessary for functionality. Second, IOMs consist of configurable input buffers, configurable output drivers, and configurable interrupt generation. Further, these modules can be added singly or in groups to a Processor Module to achieve the required I/O configuration. The culmination of this LDRD was the building of both Processor Module and Input/Output Module. The MWCU was chosen as a test system to evaluate Low-Temperature Co-fired Ceramic (LTCC) technology, desirable for high component density and good thermal characteristics.

  4. Identification of multifunctional peptides from human milk.

    PubMed

    Mandal, Santi M; Bharti, Rashmi; Porto, William F; Gauri, Samiran S; Mandal, Mahitosh; Franco, Octavio L; Ghosh, Ananta K

    2014-06-01

    Pharmaceutical industries have renewed interest in screening multifunctional bioactive peptides as a marketable product in health care applications. In this context, several animal and plant peptides with potential bioactivity have been reported. Milk proteins and peptides have received much attention as a source of health-enhancing components to be incorporated into nutraceuticals and functional foods. By using this source, 24 peptides have been fractionated and purified from human milk using RP-HPLC. Multifunctional roles including antimicrobial, antioxidant and growth stimulating activity have been evaluated in all 24 fractions. Nevertheless, only four fractions show multiple combined activities among them. Using a proteomic approach, two of these four peptides have been identified as lactoferrin derived peptide and kappa casein short chain peptide. Lactoferrin derived peptide (f8) is arginine-rich and kappa casein derived (f12) peptide is proline-rich. Both peptides (f8 and f12) showed antimicrobial activities against both Gram-positive and Gram-negative bacteria. Fraction 8 (f8) exhibits growth stimulating activity in 3T3 cell line and f12 shows higher free radical scavenging activity in comparison to other fractions. Finally, both peptides were in silico evaluated and some insights into their mechanism of action were provided. Thus, results indicate that these identified peptides have multiple biological activities which are valuable for the quick development of the neonate and may be considered as potential biotechnological products for nutraceutical industry. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L (CbpL) Contributing to Pneumococcal Pathogenesis

    PubMed Central

    Gutiérrez-Fernández, Javier; Saleh, Malek; Alcorlo, Martín; Gómez-Mejía, Alejandro; Pantoja-Uceda, David; Treviño, Miguel A.; Voß, Franziska; Abdullah, Mohammed R.; Galán-Bartual, Sergio; Seinen, Jolien; Sánchez-Murcia, Pedro A.; Gago, Federico; Bruix, Marta; Hammerschmidt, Sven; Hermoso, Juan A.

    2016-01-01

    The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca2+-binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp_Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus. PMID:27917891

  6. Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L (CbpL) Contributing to Pneumococcal Pathogenesis

    NASA Astrophysics Data System (ADS)

    Gutiérrez-Fernández, Javier; Saleh, Malek; Alcorlo, Martín; Gómez-Mejía, Alejandro; Pantoja-Uceda, David; Treviño, Miguel A.; Voß, Franziska; Abdullah, Mohammed R.; Galán-Bartual, Sergio; Seinen, Jolien; Sánchez-Murcia, Pedro A.; Gago, Federico; Bruix, Marta; Hammerschmidt, Sven; Hermoso, Juan A.

    2016-12-01

    The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca2+-binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp_Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.

  7. Pirin1 (PRN1) is a multifunctional protein that regulates quercetin, and impacts specific light and UV responses in the seed-to-seedling transition of Arabidopsis thaliana.

    PubMed

    Orozco-Nunnelly, Danielle A; Muhammad, Durreshahwar; Mezzich, Raquel; Lee, Bao-Shiang; Jayathilaka, Lasanthi; Kaufman, Lon S; Warpeha, Katherine M

    2014-01-01

    Pirins are cupin-fold proteins, implicated in apoptosis and cellular stress in eukaryotic organisms. Pirin1 (PRN1) plays a role in seed germination and transcription of a light- and ABA-regulated gene under specific conditions in the model plant system Arabidopsis thaliana. Herein, we describe that PRN1 possesses previously unreported functions that can profoundly affect early growth, development, and stress responses. In vitro-translated PRN1 possesses quercetinase activity. When PRN1 was incubated with G-protein-α subunit (GPA1) in the inactive conformation (GDP-bound), quercetinase activity was observed. Quercetinase activity was not observed when PRN1 was incubated with GPA1 in the active form (GTP-bound). Dark-grown prn1 mutant seedlings produced more quercetin after UV (317 nm) induction, compared to levels observed in wild type (WT) seedlings. prn1 mutant seedlings survived a dose of high-energy UV (254 nm) radiation that killed WT seedlings. prn1 mutant seedlings grown for 3 days in continuous white light display disoriented hypocotyl growth compared to WT, but hypocotyls of dark-grown prn1 seedlings appeared like WT. prn1 mutant seedlings transformed with GFP constructs containing the native PRN1 promoter and full ORF (PRN1::PRN1-GFP) were restored to WT responses, in that they did not survive UV (254 nm), and there was no significant hypocotyl disorientation in response to white light. prn1 mutants transformed with PRN1::PRN1-GFP were observed by confocal microscopy, where expression in the cotyledon epidermis was largely localized to the nucleus, adjacent to the nucleus, and diffuse and punctate expression occurred within some cells. WT seedlings transformed with the 35S::PRN1-GFP construct exhibited widespread expression in the epidermis of the cotyledon, also with localization in the nucleus. PRN1 may play a critical role in cellular quercetin levels and influence light- or hormonal-directed early development.

  8. Diffusible Signal Factor (DSF) Synthase RpfF of Xylella fastidiosa Is a Multifunction Protein Also Required for Response to DSF

    PubMed Central

    Ionescu, Michael; Baccari, Clelia; Da Silva, Aline Maria; Garcia, Angelica; Yokota, Kenji

    2013-01-01

    Xylella fastidiosa, like related Xanthomonas species, employs an Rpf cell-cell communication system consisting of a diffusible signal factor (DSF) synthase, RpfF, and a DSF sensor, RpfC, to coordinate expression of virulence genes. While phenotypes of a ΔrpfF strain in Xanthomonas campestris could be complemented by its own DSF, the DSF produced by X. fastidiosa (XfDSF) did not restore expression of the XfDSF-dependent genes hxfA and hxfB to a ΔrpfF strain of X. fastidiosa, suggesting that RpfF is involved in XfDSF sensing or XfDSF-dependent signaling. To test this conjecture, rpfC and rpfF of X. campestris were replaced by those of X. fastidiosa, and the contribution of each gene to the induction of a X. campestris DSF-dependent gene was assessed. As in X. fastidiosa, XfDSF-dependent signaling required both X. fastidiosa proteins RpfF and RpfC. RpfF repressed RpfC signaling activity, which in turn was derepressed by XfDSF. A mutated X. fastidiosa RpfF protein with two substitutions of glutamate to alanine in its active site was incapable of XfDSF production yet enabled a response to XfDSF, indicating that XfDSF production and the response to XfDSF are two separate functions in which RpfF is involved. This mutant was also hypervirulent to grape, demonstrating the antivirulence effects of XfDSF itself in X. fastidiosa. The Rpf system of X. fastidiosa is thus a novel example of a quorum-sensing signal synthase that is also involved in the response to the signal molecule that it synthesizes. PMID:24056101

  9. Diffusible signal factor (DSF) synthase RpfF of Xylella fastidiosa is a multifunction protein also required for response to DSF.

    PubMed

    Ionescu, Michael; Baccari, Clelia; Da Silva, Aline Maria; Garcia, Angelica; Yokota, Kenji; Lindow, Steven E

    2013-12-01

    Xylella fastidiosa, like related Xanthomonas species, employs an Rpf cell-cell communication system consisting of a diffusible signal factor (DSF) synthase, RpfF, and a DSF sensor, RpfC, to coordinate expression of virulence genes. While phenotypes of a ΔrpfF strain in Xanthomonas campestris could be complemented by its own DSF, the DSF produced by X. fastidiosa (XfDSF) did not restore expression of the XfDSF-dependent genes hxfA and hxfB to a ΔrpfF strain of X. fastidiosa, suggesting that RpfF is involved in XfDSF sensing or XfDSF-dependent signaling. To test this conjecture, rpfC and rpfF of X. campestris were replaced by those of X. fastidiosa, and the contribution of each gene to the induction of a X. campestris DSF-dependent gene was assessed. As in X. fastidiosa, XfDSF-dependent signaling required both X. fastidiosa proteins RpfF and RpfC. RpfF repressed RpfC signaling activity, which in turn was derepressed by XfDSF. A mutated X. fastidiosa RpfF protein with two substitutions of glutamate to alanine in its active site was incapable of XfDSF production yet enabled a response to XfDSF, indicating that XfDSF production and the response to XfDSF are two separate functions in which RpfF is involved. This mutant was also hypervirulent to grape, demonstrating the antivirulence effects of XfDSF itself in X. fastidiosa. The Rpf system of X. fastidiosa is thus a novel example of a quorum-sensing signal synthase that is also involved in the response to the signal molecule that it synthesizes.

  10. Multi-functional composite structures

    DOEpatents

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2010-04-27

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  11. Multi-functional composite structures

    DOEpatents

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2004-10-19

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  12. Multifunctional Thin Film Biomatrice Biosensor in a Degradable Scaffold Containing Bone Morphogenetic Protein-2 (BMP-2) for Controlled Release in Skeletal Tissue Engineering

    NASA Astrophysics Data System (ADS)

    McDaniel, Harvey; Lomax, Linda

    2001-03-01

    Bone morphonogenetic proteins (BMP-2) have been under investigation for three decades. Deminerialized bone and extracts of deminerialized bone are o steoinductive with a temporal sequence of bone induction. Native and recombi nant BMP's have shown the ability, thru growth and differentiative factors t o induce de novo bone formation both invitro and invivo. Their principle fun ction is to induce transformation of undifferentiated mesenchymal cells into osteoblasts. Native and recombinant BMP's, when purified and used without carrier disp erse after implantation and exert no effect on bone induction. The delivery system provides the missing component to successsfully applying osteogenic p roteins for clinical need. Biological and physio-chemical properties are str ictly adhered tofor a successful delivery system. The BMP delivery system ca rrier for osteo inductive payload provided; 1)non tumorgenic genecity, 2) no n immunogenecity, 3) water insoluble, 4) biosorbability with predictable enz ymatic degradation, and 5) an optimized surface for compatibility, cell migr ation and attachment with a negative surface change that encouraged target c ell attachment. Being a controlled Release System, it binded the proteins wi th predictible BMP released kinetics. Porosity with interconnecting voids pr otected the BMP from noon specific proteolysis and promoted rapid vascular a nd mesenchymal invasion. Far wide ranging clinical applications of mechanica l and biofunctional requirements were met with the BMP delivery system. Cohe sion and malleability were reqiured forcontour augmentation, and reconstruct ion of the discontinuity defects, prevented dislocation and retained the sha pe and bone replaced the system. Biological systems have elastic activity associated with them. The activi ty was current associated with a time dependant biological/biochemical react ion (enzymic activity). Bioelectric phoenomena associated with charged molec ules in a biologic structure caused

  13. Multifunctional reactive nanocomposite materials

    NASA Astrophysics Data System (ADS)

    Stamatis, Demitrios

    Many multifunctional nanocomposite materials have been developed for use in propellants, explosives, pyrotechnics, and reactive structures. These materials exhibit high reaction rates due to their developed reaction interfacial area. Two applications addressed in this work include nanocomposite powders prepared by arrested reactive milling (ARM) for burn rate modifiers and reactive structures. In burn rate modifiers, addition of reactive nanocomposite powders to aluminized propellants increases the burn rate of aluminum and thus the overall reaction rate of an energetic formulation. Replacing only a small fraction of aluminum by 8Al·MoO3 and 2B·Ti nanocomposite powders enhances the reaction rate with little change to the thermodynamic performance of the formulation; both the rate of pressure rise and maximum pressure measured in the constant volume explosion test increase. For reactive structures, nanocomposite powders with bulk compositions of 8Al·MoO3, 12Al·MoO3, and 8Al·3CuO were prepared by ARM and consolidated using a uniaxial die. Consolidated samples had densities greater than 90% of theoretical maximum density while maintaining their high reactivity. Pellets prepared using 8Al·MoO3 powders were ignited by a CO2 laser. Ignition delays increased at lower laser powers and greater pellet densities. A simplified numerical model describing heating and thermal initiation of the reactive pellets predicted adequately the observed effects of both laser power and pellet density on the measured ignition delays. To investigate the reaction mechanisms in nanocomposite thermites, two types of nanocomposite reactive materials with the same bulk compositions 8Al·MoO3 were prepared by different methods. One of the materials was manufactured by ARM and the other, so called metastable interstitial composite (MIC), by mixing of nano-scaled individual powders. Clear differences in the low-temperature redox reactions, welldetectable by differential scanning calorimetry

  14. Modular structure of chromosomal proteins HMG-14 and HMG-17: Definition of a transcriptional enhancement domain distinct from the nucleosomal binding domain

    SciTech Connect

    Trieschmann, L.; Postnikov, Y.V.; Rickers, A.; Bustin, M.

    1995-12-01

    This report describes how deletion mutants and peptides were used to identify the transcriptional enhancement domain and the nucleosome binding domain of two chromosomal proteins, HMG-14 and HMG-17. The research indicates that mutations involving C-terminal amino acids significantly reduces the ability of the nucleoproteins to enhance transcription from chromatin templates. 42 refs., 6 figs., 1 tab.

  15. Multifunctional Prenylated Peptides for Live Cell Analysis

    PubMed Central

    Wollack, James W.; Zeliadt, Nicholette A.; Mullen, Daniel G.; Amundson, Gregg; Geier, Suzanne; Falkum, Stacy; Wattenberg, Elizabeth V.; Barany, George; Distefano, Mark D.

    2009-01-01

    Protein prenylation is a common post-translational modification present in eukaryotic cells. Many key proteins involved in signal transduction pathways are prenylated and inhibition of prenylation can be useful as a therapeutic intervention. While significant progress has been made in understanding protein prenylation in vitro, we have been interested in studying this process in living cells, including the question of where prenylated molecules localize. Here, we describe the synthesis and live cell analysis of a series of fluorescently labeled multifunctional peptides, based on the C-terminus of the naturally prenylated protein CDC42. A synthetic route was developed that features a key Acm to Scm protecting group conversion. This strategy was compatible with acid-sensitive isoprenoid moieties, and allowed incorporation of an appropriate fluorophore as well as a cell-penetrating sequence (penetratin). These peptides are able to enter cells through different mechanisms, depending on the presence or absence of the penetratin vehicle and the nature of the prenyl group attached. Interestingly, prenylated peptides lacking penetratin are able to enter cells freely through an energy-independent process, and localize in a perinuclear fashion. This effect extends to a prenylated peptide that includes a full “CAAX box” sequence (specifically, CVLL). Hence, these peptides open the door for studies of protein prenylation in living cells, including enzymatic processing and intracellular peptide trafficking. Moreover, the synthetic strategy developed here should be useful for the assembly of other types of peptides that contain acid sensitive functionalities. PMID:19425596

  16. Studies in Multifunctional Drug Development: Preparation and Evaluation of 11beta-Substituted Estradiol-Drug Conjugates, Cell Membrane Targeting Imaging Agents, and Target Multifunctional Nanoparticles

    NASA Astrophysics Data System (ADS)

    Dao, KinhLuan Lenny D.

    Cancer is the second leading cause of death after cardiovascular disease in the United State. Despite extensive research in development of antitumor drugs, most of these therapeutic entities often possess nonspecific toxicity, thus they can only be used to treat tumors in higher doses or more frequently. Because of the cytotoxicity and severe side effects, the drug therapeutic window normally is limited. Beside the toxicity issue, antitumor drug are also not selectively taken up by tumor cells, thus the necessitating concentrations that would eradicate the tumor can often not be used. In addition, tumor cells tend to develop resistance against the anticancer drugs after prolonged treatment. Therefore, alleviating the systemic cytotoxicity and side effects, improving in tumor selectivity, high potency, and therapeutic efficacy are still major obstacles in the area of anticancer drug development. A more promising approach for developing a selective agent for cancer is to conjugate a potent therapeutic drug, or an imaging agent with a targeting group, such as antibody or a high binding-specificity small molecule, that selectively recognize the overexpressed antigens or proteins on tumor cells. My research combines several approaches to describe this strategy via using different targeting molecules to different diseases, as well as different potent cytotoxic drugs for different therapies. Three studies related to the preparation and biological evaluation of new therapeutic agents, such as estradiol-drug hybrids, cell membrane targeted molecular imaging agents, and multifunctional NPs will be discussed. The preliminary results of these studies indicated that our new reagents achieved their initial objectives and can be further improved for optimized synthesis and in vivo experiments. The first study describes the method in which we employed a modular assembly approach to synthesize a novel 11beta-substituted steroidal anti-estrogen. The key intermediate was synthesized

  17. Structural and Functional Modularity of the Orange Carotenoid Protein: Distinct Roles for the N- and C-Terminal Domains in Cyanobacterial Photoprotection[C][W

    PubMed Central

    Leverenz, Ryan L.; Jallet, Denis; Li, Ming-De; Mathies, Richard A.; Kirilovsky, Diana; Kerfeld, Cheryl A.

    2014-01-01

    The orange carotenoid protein (OCP) serves as a sensor of light intensity and an effector of phycobilisome (PB)–associated photoprotection in cyanobacteria. Structurally, the OCP is composed of two distinct domains spanned by a single carotenoid chromophore. Functionally, in response to high light, the OCP converts from a dark-stable orange form, OCPO, to an active red form, OCPR. The C-terminal domain of the OCP has been implicated in the dynamic response to light intensity and plays a role in switching off the OCP’s photoprotective response through its interaction with the fluorescence recovery protein. The function of the N-terminal domain, which is uniquely found in cyanobacteria, is unclear. To investigate its function, we isolated the N-terminal domain in vitro using limited proteolysis of native OCP. The N-terminal domain retains the carotenoid chromophore; this red carotenoid protein (RCP) has constitutive PB fluorescence quenching activity comparable in magnitude to that of active, full-length OCPR. A comparison of the spectroscopic properties of the RCP with OCPR indicates that critical protein–chromophore interactions within the C-terminal domain are weakened in the OCPR form. These results suggest that the C-terminal domain dynamically regulates the photoprotective activity of an otherwise constitutively active carotenoid binding N-terminal domain. PMID:24399299

  18. Spacecraft Modularity for Serviceable Satellites

    NASA Technical Reports Server (NTRS)

    Rossetti, Dino; Keer, Beth; Panek, John; Reed, Benjamin; Cepollina, Frank; Ritter, Robert

    2015-01-01

    Satellite servicing has been a proven capability of NASA since the first servicing missions in the 1980s with astronauts on the space shuttle. This capability enabled the on-orbit assembly of the International Space Station (ISS) and saved the Hubble Space Telescope (HST) mission following the discovery of the flawed primary mirror. The effectiveness and scope of servicing opportunities, especially using robotic servicers, is a function of how cooperative a spacecraft is. In this paper, modularity will be presented as a critical design aspect for a spacecraft that is cooperative from a servicing perspective. Different features of modularity are discussed using examples from HST and the Multimission Modular Spacecraft (MMS) program from the 1980s and 1990s. The benefits of modularity will be presented including those directly related to servicing and those outside of servicing including reduced costs and increased flexibility. The new Reconfigurable Operational spacecraft for Science and Exploration (ROSE) concept is introduced as an affordable implementation of modularity that provides cost savings and flexibility. Key aspects of the ROSE architecture are discussed such as the module design and the distributed avionics architecture. The ROSE concept builds on the experience from MMS and due to its modularity, would be highly suitable as a future client for on-orbit servicing.

  19. Modular Approach to Spintronics.

    PubMed

    Camsari, Kerem Yunus; Ganguly, Samiran; Datta, Supriyo

    2015-06-11

    There has been enormous progress in the last two decades, effectively combining spintronics and magnetics into a powerful force that is shaping the field of memory devices. New materials and phenomena continue to be discovered at an impressive rate, providing an ever-increasing set of building blocks that could be exploited in designing transistor-like functional devices of the future. The objective of this paper is to provide a quantitative foundation for this building block approach, so that new discoveries can be integrated into functional device concepts, quickly analyzed and critically evaluated. Through careful benchmarking against available theory and experiment we establish a set of elemental modules representing diverse materials and phenomena. These elemental modules can be integrated seamlessly to model composite devices involving both spintronic and nanomagnetic phenomena. We envision the library of modules to evolve both by incorporating new modules and by improving existing modules as the field progresses. The primary contribution of this paper is to establish the ground rules or protocols for a modular approach that can build a lasting bridge between materials scientists and circuit designers in the field of spintronics and nanomagnetics.

  20. Modular Isotopic Thermoelectric Generator

    SciTech Connect

    Schock, Alfred

    1981-04-03

    Advanced RTG concepts utilizing improved thermoelectric materials and converter concepts are under study at Fairchild for DOE. The design described here is based on DOE's newly developed radioisotope heat source, and on an improved silicon-germanium material and a multicouple converter module under development at Syncal. Fairchild's assignment was to combine the above into an attractive power system for use in space, and to assess the specific power and other attributes of that design. The resultant design is highly modular, consisting of standard RTG slices, each producing ~24 watts at the desired output voltage of 28 volt. Thus, the design could be adapted to various space missions over a wide range of power levels, with little or no redesign. Each RTG slice consists of a 250-watt heat source module, eight multicouple thermoelectric modules, and standard sections of insulator, housing, radiator fins, and electrical circuit. The design makes it possible to check each thermoelectric module for electrical performance, thermal contact, leaktightness, and performance stability, after the generator is fully assembled; and to replace any deficient modules without disassembling the generator or perturbing the others. The RTG end sections provide the spring-loaded supports required to hold the free-standing heat source stack together during launch vibration. Details analysis indicates that the design offers a substantial improvement in specific power over the present generator of RTGs, using the same heat source modules. There are three copies in the file.

  1. Modular Approach to Spintronics

    PubMed Central

    Camsari, Kerem Yunus; Ganguly, Samiran; Datta, Supriyo

    2015-01-01

    There has been enormous progress in the last two decades, effectively combining spintronics and magnetics into a powerful force that is shaping the field of memory devices. New materials and phenomena continue to be discovered at an impressive rate, providing an ever-increasing set of building blocks that could be exploited in designing transistor-like functional devices of the future. The objective of this paper is to provide a quantitative foundation for this building block approach, so that new discoveries can be integrated into functional device concepts, quickly analyzed and critically evaluated. Through careful benchmarking against available theory and experiment we establish a set of elemental modules representing diverse materials and phenomena. These elemental modules can be integrated seamlessly to model composite devices involving both spintronic and nanomagnetic phenomena. We envision the library of modules to evolve both by incorporating new modules and by improving existing modules as the field progresses. The primary contribution of this paper is to establish the ground rules or protocols for a modular approach that can build a lasting bridge between materials scientists and circuit designers in the field of spintronics and nanomagnetics. PMID:26066079

  2. The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains

    PubMed Central

    1996-01-01

    Mutations in the Caenorhabditis elegans gene unc-89 result in nematodes having disorganized muscle structure in which thick filaments are not organized into A-bands, and there are no M-lines. Beginning with a partial cDNA from the C. elegans sequencing project, we have cloned and sequenced the unc-89 gene. An unc-89 allele, st515, was found to contain an 84-bp deletion and a 10-bp duplication, resulting in an in- frame stop codon within predicted unc-89 coding sequence. Analysis of the complete coding sequence for unc-89 predicts a novel 6,632 amino acid polypeptide consisting of sequence motifs which have been implicated in protein-protein interactions. UNC-89 begins with 67 residues of unique sequences, SH3, dbl/CDC24, and PH domains, 7 immunoglobulins (Ig) domains, a putative KSP-containing multiphosphorylation domain, and ends with 46 Ig domains. A polyclonal antiserum raised to a portion of unc-89 encoded sequence reacts to a twitchin-sized polypeptide from wild type, but truncated polypeptides from st515 and from the amber allele e2338. By immunofluorescent microscopy, this antiserum localizes to the middle of A-bands, consistent with UNC-89 being a structural component of the M-line. Previous studies indicate that myofilament lattice assembly begins with positional cues laid down in the basement membrane and muscle cell membrane. We propose that the intracellular protein UNC-89 responds to these signals, localizes, and then participates in assembling an M-line. PMID:8603916

  3. Multifunctional nanoparticles for cancer immunotherapy

    PubMed Central

    Saleh, Tayebeh; Shojaosadati, Seyed Abbas

    2016-01-01

    ABSTRACT During the last decades significant progress has been made in the field of cancer immunotherapy. However, cancer vaccines have not been successful in clinical trials due to poor immunogenicity of antigen, limitations of safety associated with traditional systemic delivery as well as the complex regulation of the immune system in tumor microenvironment. In recent years, nanotechnology-based delivery systems have attracted great interest in the field of immunotherapy since they provide new opportunities to fight the cancer. In particular, for delivery of cancer vaccines, multifunctional nanoparticles present many advantages such as targeted delivery to immune cells, co-delivery of therapeutic agents, reduced adverse outcomes, blocked immune checkpoint molecules, and amplify immune activation via the use of stimuli-responsive or immunostimulatory materials. In this review article, we highlight recent progress and future promise of multifunctional nanoparticles that have been applied to enhance the efficiency of cancer vaccines. PMID:26901287

  4. Multifunctional magnetic nanoparticles: design, synthesis, and biomedical applications.

    PubMed

    Gao, Jinhao; Gu, Hongwei; Xu, Bing

    2009-08-18

    The combination of nanotechnology and molecular biology has developed into an emerging research area: nanobiotechnology. Magnetic nanoparticles are well-established nanomaterials that offer controlled size, ability to be manipulated externally, and enhancement of contrast in magnetic resonance imaging (MRI). As a result, these nanoparticles could have many applications in biology and medicine, including protein purification, drug delivery, and medical imaging. Because of the potential benefits of multimodal functionality in biomedical applications, researchers would like to design and fabricate multifunctional magnetic nanoparticles. Currently, there are two strategies to fabricate magnetic nanoparticle-based multifunctional nanostructures. The first, molecular functionalization, involves attaching antibodies, proteins, and dyes to the magnetic nanoparticles. The other method integrates the magnetic nanoparticles with other functional nanocomponents, such as quantum dots (QDs) or metallic nanoparticles. Because they can exhibit several features synergistically and deliver more than one function simultaneously, such multifunctional magnetic nanoparticles could have unique advantages in biomedical applications. In this Account, we review examples of the design and biomedical application of multifunctional magnetic nanoparticles. After their conjugation with proper ligands, antibodies, or proteins, the biofunctional magnetic nanoparticles exhibit highly selective binding. These results indicate that such nanoparticles could be applied to biological medical problems such as protein purification, bacterial detection, and toxin decorporation. The hybrid nanostructures, which combine magnetic nanoparticles with other nanocomponents, exhibit paramagnetism alongside features such as fluorescence or enhanced optical contrast. Such structures could provide a platform for enhanced medical imaging and controlled drug delivery. We expect that the combination of unique structural

  5. Multifunctional Information Distribution System (MIDS)

    DTIC Science & Technology

    2015-12-01

    Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-554 Multifunctional Information Distribution System (MIDS) As of FY 2017 President’s Budget...Program Office Estimate RDT&E - Research, Development, Test, and Evaluation SAR - Selected Acquisition Report SCP - Service Cost Position TBD - To Be... selectable levels Multiple selectable levels >=200 with IF for 1000 200 with IF Multiple selectable levels LVT(2) Multiple selectable levels Multiple

  6. Effective Design of Multifunctional Peptides by Combining Compatible Functions

    PubMed Central

    Diener, Christian; Garza Ramos Martínez, Georgina; Moreno Blas, Daniel; Castillo González, David A.; Corzo, Gerardo; Castro-Obregon, Susana; Del Rio, Gabriel

    2016-01-01

    Multifunctionality is a common trait of many natural proteins and peptides, yet the rules to generate such multifunctionality remain unclear. We propose that the rules defining some protein/peptide functions are compatible. To explore this hypothesis, we trained a computational method to predict cell-penetrating peptides at the sequence level and learned that antimicrobial peptides and DNA-binding proteins are compatible with the rules of our predictor. Based on this finding, we expected that designing peptides for CPP activity may render AMP and DNA-binding activities. To test this prediction, we designed peptides that embedded two independent functional domains (nuclear localization and yeast pheromone activity), linked by optimizing their composition to fit the rules characterizing cell-penetrating peptides. These peptides presented effective cell penetration, DNA-binding, pheromone and antimicrobial activities, thus confirming the effectiveness of our computational approach to design multifunctional peptides with potential therapeutic uses. Our computational implementation is available at http://bis.ifc.unam.mx/en/software/dcf. PMID:27096600

  7. Shortened OR time and decreased patient risk through use of a modular surgical instrument with artificial intelligence.

    PubMed

    Miller, David J; Nelson, Carl A; Oleynikov, Dmitry

    2009-05-01

    With a limited number of access ports, minimally invasive surgery (MIS) often requires the complete removal of one tool and reinsertion of another. Modular or multifunctional tools can be used to avoid this step. In this study, soft computing techniques are used to optimally arrange a modular tool's functional tips, allowing surgeons to deliver treatment of improved quality in less time, decreasing overall cost. The investigators watched University Medical Center surgeons perform MIS procedures (e.g., cholecystectomy and Nissen fundoplication) and recorded the procedures to digital video. The video was then used to analyze the types of instruments used, the duration of each use, and the function of each instrument. These data were aggregated with fuzzy logic techniques using four membership functions to quantify the overall usefulness of each tool. This allowed subsequent optimization of the arrangement of functional tips within the modular tool to decrease overall time spent changing instruments during simulated surgical procedures based on the video recordings. Based on a prototype and a virtual model of a multifunction laparoscopic tool designed by the investigators that can interchange six different instrument tips through the tool's shaft, the range of tool change times is approximately 11-13 s. Using this figure, estimated time savings for the procedures analyzed ranged from 2.5 to over 32 min, and on average, total surgery time can be reduced by almost 17% by using the multifunction tool.

  8. Modular Stirling Radioisotope Generator

    NASA Technical Reports Server (NTRS)

    Schmitz, Paul C.; Mason, Lee S.; Schifer, Nicholas A.

    2015-01-01

    High efficiency radioisotope power generators will play an important role in future NASA space exploration missions. Stirling Radioisotope Generators (SRG) have been identified as a candidate generator technology capable of providing mission designers with an efficient, high specific power electrical generator. SRGs high conversion efficiency has the potential to extend the limited Pu-238 supply when compared with current Radioisotope Thermoelectric Generators (RTG). Due to budgetary constraints, the Advanced Stirling Radioisotope Generator (ASRG) was canceled in the fall of 2013. Over the past year a joint study by NASA and DOE called the Nuclear Power Assessment Study (NPAS) recommended that Stirling technologies continue to be explored. During the mission studies of the NPAS, spare SRGs were sometimes required to meet mission power system reliability requirements. This led to an additional mass penalty and increased isotope consumption levied on certain SRG-based missions. In an attempt to remove the spare power system, a new generator architecture is considered which could increase the reliability of a Stirling generator and provide a more fault-tolerant power system. This new generator called the Modular Stirling Radioisotope Generator (MSRG) employs multiple parallel Stirling convertor/controller strings, all of which share the heat from the General Purpose Heat Source (GPHS) modules. For this design, generators utilizing one to eight GPHS modules were analyzed, which provide about 50 to 450 watts DC to the spacecraft, respectively. Four Stirling convertors are arranged around each GPHS module resulting in from 4 to 32 Stirling/controller strings. The convertors are balanced either individually or in pairs, and are radiatively coupled to the GPHS modules. Heat is rejected through the housing/radiator which is similar in construction to the ASRG. Mass and power analysis for these systems indicate that specific power may be slightly lower than the ASRG and

  9. Modular Stirling Radioisotope Generator

    NASA Technical Reports Server (NTRS)

    Schmitz, Paul C.; Mason, Lee S.; Schifer, Nicholas A.

    2016-01-01

    High-efficiency radioisotope power generators will play an important role in future NASA space exploration missions. Stirling Radioisotope Generators (SRGs) have been identified as a candidate generator technology capable of providing mission designers with an efficient, high-specific-power electrical generator. SRGs high conversion efficiency has the potential to extend the limited Pu-238 supply when compared with current Radioisotope Thermoelectric Generators (RTGs). Due to budgetary constraints, the Advanced Stirling Radioisotope Generator (ASRG) was canceled in the fall of 2013. Over the past year a joint study by NASA and the Department of Energy (DOE) called the Nuclear Power Assessment Study (NPAS) recommended that Stirling technologies continue to be explored. During the mission studies of the NPAS, spare SRGs were sometimes required to meet mission power system reliability requirements. This led to an additional mass penalty and increased isotope consumption levied on certain SRG-based missions. In an attempt to remove the spare power system, a new generator architecture is considered, which could increase the reliability of a Stirling generator and provide a more fault-tolerant power system. This new generator called the Modular Stirling Radioisotope Generator (MSRG) employs multiple parallel Stirling convertor/controller strings, all of which share the heat from the General Purpose Heat Source (GPHS) modules. For this design, generators utilizing one to eight GPHS modules were analyzed, which provided about 50 to 450 W of direct current (DC) to the spacecraft, respectively. Four Stirling convertors are arranged around each GPHS module resulting in from 4 to 32 Stirling/controller strings. The convertors are balanced either individually or in pairs, and are radiatively coupled to the GPHS modules. Heat is rejected through the housing/radiator, which is similar in construction to the ASRG. Mass and power analysis for these systems indicate that specific

  10. Transglutaminase type 2: A multifunctional protein chaperone?

    PubMed Central

    Rossin, Federica; D’Eletto, Manuela; Farrace, Maria Grazia; Piacentini, Mauro

    2014-01-01

    Macroautophagy selectively degrades dysfunctional mitochondria by a process known as mitophagy. The purpose of the study published in Cell Death and Differentiation was to investigate the involvement of transglutaminase 2 (TG2) in the turnover and degradation of damaged mitochondria and its effects on cell metabolism. PMID:27308365

  11. Implantable, multifunctional, bioresorbable optics

    PubMed Central

    Tao, Hu; Kainerstorfer, Jana M.; Siebert, Sean M.; Pritchard, Eleanor M.; Sassaroli, Angelo; Panilaitis, Bruce J. B.; Brenckle, Mark A.; Amsden, Jason J.; Levitt, Jonathan; Fantini, Sergio; Kaplan, David L.; Omenetto, Fiorenzo G.

    2012-01-01

    Advances in personalized medicine are symbiotic with the development of novel technologies for biomedical devices. We present an approach that combines enhanced imaging of malignancies, therapeutics, and feedback about therapeutics in a single implantable, biocompatible, and resorbable device. This confluence of form and function is accomplished by capitalizing on the unique properties of silk proteins as a mechanically robust, biocompatible, optically clear biomaterial matrix that can house, stabilize, and retain the function of therapeutic components. By developing a form of high-quality microstructured optical elements, improved imaging of malignancies and of treatment monitoring can be achieved. The results demonstrate a unique family of devices for in vitro and in vivo use that provide functional biomaterials with built-in optical signal and contrast enhancement, demonstrated here with simultaneous drug delivery and feedback about drug delivery with no adverse biological effects, all while slowly degrading to regenerate native tissue. PMID:23150544

  12. Modular Power Standard for Space Explorations Missions

    NASA Technical Reports Server (NTRS)

    Oeftering, Richard C.; Gardner, Brent G.

    2016-01-01

    Future human space exploration will most likely be composed of assemblies of multiple modular spacecraft elements with interconnected electrical power systems. An electrical system composed of a standardized set modular building blocks provides significant development, integration, and operational cost advantages. The modular approach can also provide the flexibility to configure power systems to meet the mission needs. A primary goal of the Advanced Exploration Systems (AES) Modular Power System (AMPS) project is to establish a Modular Power Standard that is needed to realize these benefits. This paper is intended to give the space exploration community a "first look" at the evolving Modular Power Standard and invite their comments and technical contributions.

  13. Eigenvalue Spectra of Modular Networks

    NASA Astrophysics Data System (ADS)

    Peixoto, Tiago P.

    2013-08-01

    A large variety of dynamical processes that take place on networks can be expressed in terms of the spectral properties of some linear operator which reflects how the dynamical rules depend on the network topology. Often, such spectral features are theoretically obtained by considering only local node properties, such as degree distributions. Many networks, however, possess large-scale modular structures that can drastically influence their spectral characteristics and which are neglected in such simplified descriptions. Here, we obtain in a unified fashion the spectrum of a large family of operators, including the adjacency, Laplacian, and normalized Laplacian matrices, for networks with generic modular structure, in the limit of large degrees. We focus on the conditions necessary for the merging of the isolated eigenvalues with the continuous band of the spectrum, after which the planted modular structure can no longer be easily detected by spectral methods. This is a crucial transition point which determines when a modular structure is strong enough to affect a given dynamical process. We show that this transition happens in general at different points for the different matrices, and hence the detectability threshold can vary significantly, depending on the operator chosen. Equivalently, the sensitivity to the modular structure of the different dynamical processes associated with each matrix will be different, given the same large-scale structure present in the network. Furthermore, we show that, with the exception of the Laplacian matrix, the different transitions coalesce into the same point for the special case where the modules are homogeneous but separate otherwise.

  14. A Detailed Modular Analysis of Heat-Shock Protein Dynamics under Acute and Chronic Stress and Its Implication in Anxiety Disorders

    PubMed Central

    Sriram, K.; Rodriguez-Fernandez, Maria; Doyle, Francis J.

    2012-01-01

    Physiological and psychological stresses cause anxiety disorders such as depression and post-traumatic stress disorder (PTSD) and induce drastic changes at a molecular level in the brain. To counteract this stress, the heat-shock protein (HSP) network plays a vital role in restoring the homeostasis of the system. To study the stress-induced dynamics of heat-shock network, we analyzed three modules of the HSP90 network—namely trimerization reactions, phosphorylation–dephosphorylation reactions, and the conversion of HSP90 from an open to a closed conformation—and constructed a corresponding nonlinear differential equation model based on mass action kinetics laws. The kinetic parameters of the model were obtained through global optimization, and sensitivity analyses revealed that the most sensitive parameters are the kinase and phosphatase that drive the phosphorylation–dephosphorylation reactions. Bifurcation analysis carried out with the estimated kinetic parameters of the model with stress as bifurcation parameter revealed the occurrence of “mushroom”, a type of complex dynamics in which S-shaped and Z-shaped hysteretic bistable forms are present together. We mapped the molecular events responsible for generating the mushroom dynamics under stress and interpreted the occurrence of the S-shaped hysteresis to a normal level of stress, and the Z-shaped hysteresis to the HSP90 variations under acute and chronic stress in the fear conditioned system, and further, we hypothesized that this can be extended to stress-related disorders such as depression and PTSD in humans. Finally, we studied the effect of parameter variations on the mushroom dynamics to get insight about the role of phosphorylation–dephosphorylation parameters in HSP90 network in bringing about complex dynamics such as isolas, where the stable steady states in a bistable system are isolated and separated from each other and not connected by an unstable steady state. PMID:22937003

  15. A detailed modular analysis of heat-shock protein dynamics under acute and chronic stress and its implication in anxiety disorders.

    PubMed

    Sriram, K; Rodriguez-Fernandez, Maria; Doyle, Francis J

    2012-01-01

    Physiological and psychological stresses cause anxiety disorders such as depression and post-traumatic stress disorder (PTSD) and induce drastic changes at a molecular level in the brain. To counteract this stress, the heat-shock protein (HSP) network plays a vital role in restoring the homeostasis of the system. To study the stress-induced dynamics of heat-shock network, we analyzed three modules of the HSP90 network--namely trimerization reactions, phosphorylation-dephosphorylation reactions, and the conversion of HSP90 from an open to a closed conformation--and constructed a corresponding nonlinear differential equation model based on mass action kinetics laws. The kinetic parameters of the model were obtained through global optimization, and sensitivity analyses revealed that the most sensitive parameters are the kinase and phosphatase that drive the phosphorylation-dephosphorylation reactions. Bifurcation analysis carried out with the estimated kinetic parameters of the model with stress as bifurcation parameter revealed the occurrence of "mushroom", a type of complex dynamics in which S-shaped and Z-shaped hysteretic bistable forms are present together. We mapped the molecular events responsible for generating the mushroom dynamics under stress and interpreted the occurrence of the S-shaped hysteresis to a normal level of stress, and the Z-shaped hysteresis to the HSP90 variations under acute and chronic stress in the fear conditioned system, and further, we hypothesized that this can be extended to stress-related disorders such as depression and PTSD in humans. Finally, we studied the effect of parameter variations on the mushroom dynamics to get insight about the role of phosphorylation-dephosphorylation parameters in HSP90 network in bringing about complex dynamics such as isolas, where the stable steady states in a bistable system are isolated and separated from each other and not connected by an unstable steady state.

  16. Product modular design incorporating preventive maintenance issues

    NASA Astrophysics Data System (ADS)

    Gao, Yicong; Feng, Yixiong; Tan, Jianrong

    2016-03-01

    Traditional modular design methods lead to product maintenance problems, because the module form of a system is created according to either the function requirements or the manufacturing considerations. For solving these problems, a new modular design method is proposed with the considerations of not only the traditional function related attributes, but also the maintenance related ones. First, modularity parameters and modularity scenarios for product modularity are defined. Then the reliability and economic assessment models of product modularity strategies are formulated with the introduction of the effective working age of modules. A mathematical model used to evaluate the difference among the modules of the product so that the optimal module of the product can be established. After that, a multi-objective optimization problem based on metrics for preventive maintenance interval different degrees and preventive maintenance economics is formulated for modular optimization. Multi-objective GA is utilized to rapidly approximate the Pareto set of optimal modularity strategy trade-offs between preventive maintenance cost and preventive maintenance interval difference degree. Finally, a coordinate CNC boring machine is adopted to depict the process of product modularity. In addition, two factorial design experiments based on the modularity parameters are constructed and analyzed. These experiments investigate the impacts of these parameters on the optimal modularity strategies and the structure of module. The research proposes a new modular design method, which may help to improve the maintainability of product in modular design.

  17. Modular process modeling for OPC

    NASA Astrophysics Data System (ADS)

    Keck, M. C.; Bodendorf, C.; Schmidtling, T.; Schlief, R.; Wildfeuer, R.; Zumpe, S.; Niehoff, M.

    2007-03-01

    Modular OPC modeling, describing mask, optics, resist and etch processes separately is an approach to keep efforts for OPC manageable. By exchanging single modules of a modular OPC model, a fast response to process changes during process development is possible. At the same time efforts can be reduced, since only single modular process steps have to be re-characterized as input for OPC modeling as the process is adjusted and optimized. Commercially available OPC tools for full chip processing typically make use of semi-empirical models. The goal of our work is to investigate to what extent these OPC tools can be applied for modeling of single process steps as separate modules. For an advanced gate level process we analyze the modeling accuracy over different process conditions (focus and dose) when combining models for each process step - optics, resist and etch - for differing single processes to a model describing the total process.

  18. Modular assembly of optical nanocircuits.

    PubMed

    Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

    2014-05-29

    A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic 'lumped' circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

  19. Modular multichannel surface plasmon spectrometer

    NASA Astrophysics Data System (ADS)

    Neuert, G.; Kufer, S.; Benoit, M.; Gaub, H. E.

    2005-05-01

    We have developed a modular multichannel surface plasmon resonance (SPR) spectrometer on the basis of a commercially available hybrid sensor chip. Due to its modularity this inexpensive and easy to use setup can readily be adapted to different experimental environments. High temperature stability is achieved through efficient thermal coupling of individual SPR units. With standard systems the performance of the multichannel instrument was evaluated. The absorption kinetics of a cysteamine monolayer, as well as the concentration dependence of the specific receptor-ligand interaction between biotin and streptavidin was measured.

  20. Modular multivariable control improves hydrocracking

    SciTech Connect

    Chia, T.L.; Lefkowitz, I.; Tamas, P.D.

    1996-10-01

    Modular multivariable control (MMC), a system of interconnected, single process variable controllers, can be a user-friendly, reliable and cost-effective alternative to centralized, large-scale multivariable control packages. MMC properties and features derive directly from the properties of the coordinated controller which, in turn, is based on internal model control technology. MMC was applied to a hydrocracking unit involving two process variables and three controller outputs. The paper describes modular multivariable control, MMC properties, tuning considerations, application at the DCS level, constraints handling, and process application and results.

  1. Inherent controllability in modular ALMRs

    SciTech Connect

    Sackett, J.I.; Sevy, R.H.; Wei, T.Y.C.

    1989-01-01

    As part of recent development efforts on advanced reactor designs ANL has proposed the IFR (Integral Fast Reactor) concept. The IFR concept is currently being applied to modular sized reactors which would be built in multiple power paks together with an integrated fuel cycle facility. It has been amply demonstrated that the concept as applied to the modular designs has significant advantages in regard to ATWS transients. Attention is now being focussed on determining whether or not those advantages deriving from the traits of the IFR can be translated to the operational/DBA (design basis accident) class of transients. 5 refs., 3 figs., 3 tabs.

  2. Modular Firewalls for Storage Areas

    NASA Technical Reports Server (NTRS)

    Fedor, O. H.; Owens, L. J.

    1986-01-01

    Giant honeycomb structures assembled in modular units. Flammable materials stored in cells. Walls insulated with firebrick to prevent spread of fire among cells. Portable, modular barrier withstands heat of combustion for limited time and confines combustion products horizontally to prevent fire from spreading. Barrier absorbs heat energy by ablation and not meant to be reused. Designed to keep fires from spreading among segments of solid rocket propellant in storage, barrier erected between storage units of other flammable or explosive materials; tanks of petroleum or liquid natural gas. Barrier adequate for most industrial purposes.

  3. Modular electron transfer circuits for synthetic biology

    PubMed Central

    Agapakis, Christina M

    2010-01-01

    Electron transfer is central to a wide range of essential metabolic pathways, from photosynthesis to fermentation. The evolutionary diversity and conservation of proteins that transfer electrons makes these pathways a valuable platform for engineered metabolic circuits in synthetic biology. Rational engineering of electron transfer pathways containing hydrogenases has the potential to lead to industrial scale production of hydrogen as an alternative source of clean fuel and experimental assays for understanding the complex interactions of multiple electron transfer proteins in vivo. We designed and implemented a synthetic hydrogen metabolism circuit in Escherichia coli that creates an electron transfer pathway both orthogonal to and integrated within existing metabolism. The design of such modular electron transfer circuits allows for facile characterization of in vivo system parameters with applications toward further engineering for alternative energy production. PMID:21468209

  4. The discovery of modular binding domains: building blocks of cell signalling.

    PubMed

    Mayer, Bruce J

    2015-11-01

    Cell signalling - the ability of a cell to process information from the environment and change its behaviour in response - is a central property of life. Signalling depends on proteins that are assembled from a toolkit of modular domains, each of which confers a specific activity or function. The discovery of modular protein- and lipid-binding domains was a crucial turning point in understanding the logic and evolution of signalling mechanisms.

  5. Structure-power multifunctional materials for UAV's

    NASA Astrophysics Data System (ADS)

    Thomas, James; Qidwai, Muhammad A.; Matic, Peter; Everett, Richard; Gozdz, Antoni S.; Keennon, Matt; Grasmeyer, Joel

    2002-07-01

    This paper presents multifunctional structure-plus-power developments being pursued under DARPA sponsorship with the focus on structure-battery components for unmanned air vehicles (UAV). New design strategies, analysis methods, performance indices, and prototypes for multifunctional structure-battery materials are described along with the development of two UAV prototypes with structure-battery implementation.

  6. Locally rare species influence grassland ecosystem multifunctionality.

    PubMed

    Soliveres, Santiago; Manning, Peter; Prati, Daniel; Gossner, Martin M; Alt, Fabian; Arndt, Hartmut; Baumgartner, Vanessa; Binkenstein, Julia; Birkhofer, Klaus; Blaser, Stefan; Blüthgen, Nico; Boch, Steffen; Böhm, Stefan; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Heinze, Johannes; Hölzel, Norbert; Jung, Kirsten; Klaus, Valentin H; Klein, Alexandra-Maria; Kleinebecker, Till; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Morris, E Kathryn; Müller, Jörg; Oelmann, Yvonne; Overmann, Jörg; Pašalić, Esther; Renner, Swen C; Rillig, Matthias C; Schaefer, H Martin; Schloter, Michael; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Sikorski, Johannes; Socher, Stephanie A; Solly, Emily F; Sonnemann, Ilja; Sorkau, Elisabeth; Steckel, Juliane; Steffan-Dewenter, Ingolf; Stempfhuber, Barbara; Tschapka, Marco; Türke, Manfred; Venter, Paul; Weiner, Christiane N; Weisser, Wolfgang W; Werner, Michael; Westphal, Catrin; Wilcke, Wolfgang; Wolters, Volkmar; Wubet, Tesfaye; Wurst, Susanne; Fischer, Markus; Allan, Eric

    2016-05-19

    Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity-multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.

  7. Locally rare species influence grassland ecosystem multifunctionality

    PubMed Central

    Manning, Peter; Prati, Daniel; Gossner, Martin M.; Alt, Fabian; Arndt, Hartmut; Baumgartner, Vanessa; Binkenstein, Julia; Birkhofer, Klaus; Blaser, Stefan; Blüthgen, Nico; Boch, Steffen; Böhm, Stefan; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Heinze, Johannes; Hölzel, Norbert; Jung, Kirsten; Klaus, Valentin H.; Klein, Alexandra-Maria; Kleinebecker, Till; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Morris, E. Kathryn; Müller, Jörg; Oelmann, Yvonne; Overmann, Jörg; Pašalić, Esther; Renner, Swen C.; Rillig, Matthias C.; Schaefer, H. Martin; Schloter, Michael; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Sikorski, Johannes; Socher, Stephanie A.; Solly, Emily F.; Sonnemann, Ilja; Sorkau, Elisabeth; Steckel, Juliane; Steffan-Dewenter, Ingolf; Stempfhuber, Barbara; Tschapka, Marco; Türke, Manfred; Venter, Paul; Weiner, Christiane N.; Weisser, Wolfgang W.; Werner, Michael; Westphal, Catrin; Wilcke, Wolfgang; Wolters, Volkmar; Wubet, Tesfaye; Wurst, Susanne; Fischer, Markus; Allan, Eric

    2016-01-01

    Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity–multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities. PMID:27114572

  8. Generic Automated Multi-function Finger Design

    NASA Astrophysics Data System (ADS)

    Honarpardaz, M.; Tarkian, M.; Sirkett, D.; Ölvander, J.; Feng, X.; Elf, J.; Sjögren, R.

    2016-11-01

    Multi-function fingers that are able to handle multiple workpieces are crucial in improvement of a robot workcell. Design automation of multi-function fingers is highly demanded by robot industries to overcome the current iterative, time consuming and complex manual design process. However, the existing approaches for the multi-function finger design automation are unable to entirely meet the robot industries’ need. This paper proposes a generic approach for design automation of multi-function fingers. The proposed approach completely automates the design process and requires no expert skill. In addition, this approach executes the design process much faster than the current manual process. To validate the approach, multi-function fingers are successfully designed for two case studies. Further, the results are discussed and benchmarked with existing approaches.

  9. Modularity in Cognition: Framing the Debate

    ERIC Educational Resources Information Center

    Barrett, H. Clark; Kurzban, Robert

    2006-01-01

    Modularity has been the subject of intense debate in the cognitive sciences for more than 2 decades. In some cases, misunderstandings have impeded conceptual progress. Here the authors identify arguments about modularity that either have been abandoned or were never held by proponents of modular views of the mind. The authors review arguments that…

  10. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  11. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  12. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  13. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  14. 48 CFR 3417.70 - Modular contracting.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 7 2013-10-01 2012-10-01 true Modular contracting. 3417... REGULATION CONTRACTING METHODS AND CONTRACT TYPES SPECIAL CONTRACTING METHODS Modular Contracting 3417.70 Modular contracting. (a) FSA—May incrementally conduct successive procurements of modules of overall...

  15. The Modular Mind and Intrapersonal Communication Processes.

    ERIC Educational Resources Information Center

    Stacks, Don W.

    Based on a prior model on modularity of the brain, a new modular model of intrapersonal communication was developed which focuses on brain processing, encompassing both the structures and the functions of those structures in the creation of messages. The modular mind is a bio-social model of communication which presupposes a relationship between…

  16. Evolution and the Modularity of Mindreading.

    ERIC Educational Resources Information Center

    Moore, Chris

    1996-01-01

    Reviews Baron-Cohen's study of autism and an explanatory theory called modularity of mindreading, which proposed a domain-specific modular psychological model based on evolutionary, developmental, psychopathological, and neurobiological considerations. Enumerates problems with the modularity approach and emphasized the evolution of domain general…

  17. Modular Instruction Under Restricted Conditions.

    ERIC Educational Resources Information Center

    Utomo, Tjipto; Ruijter, Kees

    1984-01-01

    Describes the evaluation and reconstruction of a transport phenomena course given at the Bandung Institute of Technology which had a 70 percent failure rate. Discusses the teacher-paced modular instruction technique designed to replace the original course material and its results in terms of student performance over a three-year period. (JM)

  18. Rapidly Deployed Modular Telemetry System

    NASA Technical Reports Server (NTRS)

    Varnavas, Kosta A. (Inventor); Sims, William Herbert, III (Inventor)

    2013-01-01

    The present invention is a telemetry system, and more specifically is a rapidly deployed modular telemetry apparatus which utilizes of SDR technology and the FPGA programming capability to reduce the number of hardware components and programming required to deploy a telemetry system.

  19. Electrospun multifunctional tissue engineering scaffolds

    NASA Astrophysics Data System (ADS)

    Wang, Chong; Wang, Min

    2014-03-01

    Tissue engineering holds great promises in providing successful treatments of human body tissue loss that current methods are unable to treat or unable to achieve satisfactory clinical outcomes. In scaffold-based tissue engineering, a highperformance scaffold underpins the success of a tissue engineering strategy and a major direction in the field is to create multifunctional tissue engineering scaffolds for enhanced biological performance and for regenerating complex body tissues. Electrospinning can produce nanofibrous scaffolds that are highly desirable for tissue engineering. The enormous interest in electrospinning and electrospun fibrous structures by the science, engineering and medical communities has led to various developments of the electrospinning technology and wide investigations of electrospun products in many industries, including biomedical engineering, over the past two decades. It is now possible to create novel, multicomponent tissue engineering scaffolds with multiple functions. This article provides a concise review of recent advances in the R & D of electrospun multifunctional tissue engineering scaffolds. It also presents our philosophy and research in the designing and fabrication of electrospun multicomponent scaffolds with multiple functions.

  20. Phototriggered multifunctional drug delivery device

    NASA Astrophysics Data System (ADS)

    Härtner, S.; Kim, H.-C.; Hampp, N.

    2006-02-01

    Although phototriggered cleavage of chemical bonds induced by single-photon or two-photon-absorption provides attractive tools for controlled drug delivery, the choice of drugs is still limited by the linker system to which the therapeutic molecules need to be bound covalently. The use of a multifunctional linker system suitable for coupling a broad spectrum of drugs to the polymeric carrier will open a new field for drug delivery. We have developed a novel photocleavable multifunctional linker system based on coumarin dimers, whose unique photochemical behavior are well characterized. As a first example, an acrylic polymer-drug conjugate with antimetabolites is explored. The cleavage of the link between the drug and the polymer backbone is triggered by both single- as well as two-photon absorption. The release of the drug is investigated. It is possible to manufacture a polymeric drug delivery device with several drugs in different areas. In particular the two-photon-absorption induced process offers the possibility to address the drug of interest owing to the superior spatial resolution. The key to such devices is a versatile linker-system which can be adopted to work with various drug compounds.

  1. The tight junction: a multifunctional complex.

    PubMed

    Schneeberger, Eveline E; Lynch, Robert D

    2004-06-01

    Multicellular organisms are separated from the external environment by a layer of epithelial cells whose integrity is maintained by intercellular junctional complexes composed of tight junctions, adherens junctions, and desmosomes, whereas gap junctions provide for intercellular communication. The aim of this review is to present an updated overview of recent developments in the area of tight junction biology. In a relatively short time, our knowledge of the tight junction has evolved from a relatively simple view of it being a permeability barrier in the paracellular space and a fence in the plane of the plasma membrane to one of it acting as a multicomponent, multifunctional complex that is involved in regulating numerous and diverse cell functions. A group of integral membrane proteins-occludin, claudins, and junction adhesion molecules-interact with an increasingly complex array of tight junction plaque proteins not only to regulate paracellular solute and water flux but also to integrate such diverse processes as gene transcription, tumor suppression, cell proliferation, and cell polarity.

  2. Engineering the bio-nano interface using a multi-functional polymer coating

    NASA Astrophysics Data System (ADS)

    Wang, Wentao

    for the surface engineering of QDs. Third, modulation of the nanoparticle's interaction with biological systems requires access to an effective conjugation of these materials with bioactive targets in a controlled manner. To fulfill this goal, we have developed several zwitterion-based multifunctional ligands presenting tunable functional groups, including carboxyl, amine, azide and biotin. This has allowed conjugation of the QDs to biomolecules via bio-orthogonal coupling chemistries, including (1) amine-isothiocyanate reaction; (2) biotin-streptavidin self-assembly; (3) copper-free click chemistry. The resulted QD-bioconjugates have been tested in sensor design and for cell imaging. We also find that the efficiency of polyhistidine-mediated metal coordination is not only determined by the ligand lateral extension but also greatly influenced by the nature of metal coordination on the QDs. In Chapter 3, we have applied the various multi-coordinating and multi-reactive polymers, in particular, those presenting lipoic acid and PEG for the functionalization of gold nanoparticles and nanorods. Gold nanocrystals coated with this polymer exhibit excellent long-term colloidal stability over a broad range of conditions, and furthermore prevent the formation of protein corona. This was verified using dynamic light scattering measurements combined with agarose gel electrophoresis. The diffusion properties of polymer-coated nanocrystals were further characterized using dynamic light scattering; this has yielded valuable information on the nature of the interparticle interactions in biological media. In Chapter 4, an additional set of modular ligands were synthesized and applied for the surface modification of iron oxide nanoparticles. These ligands feature several dopamines for tight binding on iron oxide nanoparticle surface, a short PEG for water solubility and reactive groups (amine, carboxyl, azide and thiol) for bioconjugation. Nanoparticles functionalized with these

  3. Multiplexed modular genetic targeting of quantum dots.

    PubMed

    Saurabh, Saumya; Beck, Lauren E; Maji, Suvrajit; Baty, Catherine J; Wang, Yi; Yan, Qi; Watkins, Simon C; Bruchez, Marcel P

    2014-11-25

    While DNA-directed nanotechnology is now a well-established platform for bioinspired nanoscale assembly in vitro, the direct targeting of various nanomaterials in living biological systems remains a significant challenge. Hybrid biological systems with integrated and targeted nanomaterials may have interesting and exploitable properties, so methods for targeting various nanomaterials to precise biological locations are required. Fluorescence imaging has benefited from the use of nanoparticles with superior optical properties compared to fluorescent organic dyes or fluorescent proteins. While single-particle tracking (SPT) in living cells with genetically encoded proteins is limited to very short trajectories, the high photon output of genetically targeted and multiplexed quantum dots (QDs) would enable long-trajectory analysis of multiple proteins. However, challenges with genetic targeting of QDs limit their application in these experiments. In this report, we establish a modular method for targeting QD nanoparticles selectively to multiple genetically encoded tags by precomplexing QD-streptavidin conjugates with cognate biotinylated hapten molecules. This approach enables labeling and SPT of multiple genetically encoded proteins on living cells at high speed and can label expressed proteins in the cytosol upon microinjection into living cells. While we demonstrate labeling with three distinct QD conjugates, the approach can be extended to other specific hapten-affinity molecule interactions and alternative nanoparticles, enabling precise directed targeting of nanoparticles in living biological systems.

  4. Playing Modular Puzzle with Adhesion/Growth-Regulatory Galectins: Design and Testing of a Hybrid to Unravel Structure-Activity Relationships.

    PubMed

    Ludwig, Anna-Kristin; Vértesy, Sabine; Michalak, Malwina; Manning, Joachim C; Andre, Sabine; Kubler, Dieter; Kopitz, Jurgen; Kaltner, Herbert; Gabius, Hans-Joachim

    2016-01-01

    The potent multifunctionality of human galectins is based on their modular structure in a not yet fully understood manner. A strategy to dissect the contributions of individual sequence stretches to lectin activity is based on engineering variants of the natural proteins, which are composed of novel combinations of distinct parts. On proof-of-principle level, we here describe the design of a hybrid constituted by the N-terminal tail of chimera-type galectin-3 and the Nterminal carbohydrate recognition domain of tandem-repeat-type galectin-8, its production, purification and its serine phosphorylation characteristic for galectin- 3's tail. As measured for the respective parental proteins, its binding to (neo)glycoproteins is specific for β-galactosides and inhibitable by lactose, with KD-value closer to galectin-8 than galectin-3. Cell surface staining indicated similarity of the hybrid's reactivity to O-glycans and sensitivity for sialylation to respective properties of tandem-repeattype galectin-8 and its N-terminal domain. Applied as histochemical tool on tissue sections of murine jejunum and epididymis, intense lactose-inhibitable signals were recorded intracellularly, with a distribution profile akin to that of galectin-3. Tested as agglutinin, the hybrid was potent, excelling wild-type control galectins. The chimera-type design can thus serve as platform for tuning crosslinking activity.

  5. Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges.

    PubMed

    Yuzawa, Satoshi; Keasling, Jay D; Katz, Leonard

    2017-04-01

    Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. We have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals.

  6. Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges

    SciTech Connect

    Yuzawa, Satoshi; Keasling, Jay D.; Katz, Leonard

    2016-11-16

    Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. Finally, we have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals.

  7. Synthetic approaches to multifunctional indenes

    PubMed Central

    López-Pérez, Sara; Dinarès, Immaculada

    2011-01-01

    Summary The synthesis of multifunctional indenes with at least two different functional groups has not yet been extensively explored. Among the plausible synthetic routes to 3,5-disubstituted indenes bearing two different functional groups, such as the [3-(aminoethyl)inden-5-yl)]amines, a reasonable pathway involves the (5-nitro-3-indenyl)acetamides as key intermediates. Although several multistep synthetic approaches can be applied to obtain these advanced intermediates, we describe herein their preparation by an aldol-type reaction between 5-nitroindan-1-ones and the lithium salt of N,N-disubstituted acetamides, followed immediately by dehydration with acid. This classical condensation process, which is neither simple nor trivial despite its apparent directness, permits an efficient entry to a variety of indene-based molecular modules, which could be adapted to a range of functionalized indanones. PMID:22238553

  8. Toward multifunctional "clickable" diamond nanoparticles.

    PubMed

    Khanal, Manakamana; Turcheniuk, Volodymyr; Barras, Alexandre; Rosay, Elodie; Bande, Omprakash; Siriwardena, Aloysius; Zaitsev, Vladimir; Pan, Guo-Hui; Boukherroub, Rabah; Szunerits, Sabine

    2015-04-07

    Nanodiamonds (NDs) are among the most promising new carbon based materials for biomedical applications, and the simultaneous integration of various functions onto NDs is an urgent necessity. A multifunctional nanodiamond based formulation is proposed here. Our strategy relies on orthogonal surface modification using different dopamine anchors. NDs simultaneously functionalized with triethylene glycol (EG) and azide (-N3) functions were fabricated through a stoichiometrically controlled integration of the dopamine ligands onto the surface of hydroxylated NDs. The presence of EG functionalities rendered NDs soluble in water and biological media, while the -N3 group allowed postsynthetic modification of the NDs using "click" chemistry. As a proof of principle, alkynyl terminated di(amido amine) ligands were linked to these ND particles.

  9. Metalenses: Versatile multifunctional photonic components.

    PubMed

    Khorasaninejad, Mohammadreza; Capasso, Federico

    2017-10-05

    Recent progress in metasurface designs fueled by advanced-fabrication techniques has led to the realization of ultrathin, lightweight, and flat lenses (metalenses) with unprecedented functionalities. Due to straightforward fabrication, generally requiring a single-step lithography, and possibility of vertical integration, these planar lenses can potentially replace or complement their conventional refractive and diffractive counterparts leading to further miniaturization of high performance optical devices and systems. Here, we give a brief overview of the evolution of metalenses with an emphasis on the visible and near-infrared spectrum and summarize their important features: diffraction-limited focusing, high quality imaging and multifunctionalities. Future challenges including aberrations' corrections, as well as current issues and solutions are discussed. We conclude by providing an outlook of this technology platform and by identifying future promising directions. Copyright © 2017, American Association for the Advancement of Science.

  10. Multifunctionalities driven by ferroic domains

    SciTech Connect

    Yang, J. C.; Huang, Y. L.; Chu, Y. H.; He, Q.

    2014-08-14

    Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

  11. Multifunction display system, volume 1

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The design and construction of a multifunction display man/machine interface for use with a 4 pi IBM-360 System are described. The system is capable of displaying superimposed volatile alphanumeric and graphical data on a 512 x 512 element plasma panel, and holographically stored multicolor archival information. The volatile data may be entered from a keyboard or by means of an I/O interface to the 360 system. A 2-page memory local to the display is provided for storing the entered data. The archival data is stored as a phase hologram on a vinyl tape strip. This data is accessible by means of a rapid transport system which responds to inputs provided by the I/O channel on the keyboard. As many as 500 frames may be stored on a tape strip for access in under 6 seconds.

  12. Multifunctional composites for energy storage

    NASA Astrophysics Data System (ADS)

    Shuvo, Mohammad Arif I.; Karim, Hasanul; Rajib, Md; Delfin, Diego; Lin, Yirong

    2014-03-01

    Electrochemical super-capacitors have become one of the most important topics in both academia and industry as novel energy storage devices because of their high power density, long life cycles, and high charge/discharge efficiency. Recently, there has been an increasing interest in the development of multifunctional structural energy storage devices such as structural super-capacitors for applications in aerospace, automobiles and portable electronics. These multifunctional structural super-capacitors provide lighter structures combining energy storage and load bearing functionalities. Due to their superior materials properties, carbon fiber composites have been widely used in structural applications for aerospace and automotive industries. Besides, carbon fiber has good electrical conductivity which will provide lower equivalent series resistance; therefore, it can be an excellent candidate for structural energy storage applications. Hence, this paper is focused on performing a pilot study for using nanowire/carbon fiber hybrids as building materials for structural energy storage materials; aiming at enhancing the charge/discharge rate and energy density. This hybrid material combines the high specific surface area of carbon fiber and pseudo-capacitive effect of metal oxide nanowires which were grown hydrothermally in an aligned fashion on carbon fibers. The aligned nanowire array could provide a higher specific surface area that leads to high electrode-electrolyte contact area and fast ion diffusion rates. Scanning Electron Microscopy (SEM) and XRay Diffraction (XRD) measurements were used for the initial characterization of this nanowire/carbon fiber hybrid material system. Electrochemical testing has been performed using a potentio-galvanostat. The results show that gold sputtered nanowire hybrid carbon fiber provides 65.9% better performance than bare carbon fiber cloth as super-capacitor.

  13. Modular assembly of genes and the evolution of new functions.

    PubMed

    Patthy, László

    2003-07-01

    Modular assembly of novel genes from existing genes has long been thought to be an important source of evolutionary novelty. Thanks to major advances in genomic studies it has now become clear that this mechanism contributed significantly to the evolution of novel biological functions in different evolutionary lineages. Analyses of completely sequenced bacterial, archaeal and eukaryotic genomes has revealed that modular assembly of novel constituents of various eukaryotic intracellular signalling pathways played a major role in the evolution of eukaryotes. Comparison of the genomes of single-celled eukaryotes, multicellular plants and animals has also shown that the evolution of multicellularity was accompanied by the assembly of numerous novel extracellular matrix proteins and extracellular signalling proteins that are absolutely essential for multicellularity. There is now strong evidence that exon-shuffling played a general role in the assembly of the modular proteins involved in extracellular communications of metazoa. Although some of these proteins seem to be shared by all major groups of metazoa, others are restricted to certain evolutionary lineages. The genomic features of the chordates appear to have favoured intronic recombination as evidenced by the fact that exon-shuffling continued to be a major source of evolutionary novelty during vertebrate evolution.

  14. Structural basis for multifunctional roles of mammalian aminopeptidase N

    PubMed Central

    Chen, Lang; Lin, Yi-Lun; Peng, Guiqing; Li, Fang

    2012-01-01

    Mammalian aminopeptidase N (APN) plays multifunctional roles in many physiological processes, including peptide metabolism, cell motility and adhesion, and coronavirus entry. Here we determined crystal structures of porcine APN at 1.85 Å resolution and its complexes with a peptide substrate and a variety of inhibitors. APN is a cell surface-anchored and seahorse-shaped zinc-aminopeptidase that forms head-to-head dimers. Captured in a catalytically active state, these structures of APN illustrate a detailed catalytic mechanism for its aminopeptidase activity. The active site and peptide-binding channel of APN reside in cavities with wide openings, allowing easy access to peptides. The cavities can potentially open up further to bind the exposed N terminus of proteins. The active site anchors the N-terminal neutral residue of peptides/proteins, and the peptide-binding channel binds the remainder of the peptides/proteins in a sequence-independent fashion. APN also provides an exposed outer surface for coronavirus binding, without its physiological functions being affected. These structural features enable APN to function ubiquitously in peptide metabolism, interact with other proteins to mediate cell motility and adhesion, and serve as a coronavirus receptor. This study elucidates multifunctional roles of APN and can guide therapeutic efforts to treat APN-related diseases. PMID:23071329

  15. Modular Stellarator Fusion Reactor concept

    SciTech Connect

    Miller, R.L.; Krakowski, R.A.

    1981-08-01

    A preliminary conceptual study is made of the Modular Stellarator Reactor (MSR). A steady-state ignited, DT-fueled, magnetic fusion reactor is proposed for use as a central electric-power station. The MSR concept combines the physics of the classic stellarator confinement topology with an innovative, modular-coil design. Parametric tradeoff calculations are described, leading to the selection of an interim design point for a 4-GWt plant based on Alcator transport scaling and an average beta value of 0.04 in an l = 2 system with a plasma aspect ratio of 11. The physics basis of the design point is described together with supporting magnetics, coil-force, and stress computations. The approach and results presented herein will be modified in the course of ongoing work to form a firmer basis for a detailed conceptual design of the MSR.

  16. Relaxation labeling using modular operators

    SciTech Connect

    Duncan, J.S.; Frei, W.

    1983-01-01

    Probabilistic relaxation labeling has been shown to be useful in image processing, pattern recognition, and artificial intelligence. The approaches taken to date have been encumbered with computationally extensive summations which generally prevent real-time operation and/or easy hardware implementation. The authors present a new and unique approach to the relaxation labeling problem using modular, VLSI-oriented hierarchical complex operators. One of the fundamental concepts of this work is the representation of the probability distribution of the possible labels for a given object (pixel) as an ellipse, which may be summed with neighboring object's distribution ellipses, resulting in a new, relaxed label space. The mathematical development of the elliptical approach will be presented and compared to more classical approaches, and a hardware block diagram that shows the implementation of the relaxation scheme using vlsi chips will be presented. Finally, results will be shown which illustrate applications of the modular scheme, iteratively, to both edges and lines. 13 references.

  17. Modular hydrodam: concept definition study

    SciTech Connect

    Not Available

    1981-07-01

    The purpose of this investigation was to explore the potential for developing economical new ultra low-head (6 to 10 ft) sites using an innovative concept known as the Modular Hydrodam (MH). This concept combines the benefits of shop fabrication, installation of equipment in truck transportable, waterproof power modules, and prefabricated gate sections that can be located between the power modules. The size and weight of the power module permits it to be fully assembled and checked out in the manufacturer's shop. The module can then be broken down into four pieces and shipped by truck to the site. Once in place, concrete ballast will be added, as necessary, to prevent flotation. The following aspects were investigated: tubular and cross flow turbines; modularized components; the use of a cable support system for horizontal stability of the dam and powerhouse; and construction in the wet as well as in the dry.

  18. Modular Platforms for Optofluidic Systems

    NASA Astrophysics Data System (ADS)

    Brammer, Marko; Mappes, Timo

    2014-01-01

    Optofluidics is increasingly gaining impact in a number of different fields of research, namely biology and medicine, environmental monitoring and green energy. However, the market for optofluidic products is still in the early development phase. In this manuscript, we discuss modular platforms as a potential concept to facilitate the transfer of optofluidic sensing systems to an industrial implementation. We present microfluidic and optical networks as a basis for the interconnection of optofluidic sensor modules. Finally, we show the potential for entire optofluidic networks

  19. PTERA - Modular Aircraft Flight Test

    NASA Image and Video Library

    2016-01-13

    Aerospace testing can be costly and time consuming but a new modular, subscale remotely piloted aircraft offers NASA researchers more affordable options for developing a wide range of cutting edge aviation and space technologies. The Prototype-Technology Evaluation and Research Aircraft (PTERA), developed by Area-I, Inc., of Kennesaw, Georgia, is an extremely versatile and high quality, yet inexpensive, flying laboratory bridging the gap between wind tunnels and crewed flight testing.

  20. Modular Platforms for Optofluidic Systems

    NASA Astrophysics Data System (ADS)

    Brammer, Marko; Mappes, Timo

    2013-02-01

    Optofluidics is increasingly gaining impact in a number of different fields of research, namely biology and medicine, environmental monitoring and green energy. However, the market for optofluidic products is still in the early development phase. In this manuscript, we discuss modular platforms as a potential concept to facilitate the transfer of optofluidic sensing systems to an industrial implementation. We present microfluidic and optical networks as a basis for the interconnection of optofluidic sensor modules. Finally, we show the potential for entire optofluidic networks.

  1. Modular Platforms for Optofluidic Systems

    NASA Astrophysics Data System (ADS)

    Brammer, Marko; Mappes, Timo

    2014-01-01

    Optofluidics is increasingly gaining impact in a number of different fields of research, namely biology and medicine, environmental monitoring and green energy. However, the market for optofluidic products is still in the early development phase. In this manuscript, we discuss modular platforms as a potential concept to facilitate the transfer of optofluidic sensing systems to an industrial implementation. We present microfluidic and optical networks as a basis for the interconnection of optofluidic sensor modules. Finally, we show the potential for entire optofluidic networks

  2. Multidimensional bioseparation with modular microfluidics

    DOEpatents

    Chirica, Gabriela S.; Renzi, Ronald F.

    2013-08-27

    A multidimensional chemical separation and analysis system is described including a prototyping platform and modular microfluidic components capable of rapid and convenient assembly, alteration and disassembly of numerous candidate separation systems. Partial or total computer control of the separation system is possible. Single or multiple alternative processing trains can be tested, optimized and/or run in parallel. Examples related to the separation and analysis of human bodily fluids are given.

  3. CAMAC modular programmable function generator

    SciTech Connect

    Turner, G.W.; Suehiro, S.; Hendricks, R.W.

    1980-12-01

    A CAMAC modular programmable function generator has been developed. The device contains a 1024 word by 12-bit memory, a 12-bit digital-to-analog converter with a 600 ns settling time, an 18-bit programmable frequency register, and two programmable trigger output registers. The trigger registers can produce programmed output logic transitions at various (binary) points in the output function curve, and are used to synchronize various other data acquisition devices with the function curve.

  4. Estimation of inter-modular connectivity from the local field potentials in a hierarchical modular network

    NASA Astrophysics Data System (ADS)

    Cui, Xue-Mei; Kim, Won Sup; Hwang, Dong-Uk; Han, Seung Kee

    2015-05-01

    We propose a method of estimating inter-modular connectivity in a hierarchical modular network. The method is based on an analysis of inverse phase synchronization applied to the local field potentials on a hierarchical modular network of phase oscillators. For a strong-coupling strength, the inverse phase synchronization index of the local field potentials for two modules depends linearly on the corresponding inter-modular connectivity defined as the number of links connecting the modules. The method might enable us to estimate the inter-modular connectivity in various complex systems from the inverse phase synchronization index of the mesoscopic modular activities.

  5. Multifunctional PEGylated nanoclusters for biomedical applications.

    PubMed

    Peng, Erwin; Choo, Eugene Shi Guang; Tan, Cherie Shi Hua; Tang, Xiaosheng; Sheng, Yang; Xue, Junmin

    2013-07-07

    A simple and versatile synthesis method to form water soluble multifunctional nanoclusters using polyethylene glycol (PEG) functionalized poly(maleic anhydride-alt-1-octadecene) amphiphilic brush copolymers (PMAO-g-PEG) was presented. Simply by tuning the core size and the initial nanocrystal concentration, manganese ferrite nanoparticles (MFNPs) were used to demonstrate the versatility of tuning the loading amount of the nanoclusters. The resultant nanoclusters were found to have a well-controlled spherical shape. When Zn-doped AgInS2 quantum dots (AIZS QDs) were loaded together with the MFNP nanocrystals, bi-functional nanoclusters with fluorescent and magnetic behaviors were obtained. Such bi-functional nanoclusters were also successfully demonstrated for cellular bio-imaging. Moreover, the presence of another type of nanocrystals together with MFNPs was found to have a negligible effect on the overall properties of the nanoclusters as demonstrated by the MR relaxivity test. From the time-dependent colloidal stability test, it was found that the presence of the PEG chain grafted onto PMAO was able to reduce protein adsorption onto the nanocluster surface. An in vitro study on NIH/3T3 demonstrated the biocompatibility of the nanoclusters. Such biocompatible and colloidally stable nanoclusters with an approximate size of 80-120 nm were suitable for both MRI and cell labeling applications.

  6. Counteraction of the multifunctional restriction factor tetherin

    PubMed Central

    Sauter, Daniel

    2014-01-01

    The interferon-inducible restriction factor tetherin (also known as CD317, BST-2 or HM1.24) has emerged as a key component of the antiviral immune response. Initially, tetherin was shown to restrict replication of various enveloped viruses by inhibiting the release of budding virions from infected cells. More recently, it has become clear that tetherin also acts as a pattern recognition receptor inducing NF-κB-dependent proinflammatory gene expression in virus infected cells. Whereas the ability to restrict virion release is highly conserved among mammalian tetherin orthologs and thus probably an ancient function of this protein, innate sensing seems to be an evolutionarily recent activity. The potent and broad antiviral activity of tetherin is reflected by the fact that many viruses evolved means to counteract this restriction factor. A continuous arms race with viruses has apparently driven the evolution of different isoforms of tetherin with different functional properties. Interestingly, tetherin has also been implicated in cellular processes that are unrelated to immunity, such as the organization of the apical actin network and membrane microdomains or stabilization of the Golgi apparatus. In this review, I summarize our current knowledge of the different functions of tetherin and describe the molecular strategies that viruses have evolved to antagonize or evade this multifunctional host restriction factor. PMID:24782851

  7. Multifunctional aliphatic polyester nanofibers for tissue engineering

    PubMed Central

    Zhan, Jianan; Singh, Anirudha; Zhang, Zhe; Huang, Ling; Elisseeff, Jennifer H.

    2012-01-01

    Electrospun fibers based on aliphatic polyesters, such as poly(ε-caprolactone) (PCL), have been widely used in regenerative medicine and drug delivery applications due to their biocompatibility, low cost and ease of fabrication. However, these aliphatic polyester fibers are hydrophobic in nature, resulting in poor wettability, and they lack functional groups for decorating the scaffold with chemical and biological cues. Current strategies employed to overcome these challenges include coating and blending the fibers with bioactive components or chemically modifying the fibers with plasma treatment and reactants. In the present study, we report on designing multifunctional electrospun nanofibers based on the inclusion complex of PCL-α-cyclodextrin (PCL-α-CD), which provides both structural support and multiple functionalities for further conjugation of bioactive components. This strategy is independent of any chemical modification of the PCL main chain, and electrospinning of PCL-α-CD is as easy as electrospinning PCL. Here, we describe synthesis of the PCL-α-CD electrospun nanofibers, elucidate composition and structure, and demonstrate the utility of functional groups on the fibers by conjugating a fluorescent small molecule and a polymeric-nanobead to the nanofibers. Furthermore, we demonstrate the application of PCL-α-CD nanofibers for promoting osteogenic differentiation of human adipose-derived stem cells (hADSCs), which induced a higher level of expression of osteogenic markers and enhanced production of extracellular matrix (ECM) proteins or molecules compared with control PCL fibers. PMID:23507886

  8. Advanced Multifunctional MMOD Shield: Radiation Shielding Assessment

    NASA Technical Reports Server (NTRS)

    Rojdev, Kristina; Christiansen, Eric

    2013-01-01

    Deep space missions must contend with a harsh radiation environment Impacts to crew and electronics. Need to invest in multifunctionality for spacecraft optimization. MMOD shield. Goals: Increase radiation mitigation potential. Retain overall MMOD shielding performance.

  9. Microbial diversity drives multifunctionality in terrestrial ecosystems

    PubMed Central

    Delgado-Baquerizo, Manuel; Maestre, Fernando T.; Reich, Peter B.; Jeffries, Thomas C.; Gaitan, Juan J.; Encinar, Daniel; Berdugo, Miguel; Campbell, Colin D.; Singh, Brajesh K.

    2016-01-01

    Despite the importance of microbial communities for ecosystem services and human welfare, the relationship between microbial diversity and multiple ecosystem functions and services (that is, multifunctionality) at the global scale has yet to be evaluated. Here we use two independent, large-scale databases with contrasting geographic coverage (from 78 global drylands and from 179 locations across Scotland, respectively), and report that soil microbial diversity positively relates to multifunctionality in terrestrial ecosystems. The direct positive effects of microbial diversity were maintained even when accounting simultaneously for multiple multifunctionality drivers (climate, soil abiotic factors and spatial predictors). Our findings provide empirical evidence that any loss in microbial diversity will likely reduce multifunctionality, negatively impacting the provision of services such as climate regulation, soil fertility and food and fibre production by terrestrial ecosystems. PMID:26817514

  10. Microbial diversity drives multifunctionality in terrestrial ecosystems.

    PubMed

    Delgado-Baquerizo, Manuel; Maestre, Fernando T; Reich, Peter B; Jeffries, Thomas C; Gaitan, Juan J; Encinar, Daniel; Berdugo, Miguel; Campbell, Colin D; Singh, Brajesh K

    2016-01-28

    Despite the importance of microbial communities for ecosystem services and human welfare, the relationship between microbial diversity and multiple ecosystem functions and services (that is, multifunctionality) at the global scale has yet to be evaluated. Here we use two independent, large-scale databases with contrasting geographic coverage (from 78 global drylands and from 179 locations across Scotland, respectively), and report that soil microbial diversity positively relates to multifunctionality in terrestrial ecosystems. The direct positive effects of microbial diversity were maintained even when accounting simultaneously for multiple multifunctionality drivers (climate, soil abiotic factors and spatial predictors). Our findings provide empirical evidence that any loss in microbial diversity will likely reduce multifunctionality, negatively impacting the provision of services such as climate regulation, soil fertility and food and fibre production by terrestrial ecosystems.

  11. Targeting Prostate Cancer with Multifunctional Nanoparticles

    DTIC Science & Technology

    2015-10-01

    AWARD NUMBER: W81XWH-14-1-0487 TITLE: Targeting Prostate Cancer with Multifunctional Nanoparticles PRINCIPAL INVESTIGATOR: Darryl Martin...Targeting Prostate Cancer with Multifunctional Nanoparticles 5b. GRANT NUMBER W81XWH-14-1-0487 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Darryl...STATEMENT Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Prostate cancer cells were transfected with claudin siRNA

  12. Multifunctional magnetic quantum dots for cancer theranostics.

    PubMed

    Singh, Surinder P

    2011-02-01

    The development of an innovative platform for cancer theranostics that will be capable of noninvasive imaging and treatment of cancerous tumors using biocompatible and multifunctional Fe3O4-ZnO core-shell magnetic quantum dots (M-QDs) is being explored. This multi-functional approach will facilitate deep tumor targeting using a combination of a specific cancer marker and an external magnetic field will simultaneously provide therapy that may evolve as a new paradigm in cancer theranostics.

  13. Cell-type-specific expression of murine multifunctional galectin-3 and its association with follicular atresia/luteolysis in contrast to pro-apoptotic galectins-1 and -7.

    PubMed

    Lohr, Michaela; Kaltner, Herbert; Lensch, Martin; André, Sabine; Sinowatz, Fred; Gabius, Hans-Joachim

    2008-09-01

    Galectin-3 is a multifunctional protein with modular design. A distinct expression profile was determined in various murine organs when set into relation to homodimeric galectins-1 and -7. Fittingly, the signature of putative transcription-factor-binding sites in the promoter region of the galectin-3 gene affords a toolbox for a complex combinatorial regulation, distinct from the respective sequence stretches in galectins-1 and -7. A striking example for cell-type specificity was the ovary, where these two lectins were confined to the surface epithelium. Immunohistochemically, galectin-3 was found in macrophages of the cortical interstitium between developing follicles and medullary interstitium, matching the distribution of the F4/80 antigen. With respect to atresia and luteolysis strong signals in granulosa cells of atretic preantral but not antral follicles and increasing positivity in corpora lutea upon regression coincided with DNA fragmentation. Labeled galectin-3 revealed lactose-inhibitable binding to granulosa cells. Also, slender processes of vital granulosa cells which extended into the zona pellucida were positive. This study demonstrates cell-type specificity and cycle-associated regulation for galectin-3 with increased presence in atretic preantral follicles and in late stages of luteolysis.

  14. Modular Multi-Function Multi-Band Airborne Radio System (MFBARS). Volume II. Detailed Report.

    DTIC Science & Technology

    1981-06-01

    to the complexity of extra hardware (or software) required to perform the calculation , and the time required to make the calculation . Similarly, the...cal- culate range and bearing from the aircraft to the beacon relative to true north. The computer also calculates the times of occurrence of...to be performed on each digitized sample. Assuming sampling each of 14 output signals at a 15 MHz rate, there must be a calculated output value from

  15. Mussel-Inspired Surface Chemistry for Multifunctional Coatings

    NASA Astrophysics Data System (ADS)

    Lee, Haeshin; Dellatore, Shara M.; Miller, William M.; Messersmith, Phillip B.

    2007-10-01

    We report a method to form multifunctional polymer coatings through simple dip-coating of objects in an aqueous solution of dopamine. Inspired by the composition of adhesive proteins in mussels, we used dopamine self-polymerization to form thin, surface-adherent polydopamine films onto a wide range of inorganic and organic materials, including noble metals, oxides, polymers, semiconductors, and ceramics. Secondary reactions can be used to create a variety of ad-layers, including self-assembled monolayers through deposition of long-chain molecular building blocks, metal films by electroless metallization, and bioinert and bioactive surfaces via grafting of macromolecules.

  16. Mussel-Inspired Surface Chemistry for Multifunctional Coatings

    PubMed Central

    Lee, Haeshin; Dellatore, Shara M.; Miller, William M.; Messersmith, Phillip B.

    2008-01-01

    We report a method to form multifunctional polymer coatings through simple dip-coating of objects in an aqueous solution of dopamine. Inspired by the composition of adhesive proteins in mussels, we used dopamine self-polymerization to form thin, surface-adherent polydopamine films onto a wide range of inorganic and organic materials, including noble metals, oxides, polymers, semiconductors, and ceramics. Secondary reactions can be used to create a variety of ad-layers, including self-assembled monolayers through deposition of long-chain molecular building blocks, metal films by electroless metallization, and bioinert and bioactive surfaces via grafting of macromolecules. PMID:17947576

  17. Modular Automated Processing System (MAPS) for analysis of biological samples.

    SciTech Connect

    Gil, Geun-Cheol; Chirica, Gabriela S.; Fruetel, Julia A.; VanderNoot, Victoria A.; Branda, Steven S.; Schoeniger, Joseph S.; Throckmorton, Daniel J.; Brennan, James S.; Renzi, Ronald F.

    2010-10-01

    We have developed a novel modular automated processing system (MAPS) that enables reliable, high-throughput analysis as well as sample-customized processing. This system is comprised of a set of independent modules that carry out individual sample processing functions: cell lysis, protein concentration (based on hydrophobic, ion-exchange and affinity interactions), interferent depletion, buffer exchange, and enzymatic digestion of proteins of interest. Taking advantage of its unique capacity for enclosed processing of intact bioparticulates (viruses, spores) and complex serum samples, we have used MAPS for analysis of BSL1 and BSL2 samples to identify specific protein markers through integration with the portable microChemLab{trademark} and MALDI.

  18. Functional trait diversity maximizes ecosystem multifunctionality.

    PubMed

    Gross, Nicolas; Le Bagousse-Pinguet, Yoann; Liancourt, Pierre; Berdugo, Miguel; Gotelli, Nicholas J; Maestre, Fernando T

    2017-05-01

    Understanding the relationship between biodiversity and ecosystem functioning has been a core ecological research topic over the last decades. Although a key hypothesis is that the diversity of functional traits determines ecosystem functioning, we do not know how much trait diversity is needed to maintain multiple ecosystem functions simultaneously (multifunctionality). Here, we uncovered a scaling relationship between the abundance distribution of two key plant functional traits (specific leaf area, maximum plant height) and multifunctionality in 124 dryland plant communities spread over all continents except Antarctica. For each trait, we found a strong empirical relationship between the skewness and the kurtosis of the trait distributions that cannot be explained by chance. This relationship predicted a strikingly high trait diversity within dryland plant communities, which was associated with a local maximization of multifunctionality. Skewness and kurtosis had a much stronger impact on multifunctionality than other important multifunctionality drivers such as species richness and aridity. The scaling relationship identified here quantifies how much trait diversity is required to maximize multifunctionality locally. Trait distributions can be used to predict the functional consequences of biodiversity loss in terrestrial ecosystems.

  19. Does multifunctionality matter to US farmers? Farmer motivations and conceptions of multifunctionality in dairy systems.

    PubMed

    Brummel, Rachel F; Nelson, Kristen C

    2014-12-15

    The concept of multifunctionality describes and promotes the multiple non-production benefits that emerge from agricultural systems. The notion of multifunctional agriculture was conceived in a European context and largely has been used in European policy arenas to promote and protect the non-production goods emerging from European agriculture. Thus scholars and policy-makers disagree about the relevance of multifunctionality for United States agricultural policy and US farmers. In this study, we explore lived expressions of multifunctional agriculture at the farm-level to examine the salience of the multifunctionality concept in the US. In particular, we investigate rotational grazing and confinement dairy farms in the eastern United States as case studies of multifunctional and productivist agriculture. We also analyze farmer motivations for transitioning from confinement dairy to rotational grazing systems. Through interviews with a range of dairy producers in Wisconsin, Pennsylvania, and New York, we found that farmers were motivated by multiple factors--including improved cow health and profitability--to transition to rotational grazing systems to achieve greater farm-level multifunctionality. Additionally, rotational grazing farmers attributed a broader range of production and non-production benefits to their farm practice than confinement dairy farmers. Further, rotational grazing dairy farmers described a system-level notion of multifunctionality based on the interdependence of multiple benefits across scales--from the farm to the national level--emerging from grazing operations. We find that the concept of multifunctionality could be expanded in the US to address the interdependence of benefits emerging from farming practices, as well as private benefits to farmers. We contend that understanding agricultural benefits as experienced by the farmer is an important contribution to enriching the multifunctionality concept in the US context, informing agri

  20. Modular microrobot for swimming in heterogeneous environments

    NASA Astrophysics Data System (ADS)

    Cheang, U. Kei; Meshkati, Meshkati; Fu, Henry; Kim, Minjun; Drexel University Team; University of Nevada, Reno Team

    2015-11-01

    One of the difficulties in navigating in vivo is to overcome many types of environments. This includes blood vessels of different diameters, fluids with different mechanical properties, and physical barriers. Inspired by conventional modular robotics, we demonstrate modular microrobotics using magnetic particles as the modular units to change size and shape through docking and undocking. Much like the vast variety of microorganisms navigating many different bio-environments, modular microswimmers have the ability to dynamically adapt different environments by reconfiguring the swimmers' physical characteristics. We model the docking as magnetic assembly and undocking mechanisms as deformation by hydrodynamic forces. We characterize the swimming capability of the modular microswimmer with different size and shapes. Finally, we demonstrate modular microrobotics by assembling a three-bead microswimmer into a nine-bead microswimmer, and then disassemble it into several independently swimming microswimmers..

  1. Modular Design in Treaty Verification Equipment

    SciTech Connect

    Macarthur, Duncan Whittemore; Benz, Jacob; Tolk, Keith; Weber, Tom

    2015-01-27

    It is widely believed that modular design is a good thing. However, there are often few explicit arguments, or even an agreed range of definitions, to back up this belief. In this paper, we examine the potential range of design modularity, the implications of various amounts of modularity, and the advantages and disadvantages of each level of modular construction. We conclude with a comparison of the advantages and disadvantages of each type, as well as discuss many caveats that should be observed to take advantage of the positive features of modularity and minimize the effects of the negative. The tradeoffs described in this paper will be evaluated during the conceptual design to determine what amount of modularity should be included.

  2. Modular workcells: modern methods for laboratory automation.

    PubMed

    Felder, R A

    1998-12-01

    Laboratory automation is beginning to become an indispensable survival tool for laboratories facing difficult market competition. However, estimates suggest that only 8% of laboratories will be able to afford total laboratory automation systems. Therefore, automation vendors have developed alternative hardware configurations called 'modular automation', to fit the smaller laboratory. Modular automation consists of consolidated analyzers, integrated analyzers, modular workcells, and pre- and post-analytical automation. These terms will be defined in this paper. Using a modular automation model, the automated core laboratory will become a site where laboratory data is evaluated by trained professionals to provide diagnostic information to practising physicians. Modem software information management and process control tools will complement modular hardware. Proper standardization that will allow vendor-independent modular configurations will assure success of this revolutionary new technology.

  3. Modular, Hierarchical Learning By Artificial Neural Networks

    NASA Technical Reports Server (NTRS)

    Baldi, Pierre F.; Toomarian, Nikzad

    1996-01-01

    Modular and hierarchical approach to supervised learning by artificial neural networks leads to neural networks more structured than neural networks in which all neurons fully interconnected. These networks utilize general feedforward flow of information and sparse recurrent connections to achieve dynamical effects. The modular organization, sparsity of modular units and connections, and fact that learning is much more circumscribed are all attractive features for designing neural-network hardware. Learning streamlined by imitating some aspects of biological neural networks.

  4. Modular, Hierarchical Learning By Artificial Neural Networks

    NASA Technical Reports Server (NTRS)

    Baldi, Pierre F.; Toomarian, Nikzad

    1996-01-01

    Modular and hierarchical approach to supervised learning by artificial neural networks leads to neural networks more structured than neural networks in which all neurons fully interconnected. These networks utilize general feedforward flow of information and sparse recurrent connections to achieve dynamical effects. The modular organization, sparsity of modular units and connections, and fact that learning is much more circumscribed are all attractive features for designing neural-network hardware. Learning streamlined by imitating some aspects of biological neural networks.

  5. Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: a docking and molecular dynamics study.

    PubMed

    Anand, Swadha; Mohanty, Debasisa

    2012-05-28

    Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains. During the catalysis of various reductive steps these domains act on a substrate moiety which is covalently attached to the phosphopantetheine (P-pant) group of the holo-Acyl Carrier Protein (holo-ACP) domain, thus necessitating the formation of holo-ACP:DH and holo-ACP:KR complexes. Even though three dimensional structures are available for DH, KR and ACP domains, no structures are available for DH or KR domains in complex with ACP or substrate moieties. Since Ser of holo-ACP is covalently attached to a large phosphopantetheine group, obtaining complexes involving holo-ACP by standard protein-protein docking has been a difficult task. We have modeled the holo-ACP:DH and holo-ACP:KR complexes for identifying specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. A novel combination of protein-protein and protein-ligand docking has been used to first model complexes involving apo-ACP and then dock the phosphopantetheine and substrate moieties using covalent connectivity between ACP, phosphopantetheine and substrate moiety as constraints. The holo-ACP:DH and holo-ACP:KR complexes obtained from docking have been further refined by restraint free explicit solvent MD simulations to incorporate effects of ligand and receptor flexibilities. The results from 50 ns MD simulations reveal that substrate enters into a deep tunnel in DH domain while in case of KR domain the substrate binds a shallow surface exposed cavity. Interestingly, in case of DH domain the predicted binding site overlapped with the binding site in the inhibitor bound crystal structure of FabZ, the DH domain from E.Coli FAS. In case of KR domain, the substrate binding site identified by our simulations was in proximity of

  6. Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: a docking and molecular dynamics study

    PubMed Central

    2012-01-01

    Background Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains. During the catalysis of various reductive steps these domains act on a substrate moiety which is covalently attached to the phosphopantetheine (P-pant) group of the holo-Acyl Carrier Protein (holo-ACP) domain, thus necessitating the formation of holo-ACP:DH and holo-ACP:KR complexes. Even though three dimensional structures are available for DH, KR and ACP domains, no structures are available for DH or KR domains in complex with ACP or substrate moieties. Since Ser of holo-ACP is covalently attached to a large phosphopantetheine group, obtaining complexes involving holo-ACP by standard protein-protein docking has been a difficult task. Results We have modeled the holo-ACP:DH and holo-ACP:KR complexes for identifying specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. A novel combination of protein-protein and protein-ligand docking has been used to first model complexes involving apo-ACP and then dock the phosphopantetheine and substrate moieties using covalent connectivity between ACP, phosphopantetheine and substrate moiety as constraints. The holo-ACP:DH and holo-ACP:KR complexes obtained from docking have been further refined by restraint free explicit solvent MD simulations to incorporate effects of ligand and receptor flexibilities. The results from 50 ns MD simulations reveal that substrate enters into a deep tunnel in DH domain while in case of KR domain the substrate binds a shallow surface exposed cavity. Interestingly, in case of DH domain the predicted binding site overlapped with the binding site in the inhibitor bound crystal structure of FabZ, the DH domain from E.Coli FAS. In case of KR domain, the substrate binding site identified by our simulations

  7. 7SK small nuclear RNA, a multifunctional transcriptional regulatory RNA with gene-specific features.

    PubMed

    Egloff, Sylvain; Studniarek, Cécilia; Kiss, Tamás

    2017-08-18

    The 7SK small nuclear RNA is a multifunctional transcriptional regulatory RNA that controls the nuclear activity of the positive transcription elongation factor b (P-TEFb), specifically targets P-TEFb to the promoter regions of selected protein-coding genes and promotes transcription of RNA polymerase II-specific spliceosomal small nuclear RNA genes.

  8. Local bulk physics from intersecting modular Hamiltonians

    NASA Astrophysics Data System (ADS)

    Kabat, Daniel; Lifschytz, Gilad

    2017-06-01

    We show that bulk quantities localized on a minimal surface homologous to a boundary region correspond in the CFT to operators that commute with the modular Hamiltonian associated with the boundary region. If two such minimal surfaces intersect at a point in the bulk then CFT operators which commute with both extended modular Hamiltonians must be localized at the intersection point. We use this to construct local bulk operators purely from CFT considerations, without knowing the bulk metric, using intersecting modular Hamiltonians. For conformal field theories at zero and finite temperature the appropriate modular Hamiltonians are known explicitly and we recover known expressions for local bulk observables.

  9. Modular open RF architecture: extending VICTORY to RF systems

    NASA Astrophysics Data System (ADS)

    Melber, Adam; Dirner, Jason; Johnson, Michael

    2015-05-01

    Radio frequency products spanning multiple functions have become increasingly critical to the warfighter. Military use of the electromagnetic spectrum now includes communications, electronic warfare (EW), intelligence, and mission command systems. Due to the urgent needs of counterinsurgency operations, various quick reaction capabilities (QRCs) have been fielded to enhance warfighter capability. Although these QRCs were highly successfully in their respective missions, they were designed independently resulting in significant challenges when integrated on a common platform. This paper discusses how the Modular Open RF Architecture (MORA) addresses these challenges by defining an open architecture for multifunction missions that decomposes monolithic radio systems into high-level components with welldefined functions and interfaces. The functional decomposition maximizes hardware sharing while minimizing added complexity and cost due to modularization. MORA achieves significant size, weight and power (SWaP) savings by allowing hardware such as power amplifiers and antennas to be shared across systems. By separating signal conditioning from the processing that implements the actual radio application, MORA exposes previously inaccessible architecture points, providing system integrators with the flexibility to insert third-party capabilities to address technical challenges and emerging requirements. MORA leverages the Vehicular Integration for Command, Control, Communication, Computers, Intelligence, Surveillance, and Reconnaissance (C4ISR)/EW Interoperability (VICTORY) framework. This paper concludes by discussing how MORA, VICTORY and other standards such as OpenVPX are being leveraged by the U.S. Army Research, Development, and Engineering Command (RDECOM) Communications Electronics Research, Development, and Engineering Center (CERDEC) to define a converged architecture enabling rapid technology insertion, interoperability and reduced SWaP.

  10. Multifunctional self-assembled monolayers

    SciTech Connect

    Zawodzinski, T.; Bar, G.; Rubin, S.; Uribe, F.; Ferrais, J.

    1996-06-01

    This is the final report of at three year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The specific goals of this research project were threefold: to develop multifunctional self-assembled monolayers, to understand the role of monolayer structure on the functioning of such systems, and to apply this knowledge to the development of electrochemical enzyme sensors. An array of molecules that can be used to attach electrochemically active biomolecules to gold surfaces has been synthesized. Several members of a class of electroactive compounds have been characterized and the factors controlling surface modification are beginning to be characterized. Enzymes have been attached to self-assembled molecules arranged on the gold surface, a critical step toward the ultimate goal of this project. Several alternative enzyme attachment strategies to achieve robust enzyme- modified surfaces have been explored. Several means of juxtaposing enzymes and mediators, electroactive compounds through which the enzyme can exchange electrons with the electrode surface, have also been investigated. Finally, the development of sensitive biosensors based on films loaded with nanoscale-supported gold particles that have surface modified with the self-assembled enzyme and mediator have been explored.

  11. Multifunction automated crawling system (MACS)

    NASA Astrophysics Data System (ADS)

    Bar-Cohen, Yoseph; Backes, Paul G.; Joffe, Benjamin

    1996-11-01

    Nondestructive evaluation instruments and sensors are becoming smaller with enhanced computer controlled capability and increasingly use commercially available hardware and software. Further, robotic instruments are being developed to serve as mobility platforms allowing automation of the inspection process. This combination of miniaturized sensing and robotics technology enables hybrid miniature technology solutions for identified aircraft inspection needs. Integration of inspection and robotics technologies is benefited by the use of a standard computing platform. JPL investigated the application of telerobotic technology to inspection of aircraft structures using capabilities that were developed for use in space exploration. A miniature crawler that can travel on the surface of aircraft using suction cups for adherence was developed and is called multifunction automated crawling systems (MACS). MACS is an operational tool that can perform rapid large area inspection of aircraft, which has a relatively large platform to carry miniature inspection instruments payload. The capability of MACS and the trend towards autonomous inspection crawlers will be reviewed and discussed in this paper.

  12. Multifunctional nanorods for gene delivery

    NASA Astrophysics Data System (ADS)

    Salem, Aliasger K.; Searson, Peter C.; Leong, Kam W.

    2003-10-01

    The goal of gene therapy is to introduce foreign genes into somatic cells to supplement defective genes or provide additional biological functions, and can be achieved using either viral or synthetic non-viral delivery systems. Compared with viral vectors, synthetic gene-delivery systems, such as liposomes and polymers, offer several advantages including ease of production and reduced risk of cytotoxicity and immunogenicity, but their use has been limited by the relatively low transfection efficiency. This problem mainly stems from the difficulty in controlling their properties at the nanoscale. Synthetic inorganic gene carriers have received limited attention in the gene-therapy community, the only notable example being gold nanoparticles with surface-immobilized DNA applied to intradermal genetic immunization by particle bombardment. Here we present a non-viral gene-delivery system based on multisegment bimetallic nanorods that can simultaneously bind compacted DNA plasmids and targeting ligands in a spatially defined manner. This approach allows precise control of composition, size and multifunctionality of the gene-delivery system. Transfection experiments performed in vitro and in vivo provide promising results that suggest potential in genetic vaccination applications.

  13. Fusion of nacre, mussel, and lotus leaf: bio-inspired graphene composite paper with multifunctional integration.

    PubMed

    Zhong, Da; Yang, Qinglin; Guo, Lin; Dou, Shixue; Liu, Kesong; Jiang, Lei

    2013-07-07

    Multifunctional integration is an inherent characteristic for biological materials with multiscale structures. Learning from nature is an effective approach for scientists and engineers to construct multifunctional materials. In nature, mollusks (abalone), mussels, and the lotus have evolved different and optimized solutions to survive. Here, bio-inspired multifunctional graphene composite paper was fabricated in situ through the fusion of the different biological solutions from nacre (brick-and-mortar structure), mussel adhesive protein (adhesive property and reducing character), and the lotus leaf (self-cleaning effect). Owing to the special properties (self-polymerization, reduction, and adhesion), dopamine could be simultaneously used as a reducing agent for graphene oxide and as an adhesive, similar to the mortar in nacre, to crosslink the adjacent graphene. The resultant nacre-like graphene paper exhibited stable superhydrophobicity, self-cleaning, anti-corrosion, and remarkable mechanical properties underwater.

  14. Modular passive solar heating system

    SciTech Connect

    Hunter, B.D.

    1985-03-19

    A modular passive solar energy storage system comprises a plurality of heat tubes which are arranged to form a flat plate solar collector and are releasably connected to a water reservoir by, and are part of, double-walled heat exchangers which penetrate to the water reservoir and enhance the heat transfer characteristics between the collector and the reservoir. The flat plate collector-heat exchanger disassembly, the collector housing, and the reservoir are integrated into a relatively light weight, unitary structural system in which the reservoir is a primary structural element. In addition to light weight, the system features high efficiency and ease of assembly and maintenance.

  15. Modular design attitude control system

    NASA Technical Reports Server (NTRS)

    Chichester, F. D.

    1984-01-01

    A sequence of single axismodels and a series of reduced state linear observers of minimum order are used to reconstruct inaccessible variables pertaining to the modular attitude control of a rigid body flexible suspension model of a flexible spacecraft. The single axis models consist of two, three, four, and five rigid bodies, each interconnected by a flexible shaft passing through the mass centers of the bodies. Modal damping is added to each model. Reduced state linear observers are developed for synthesizing the inaccessible modal state variables for each modal model.

  16. Modular design attitude control system

    NASA Technical Reports Server (NTRS)

    Chichester, F. D.

    1983-01-01

    Application of modular control techniques to the attitude control of a prototype flexible spacecraft and a prototype flexible space platform was further developed by determining numerical values for the physical parameters of a four body approximation of the MSFC/hybrid deployable truss incorporated in the space platform model, generating sensitivity coefficients for the model of the flexible spacecraft, evaluating the changes in the digital computer simulation of the flexible spacecraft resulting from the addition of another rigid body to the model and comparing attitude control effectiveness with actuators on more than one rigid body of the model with that for the case in which the actuators were restricted to one body.

  17. Cascading dynamics in modular networks

    NASA Astrophysics Data System (ADS)

    Galstyan, Aram; Cohen, Paul

    2007-03-01

    In this paper we study a simple cascading process in a structured heterogeneous population, namely, a network composed of two loosely coupled communities. We demonstrate that under certain conditions the cascading dynamics in such a network has a two-tiered structure that characterizes activity spreading at different rates in the communities. We study the dynamics of the model using both simulations and an analytical approach based on annealed approximation and obtain good agreement between the two. Our results suggest that network modularity might have implications in various applications, such as epidemiology and viral marketing.

  18. Integrated modular engine - Reliability assessment

    NASA Astrophysics Data System (ADS)

    Parsley, R. C.; Ward, T. B.

    1992-07-01

    A major driver in the increased interest in integrated modular engine configurations is the desire for ultra reliability for future rocket propulsion systems. The concept of configuring multiple sets of turbomachinery networked to multiple thrust chamber assemblies has been identified as an approach with potential to achieve significant reliability enhancement. This paper summarizes the results of a reliability study comparing networked systems vs. discrete engine installations, both with and without major module and engine redundancy. The study was conducted for gas generator, expander, and staged combustion cycles. The results are representative of either booster or upper-stage applications and are indicative of either plug or nonplug installation philosophies.

  19. Mussel-inspired dendritic polymers as universal multifunctional coatings.

    PubMed

    Wei, Qiang; Achazi, Katharina; Liebe, Hendrik; Schulz, Andrea; Noeske, Paul-Ludwig Michael; Grunwald, Ingo; Haag, Rainer

    2014-10-20

    A rapid and universal approach for multifunctional material coatings was developed based on a mussel-inspired dendritic polymer. This new kind of polymer mimics not only the functional groups of mussel foot proteins (mfps) but also their molecular weight and molecular structure. The large number of catechol and amine groups set the basis for heteromultivalent anchoring and crosslinking. The molecular weight reaches 10 kDa, which is similar to the most adhesive mussel foot protein mfp-5. Also, the dendritic structure exposes its functional groups on the surface like the folded proteins. As a result, a very stable coating can be prepared on virtually any type of material surface within 10 min by a simple dip-coating method, which is as fast as the formation of mussel byssal threads in nature. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Fusion of nacre, mussel, and lotus leaf: bio-inspired graphene composite paper with multifunctional integration

    NASA Astrophysics Data System (ADS)

    Zhong, Da; Yang, Qinglin; Guo, Lin; Dou, Shixue; Liu, Kesong; Jiang, Lei

    2013-06-01

    Multifunctional integration is an inherent characteristic for biological materials with multiscale structures. Learning from nature is an effective approach for scientists and engineers to construct multifunctional materials. In nature, mollusks (abalone), mussels, and the lotus have evolved different and optimized solutions to survive. Here, bio-inspired multifunctional graphene composite paper was fabricated in situ through the fusion of the different biological solutions from nacre (brick-and-mortar structure), mussel adhesive protein (adhesive property and reducing character), and the lotus leaf (self-cleaning effect). Owing to the special properties (self-polymerization, reduction, and adhesion), dopamine could be simultaneously used as a reducing agent for graphene oxide and as an adhesive, similar to the mortar in nacre, to crosslink the adjacent graphene. The resultant nacre-like graphene paper exhibited stable superhydrophobicity, self-cleaning, anti-corrosion, and remarkable mechanical properties underwater.Multifunctional integration is an inherent characteristic for biological materials with multiscale structures. Learning from nature is an effective approach for scientists and engineers to construct multifunctional materials. In nature, mollusks (abalone), mussels, and the lotus have evolved different and optimized solutions to survive. Here, bio-inspired multifunctional graphene composite paper was fabricated in situ through the fusion of the different biological solutions from nacre (brick-and-mortar structure), mussel adhesive protein (adhesive property and reducing character), and the lotus leaf (self-cleaning effect). Owing to the special properties (self-polymerization, reduction, and adhesion), dopamine could be simultaneously used as a reducing agent for graphene oxide and as an adhesive, similar to the mortar in nacre, to crosslink the adjacent graphene. The resultant nacre-like graphene paper exhibited stable superhydrophobicity, self