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Sample records for design rational snake

  1. Identification of New Snake Venom Metalloproteinase Inhibitors Using Compound Screening and Rational Peptide Design

    PubMed Central

    2012-01-01

    The majority of snakebite envenomations in Central America are caused by the viperid species Bothrops asper, whose venom contains a high proportion of zinc-dependent metalloproteinases that play a relevant role in the pathogenesis of hemorrhage characteristic of these envenomations. Broad metalloproteinase inhibitors, such as the peptidomimetic hydroxamate Batimastat, have been shown to inhibit snake venom metalloproteinases (SVMP). However, the difficulty in having open public access to Batimastat and similar molecules highlights the need to design new inhibitors of SVMPs that could be applied in the treatment of snakebite envenomations. We have chosen the SVMP BaP1 as a model to search for new inhibitors using different strategies, that is, screening of the Prestwick Chemical Library and rational peptide design. Results from these approaches provide clues on the structural requirements for efficient BaP1 inhibition and pave the way for the design of new inhibitors of SVMP. PMID:24900507

  2. Identification of new snake venom metalloproteinase inhibitors using compound screening and rational Peptide design.

    PubMed

    Villalta-Romero, Fabián; Gortat, Anna; Herrera, Andrés E; Arguedas, Rebeca; Quesada, Javier; de Melo, Robson Lopes; Calvete, Juan J; Montero, Mavis; Murillo, Renato; Rucavado, Alexandra; Gutiérrez, José María; Pérez-Payá, Enrique

    2012-07-12

    The majority of snakebite envenomations in Central America are caused by the viperid species Bothrops asper, whose venom contains a high proportion of zinc-dependent metalloproteinases that play a relevant role in the pathogenesis of hemorrhage characteristic of these envenomations. Broad metalloproteinase inhibitors, such as the peptidomimetic hydroxamate Batimastat, have been shown to inhibit snake venom metalloproteinases (SVMP). However, the difficulty in having open public access to Batimastat and similar molecules highlights the need to design new inhibitors of SVMPs that could be applied in the treatment of snakebite envenomations. We have chosen the SVMP BaP1 as a model to search for new inhibitors using different strategies, that is, screening of the Prestwick Chemical Library and rational peptide design. Results from these approaches provide clues on the structural requirements for efficient BaP1 inhibition and pave the way for the design of new inhibitors of SVMP. PMID:24900507

  3. Snakes! Snakes! Snakes!

    ERIC Educational Resources Information Center

    Nature Naturally, 1983

    1983-01-01

    Designed for students in grades 4-6, the teaching unit presents illustrations and facts about snakes. Topics include common snakes found in the United States, how snakes eat, how snakes shed their skin, poisonous snakes, the Eastern Indigo snake, and the anatomy of a snake. A student page includes a crossword puzzle and surprising snake facts. A…

  4. Rational design of nanomaterials for water treatment

    NASA Astrophysics Data System (ADS)

    Li, Renyuan; Zhang, Lianbin; Wang, Peng

    2015-10-01

    The ever-increasing human demand for safe and clean water is gradually pushing conventional water treatment technologies to their limits. It is now a popular perception that the solutions to the existing and future water challenges will hinge upon further developments in nanomaterial sciences. The concept of rational design emphasizes on `design-for-purpose' and it necessitates a scientifically clear problem definition to initiate the nanomaterial design. The field of rational design of nanomaterials for water treatment has experienced a significant growth in the past decade and is poised to make its contribution in creating advanced next-generation water treatment technologies in the years to come. Within the water treatment context, this review offers a comprehensive and in-depth overview of the latest progress in rational design, synthesis and applications of nanomaterials in adsorption, chemical oxidation and reduction reactions, membrane-based separation, oil-water separation, and synergistic multifunctional all-in-one nanomaterials/nanodevices. Special attention is paid to the chemical concepts related to nanomaterial design throughout the review.

  5. Rational design of nanomaterials for water treatment.

    PubMed

    Li, Renyuan; Zhang, Lianbin; Wang, Peng

    2015-11-01

    The ever-increasing human demand for safe and clean water is gradually pushing conventional water treatment technologies to their limits. It is now a popular perception that the solutions to the existing and future water challenges will hinge upon further developments in nanomaterial sciences. The concept of rational design emphasizes on 'design-for-purpose' and it necessitates a scientifically clear problem definition to initiate the nanomaterial design. The field of rational design of nanomaterials for water treatment has experienced a significant growth in the past decade and is poised to make its contribution in creating advanced next-generation water treatment technologies in the years to come. Within the water treatment context, this review offers a comprehensive and in-depth overview of the latest progress in rational design, synthesis and applications of nanomaterials in adsorption, chemical oxidation and reduction reactions, membrane-based separation, oil-water separation, and synergistic multifunctional all-in-one nanomaterials/nanodevices. Special attention is paid to the chemical concepts related to nanomaterial design throughout the review.

  6. Computational Methods Applied to Rational Drug Design

    PubMed Central

    Ramírez, David

    2016-01-01

    Due to the synergic relationship between medical chemistry, bioinformatics and molecular simulation, the development of new accurate computational tools for small molecules drug design has been rising over the last years. The main result is the increased number of publications where computational techniques such as molecular docking, de novo design as well as virtual screening have been used to estimate the binding mode, site and energy of novel small molecules. In this work I review some tools, which enable the study of biological systems at the atomistic level, providing relevant information and thereby, enhancing the process of rational drug design. PMID:27708723

  7. Rational design and synthesis of Janus composites.

    PubMed

    Liang, Fuxin; Zhang, Chengliang; Yang, Zhenzhong

    2014-10-29

    Janus composites with two different components divided on the same object have gained growing interest in many fields, such as solid emulsion stabilizers, sensors, optical probes and self-propellers. Over the past twenty years, various synthesis methods have been developed including Pickering emulsion interfacial modification, block copolymer self-assembly, microfluidics, electro co-jetting, and swelling emulsion polymerization. Anisotropic shape and asymmetric spatial distribution of compositions and functionalities determine their unique performances. Rational design and large scale synthesis of functional Janus materials are crucial for the systematical characterization of performance and exploitation of practical applications.

  8. Rational Experimental Design for Electrical Resistivity Imaging

    NASA Astrophysics Data System (ADS)

    Mitchell, V.; Pidlisecky, A.; Knight, R.

    2008-12-01

    Over the past several decades advances in the acquisition and processing of electrical resistivity data, through multi-channel acquisition systems and new inversion algorithms, have greatly increased the value of these data to near-surface environmental and hydrological problems. There has, however, been relatively little advancement in the design of actual surveys. Data acquisition still typically involves using a small number of traditional arrays (e.g. Wenner, Schlumberger) despite a demonstrated improvement in data quality from the use of non-standard arrays. While optimized experimental design has been widely studied in applied mathematics and the physical and biological sciences, it is rarely implemented for non-linear problems, such as electrical resistivity imaging (ERI). We focus specifically on using ERI in the field for monitoring changes in the subsurface electrical resistivity structure. For this application we seek an experimental design method that can be used in the field to modify the data acquisition scheme (spatial and temporal sampling) based on prior knowledge of the site and/or knowledge gained during the imaging experiment. Some recent studies have investigated optimized design of electrical resistivity surveys by linearizing the problem or with computationally-intensive search algorithms. We propose a method for rational experimental design based on the concept of informed imaging, the use of prior information regarding subsurface properties and processes to develop problem-specific data acquisition and inversion schemes. Specifically, we use realistic subsurface resistivity models to aid in choosing source configurations that maximize the information content of our data. Our approach is based on first assessing the current density within a region of interest, in order to provide sufficient energy to the region of interest to overcome a noise threshold, and then evaluating the direction of current vectors, in order to maximize the

  9. Rational Design of Biobetters with Enhanced Stability.

    PubMed

    Courtois, Fabienne; Schneider, Curtiss P; Agrawal, Neeraj J; Trout, Bernhardt L

    2015-08-01

    Biotherapeutics are the fastest growing class of pharmaceutical with a rapidly evolving market facing the rise of biosimilar and biobetter products. In contrast to a biosimilar, which is derived from the same gene sequence as the innovator product, a biobetter has enhanced properties, such as enhanced efficacy or reduced immunogenicity. Little work has been carried out so far to increase the intrinsic stability of biotherapeutics via sequence changes, even though, aggregation, the primary degradation pathway of proteins, leads to issues ranging from manufacturing failure to immunological response and to loss of therapeutic activity. Using our spatial aggregation propensity tool as a first step to a rational design approach to identify aggregation-prone regions, biobetters of rituximab have been produced with enhanced stability by introducing site-specific mutations. Significant stabilization against aggregation was achieved for rituximab with no decrease in its binding affinity to the antigen.

  10. Metalated Hexaphyrins: From Understanding to Rational Design.

    PubMed

    Alonso, Mercedes; Pinter, Balazs; Geerlings, Paul; De Proft, Frank

    2015-12-01

    The heretofore unpredictable behavior of [26] and [28]hexaphyrins upon metalation has been elucidated through quantum chemical calculations. It is demonstrated that the molecular topology of Group 10 and Group 11 metal complexes of hexaphyrins depends on sensitive interplay between the intrinsic ligand strain and the metal-ligand interaction strength. As such, the aromaticity of the ligand and effective charge of the metal are revealed as key factors determining the binding mode and the preference for Möbius or Hückel structures. These findings offer a new perspective to rationalize experimental observations for metalated hexaphyrins. More importantly, the proposed guidelines could be useful for designing novel complexes of hexaphyrins, such as a hitherto unknown Möbius [26]hexaphyrin complex. PMID:26462865

  11. Rationally designed substrates for SERS biosensing

    NASA Astrophysics Data System (ADS)

    Yan, Bo

    The large electromagnetic field enhancement provided by nanostructured noble metal surfaces forms the foundation for a series of enabling optical analytical techniques, such as surface enhanced Raman spectroscopy (SERS), surface enhanced IR absorption spectroscopy (SEIRA), surface enhanced fluorescent microscopy (SEF), to name only a few. Critical sensing applications have, however, other substrate requirements than mere peak signal enhancement. The substrate needs to be reliable, provide reproducible signal enhancements, and be amenable to a combination with microfluidic chips or other integrated sensor platforms. These needs motivate the development of engineerable SERS substrate "chips" with defined near- and far-field responses. In this dissertation, two types of rationally designed SERS substrates - nanoparticle cluster arrays (NCAs) and SERS stamp - will be introduced and characterized. NCAs were fabricated through a newly developed template guided self-assembly fabrication approach, in which chemically synthesized nanoparticles are integrated into predefined patterns using a hybrid top-down/bottom-up approach. Since this method relies on chemically defined building blocks, it can overcome the resolution limit of conventional lithographical methods and facilitates higher structural complexity. NCAs sustain near-field interactions within individual clusters as well as between entire neighboring clusters and create a multi-scale cascaded E-field enhancement throughout the entire array. SERS stamps were generated using an oblique angle metal deposition on a lithographically defined piston. When mounted on a nanopositioning stage, the SERS stamps were enabled to contact biological surfaces with pristine nanostructured metal surfaces for a label-free spectroscopic characterization. The developed engineered substrates were applied and tested in critical sensing applications, including the ultra-trace detection of explosive vapors, the rapid discrimination of

  12. Rationally designing the mechanical properties of protein hydrogels

    NASA Astrophysics Data System (ADS)

    Cao, Yi

    Naturally occurring biomaterials possess diverse mechanical properties, which are critical to their unique biological functions. However, it remains challenging to rationally control the mechanical properties of synthetic biomaterials. Here we provide a bottom-up approach to rationally design the mechanical properties of protein-based hydrogels. We first use atomic fore microscope (AFM) based single-molecule force spectroscopy to characterize the mechanical stability of individual protein building blocks. We then rationally design the mechanical properties of hydrogels by selecting different combination of protein building blocks of known mechanical properties. As a proof-of-principle, we demonstrate the engineering of hydrogels of distinct extensibility and toughness. This simple combinatorial approach allows direct translation of the mechanical properties of proteins from the single molecule level to the macroscopic level and represents an important step towards rationally designing the mechanical properties of biomaterials.

  13. Rational design of all organic polymer dielectrics

    NASA Astrophysics Data System (ADS)

    Sharma, Vinit; Wang, Chenchen; Lorenzini, Robert G.; Ma, Rui; Zhu, Qiang; Sinkovits, Daniel W.; Pilania, Ghanshyam; Oganov, Artem R.; Kumar, Sanat; Sotzing, Gregory A.; Boggs, Steven A.; Ramprasad, Rampi

    2014-09-01

    To date, trial and error strategies guided by intuition have dominated the identification of materials suitable for a specific application. We are entering a data-rich, modelling-driven era where such Edisonian approaches are gradually being replaced by rational strategies, which couple predictions from advanced computational screening with targeted experimental synthesis and validation. Here, consistent with this emerging paradigm, we propose a strategy of hierarchical modelling with successive downselection stages to accelerate the identification of polymer dielectrics that have the potential to surpass ‘standard’ materials for a given application. Successful synthesis and testing of some of the most promising identified polymers and the measured attractive dielectric properties (which are in quantitative agreement with predictions) strongly supports the proposed approach to material selection.

  14. Rational drug design paradigms: the odyssey for designing better drugs.

    PubMed

    Kellici, Tahsin; Ntountaniotis, Dimitrios; Vrontaki, Eleni; Liapakis, George; Moutevelis-Minakakis, Panagiota; Kokotos, George; Hadjikakou, Sotiris; Tzakos, Andreas G; Afantitis, Antreas; Melagraki, Georgia; Bryant, Sharon; Langer, Thierry; Di Marzo, Vincenzo; Mavromoustakos, Thomas

    2015-01-01

    Due to the time and effort requirements for the development of a new drug, and the high attrition rates associated with this developmental process, there is an intense effort by academic and industrial researchers to find novel ways for more effective drug development schemes. The first step in the discovery process of a new drug is the identification of the lead compound. The modern research tendency is to avoid the synthesis of new molecules based on chemical intuition, which is time and cost consuming, and instead to apply in silico rational drug design. This approach reduces the consumables and human personnel involved in the initial steps of the drug design. In this review real examples from our research activity aiming to discover new leads will be given for various dire warnings diseases. There is no recipe to follow for discovering new leads. The strategy to be followed depends on the knowledge of the studied system and the experience of the researchers. The described examples constitute successful and unsuccessful efforts and reflect the reality which medicinal chemists have to face in drug design and development. The drug stability is also discussed in both organic molecules and metallotherapeutics. This is an important issue in drug discovery as drug metabolism in the body can lead to various toxic and undesired molecules.

  15. Rational drug design paradigms: the odyssey for designing better drugs.

    PubMed

    Kellici, Tahsin; Ntountaniotis, Dimitrios; Vrontaki, Eleni; Liapakis, George; Moutevelis-Minakakis, Panagiota; Kokotos, George; Hadjikakou, Sotiris; Tzakos, Andreas G; Afantitis, Antreas; Melagraki, Georgia; Bryant, Sharon; Langer, Thierry; Di Marzo, Vincenzo; Mavromoustakos, Thomas

    2015-01-01

    Due to the time and effort requirements for the development of a new drug, and the high attrition rates associated with this developmental process, there is an intense effort by academic and industrial researchers to find novel ways for more effective drug development schemes. The first step in the discovery process of a new drug is the identification of the lead compound. The modern research tendency is to avoid the synthesis of new molecules based on chemical intuition, which is time and cost consuming, and instead to apply in silico rational drug design. This approach reduces the consumables and human personnel involved in the initial steps of the drug design. In this review real examples from our research activity aiming to discover new leads will be given for various dire warnings diseases. There is no recipe to follow for discovering new leads. The strategy to be followed depends on the knowledge of the studied system and the experience of the researchers. The described examples constitute successful and unsuccessful efforts and reflect the reality which medicinal chemists have to face in drug design and development. The drug stability is also discussed in both organic molecules and metallotherapeutics. This is an important issue in drug discovery as drug metabolism in the body can lead to various toxic and undesired molecules. PMID:25747445

  16. Computational approaches for rational design of proteins with novel functionalities.

    PubMed

    Tiwari, Manish Kumar; Singh, Ranjitha; Singh, Raushan Kumar; Kim, In-Won; Lee, Jung-Kul

    2012-01-01

    Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.

  17. Rational Design of Immunostimulatory siRNAs

    PubMed Central

    Gantier, Michael P; Tong, Stephen; Behlke, Mark A; Irving, Aaron T; Lappas, Martha; Nilsson, Ulrika W; Latz, Eicke; McMillan, Nigel AJ; Williams, Bryan RG

    2010-01-01

    Short-interfering RNAs (siRNAs) have engendered much enthusiasm for their ability to silence the expression of specific genes. However, it is now well established that siRNAs, depending on their sequence, can be variably sensed by the innate immune system through recruitment of toll-like receptors 7 and 8 (TLR7/8). Here, we aimed to identify sequence-based modifications allowing for the design of bifunctional siRNAs with both proinflammatory and specific silencing activities, and with potentially increased therapeutic benefits. We found that the introduction of a micro-RNA (miRNA)-like nonpairing uridine-bulge in the passenger strand robustly increased immunostimulatory activity on human immune cells. This sequence modification had no effect on the silencing efficiency of the siRNA. Increased immunostimulation with the uridine-bulge design was specific to human cells, and conserved silencing efficiency required a Dicer-substrate scaffold. The increased cytokine production with the uridine-bulge design resulted in enhanced protection against Semliki Forest virus (SFV) infection, in viral assays. Thus, we characterize a design scaffold applicable to any given siRNA sequence, that results in increased innate immune activation without affecting gene silencing. Our data suggest that this sequence modification coupled with structural modification differentially recruits human TLR8 over TLR7, and could have potential application in antiviral therapies. PMID:20125126

  18. Rational design of efficient modular cells.

    PubMed

    Trinh, Cong T; Liu, Yan; Conner, David J

    2015-11-01

    The modular cell design principle is formulated to devise modular (chassis) cells. These cells can be assembled with exchangeable production modules in a plug-and-play fashion to build microbial cell factories for efficient combinatorial biosynthesis of novel molecules, requiring minimal iterative strain optimization steps. A modular cell is designed to be auxotrophic, containing core metabolic pathways that are necessary but insufficient to support cell growth and maintenance. To be functional, it must tightly couple with an exchangeable production module containing auxiliary metabolic pathways that not only complement cell growth but also enhance production of targeted molecules. We developed a MODCELL (modular cell) framework based on metabolic pathway analysis to implement the modular cell design principle. MODCELL identifies genetic modifications and requirements to construct modular cell candidates and their associated exchangeable production modules. By defining the degree of similarity and coupling metrics, MODCELL can evaluate which exchangeable production module(s) can be tightly coupled with a modular cell candidate. We first demonstrated how MODCELL works in a step-by-step manner for example metabolic networks, and then applied it to design modular Escherichia coli cells for efficient combinatorial biosynthesis of five alcohols (ethanol, propanol, isopropanol, butanol and isobutanol) and five butyrate esters (ethyl butyrate, propyl butyrate, isopropyl butyrate, butyl butyrate and isobutyl butyrate) from pentose sugars (arabinose and xylose) and hexose sugars (glucose, mannose, and galactose) under anaerobic conditions. We identified three modular cells, MODCELL1, MODCELL2 and MODCELL3, that can couple well with Group 1 of modules (ethanol, isobutanol, butanol, ethyl butyrate, isobutyl butyrate, butyl butyrate), Group 2 (isopropanol, isopropyl butyrate), and Group 3 (propanol, isopropanol), respectively. We validated the design of MODCELL1 for anaerobic

  19. Object design using blending of rational Timmer

    NASA Astrophysics Data System (ADS)

    Ramli, Norhidayah; Ali, Jamaludin Md.

    2014-07-01

    Timmer function was introduced by Harry Timmer but the function did not get enough exposure since it did not satisfy the convex hull property. This function is an advance of Bezier function. The function is used in this paper as it produce a curve that near the control polygon and it easier to use as blending function. This function is being started with Timmer cubic function. This study is carried out to extend the previous research which using the Timmer function by deriving the higher order Timmer blending function such as quartic and quantic function. The design of object using Timmer quintic blending function derivation is implemented. The usage of quintic Timmer function is to make the manipulation of control points easier and will produce the higher order blending design.

  20. Rational Design of Zinc Phosphide Heterojunction Photovoltaics

    NASA Astrophysics Data System (ADS)

    Bosco, Jeffrey Paul

    The prospect of terawatt-scale electricity generation using a photovoltaic (PV) device places strict requirements on the active semiconductor optoelectronic properties and elemental abundance. After reviewing the constraints placed on an ``earth-abundant'' solar absorber, we find zinc phosphide (α-Zn 3P2) to be an ideal candidate. In addition to its near-optimal direct band gap of 1.5 eV, high visible-light absorption coefficient (>10. 4cm-1), and long minority-carrier diffusion length (>5 μm), Zn3P 2 is composed of abundant Zn and P elements and has excellent physical properties for scalable thin-film deposition. However, to date, a Zn 3P2 device of sufficient efficiency for commercial applications has not been demonstrated. Record efficiencies of 6.0% for multicrystalline and 4.3% for thin-film cells have been reported, respectively. Performance has been limited by the intrinsic p-type conductivity of Zn3P 2 which restricts us to Schottky and heterojunction device designs. Due to our poor understanding of Zn3P2 interfaces, an ideal heterojunction partner has not yet been found. The goal of this thesis is to explore the upper limit of solar conversion efficiency achievable with a Zn3P2 absorber through the design of an optimal heterojunction PV device. To do so, we investigate three key aspects of material growth, interface energetics, and device design. First, the growth of Zn3P2 on GaAs(001) is studied using compound-source molecular-beam epitaxy (MBE). We successfully demonstrate the pseudomorphic growth of Zn3P2 epilayers of controlled orientation and optoelectronic properties. Next, the energy-band alignments of epitaxial Zn3P2 and II-VI and III-V semiconductor interfaces are measured via high-resolution x-ray photoelectron spectroscopy in order to determine the most appropriate heterojunction partner. From this work, we identify ZnSe as a nearly ideal n-type emitter for a Zn3P 2 PV device. Finally, various II-VI/Zn3P2 heterojunction solar cells designs are

  1. [Democratic institutional design in health care priority setting and rationing].

    PubMed

    Landwehr, Claudia

    2012-01-01

    Decisions on priority setting and rationing in health care have both informational and distributional aspects, which is why they require expert knowledge and specialised bodies on the one hand and democratic consent on the other hand. The paper presents normative criteria for the evaluation and empirical categories for the description and comparison of respective bodies. As procedural decisions always have implications for resulting distributional decisions, the bodies charged with priority setting and rationing decisions must be subject to democratic institutional design. (As supplied by publisher).

  2. Rational Design of a Structural and Functional Nitric Oxide Reductase

    SciTech Connect

    Yeung, N.; Lin, Y; Gao, Y; Zhao, X; Russell, B; Lei, L; Miner, L; Robinson, H; Lu, Y

    2009-01-01

    Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally, it is more difficult to design functional proteins. In comparison to recent successes in designing non-metalloproteins, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes. This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem FeB centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico.

  3. Rational design and nanofabrication of gecko-inspired fibrillar adhesives.

    PubMed

    Hu, Shihao; Xia, Zhenhai

    2012-08-20

    Gecko feet integrate many intriguing functions such as strong adhesion, easy detachment, and self-cleaning. Mimicking gecko toe pad structure leads to the development of new types of fibrillar adhesives useful for various applications. In this Concept article, in addition to the design of adhesive mimics by replicating gecko geometric features, we show a new trend of rational design by adding other physical, chemical, and biological principles on to the geometric merits, for enhancing robustness, responsive control, and durability. Current challenges and future directions are highlighted in the design and nanofabrication of biomimetic fibrillar adhesives.

  4. Rational principles of compound selection for combinatorial library design.

    PubMed

    Tropsha, Alexander; Zheng, Weifan

    2002-03-01

    It is practically impossible in a short period of time to synthesize and test all compounds in any large exhaustive chemical library. We discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for both targeted and diverse library design. For targeted library design, we consider principles based on the similarity to lead molecules. In the case of diverse library design, we discuss algorithms aimed at the selection of both diverse and representative subsets of the entire chemical library space. We illustrate methodologies with several practical examples.

  5. Rational design of semiconductors for photoelectrochemical water splitting

    NASA Astrophysics Data System (ADS)

    Wei, Su-Huai

    2013-12-01

    Using first-principles method as a tool, we discuss the general strategies for the rational design of semiconductors to simultaneously meet all of requirements for high-efficiency, solar-driven photoelectrochemical (PEC) water-splitting devices. Our studies demonstrate that theoretical calculations, which provided deep understanding of the underlying physics behind these PEC materials, can greatly accelerate scientific discovery of new PEC materials in this exciting field.

  6. Synthetic Biology: Rational Pathway Design for Regenerative Medicine.

    PubMed

    Davies, Jamie A

    2016-01-01

    Rational pathway design is the invention of an optimally efficient route from one state (e.g. chemical structure, state of differentiation, physiological state) to another, based on knowledge of biological processes: it contrasts with the use of natural pathways that have evolved by natural selection. Synthetic biology is a hybrid discipline of biology and engineering that offers a means for rationally designed pathways to be realized in living cells. Several areas of regenerative medicine could benefit from rational pathway design, including derivation of patient-specific stem cells, directed differentiation of stem cells, replicating physiological function in an alternative cell type, construction of custom interface tissues and building fail-safe systems into transplanted tissues. Synthetic biological approaches offer the potential for construction of these, for example controllable ex vivo stem cell niches, genetic networks for direct transdifferentiation from adult fibroblast to restricted stem cell without going via induced pluripotent stem cells, signalling pathways for realizing physiological regulation in alternative cell types, morphological modules for producing self-constructing novel 'tissues' and 'kill-switches' for therapeutically applied stem cells. Given the potential of this approach, a closer convergence of the regenerative medicine and synthetic biology research fields seems timely.

  7. Host defense mechanism-based rational design of live vaccine.

    PubMed

    Jang, Yo Han; Byun, Young Ho; Lee, Kwang-Hee; Park, Eun-Sook; Lee, Yun Ha; Lee, Yoon-Jae; Lee, Jinhee; Kim, Kyun-Hwan; Seong, Baik Lin

    2013-01-01

    Live attenuated vaccine (LAV), mimicking natural infection, provides an excellent protection against microbial infection. The development of LAV, however, still remains highly empirical and the rational design of clinically useful LAV is scarcely available. Apoptosis and caspase activation are general host antiviral responses in virus-infected cells. Utilizing these tightly regulated host defense mechanisms, we present a novel apoptosis-triggered attenuation of viral virulence as a rational design of live attenuated vaccine with desired levels of safety, efficacy, and productivity. Mutant influenza viruses carrying caspase recognition motifs in viral NP and the interferon-antagonist NS1 proteins were highly attenuated both in vitro and in vivo by caspase-mediated cleavage of those proteins in infected cells. Both viral replication and interferon-resistance were substantially reduced, resulting in a marked attenuation of virulence of the virus. Despite pronounced attenuation, the viruses demonstrated high growth phenotype in embryonated eggs at lower temperature, ensuring its productivity. A single dose vaccination with the mutant virus elicited high levels of systemic and mucosal antibody responses and provided complete protection against both homologous and heterologous lethal challenges in mouse model. While providing a practical means to generate seasonal or pandemic influenza live vaccines, the sensitization of viral proteins to pathogen-triggered apoptotic signals presents a potentially universal, mechanism-based rational design of live vaccines against many viral infections.

  8. Evolving protocells to prototissues: rational design of a missing link.

    PubMed

    Mantri, Shiksha; Sapra, K Tanuj

    2013-10-01

    Realization of a functional artificial cell, the so-called protocell, is a major challenge posed by synthetic biology. A subsequent goal is to use the protocellular units for the bottom-up assembly of prototissues. There is, however, a looming chasm in our knowledge between protocells and prototissues. In the present paper, we give a brief overview of the work on protocells to date, followed by a discussion on the rational design of key structural elements specific to linking two protocellular bilayers. We propose that designing synthetic parts capable of simultaneous insertion into two bilayers may be crucial in the hierarchical assembly of protocells into a functional prototissue. PMID:24059502

  9. Rational design of inorganic dielectric materials with expected permittivity

    NASA Astrophysics Data System (ADS)

    Xie, Congwei; Oganov, Artem R.; Dong, Dong; Liu, Ning; Li, Duan; Debela, Tekalign Terfa

    2015-11-01

    Techniques for rapid design of dielectric materials with appropriate permittivity for many important technological applications are urgently needed. It is found that functional structure blocks (FSBs) are helpful in rational design of inorganic dielectrics with expected permittivity. To achieve this, coordination polyhedra are parameterized as FSBs and a simple empirical model to evaluate permittivity based on these FSB parameters is proposed. Using this model, a wide range of examples including ferroelectric, high/low permittivity materials are discussed, resulting in several candidate materials for experimental follow-up.

  10. Rational design of inorganic dielectric materials with expected permittivity

    PubMed Central

    Xie, Congwei; Oganov, Artem R.; Dong, Dong; Liu, Ning; Li, Duan; Debela, Tekalign Terfa

    2015-01-01

    Techniques for rapid design of dielectric materials with appropriate permittivity for many important technological applications are urgently needed. It is found that functional structure blocks (FSBs) are helpful in rational design of inorganic dielectrics with expected permittivity. To achieve this, coordination polyhedra are parameterized as FSBs and a simple empirical model to evaluate permittivity based on these FSB parameters is proposed. Using this model, a wide range of examples including ferroelectric, high/low permittivity materials are discussed, resulting in several candidate materials for experimental follow-up. PMID:26617342

  11. Rational design of inorganic dielectric materials with expected permittivity.

    PubMed

    Xie, Congwei; Oganov, Artem R; Dong, Dong; Liu, Ning; Li, Duan; Debela, Tekalign Terfa

    2015-11-30

    Techniques for rapid design of dielectric materials with appropriate permittivity for many important technological applications are urgently needed. It is found that functional structure blocks (FSBs) are helpful in rational design of inorganic dielectrics with expected permittivity. To achieve this, coordination polyhedra are parameterized as FSBs and a simple empirical model to evaluate permittivity based on these FSB parameters is proposed. Using this model, a wide range of examples including ferroelectric, high/low permittivity materials are discussed, resulting in several candidate materials for experimental follow-up.

  12. Rational design and synthesis of semi-conducting polymers.

    SciTech Connect

    Wong, Bryan Matthew; Reeder, Craig; Cordaro, Joseph Gabriel

    2010-12-01

    A rational approach was used to design polymeric materials for thin-film electronics applications, whereby theoretical modeling was used to determine synthetic targets. Time-dependent density functional theory calculations were used as a tool to predict the electrical properties of conjugated polymer systems. From these results, polymers with desirable energy levels and band-gaps were designed and synthesized. Measurements of optoelectronic properties were performed on the synthesized polymers and the results were compared to those of the theoretical model. From this work, the efficacy of the model was evaluated and new target polymers were identified.

  13. Rational design of dualsteric GPCR ligands: quests and promise

    PubMed Central

    Mohr, Klaus; Tränkle, Christian; Kostenis, Evi; Barocelli, Elisabetta; De Amici, Marco; Holzgrabe, Ulrike

    2010-01-01

    Dualsteric ligands represent a novel mode of targeting G protein-coupled receptors (GPCRs). These compounds attach simultaneously to both, the orthosteric transmitter binding site and an additional allosteric binding area of a receptor protein. This approach allows the exploitation of favourable characteristics of the orthosteric and the allosteric site by a single ligand molecule. The orthosteric interaction provides high affinity binding and activation of receptors. The allosteric interaction yields receptor subtype-selectivity and, in addition, may modulate both, efficacy and intracellular signalling pathway activation. Insight into the spatial arrangement of the orthosteric and the allosteric site is far advanced in the muscarinic acetylcholine receptor, and the design of dualsteric muscarinic agonists has now been accomplished. Using the muscarinic receptor as a paradigm, this review summarizes the way from suggestive evidence for an orthosteric/allosteric overlap binding to the rational design and experimental validation of dualsteric ligands. As allosteric interactions are increasingly described for GPCRs and as insight into the spatial geometry of ligand/GPCR-complexes is growing impressively, the rational design of dualsteric drugs is a promising new approach to achieve fine-tuned GPCR-modulation. This article is part of a themed section on Molecular Pharmacology of GPCR. To view the editorial for this themed section visit http://dx.doi.org/10.1111/j.1476-5381.2010.00695.x PMID:20136835

  14. Using Fitness Landscapes for Rational Hepatitis C Immunogen Design

    NASA Astrophysics Data System (ADS)

    Hart, Gregory; Ferguson, Andrew

    2015-03-01

    Hepatitis C virus afflicts 170 million people worldwide, 2-3% of the global population. Prophylactic vaccination offers the most realistic and cost effective hope of controlling this epidemic, particularly in the developing world where expensive drug therapies are unavailable. Despite 20 years of research, the high mutability of the virus, and lack of knowledge of what constitutes effective immune responses, have impeded development of an effective vaccine. Coupling data mining of sequence databases with the Potts model, we have developed a computational approach to systematically identify viral vulnerabilities and perform rational design of vaccine immunogens. We applied our approach to the nonstructural proteins NS3, NSA, NSA, and NSB which are crucial for viral replication.The predictions of our model are in good accord with experimental measurements and clinical observations, and we have used our model to design immunogen candidates to elicit T-cell responses against vulnerable regions of theseviral proteins.

  15. Tailoring recombinant protein quality by rational media design.

    PubMed

    Brühlmann, David; Jordan, Martin; Hemberger, Jürgen; Sauer, Markus; Stettler, Matthieu; Broly, Hervé

    2015-01-01

    Clinical efficacy and safety of recombinant proteins are closely associated with their structural characteristics. The major quality attributes comprise glycosylation, charge variants (oxidation, deamidation, and C- & N-terminal modifications), aggregates, low-molecular-weight species (LMW), and misincorporation of amino acids in the protein backbone. Cell culture media design has a great potential to modulate these quality attributes due to the vital role of medium in mammalian cell culture. The purpose of this review is to provide an overview of the way both classical cell culture medium components and novel supplements affect the quality attributes of recombinant therapeutic proteins expressed in mammalian hosts, allowing rational and high-throughput optimization of mammalian cell culture media. A selection of specific and/or potent inhibitors and activators of oligosaccharide processing as well as components affecting multiple quality attributes are presented. Extensive research efforts in this field show the feasibility of quality engineering through media design, allowing to significantly modulate the protein function.

  16. Beyond directed evolution - semi-rational protein engineering and design

    PubMed Central

    Lutz, Stefan

    2010-01-01

    Over the last two decades, directed evolution has transformed the field of protein engineering. The advances in understanding protein structure and function, in no insignificant part a result of directed evolution studies, are increasingly empowering scientists and engineers to device more effective methods for manipulating and tailoring biocatalysts. Abandoning large combinatorial libraries, the focus has shifted to small, functionally-rich libraries and rational design. A critical component to the success of these emerging engineering strategies are computational tools for the evaluation of protein sequence datasets and the analysis of conformational variations of amino acids in proteins. Highlighting the opportunities and limitations of such approaches, this review focuses on recent engineering and design examples that require screening or selection of small libraries. PMID:20869867

  17. Principles underlying rational design of live attenuated influenza vaccines

    PubMed Central

    Jang, Yo Han

    2012-01-01

    Despite recent innovative advances in molecular virology and the developments of vaccines, influenza virus remains a serious burden for human health. Vaccination has been considered a primary countermeasure for prevention of influenza infection. Live attenuated influenza vaccines (LAIVs) are particularly attracting attention as an effective strategy due to several advantages over inactivated vaccines. Cold-adaptation, as a classical means for attenuating viral virulence, has been successfully used for generating safe and effective donor strains of LAIVs against seasonal epidemics and occasional pandemics. Recently, the advent of reverse genetics technique expedited a variety of rational strategies to broaden the pool of LAIVs. Considering the breadth of antigenic diversity of influenza virus, the pool of LAIVs is likely to equip us with better options for controlling influenza pandemics. With a brief reflection on classical attenuating strategies used at the initial stage of development of LAIVs, especially on the principles underlying the development of cold-adapted LAIVs, we further discuss and outline other attenuation strategies especially with respect to the rationales for attenuation, and their practicality for mass production. Finally, we propose important considerations for a rational vaccine design, which will provide us with practical guidelines for improving the safety and effectiveness of LAIVs. PMID:23596576

  18. Rationally designed molecular beacons for bioanalytical and biomedical applications.

    PubMed

    Zheng, Jing; Yang, Ronghua; Shi, Muling; Wu, Cuichen; Fang, Xiaohong; Li, Yinhui; Li, Jishan; Tan, Weihong

    2015-05-21

    Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then

  19. Rational clinical trial design for antibody mediated renal allograft injury

    PubMed Central

    Sandal, Shaifali; Zand, Martin S.

    2015-01-01

    Antibody mediated renal allograft rejection is a significant cause of acute and chronic graft loss. Recent work has revealed that AMR is a complex processes, involving B and plasma cells, donor-specific antibodies, complement, vascular endothelial cells, NK cells, Fc receptors, cytokines and chemokines. These insights have led to the development of numerous new therapies, and adaptation of others originally developed for treatment of hemetologic malignancies, autoimmune and complement mediated conditions. Here we review emerging insights into the pathophysiology of AMR as well as current and emerging therapies for both acute and chronic AMR. Finally, we discuss rational clinical trial design in light of antibody and B cell immunobiology, as well as appropriate efficacy metrics to identify robust protocols and therapeutic agents. PMID:25553476

  20. Toward rational design of electrical stimulation strategies for epilepsy control

    PubMed Central

    Sunderam, Sridhar; Gluckman, Bruce; Reato, Davide; Bikson, Marom

    2009-01-01

    Electrical stimulation is emerging as a viable alternative for epilepsy patients whose seizures are not alleviated by drugs or surgery. Its attractions are temporal and spatial specificity of action, flexibility of waveform parameters and timing, and the perception that its effects are reversible unlike resective surgery. However, despite significant advances in our understanding of mechanisms of neural electrical stimulation, clinical electrotherapy for seizures relies heavily on empirical tuning of parameters and protocols. We highlight concurrent treatment goals with potentially conflicting design constraints that must be resolved when formulating rational strategies for epilepsy electrotherapy: namely seizure reduction versus cognitive impairment, stimulation efficacy versus tissue safety, and mechanistic insight versus clinical pragmatism. First, treatment markers, objectives, and metrics relevant to electrical stimulation for epilepsy are discussed from a clinical perspective. Then the experimental perspective is presented, with the biophysical mechanisms and modalities of open-loop electrical stimulation, and the potential benefits of closed-loop control for epilepsy. PMID:19926525

  1. A rationally designed CD4 analogue inhibits experimental allergic encephalomyelitis

    NASA Astrophysics Data System (ADS)

    Jameson, Bradford A.; McDonnell, James M.; Marini, Joseph C.; Korngold, Robert

    1994-04-01

    EXPERIMENTAL allergic encephalomyelitis (EAE) is an acute inflammatory autoimmune disease of the central nervous system that can be elicited in rodents and is the major animal model for the study of multiple sclerosis (MS)1,2. The pathogenesis of both EAE and MS directly involves the CD4+ helper T-cell subset3-5. Anti-CD4 monoclonal antibodies inhibit the development of EAE in rodents6-9, and are currently being used in human clinical trials for MS. We report here that similar therapeutic effects can be achieved in mice using a small (rationally designed) synthetic analogue of the CD4 protein surface. It greatly inhibits both clinical incidence and severity of EAE with a single injection, but does so without depletion of the CD4+ subset and without the inherent immunogenicity of an antibody. Furthermore, this analogue is capable of exerting its effects on disease even after the onset of symptoms.

  2. Rational design of functional and tunable oscillating enzymatic networks

    NASA Astrophysics Data System (ADS)

    Semenov, Sergey N.; Wong, Albert S. Y.; van der Made, R. Martijn; Postma, Sjoerd G. J.; Groen, Joost; van Roekel, Hendrik W. H.; de Greef, Tom F. A.; Huck, Wilhelm T. S.

    2015-02-01

    Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

  3. New generation adjuvants--from empiricism to rational design.

    PubMed

    O'Hagan, Derek T; Fox, Christopher B

    2015-06-01

    Adjuvants are an essential component of modern vaccine development. Despite many decades of development, only a few types of adjuvants are currently included in vaccines approved for human use. In order to better understand the reasons that development of some adjuvants succeeded while many others failed, we discuss some of the common attributes of successful first generation adjuvants. Next, we evaluate current trends in the development of second generation adjuvants, including the potential advantages of rationally designed synthetic immune potentiators appropriately formulated. Finally, we discuss desirable attributes of next generation adjuvants. Throughout, we emphasize that the importance of formulation and analytical characterization in all aspects of vaccine adjuvant development is often underappreciated. We highlight the formulation factors that must be evaluated in order to optimize interactions between vaccine antigens, immune potentiators, and particulate formulations, and the resulting effects on safety, biological activity, manufacturability, and stability.

  4. New generation adjuvants--from empiricism to rational design.

    PubMed

    O'Hagan, Derek T; Fox, Christopher B

    2015-06-01

    Adjuvants are an essential component of modern vaccine development. Despite many decades of development, only a few types of adjuvants are currently included in vaccines approved for human use. In order to better understand the reasons that development of some adjuvants succeeded while many others failed, we discuss some of the common attributes of successful first generation adjuvants. Next, we evaluate current trends in the development of second generation adjuvants, including the potential advantages of rationally designed synthetic immune potentiators appropriately formulated. Finally, we discuss desirable attributes of next generation adjuvants. Throughout, we emphasize that the importance of formulation and analytical characterization in all aspects of vaccine adjuvant development is often underappreciated. We highlight the formulation factors that must be evaluated in order to optimize interactions between vaccine antigens, immune potentiators, and particulate formulations, and the resulting effects on safety, biological activity, manufacturability, and stability. PMID:26022561

  5. Rational Co-Design of Polymer Dielectrics for Energy Storage.

    PubMed

    Mannodi-Kanakkithodi, Arun; Treich, Gregory M; Huan, Tran Doan; Ma, Rui; Tefferi, Mattewos; Cao, Yang; Sotzing, Gregory A; Ramprasad, Rampi

    2016-08-01

    Although traditional materials discovery has historically benefited from intuition-driven experimental approaches and serendipity, computational strategies have risen in prominence and proven to be a powerful complement to experiments in the modern materials research environment. It is illustrated here how one may harness a rational co-design approach-involving synergies between high-throughput computational screening and experimental synthesis and testing-with the example of polymer dielectrics design for electrostatic energy storage applications. Recent co-design efforts that can potentially enable going beyond present-day "standard" polymer dielectrics (such as biaxially oriented polypropylene) are highlighted. These efforts have led to the identification of several new organic polymer dielectrics within known generic polymer subclasses (e.g., polyurea, polythiourea, polyimide), and the recognition of the untapped potential inherent in entirely new and unanticipated chemical subspaces offered by organometallic polymers. The challenges that remain and the need for additional methodological developments necessary to further strengthen the co-design concept are then presented.

  6. Rational Co-Design of Polymer Dielectrics for Energy Storage.

    PubMed

    Mannodi-Kanakkithodi, Arun; Treich, Gregory M; Huan, Tran Doan; Ma, Rui; Tefferi, Mattewos; Cao, Yang; Sotzing, Gregory A; Ramprasad, Rampi

    2016-08-01

    Although traditional materials discovery has historically benefited from intuition-driven experimental approaches and serendipity, computational strategies have risen in prominence and proven to be a powerful complement to experiments in the modern materials research environment. It is illustrated here how one may harness a rational co-design approach-involving synergies between high-throughput computational screening and experimental synthesis and testing-with the example of polymer dielectrics design for electrostatic energy storage applications. Recent co-design efforts that can potentially enable going beyond present-day "standard" polymer dielectrics (such as biaxially oriented polypropylene) are highlighted. These efforts have led to the identification of several new organic polymer dielectrics within known generic polymer subclasses (e.g., polyurea, polythiourea, polyimide), and the recognition of the untapped potential inherent in entirely new and unanticipated chemical subspaces offered by organometallic polymers. The challenges that remain and the need for additional methodological developments necessary to further strengthen the co-design concept are then presented. PMID:27167752

  7. Rationally designed oxaliplatin-nanoparticle for enhanced antitumor efficacy

    NASA Astrophysics Data System (ADS)

    Paraskar, Abhimanyu; Soni, Shivani; Roy, Bhaskar; Papa, Anne-Laure; Sengupta, Shiladitya

    2012-02-01

    Nanoscale drug delivery vehicles have been extensively studied as carriers for cancer chemotherapeutics. However, the formulation of platinum chemotherapeutics in nanoparticles has been a challenge arising from their physicochemical properties. There are only a few reports describing oxaliplatin nanoparticles. In this study, we derivatized the monomeric units of a polyisobutylene maleic acid copolymer with glucosamine, which chelates trans-1,2-diaminocyclohexane (DACH) platinum (II) through a novel monocarboxylato and O → Pt coordination linkage. At a specific polymer to platinum ratio, the complex self-assembled into a nanoparticle, where the polymeric units act as the leaving group, releasing DACH-platinum in a sustained pH-dependent manner. Sizing was done using dynamic light scatter and electron microscopy. The nanoparticles were evaluated for efficacy in vitro and in vivo. Biodistribution was quantified using inductively coupled plasma atomic absorption spectroscopy (ICP-AAS). The PIMA-GA-DACH-platinum nanoparticle was found to be more active than free oxaliplatin in vitro. In vivo, the nanoparticles resulted in greater tumor inhibition than oxaliplatin (equivalent to 5 mg kg-1 platinum dose) with minimal nephrotoxicity or body weight loss. ICP-AAS revealed significant preferential tumor accumulation of platinum with reduced biodistribution to the kidney or liver following PIMA-GA-DACH-platinum nanoparticle administration as compared with free oxaliplatin. These results indicate that the rational engineering of a novel polymeric nanoparticle inspired by the bioactivation of oxaliplatin results in increased antitumor potency with reduced systemic toxicity compared with the parent cytotoxic. Rational design can emerge as an exciting strategy in the synthesis of nanomedicines for cancer chemotherapy.

  8. Rationally designed molecular beacons for bioanalytical and biomedical applications.

    PubMed

    Zheng, Jing; Yang, Ronghua; Shi, Muling; Wu, Cuichen; Fang, Xiaohong; Li, Yinhui; Li, Jishan; Tan, Weihong

    2015-05-21

    Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then

  9. The application of rational design on phospholipase A(2) inhibitors.

    PubMed

    Mouchlis, V D; Barbayianni, E; Mavromoustakos, T M; Kokotos, G

    2011-01-01

    The phospholipase A(2) (PLA(2)) superfamily consists of different groups of enzymes which are characterized by their ability to catalyze the hydrolysis of the sn-2 ester bond in a variety of phospholipid molecules. The products of PLA(2s) activity play divergent roles in a variety of physiological processes. There are four main types of PLA(2s): the secreted PLA(2s) (sPLA(2s)), the cytosolic PLA(2s) (cPLA(2s)), the calcium-independent PLA(2s) (iPLA(2)) and the lipoprotein-associated PLA(2s) (LpPLA(2s)). Various potent and selective PLA2 inhibitors have been reported up to date and have provided outstanding support in understanding the mechanism of action and elucidating the function of these enzymes. The current review focuses on the implementation of rational design through computer-aided drug design (CADD) on the discovery and development of new PLA(2) inhibitors. PMID:21568891

  10. Rational design of a meningococcal antigen inducing broad protective immunity.

    PubMed

    Scarselli, Maria; Aricò, Beatrice; Brunelli, Brunella; Savino, Silvana; Di Marcello, Federica; Palumbo, Emmanuelle; Veggi, Daniele; Ciucchi, Laura; Cartocci, Elena; Bottomley, Matthew James; Malito, Enrico; Lo Surdo, Paola; Comanducci, Maurizio; Giuliani, Marzia Monica; Cantini, Francesca; Dragonetti, Sara; Colaprico, Annalisa; Doro, Francesco; Giannetti, Patrizia; Pallaoro, Michele; Brogioni, Barbara; Tontini, Marta; Hilleringmann, Markus; Nardi-Dei, Vincenzo; Banci, Lucia; Pizza, Mariagrazia; Rappuoli, Rino

    2011-07-13

    The sequence variability of protective antigens is a major challenge to the development of vaccines. For Neisseria meningitidis, the bacterial pathogen that causes meningitis, the amino acid sequence of the protective antigen factor H binding protein (fHBP) has more than 300 variations. These sequence differences can be classified into three distinct groups of antigenic variants that do not induce cross-protective immunity. Our goal was to generate a single antigen that would induce immunity against all known sequence variants of N. meningitidis. To achieve this, we rationally designed, expressed, and purified 54 different mutants of fHBP and tested them in mice for the induction of protective immunity. We identified and determined the crystal structure of a lead chimeric antigen that was able to induce high levels of cross-protective antibodies in mice against all variant strains tested. The new fHBP antigen had a conserved backbone that carried an engineered surface containing specificities for all three variant groups. We demonstrate that the structure-based design of multiple immunodominant antigenic surfaces on a single protein scaffold is possible and represents an effective way to create broadly protective vaccines.

  11. Rational Co-Design of Polymer Dielectrics for Energy Storage

    NASA Astrophysics Data System (ADS)

    Mannodi-Kanakkithodi, Arun; Tran, Huan; Pilania, Ghanshyam; Lookman, Turab; Ramprasad, Rampi

    While intuition-driven experiments and serendipity have guided traditional materials discovery, computational strategies have become increasingly important and a powerful complement to experiments in modern day materials research. With the example of polymer dielectrics for electrostatic energy storage applications, we demonstrate how a rational co-design approach--involving synergies between high-throughput computational screening and experimental synthesis and testing--can be harnessed for quick and efficient discovery. We highlight recent co-design efforts that can potentially lead to replacement of present-day ``standard'' polymer dielectrics (such as biaxially oriented polypropylene) not only by new organic polymer candidates within known generic polymer subclasses (e.g., polyurea, polythiourea, polyimide), but also by organometallic polymers, a hitherto untapped but promising chemical subspace. We also discuss the utilization of vast computational data (generated in the aforementioned process) towards the development of statistical learning models for relevant properties of dielectric polymers, which can further accelerate the guidance to experiments and thus the successful discovery of new materials.

  12. Protocol for rational design of covalently interacting inhibitors.

    PubMed

    Schmidt, Thomas C; Welker, Armin; Rieger, Max; Sahu, Prabhat K; Sotriffer, Christoph A; Schirmeister, Tanja; Engels, Bernd

    2014-10-20

    The inhibition potencies of covalent inhibitors mainly result from the formation of a covalent bond to the enzyme during the inhibition mechanism. This class of inhibitors has essentially been ignored in previous target-directed drug discovery projects because of concerns about possible side effects. However, their advantages, such as higher binding energies and longer drug-target residence times moved them into the focus of recent investigations. While the rational design of non-covalent inhibitors became standard the corresponding design of covalent inhibitors is still in its early stages. Potent covalent inhibitors can be retrieved from large compound libraries by covalent docking approaches but protocols are missing that can reliably predict the influence of variations in the substitution pattern on the affinity and/or reactivity of a given covalent inhibitor. Hence, the wanted property profile can only be obtained from trial-and-error proceedings. This paper presents an appropriate protocol which is able to predict improved covalent inhibitors. It uses hybrid approaches, which mix quantum mechanical (QM) and molecular mechanical (MM) methods to predict variations in the reactivity of the inhibitor. They are also used to compute the required information about the non-covalent enzyme-inhibitor complex. Docking tools are employed to improve the inhibitor with respect to the non-covalent interactions formed in the binding site. PMID:25251382

  13. Rational design of electrolyte components by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Johansson, Patrik; Jacobsson, Per

    This paper is a small review of the use of computer simulations and especially the use of standard quantum-mechanical ab initio electronic structure calculations to rationally design and investigate different choices of chemicals/systems for lithium battery electrolytes. Covered systems and strategies to enhance the performance of electrolytes will range from assisting the interpretation of vibrational spectroscopy experiments over development of potentials for molecular dynamics simulations, to the design of new lithium salts and the lithium ion coordination in liquid, polymer, and gel polymer electrolytes. Examples of studied properties include the vibrational spectra of anions and ion pairs to characterize the nature and extent of the interactions present, the lithium ion affinities of anions, important for the salt solvation and the ability to provide a high concentration of charge carriers, the HOMO energies of the anions to estimate the stability versus oxidation, the anion volumes that correlate to the anion mobility, the lithium ion coordination and dynamics to reveal the limiting steps of lithium ion transport, etc.

  14. Snake bites

    MedlinePlus

    ... bites by any of the following: Cobra Copperhead Coral snake Cottonmouth (water moccasin) Rattlesnake Various snakes found ... Swelling Thirst Tiredness Tissue damage Weakness Weak pulse Coral snake bites may be painless at first. Major ...

  15. Structure-Based, Rational Design of T Cell Receptors

    PubMed Central

    Zoete, V.; Irving, M.; Ferber, M.; Cuendet, M. A.; Michielin, O.

    2013-01-01

    Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157–165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, KD = ∼1 − 5 μM. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function, in line with the “half-life” model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method

  16. Rational design and synthesis of excavated trioctahedral Au nanocrystals

    NASA Astrophysics Data System (ADS)

    Chen, Qiaoli; Jia, Yanyan; Shen, Wei; Xie, Shuifen; Yang, Yanan; Cao, Zhenming; Xie, Zhaoxiong; Zheng, Lansun

    2015-06-01

    Excavated polyhedral nanostructures, possessing the features of high surface area and well-defined surface structure with a specific crystal facet and avoidance of aggregation, could be one of the best choices for the purpose of reducing consumption and improving performance of noble metals in many application fields. However, the formation of the excavated structures is thermodynamically unfavourable and its rational synthesis is far beyond our knowledge. In this work, taking overgrowth of Pd onto trioctahedral Au nanocrystals as a model, we present a deep insight study for synthesizing an excavated structure relying on the protection role of surfactants under suitable crystal growth kinetics. Based on the abovementioned understanding, we designed a simple and effective strategy to synthesize Au nanocrystals with excavated trioctahedral structure in one step. Due to the novel feature of the excavated structure and exposed high energy {110} facets, excavated trioctahedral Au NCs exhibited optical extinction at the near-infrared region and showed high catalytic activity towards the reduction of p-nitrophenol. Moreover, the synthetic strategy can be extended to the synthesis of excavated Au-Pd alloys.Excavated polyhedral nanostructures, possessing the features of high surface area and well-defined surface structure with a specific crystal facet and avoidance of aggregation, could be one of the best choices for the purpose of reducing consumption and improving performance of noble metals in many application fields. However, the formation of the excavated structures is thermodynamically unfavourable and its rational synthesis is far beyond our knowledge. In this work, taking overgrowth of Pd onto trioctahedral Au nanocrystals as a model, we present a deep insight study for synthesizing an excavated structure relying on the protection role of surfactants under suitable crystal growth kinetics. Based on the abovementioned understanding, we designed a simple and effective

  17. Patterning symmetry in the rational design of colloidal crystals.

    PubMed

    Romano, Flavio; Sciortino, Francesco

    2012-01-01

    Colloidal particles have the right size to form ordered structures with periodicities comparable to the wavelength of visible light. The tantalizing colours of precious opals and the colour of some species of birds are examples of polycrystalline colloidal structures found in nature. Driven by the demands of several emergent technologies, efforts have been made to develop efficient, self-assembly-based methodologies for generating colloidal single crystals with well-defined morphologies. Somewhat unfortunately, these efforts are often frustrated by the formation of structures lacking long-range order. Here we show that the rational design of patch shape and symmetry can drive patchy colloids to crystallize in a single, selected morphology by structurally eliminating undesired polymorphs. We provide a proof of this concept through the numerical investigation of triblock Janus colloids. One particular choice of patch symmetry yields, via spontaneous crystallization, a pure tetrastack lattice, a structure with attractive photonic properties, whereas another one results in a colloidal clathrate-like structure, in both cases without any interfering polymorphs. PMID:22828635

  18. Rational design and synthesis of excavated trioctahedral Au nanocrystals.

    PubMed

    Chen, Qiaoli; Jia, Yanyan; Shen, Wei; Xie, Shuifen; Yang, Yanan; Cao, Zhenming; Xie, Zhaoxiong; Zheng, Lansun

    2015-06-28

    Excavated polyhedral nanostructures, possessing the features of high surface area and well-defined surface structure with a specific crystal facet and avoidance of aggregation, could be one of the best choices for the purpose of reducing consumption and improving performance of noble metals in many application fields. However, the formation of the excavated structures is thermodynamically unfavourable and its rational synthesis is far beyond our knowledge. In this work, taking overgrowth of Pd onto trioctahedral Au nanocrystals as a model, we present a deep insight study for synthesizing an excavated structure relying on the protection role of surfactants under suitable crystal growth kinetics. Based on the abovementioned understanding, we designed a simple and effective strategy to synthesize Au nanocrystals with excavated trioctahedral structure in one step. Due to the novel feature of the excavated structure and exposed high energy {110} facets, excavated trioctahedral Au NCs exhibited optical extinction at the near-infrared region and showed high catalytic activity towards the reduction of p-nitrophenol. Moreover, the synthetic strategy can be extended to the synthesis of excavated Au-Pd alloys.

  19. Systems vaccinology: Enabling rational vaccine design with systems biological approaches.

    PubMed

    Hagan, Thomas; Nakaya, Helder I; Subramaniam, Shankar; Pulendran, Bali

    2015-09-29

    Vaccines have drastically reduced the mortality and morbidity of many diseases. However, vaccines have historically been developed empirically, and recent development of vaccines against current pandemics such as HIV and malaria has been met with difficulty. The advent of high-throughput technologies, coupled with systems biological methods of data analysis, has enabled researchers to interrogate the entire complement of a variety of molecular components within cells, and characterize the myriad interactions among them in order to model and understand the behavior of the system as a whole. In the context of vaccinology, these tools permit exploration of the molecular mechanisms by which vaccines induce protective immune responses. Here we review the recent advances, challenges, and potential of systems biological approaches in vaccinology. If the challenges facing this developing field can be overcome, systems vaccinology promises to empower the identification of early predictive signatures of vaccine response, as well as novel and robust correlates of protection from infection. Such discoveries, along with the improved understanding of immune responses to vaccination they impart, will play an instrumental role in development of the next generation of rationally designed vaccines.

  20. A thermostable exo-β-fructosidase immobilised through rational design.

    PubMed

    Martínez, Duniesky; Cutiño-Avila, Bessy; Pérez, Enrique Rosendo; Menéndez, Carmen; Hernández, Lázaro; Del Monte-Martínez, Alberto

    2014-02-15

    Thermotoga maritima exo-β-fructosidase (BfrA) secreted by a recombinant Pichia pastoris strain was optimally immobilised on Glyoxyl-Sepharose CL 4B using the Rational Design of Immobilised Derivatives (RDID) strategy. Covalent attachment of the N-glycosylated BfrA onto the activated support at pH 10 allowed total recovery of the loaded enzyme and its activity. The immobilisation process caused no variation in the catalytic properties of the enzyme and allowed further enhancement of the thermal stability. Complete inversion of cane sugar (2.04 M) in a batch stirred tank reactor at 60 °C was achieved with a productivity of 22.2 g of substrate hydrolysed/gram of biocatalyst/hour. Half-life of the immobilised enzyme of 5 days at 60 °C was determined in a continuously operated fixed-bed column reactor. Our results promote the applicability of the BfrA-immobilised biocatalyst for the complete hydrolysis of concentrated sucrose solutions under industrial conditions, especially at a high reaction temperature. PMID:24128552

  1. Rational design of enhanced photoresistance in a photoswitchable fluorescent protein

    NASA Astrophysics Data System (ADS)

    Duan, Chenxi; Byrdin, Martin; El Khatib, Mariam; Henry, Xavier; Adam, Virgile; Bourgeois, Dominique

    2015-03-01

    Fluorescent proteins are particularly susceptible to photobleaching, the permanent loss of fluorescence emission resulting from photodestruction of the chromophore. In the case of Reversibly Switchable Fluorescent Proteins (RSFPs), which can be switched back and forth between a non-fluorescent and a fluorescent state, the achievable number of switching cycles is limited by photobleaching, a process known as photofatigue. Photofatigue has become a crucial limitation in a number of advanced applications based on repeated photoswitching of RSFPs, notably in the field of super-resolution fluorescence microscopy. Here, based on our previous structural investigation of photobleaching mechanisms in IrisFP, an RSFP also capable of green-to-red photoconversion, we present the rational design of a single-mutant IrisFP-M159A that displays considerably enhanced photostability. The results suggest that, under moderate illumination intensities, photobleaching of IrisFP-like Anthozoan fluorescent proteins such as EosFP, Dendra or Dronpa derivatives is mainly driven by an oxygen-dependent mechanism resulting in the irreversible sulfoxidation of methionine 159. The photofatigue decay profiles of IrisFP and its photoresistant mutant IrisFP-M159A were investigated in different experimental conditions, in vitro and in cellulo. Although the performance of the mutant was found to be always superior, the results showed switching behaviors strongly dependent on the nanoenvironment. Thus, in general, assessment of photostability and switching properties of RSFPs should be carried out in real experimental conditions.

  2. A thermostable exo-β-fructosidase immobilised through rational design.

    PubMed

    Martínez, Duniesky; Cutiño-Avila, Bessy; Pérez, Enrique Rosendo; Menéndez, Carmen; Hernández, Lázaro; Del Monte-Martínez, Alberto

    2014-02-15

    Thermotoga maritima exo-β-fructosidase (BfrA) secreted by a recombinant Pichia pastoris strain was optimally immobilised on Glyoxyl-Sepharose CL 4B using the Rational Design of Immobilised Derivatives (RDID) strategy. Covalent attachment of the N-glycosylated BfrA onto the activated support at pH 10 allowed total recovery of the loaded enzyme and its activity. The immobilisation process caused no variation in the catalytic properties of the enzyme and allowed further enhancement of the thermal stability. Complete inversion of cane sugar (2.04 M) in a batch stirred tank reactor at 60 °C was achieved with a productivity of 22.2 g of substrate hydrolysed/gram of biocatalyst/hour. Half-life of the immobilised enzyme of 5 days at 60 °C was determined in a continuously operated fixed-bed column reactor. Our results promote the applicability of the BfrA-immobilised biocatalyst for the complete hydrolysis of concentrated sucrose solutions under industrial conditions, especially at a high reaction temperature.

  3. Rationally designed polyimides for high-energy density capacitor applications.

    PubMed

    Ma, Rui; Baldwin, Aaron F; Wang, Chenchen; Offenbach, Ido; Cakmak, Mukerrem; Ramprasad, Rampi; Sotzing, Gregory A

    2014-07-01

    Development of new dielectric materials is of great importance for a wide range of applications for modern electronics and electrical power systems. The state-of-the-art polymer dielectric is a biaxially oriented polypropylene (BOPP) film having a maximal energy density of 5 J/cm(3) and a high breakdown field of 700 MV/m, but with a limited dielectric constant (∼2.2) and a reduced breakdown strength above 85 °C. Great effort has been put into exploring other materials to fulfill the demand of continuous miniaturization and improved functionality. In this work, a series of polyimides were investigated as potential polymer materials for this application. Polyimide with high dielectric constants of up to 7.8 that exhibits low dissipation factors (<1%) and high energy density around 15 J/cm(3), which is 3 times that of BOPP, was prepared. Our syntheses were guided by high-throughput density functional theory calculations for rational design in terms of a high dielectric constant and band gap. Correlations of experimental and theoretical results through judicious variations of polyimide structures allowed for a clear demonstration of the relationship between chemical functionalities and dielectric properties.

  4. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

    PubMed Central

    Ben-Yehezkel, Tuval; Atar, Shimshi; Zur, Hadas; Diament, Alon; Goz, Eli; Marx, Tzipy; Cohen, Rafael; Dana, Alexandra; Feldman, Anna; Shapiro, Ehud; Tuller, Tamir

    2015-01-01

    Deducing generic causal relations between RNA transcript features and protein expression profiles from endogenous gene expression data remains a major unsolved problem in biology. The analysis of gene expression from heterologous genes contributes significantly to solving this problem, but has been heavily biased toward the study of the effect of 5′ transcript regions and to prokaryotes. Here, we employ a synthetic biology driven approach that systematically differentiates the effect of different regions of the transcript on gene expression up to 240 nucleotides into the ORF. This enabled us to discover new causal effects between features in previously unexplored regions of transcripts, and gene expression in natural regimes. We rationally designed, constructed, and analyzed 383 gene variants of the viral HRSVgp04 gene ORF, with multiple synonymous mutations at key positions along the transcript in the eukaryote S. cerevisiae. Our results show that a few silent mutations at the 5′UTR can have a dramatic effect of up to 15 fold change on protein levels, and that even synonymous mutations in positions more than 120 nucleotides downstream from the ORF 5′end can modulate protein levels up to 160%–300%. We demonstrate that the correlation between protein levels and folding energy increases with the significance of the level of selection of the latter in endogenous genes, reinforcing the notion that selection for folding strength in different parts of the ORF is related to translation regulation. Our measured protein abundance correlates notably(correlation up to r = 0.62 (p=0.0013)) with mean relative codon decoding times, based on ribosomal densities (Ribo-Seq) in endogenous genes, supporting the conjecture that translation elongation and adaptation to the tRNA pool can modify protein levels in a causal/direct manner. This report provides an improved understanding of transcript evolution, design principles of gene expression regulation, and suggests simple

  5. Snake bite: coral snakes.

    PubMed

    Peterson, Michael E

    2006-11-01

    North American coral snakes are distinctively colored beginning with a black snout and an alternating pattern of black, yellow, and red. They have fixed front fangs and a poorly developed system for venom delivery, requiring a chewing action to inject the venom. The severity of a coral snake bite is related to the volume of venom injected and the size of the victim. The length of the snake correlates positively with the snakes venom yield. Coral snake venom is primarily neurotoxic with little local tissue reaction or pain at the bite site. The net effect of the neurotoxins is a curare like syndrome. In canine victims there have been reports of marked hemolysis with severe anemia and hemoglobinuria. The onset of clinical signs may be delayed for as much as 10 to 18 hours. The victim begins to have alterations in mental status and develops generalized weakness and muscle fasciculations. Progression to paralysis of the limbs and respiratory muscles then follows. The best flied response to coral snake envenomation is rapid transport to a veterinary medical facility capable of 24 hour critical care and assisted ventilation. First aid treatment advocated in Australia for Elapid bites is the immediate use of a compression bandage. The victim should be hospitalized for a minimum of 48 hours for continuous monitoring. The only definitive treatment for coral snake envenomation is the administration of antivenin (M. fulvius). Once clinical signs of coral snake envenomation become manifest they progress with alarming rapidity and are difficult to reverse. If antivenin is not available or if its administration is delayed, supportive care includes respiratory support. Assisted mechanical ventilation can be used but may have to be employed for up to 48 to 72 hours.

  6. Harvesting bioenergy with rationally designed complex functional materials

    NASA Astrophysics Data System (ADS)

    Kuang, Liangju

    A key challenge in renewable energy is to capture, convert and store solar power with earth-abundant materials and environmentally benign technologies. The goal of this thesis is to develop rationally designed complex functional materials for bio-renewable energy applications. On one hand, photoconversion membrane proteins (MPs) are nature's nanoengineering feats for renewable energy management. Harnessing their functions in synthetic systems could help understand, predict, and ultimately control matter and energy at the nanoscale. This is particularly enticing in the post-genome era as recombinant or cell-free expression of many MPs with high yields becomes possible. However, the labile nature of lipid bilayers renders them unsuitable for use in a broad range of engineered systems. A knowledge gap exists about how to design robust synthetic nanomembranes as lipid-bilayer-mimics to support MP functions and how to direct hierarchical MP reconstitution into those membranes to form 2-D or 3-D ordered proteomembrane arrays. Our studies on proteorhodopsin (PR) and bacterial reaction center (BRC), the two light-harvesting MPs, reveal that a charge-interaction-directed reconstitution (CIDR) mechanism induces spontaneous reconstitution of detergent-solubilized MPs into various amphiphilic block copolymer membranes, many of which have far superior stability than lipid bilayers. Our preliminary data also suggest MPs are not enslaved by the biological membranes they derive from; rather, the chemically nonspecific material properties of MP-supporting membranes may act as allosteric regulators. Versatile chemical designs are possible to modulate the conformational energetics of MPs, hence their transport performance in synthetic systems. On the other hand, microalgae are widely regarded as a sustainable feedstock for biofuel production. Microalgae-derived biofuels have not been commercialized yet because current technologies for microalgae dewatering add a huge cost to the

  7. The Snakes and Ladders of Research: Using a Board Game to Teach the Pitfalls of Undergraduate Research Design.

    ERIC Educational Resources Information Center

    Warburton, Jeff; Madge, Clare

    1994-01-01

    Contends that the success or failure of an undergraduate research project can hinge on one or two decisions made at an early stage in the process. Describes a "Snakes and Ladders" board game used to remind students of good and bad research design practices. Includes game rules and a listing of the good and bad practices. (CFR)

  8. Rational design and investigation of polypeptide multilayer films and capsules

    NASA Astrophysics Data System (ADS)

    Zhang, Ling

    Three major concerns in the science of materials today are control over structure and function at the molecular level, biodegradability, and scalability of production. Polymeric materials, notably polyelectrolyte multilayer films, have shown considerable promise in all these areas, and for rational development of multifunctionality. Polypeptides constitute an especially interesting class of polyelectrolyte, given their inherent biodegradability, means of control over structure, methods of large-scale synthesis, and ability to encode biological information. Relatively little is known, however, about polypeptide multilayer films, despite recent advances in the general area. In this dissertation, ten heteropolypeptides were designed and synthesized by Fmoc chemistry. These peptides and homopolypeptides available from a commercial source have been used to carry out a systematic study of the physical basis of polypeptide multilayer film assembly, structure, and stability, in order to gain a greater grasp of the roles of different kinds of non-covalent interaction, degree of polymerization, and polydispersity. The data show that amino acid composition, sequence, and specific combination of anionic and cationic polypeptides together determine film growth behavior, secondary structure content, overall density, surface morphology, and susceptibility to environmental perturbations. The peptides are largely unstructured in solution but tend to form beta sheets in a multilayer film at neutral pH. Electrostatic interactions dominate polypeptide adsorption and film stability, but hydrophobic interactions and hydrogen bonding have a significant influence on internal structure and surface morphology, decreasing film density and increasing film thickness and roughness. Experimental results of polypeptide multilayer films correlate well with molecular dynamics (MD) simulation results of interpolyelectrolyte complexes (IPECs) of the same polypeptide designs. Microcrystals of pyrene

  9. Laccase engineering: from rational design to directed evolution.

    PubMed

    Mate, Diana M; Alcalde, Miguel

    2015-01-01

    Laccases are multicopper oxidoreductases considered by many in the biotechonology field as the ultimate "green catalysts". This is mainly due to their broad substrate specificity and relative autonomy (they use molecular oxygen from air as an electron acceptor and they only produce water as by-product), making them suitable for a wide array of applications: biofuel production, bioremediation, organic synthesis, pulp biobleaching, textiles, the beverage and food industries, biosensor and biofuel cell development. Since the beginning of the 21st century, specific features of bacterial and fungal laccases have been exhaustively adapted in order to reach the industrial demands for high catalytic activity and stability in conjunction with reduced production cost. Among the goals established for laccase engineering, heterologous functional expression, improved activity and thermostability, tolerance to non-natural media (organic solvents, ionic liquids, physiological fluids) and resistance to different types of inhibitors are all challenges that have been met, while obtaining a more comprehensive understanding of laccase structure-function relationships. In this review we examine the most significant advances in this exciting research area in which rational, semi-rational and directed evolution approaches have been employed to ultimately convert laccases into high value-added biocatalysts.

  10. Laccase engineering: from rational design to directed evolution.

    PubMed

    Mate, Diana M; Alcalde, Miguel

    2015-01-01

    Laccases are multicopper oxidoreductases considered by many in the biotechonology field as the ultimate "green catalysts". This is mainly due to their broad substrate specificity and relative autonomy (they use molecular oxygen from air as an electron acceptor and they only produce water as by-product), making them suitable for a wide array of applications: biofuel production, bioremediation, organic synthesis, pulp biobleaching, textiles, the beverage and food industries, biosensor and biofuel cell development. Since the beginning of the 21st century, specific features of bacterial and fungal laccases have been exhaustively adapted in order to reach the industrial demands for high catalytic activity and stability in conjunction with reduced production cost. Among the goals established for laccase engineering, heterologous functional expression, improved activity and thermostability, tolerance to non-natural media (organic solvents, ionic liquids, physiological fluids) and resistance to different types of inhibitors are all challenges that have been met, while obtaining a more comprehensive understanding of laccase structure-function relationships. In this review we examine the most significant advances in this exciting research area in which rational, semi-rational and directed evolution approaches have been employed to ultimately convert laccases into high value-added biocatalysts. PMID:25545886

  11. Sidewinding snakes on sand

    NASA Astrophysics Data System (ADS)

    Marvi, Hamidreza; Dimenichi, Dante; Chrystal, Robert; Mendelson, Joseph; Goldman, Daniel; Hu, David; Georgia Tech and Zoo Atlanta Collaboration

    2012-11-01

    Desert snakes such as the rattlesnake Crotalus cerastes propel themselves over sand using sidewinding, a mode of locomotion relying upon helical traveling waves. While sidewinding on hard ground has been described, the mechanics of movement on more natural substrates such as granular media remain poorly understood. In this experimental study, we use 3-D high speed video to characterize the motion of a sidewinder rattlesnake as it moves on a granular bed. We study the movement both on natural desert sand and in an air-fluidized bed trackway which we use to challenge the animal on different compactions of granular media. Particular attention is paid to rationalizing the snake's thrust on this media using friction and normal forces on the piles of sand created by the snake's body. The authors thank the NSF (PHY-0848894), Georgia Tech, and the Elizabeth Smithgall Watts endowment for support. We would also like to thank Zoo Atlanta staff for their generous help with this project.

  12. A rational design change methodology based on experimental and analytical modal analysis

    SciTech Connect

    Weinacht, D.J.; Bennett, J.G.

    1993-08-01

    A design methodology that integrates analytical modeling and experimental characterization is presented. This methodology represents a powerful tool for making rational design decisions and changes. An example of its implementation in the design, analysis, and testing of a precisions machine tool support structure is given.

  13. Rational design of small molecules as vaccine adjuvants.

    PubMed

    Wu, Tom Y-H; Singh, Manmohan; Miller, Andrew T; De Gregorio, Ennio; Doro, Francesco; D'Oro, Ugo; Skibinski, David A G; Mbow, M Lamine; Bufali, Simone; Herman, Ann E; Cortez, Alex; Li, Yongkai; Nayak, Bishnu P; Tritto, Elaine; Filippi, Christophe M; Otten, Gillis R; Brito, Luis A; Monaci, Elisabetta; Li, Chun; Aprea, Susanna; Valentini, Sara; Calabrό, Samuele; Laera, Donatello; Brunelli, Brunella; Caproni, Elena; Malyala, Padma; Panchal, Rekha G; Warren, Travis K; Bavari, Sina; O'Hagan, Derek T; Cooke, Michael P; Valiante, Nicholas M

    2014-11-19

    Adjuvants increase vaccine potency largely by activating innate immunity and promoting inflammation. Limiting the side effects of this inflammation is a major hurdle for adjuvant use in vaccines for humans. It has been difficult to improve on adjuvant safety because of a poor understanding of adjuvant mechanism and the empirical nature of adjuvant discovery and development historically. We describe new principles for the rational optimization of small-molecule immune potentiators (SMIPs) targeting Toll-like receptor 7 as adjuvants with a predicted increase in their therapeutic indices. Unlike traditional drugs, SMIP-based adjuvants need to have limited bioavailability and remain localized for optimal efficacy. These features also lead to temporally and spatially restricted inflammation that should decrease side effects. Through medicinal and formulation chemistry and extensive immunopharmacology, we show that in vivo potency can be increased with little to no systemic exposure, localized innate immune activation and short in vivo residence times of SMIP-based adjuvants. This work provides a systematic and generalizable approach to engineering small molecules for use as vaccine adjuvants.

  14. Rational Design of Molecular Ferroelectric Materials and Nanostructures

    SciTech Connect

    Ducharme, Stephen

    2012-09-25

    The purpose of this project was to gain insight into the properties of molecular ferroelectrics through the detailed study of oligomer analogs of polyvinylidene fluoride (PVDF). By focusing on interactions at both the molecular level and the nanoscale level, we expect to gain improved understanding about the fundamental mechanism of ferroelectricity and its key properties. The research consisted of three complementary components: 1) Rational synthesis of VDF oligomers by Prof. Takacs' group; 2) Detailed structural and electrical studies of thin by Prof. Ducharme's Group; and 3) First-principles computational studies by DOE Lab Partner Dr. Serge Nakhman-son at Argonne National Laboratory. The main results of the work was a detailed understanding of the relationships between the molecular interactions and macroscopic phenomenology of fer-roelectricity VDF oligomers. This is valuable information supporting the development of im-proved electromechanical materials for, e.g., sonar, ultrasonic imaging, artificial muscles, and compliant actuators. Other potential applications include nonvolatile ferroelectric memories, heat-sensing imaging arrays, photovoltaic devices, and functional biomimetic materials. The pro-ject contributed to the training and professional development of undergraduate students and graduate students, post-doctoral assistants, and a high-school teacher. Project personnel took part in several outreach and education activities each year.

  15. Rational approaches to design of therapeutics targeting molecular markers.

    PubMed

    Klasa, R J; List, A F; Cheson, B D

    2001-01-01

    This paper introduces novel therapeutic strategies focusing on a molecular marker relevant to a particular hematologic malignancy. Four different approaches targeting specific molecules in unique pathways will be presented. The common theme will be rational target selection in a strategy that has reached the early phase of human clinical trial in one malignancy, but with a much broader potential applicability to the technology. In Section I Dr. Richard Klasa presents preclinical data on the use of antisense oligonucleotides directed at the bcl-2 gene message to specifically downregulate Bcl-2 protein expression in non-Hodgkin's lymphomas and render the cells more susceptible to the induction of apoptosis. In Section II Dr. Alan List reviews the targeting of vascular endothelial growth factor (VEGF) and its receptor in anti-angiogenesis strategies for acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). In Section III Dr. Bruce Cheson describes recent progress in inhibiting cell cycle progression by selectively disrupting cyclin D1 with structurally unique compounds such as flavopiridol in mantle cell lymphoma as well as describing a new class of agents that affect proteasome degradation pathways.

  16. From bricolage to BioBricks™: Synthetic biology and rational design.

    PubMed

    Lewens, Tim

    2013-12-01

    Synthetic biology is often described as a project that applies rational design methods to the organic world. Although humans have influenced organic lineages in many ways, it is nonetheless reasonable to place synthetic biology towards one end of a continuum between purely 'blind' processes of organic modification at one extreme, and wholly rational, design-led processes at the other. An example from evolutionary electronics illustrates some of the constraints imposed by the rational design methodology itself. These constraints reinforce the limitations of the synthetic biology ideal, limitations that are often freely acknowledged by synthetic biology's own practitioners. The synthetic biology methodology reflects a series of constraints imposed on finite human designers who wish, as far as is practicable, to communicate with each other and to intervene in nature in reasonably targeted and well-understood ways. This is better understood as indicative of an underlying awareness of human limitations, rather than as expressive of an objectionable impulse to mastery over nature.

  17. Nanoscale design of snake skin for reptation locomotions via friction anisotropy.

    PubMed

    Hazel, J; Stone, M; Grace, M S; Tsukruk, V V

    1999-05-01

    Multi-mode scanning probe microscopy is employed to investigate the nanostructure of dermal samples from three types of snakes. Sophisticated friction modifying nanostructures are described. These include an ordered microfibrillar array that can function to achieve mission adaptable friction characteristics. Significant reduction of adhesive forces in the contact areas caused by the 'double-ridge' nanoscale microfibrillar geometry provides ideal conditions for sliding in forward direction with minimum adhesive forces and friction. Low surface adhesion in these local contact points may reduce local wear and skin contamination by environmental debris. The highly asymmetric, 'pawl-like' profile of the microfibrillar ends with radius of curvature 20-40 nm induces friction anisotropy in forward backward motions and serves as an effective stopper for backward motion preserving low friction for forward motion. The system of continuous micropores penetrating through the snake skin may serve as a delivery system for lubrication/anti-adhesive lipid mixture that provides for boundary lubrication of snake skins.

  18. Application of Absorption Modeling in Rational Design of Drug Product Under Quality-by-Design Paradigm.

    PubMed

    Kesisoglou, Filippos; Mitra, Amitava

    2015-09-01

    Physiologically based absorption models can be an important tool in understanding product performance and hence implementation of Quality by Design (QbD) in drug product development. In this report, we show several case studies to demonstrate the potential application of absorption modeling in rational design of drug product under the QbD paradigm. The examples include application of absorption modeling—(1) prior to first-in-human studies to guide development of a formulation with minimal sensitivity to higher gastric pH and hence reduced interaction when co-administered with PPIs and/or H2RAs, (2) design of a controlled release formulation with optimal release rate to meet trough plasma concentrations and enable QD dosing, (3) understanding the impact of API particle size distribution on tablet bioavailability and guide formulation design in late-stage development, (4) assess impact of API phase change on product performance to guide specification setting, and (5) investigate the effect of dissolution rate changes on formulation bioperformance and enable appropriate specification setting. These case studies are meant to highlight the utility of physiologically based absorption modeling in gaining a thorough understanding of the product performance and the critical factors impacting performance to drive design of a robust drug product that would deliver the optimal benefit to the patients.

  19. Rational Design of Cancer-Targeted Benzoselenadiazole by RGD Peptide Functionalization for Cancer Theranostics.

    PubMed

    Yang, Liye; Li, Wenying; Huang, Yanyu; Zhou, Yangliang; Chen, Tianfeng

    2015-09-01

    A cancer-targeted conjugate of the selenadiazole derivative BSeC (benzo[1,2,5] selenadiazole-5-carboxylic acid) with RGD peptide as targeting molecule and PEI (polyethylenimine) as a linker is rationally designed and synthesized in the present study. The results show that RGD-PEI-BSeC forms nanoparticles in aqueous solution with a core-shell nanostructure and high stability under physiological conditions. This rational design effectively enhances the selective cellular uptake and cellular retention of BSeC in human glioma cells, and increases its selectivity between cancer and normal cells. The nanoparticles enter the cells through receptor-mediated endocytosis via clathrin-mediated and nystatin-dependent lipid raft-mediated pathways. Internalized nanoparticles trigger glioma cell apoptosis by activation of ROS-mediated p53 phosphorylation. Therefore, this study provides a strategy for the rational design of selenium-containing cancer-targeted theranostics.

  20. Rational design of an organometallic glutathione transferase inhibitor

    SciTech Connect

    Ang, W.H.; Parker, L.J.; De Luca, A.; Juillerat-Jeanneret, L.; Morton, C.J.; LoBello, M.; Parker, M.W.; Dyson, P.J.

    2010-08-17

    A hybrid organic-inorganic (organometallic) inhibitor was designed to target glutathione transferases. The metal center is used to direct protein binding, while the organic moiety acts as the active-site inhibitor. The mechanism of inhibition was studied using a range of biophysical and biochemical methods.

  1. Rational design of mirror-like peptides with alanine regulation.

    PubMed

    Li, Weizhong; Tan, Tingting; Xu, Wei; Xu, Lin; Dong, Na; Ma, Deying; Shan, Anshan

    2016-02-01

    To generate effective antimicrobial peptides (AMPs) with good antimicrobial activities and cell selectivity, many synthetic strategies have been implemented to facilitate the development of AMPs. However, these synthetic strategies represent only a small proportion of the methods used for the development of AMPs and are not optimal with the requirements needed for the design of AMPs. In this investigation, we designed a mirror-like structure with a lower charge and a higher number of hydrophobic amino acids. The amino acid sequence of the designed mirror-like peptides was XXYXXXYXXXYXX [X represents L (Leu) and/or A (Ala); Y represents K (Lys)]. These mirror-like peptides displayed antimicrobial activity against both Gram-positive and Gram-negative bacteria. Hemolysis activity and cytotoxicity, detected by using human red blood cells (hRBCs) and human embryonic kidney cells (HEK293), respectively, demonstrated that the frequency of Ala residues in this structure had a regulatory effect on the high hydrophobic region. In particular, KL4A6 showed a greater antimicrobial potency than the other three mirror-like peptides, folded into an α-helical structure, and displayed the highest therapeutic index, suggesting its good cell selectivity. Observations from fluorescence spectroscopy, flow cytometry, and electron microscopy experiments indicated that KL4A6 exhibited good membrane penetration potential by inducing membrane blebbing, disruption and lysis. Therefore, generating mirror-like peptides is a promising strategy for designing effective AMPs with regions of high hydrophobicity.

  2. Rationally designed gibbous stimuli-responsive colloidal nanoparticles.

    PubMed

    Lu, Chunliang; Urban, Marek

    2015-03-24

    Multiphase colloidal copolymer nanoparticles, if properly designed, offer a number of unique properties and well-documented technological opportunities for drug delivery, nanolithography, high surface area colloidal crystals, or hollow nanoparticles, to name just a few. Using a simple free radical polymerization process, we synthesized copolymer nanoparticles with controlled stimuli-responsive phase-separated gibbosities. The topography of the gibbous phase can be controlled by the copolymer composition and polymerization conditions. When pH-sensitive monomers were copolymerized onto surface bulges, pH changes resulted in localized gibbous phase dimensional changes. Facilitated by monomer diffusion into interfacial particle seed solution regions, localized polymerization near the surface is responsible for the formation of phase-separated gibbous topographies. This general approach may offer a number of possibilities for controllable design of ordered heterogeneous copolymer morphologies for a variety of applications.

  3. Rational Design of Pathogen-Mimicking Amphiphilic Materials as Nanoadjuvants

    NASA Astrophysics Data System (ADS)

    Ulery, Bret D.; Petersen, Latrisha K.; Phanse, Yashdeep; Kong, Chang Sun; Broderick, Scott R.; Kumar, Devender; Ramer-Tait, Amanda E.; Carrillo-Conde, Brenda; Rajan, Krishna; Wannemuehler, Michael J.; Bellaire, Bryan H.; Metzger, Dennis W.; Narasimhan, Balaji

    2011-12-01

    An opportunity exists today for cross-cutting research utilizing advances in materials science, immunology, microbial pathogenesis, and computational analysis to effectively design the next generation of adjuvants and vaccines. This study integrates these advances into a bottom-up approach for the molecular design of nanoadjuvants capable of mimicking the immune response induced by a natural infection but without the toxic side effects. Biodegradable amphiphilic polyanhydrides possess the unique ability to mimic pathogens and pathogen associated molecular patterns with respect to persisting within and activating immune cells, respectively. The molecular properties responsible for the pathogen-mimicking abilities of these materials have been identified. The value of using polyanhydride nanovaccines was demonstrated by the induction of long-lived protection against a lethal challenge of Yersinia pestis following a single administration ten months earlier. This approach has the tantalizing potential to catalyze the development of next generation vaccines against diseases caused by emerging and re-emerging pathogens.

  4. Regular Expressions at Their Best: A Case for Rational Design

    NASA Astrophysics Data System (ADS)

    Le Maout, Vincent

    Regular expressions are often an integral part of program customization and many algorithms have been proposed for transforming them into suitable data structures. These algorithms can be divided into two main classes: backtracking or automaton-based algorithms. Surprisingly, the latter class draws less attention than the former, even though automaton-based algorithms represent the oldest and by far the fastest solutions when carefully designed. Only two open-source automaton-based implementations stand out: PCRE and the recent RE2 from Google. We have developed, and present here, a competitive automaton-based regular expression engine on top of the LGPL C++ Automata Standard Template Library (ASTL), whose efficiency and scalability remain unmatched and which distinguishes itself through a unique and rigorous STL-like design.

  5. On the rational design of compressible flow ejectors

    NASA Technical Reports Server (NTRS)

    Ortwerth, P. J.

    1979-01-01

    A fluid mechanics review of chemical laser ejectors is presented. The characteristics of ejectors with single and multiple driver nozzles are discussed. Methods to compute an optimized performance map in which secondary Mach number and performance are computed versus mass ratio, to compute the flow distortion at each optimized condition, and to determine the thrust area for the design point to match diffuser impedence are examined.

  6. Rational Design of Proteasome Inhibitors as Antimalarial Drugs.

    PubMed

    Le Chapelain, Camille; Groll, Michael

    2016-05-23

    One life, two strategies: Crucial structural differences between the human and the Plasmodium falciparum proteasomes were recently identified. A combination of cryo-EM and functional characterization enabled the design of a selective antimalarial proteasome inhibitor that shows low toxicity in the host. When used with artemisinin, this ligand offers a new approach for the efficient treatment of malaria at all stages of the parasite lifecycle.

  7. Rational Design of Antirheumatic Prodrugs Specific for Sites of Inflammation

    PubMed Central

    Onuoha, Shimobi C.; Ferrari, Mathieu; Sblattero, Daniele

    2015-01-01

    Objective Biologic drugs, such as the anti–tumor necrosis factor (anti‐TNF) antibody adalimumab, have represented a breakthrough in the treatment of rheumatoid arthritis. Yet, concerns remain over their lack of efficacy in a sizable proportion of patients and their potential for systemic side effects such as infection. Improved biologic prodrugs specifically targeted to the site of inflammation have the potential to alleviate current concerns surrounding biologic anticytokine therapies. The purpose of this study was to design, construct, and evaluate in vitro and ex vivo the targeting and antiinflammatory capacity of activatable bispecific antibodies. Methods Activatable dual variable domain (aDVD) antibodies were designed and constructed to target intercellular adhesion molecule 1 (ICAM‐1), which is up‐regulated at sites of inflammation, and anti‐TNF antibodies (adalimumab and infliximab). These bispecific molecules included an external arm that targets ICAM‐1 and an internal arm that comprises the therapeutic domain of an anti‐TNF antibody. Both arms were linked to matrix metalloproteinase (MMP)–cleavable linkers. The constructs were tested for their ability to bind and neutralize both in vitro and ex vivo targets. Results Intact aDVD constructs demonstrated significantly reduced binding and anti‐TNF activity in the prodrug formulation as compared to the parent antibodies. Human synovial fluid and physiologic concentrations of MMP enzyme were capable of cleaving the external domain of the antibody, revealing a fully active molecule. Activated antibodies retained the same binding and anti‐TNF inhibitory capacities as the parent molecules. Conclusion The design of a biologic prodrug with enhanced specificity for sites of inflammation (synovium) and reduced specificity for off‐target TNF is described. This construct has the potential to form a platform technology that is capable of enhancing the therapeutic index of drugs for the treatment of

  8. Approaches to the rational design of selective melanocortin receptor antagonists

    PubMed Central

    Hruby, Victor J; Cai, Minying; Nyberg, Joel; Muthu, Dhanasekaran

    2015-01-01

    Introduction When establishing the physiological roles of specific receptors in normal and disease states, it is critical to have selective antagonist ligands for each receptor in a receptor system with several subtypes. The melanocortin receptors have five subtypes referred to as the melanocortin 1 receptor, melanocortin 2 receptor, melanocortin 3 receptor, melanocortin 4 receptor and melanocortin 5 receptor, and they are of critical importance for many aspects of human health and disease. Areas covered This article reviews the current efforts to design selective antagonistic ligands for the five human melanocortin receptors summarizing the currently published orthosteric and allosteric antagonists for each of these receptors. Expert opinion Though there has been progress, there are still few drugs available that address the many significant biological activities and diseases that are associated with these receptors, which is possibly due to the lack of receptor selectivity that these designed ligands are currently showing. The authors believe that further studies into the antagonists’ 3D conformational and topographical properties in addition to future mutagenesis studies will provide greater insight into these ligands which could play a role in the treatment of various diseases in the future. PMID:22646078

  9. Progress toward a rationally designed, chemically powered rotary molecular motor.

    PubMed

    Kelly, T Ross; Cai, Xiaolu; Damkaci, Fehmi; Panicker, Sreeletha B; Tu, Bin; Bushell, Simon M; Cornella, Ivan; Piggott, Matthew J; Salives, Richard; Cavero, Marta; Zhao, Yajun; Jasmin, Serge

    2007-01-17

    Building on prototype 1, which achieves 120 degrees of phosgene-powered unidirectional rotation to rotamer 6 (see Figure 5 in the full article), 7 was designed to accomplish repeated unidirectional rotation (see Scheme 7). Compound 7 contains an amino group on each blade of the triptycene and a 4-(dimethylamino)pyridine (DMAP) unit to selectively deliver phosgene (or its equivalent) to the amine in the "firing position". The synthesis of 7 is described: the key constructive steps are a benzyne addition to an anthracene to generate the triptycene, a stilbene photocyclization to construct the helicene, and a Stille coupling to incorporate the DMAP unit. The DMAP unit was shown to regioselectively relay 1,1'-carbonyldiimidazole (but not phosgene) to the proximal amino group, as designed, but rotation of the triptycene does not occur. Extensive attempts to troubleshoot the problem led to the conclusion that the requisite intramolecular urethane formation, as demonstrated in the prototype (1 --> 4), does not occur with 7 (to give 85) or 97 (to give 100). We speculate that either (i) hydrogen bonding between the hydroxypropyl group and functionality present in 7 but absent from 1 or (ii) a Bürgi-Dunitz (or similar) interaction involving the DMAP (see 106) prevents achievement of a conformation conducive to intramolecular urethane formation. PMID:17212418

  10. Intestinal targeting of drugs: rational design approaches and challenges.

    PubMed

    Filipski, Kevin J; Varma, Manthena V; El-Kattan, Ayman F; Ambler, Catherine M; Ruggeri, Roger B; Goosen, Theunis C; Cameron, Kimberly O

    2013-01-01

    Targeting drugs to the gastrointestinal tract has been and continues to be an active area of research. Gut-targeting is an effective means of increasing the local concentration of active substance at the desired site of action while minimizing concentrations elsewhere in the body that could lead to unwanted side-effects. Several approaches to intestinal targeting exist. Physicochemical property manipulation can drive molecules to large, polar, low absorption space or alternatively to lipophilic, high clearance space in order to minimize systemic exposure. Design of compounds that are substrates for transporters within the gastrointestinal tract, either uptake or efflux, or at the hepato-biliary interface, may help to increase intestinal concentration. Prodrug strategies have been shown to be effective particularly for colon targeting, and several different technology formulation approaches are currently being researched. This review provides examples of various approaches to intestinal targeting, and discusses challenges and areas in need of future scientific advances.

  11. Synthesis of a Potent Vinblastine: Rationally Designed Added Benign Complexity.

    PubMed

    Allemann, Oliver; Brutsch, Manuela; Lukesh, John C; Brody, Daniel M; Boger, Dale L

    2016-07-13

    Many natural products, including vinblastine, have not been easily subjected to simplifications in their structures by synthetic means or modifications by late-stage semisynthetic derivatization in ways that enhance their biological potency. Herein, we detail a synthetic vinblastine that incorporates added benign complexity (ABC), which improves activity 10-fold, and is now accessible as a result of advances in the total synthesis of the natural product. The compound incorporates designed added molecular complexity but no new functional groups and maintains all existing structural and conformational features of the natural product. It constitutes a member of an analogue class presently inaccessible by semisynthetic derivatization of the natural product, by its late-stage functionalization, or by biosynthetic means. Rather, it was accessed by synthetic means, using an appropriately modified powerful penultimate single-step vindoline-catharanthine coupling strategy that proceeds with a higher diastereoselectivity than found for the natural product itself. PMID:27356080

  12. Rational Design of Calpain Inhibitors Based on Calpastatin Peptidomimetics.

    PubMed

    Low, Kristin E; Ler, Spencer; Chen, Kevin J; Campbell, Robert L; Hickey, Jennifer L; Tan, Joanne; Scully, Conor C G; Davies, Peter L; Yudin, Andrei K; Zaretsky, Serge

    2016-06-01

    Our previously reported structures of calpain bound to its endogenous inhibitor calpastatin have motivated the use of aziridine aldehyde-mediated peptide macrocyclization toward the design of cyclic peptides and peptidomimetics as calpain inhibitors. Inspired by nature's hint that a β-turn loop within calpastatin forms a broad interaction around calpain's active site cysteine, we have constructed and tested a library of 45 peptidic compounds based on this loop sequence. Four molecules have shown reproducibly low micromolar inhibition of calpain-2. Further systematic sequence changes led to the development of probes that displayed increased potency and specificity of inhibition against calpain over other cysteine proteases. Calculated Ki values were in the low micromolar range, rivaling other peptidomimetic calpain inhibitors and presenting an improved selectivity profile against other therapeutically relevant proteases. Competitive and mixed inhibition against calpain-2 was observed, and an allosteric inhibition site on the enzyme was identified for a noncompetitive inhibitor.

  13. Kinetic resolution of oxazinones: rational exploration of chemical space through the design of experiments.

    PubMed

    Renzi, Polyssena; Kronig, Christel; Carlone, Armando; Eröksüz, Serap; Berkessel, Albrecht; Bella, Marco

    2014-09-01

    The organocatalytic kinetic resolution of 4-substituted oxazinones has been optimised (selectivity factor S up to 98, chiral oxazinone ee values up to 99.6 % (1 a-g) and product ee values up to 90 % (3 a-g)) in a rational way by applying the Design of Experiments (DoE) approach.

  14. Utilizing interfaces: One-step forward for rational design of heterogeneous catalysts

    SciTech Connect

    Kim H. Y.

    2013-06-20

    As far as heterogeneous catalysts are a composite material, physicochemical properties of the interfaces between individual components should be extensively studied for rational design of catalysts with desired properties. Here, I will present recent computational achievements in following three heterogeneous catalysts where the interface between composing materials plays a critical role

  15. Rational ligand design for the arylation of hindered primary amines guided by reaction progress kinetic analysis.

    PubMed

    Ruiz-Castillo, Paula; Blackmond, Donna G; Buchwald, Stephen L

    2015-03-01

    We report the Pd-catalyzed arylation of very hindered α,α,α-trisubstituted primary amines. Kinetics-based mechanistic analysis and rational design have led to the development of two biarylphosphine ligands that allow the transformation to proceed with excellent efficiency. The process was effective in coupling a wide range of functionalized aryl and heteroaryl halides under mild conditions.

  16. Rational design and interaction studies of combilexins towards duplex DNA.

    PubMed

    Dileep, K V; Vijeesh, V; Remya, C

    2016-03-01

    DNA, which is the genetic material, plays a predominant role in all living organisms. Alterations in the structure and function of this genetic material correlate with complex diseases such as cancer. A number of anticancer drugs exert their action by binding to DNA. Although DNA binding compounds exert genotoxicity, there is a high demand for novel DNA binding molecules because they can be further developed into anticancer drugs. In the present study, the mode of interaction of two compounds, 2,4-D and tacrine, has been determined to be minor groove binding and intercalation, respectively. Subsequently, from their binding modes, novel combilexin molecules were designed using computational tools and their mode of binding and affinities towards DNA were determined through a series of molecular modeling experiments such as molecular docking, molecular dynamics and binding free energy calculations. The entire study focuses on the potential effects of combilexins compared to intercalators and minor groove binders. The combilexins deduced from the current study may be considered as lead compounds for the development of better anticancer drugs.

  17. Rational design of a split-Cas9 enzyme complex

    DOE PAGES

    Wright, Addison V.; Sternberg, Samuel H.; Taylor, David W.; Staahl, Brett T.; Bardales, Jorge A.; Kornfeld, Jack E.; Doudna, Jennifer A.

    2015-02-23

    Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. The lobes do not interactmore » on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications.« less

  18. Rational design of a split-Cas9 enzyme complex

    SciTech Connect

    Wright, Addison V.; Sternberg, Samuel H.; Taylor, David W.; Staahl, Brett T.; Bardales, Jorge A.; Kornfeld, Jack E.; Doudna, Jennifer A.

    2015-02-23

    Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. The lobes do not interact on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications.

  19. Rational design of the car hearth of a tunnel furnace

    SciTech Connect

    Kryzhanovskii, K.S.; Chernyi, V.I.; Dunaevskii, O.M.; Mokhort, V.N.; Sedoi, N.I.

    1985-09-01

    In tunnel furnaces the heat losses into the environment amount to 15-20% of the burnt-fuel heat. The heat is essentially lost through the car (carrier) hearth into the corridor of the furnace bottom. A light-weight car has been designed that is thermally insulated using a high-alumina kaolin fiber of the VGR-130 mark. The car-hearth weight was reduced by 1.5 times by using a light-weight fireclay and incorporating an air space within the hearth. Using the method of finite differences, the authors determined the dynamics of temperature field variation along the height of the car-hearth before and after its reconstruction as applied to the firing parameters of the products in the tunnel furnace. The results of the determinations are presented. An additional thermal insulation of the car hearth using a 15-20 mm thick high-alumina kaolin fiber also makes it possible to reduce the heat losses in the furnace-bottom corridor by 30-40%, and thereby, to decrease the maximum temperature in the corridor from 90 to 60 degrees C, which significantly improves energy efficiency.

  20. Rational design of a split-Cas9 enzyme complex

    PubMed Central

    Wright, Addison V.; Sternberg, Samuel H.; Taylor, David W.; Staahl, Brett T.; Bardales, Jorge A.; Kornfeld, Jack E.; Doudna, Jennifer A.

    2015-01-01

    Cas9, an RNA-guided DNA endonuclease found in clustered regularly interspaced short palindromic repeats (CRISPR) bacterial immune systems, is a versatile tool for genome editing, transcriptional regulation, and cellular imaging applications. Structures of Streptococcus pyogenes Cas9 alone or bound to single-guide RNA (sgRNA) and target DNA revealed a bilobed protein architecture that undergoes major conformational changes upon guide RNA and DNA binding. To investigate the molecular determinants and relevance of the interlobe rearrangement for target recognition and cleavage, we designed a split-Cas9 enzyme in which the nuclease lobe and α-helical lobe are expressed as separate polypeptides. Although the lobes do not interact on their own, the sgRNA recruits them into a ternary complex that recapitulates the activity of full-length Cas9 and catalyzes site-specific DNA cleavage. The use of a modified sgRNA abrogates split-Cas9 activity by preventing dimerization, allowing for the development of an inducible dimerization system. We propose that split-Cas9 can act as a highly regulatable platform for genome-engineering applications. PMID:25713377

  1. Rationally Designed Peptidomimetic Modulators of Aβ Toxicity in Alzheimer's Disease

    NASA Astrophysics Data System (ADS)

    Rajasekhar, K.; Suresh, S. N.; Manjithaya, Ravi; Govindaraju, T.

    2015-01-01

    Alzheimer's disease is one of the devastating illnesses mankind is facing in the 21st century. The main pathogenic event in Alzheimer's disease is believed to be the aggregation of the β-amyloid (Aβ) peptides into toxic aggregates. Molecules that interfere with this process may act as therapeutic agents for the treatment of the disease. Use of recognition unit based peptidomimetics as inhibitors are a promising approach, as they exhibit greater protease stability compared to natural peptides. Here, we present peptidomimetic inhibitors of Aβ aggregation designed based on the KLVFF (P1) sequence that is known to bind Aβ aggregates. We improved inhibition efficiency of P1 by introducing multiple hydrogen bond donor-acceptor moieties (thymine/barbiturate) at the N-terminal (P2 and P3), and blood serum stability by modifying the backbone by incorporating sarcosine (N-methylglycine) units at alternate positions (P4 and P5). The peptidomimetics showed moderate to good activity in both inhibition and dissolution of Aβ aggregates as depicted by thioflavin assay, circular dichroism (CD) measurements and microscopy (TEM). The activity of P4 and P5 were studied in a yeast cell model showing Aβ toxicity. P4 and P5 could rescue yeast cells from Aβ toxicity and Aβ aggregates were cleared by the process of autophagy.

  2. Resistance identification and rational process design in Capacitive Deionization.

    PubMed

    Dykstra, J E; Zhao, R; Biesheuvel, P M; van der Wal, A

    2016-01-01

    Capacitive Deionization (CDI) is an electrochemical method for water desalination employing porous carbon electrodes. To enhance the performance of CDI, identification of electronic and ionic resistances in the CDI cell is important. In this work, we outline a method to identify these resistances. We illustrate our method by calculating the resistances in a CDI cell with membranes (MCDI) and by using this knowledge to improve the cell design. To identify the resistances, we derive a full-scale MCDI model. This model is validated against experimental data and used to calculate the ionic resistances across the MCDI cell. We present a novel way to measure the electronic resistances in a CDI cell, as well as the spacer channel thickness and porosity after assembly of the MCDI cell. We identify that for inflow salt concentrations of 20 mM the resistance is mainly located in the spacer channel and the external electrical circuit, not in the electrodes. Based on these findings, we show that the carbon electrode thickness can be increased without significantly increasing the energy consumption per mol salt removed, which has the advantage that the desalination time can be lengthened significantly.

  3. Rational design of vaccines against enveloped RNA viruses.

    PubMed

    Stephenson, J R

    1985-03-01

    The enveloped RNA viruses are responsible for many important infectious diseases both in the UK and worldwide. The most familiar of these would probably be influenza, measles, mumps, rubella, rabies, dengue and yellow fever. Conventional vaccines against all of the most widespread diseases have been available for several years, although with widely varying degrees of safety and efficacy. Although vaccines against diseases such as measles, rubella, and yellow fever have been fairly successful, all vaccines against diseases caused by this group of viruses still have several drawbacks and are in need of improvement for a variety of reasons. During the past decade our knowledge in several diverse areas of the biological sciences has expanded to the extent that it can now be combined and serious attempts made to design and engineer biological molecules with immunogenic potential. First, significant advances have been made in elucidating the mechanisms operating in the immune defence network and in determining the structure of both immunogenic molecules and the components of the immune system with which they interact. Second, the development of recombinant DNA technology has enabled biological molecules to be synthesized under conditions not restricted by the characteristics of their parent organism. Such molecules can then be altered in such a way as to improve their efficiency and their level of production. It is the purpose of this paper to outline the problems associated with the production of vaccines against enveloped RNA viruses and to discuss how recent advances in knowledge and techniques can help to overcome these problems. PMID:2408398

  4. Acentric lattice electro-optic materials by rational design

    NASA Astrophysics Data System (ADS)

    Dalton, Larry; Robinson, Bruce; Jen, Alex; Ried, Philip; Eichinger, Bruce; Sullivan, Philip; Akelaitis, Andrew; Bale, Denise; Haller, Marnie; Luo, Jingdong; Liu, Sen; Liao, Yi; Firestone, Kimberly; Bhatambrekar, Nishant; Bhattacharjee, Sanchali; Sinness, Jessica; Hammond, Scott; Buker, Nicholas; Snoeberger, Robert; Lingwood, Mark; Rommel, Harry; Amend, Joe; Jang, Sei-Hum; Chen, Antao; Steier, William

    2005-08-01

    Quantum and statistical mechanical calculations have been used to guide the improvement of the macroscopic electro-optic activity of organic thin film materials to values greater than 300 pm/V at telecommunication wavelengths. Various quantum mechanical methods (Hartree-Fock, INDO, and density functional theory) have been benchmarked and shown to be reliable for estimating trends in molecular first hyperpolarizability, β, for simple variation of donor, bridge, and acceptor structures of charge-transfer (dipolar) chromophores. β values have been increased significantly over the past five years and quantum mechanical calculations suggest that they can be further significantly improved. Statistical mechanical calculations, including pseudo-atomistic Monte Carlo calculations, have guided the design of the super/supramolecular structures of chromophores so that they assemble, under the influence of electric field poling, into macroscopic lattices with high degrees of acentric order. Indeed, during the past year, chromophores doped into single- and multi-chromophore-containing dendrimer materials to form binary glasses have yielded thin films that exhibit electro-optic activities at telecommunication wavelengths of greater than 300 pm/V. Such materials may be viewed as intermediate between chromophore/polymer composites and crystalline organic chromophore materials. Theory suggests that further improvements of electro-optic activity are possible. Auxiliary properties of these materials, including optical loss, thermal and photochemical stability, and processability are discussed. Such organic electro-optic materials have been incorporated into silicon photonic circuitry for active wavelength division multiplexing, reconfigurable optical add/drop multiplexing, and high bandwidth optical rectification. A variety of all-organic devices, including stripline, cascaded prism, Fabry-Perot etalon, and ring microresonator devices, have been fabricated and evaluated.

  5. Rational Design of Plasmonic Nanoparticles for Enhanced Cavitation and Cell Perforation.

    PubMed

    Lachaine, Rémi; Boutopoulos, Christos; Lajoie, Pierre-Yves; Boulais, Étienne; Meunier, Michel

    2016-05-11

    Metallic nanoparticles are routinely used as nanoscale antenna capable of absorbing and converting photon energy with subwavelength resolution. Many applications, notably in nanomedicine and nanobiotechnology, benefit from the enhanced optical properties of these materials, which can be exploited to image, damage, or destroy targeted cells and subcellular structures with unprecedented precision. Modern inorganic chemistry enables the synthesis of a large library of nanoparticles with an increasing variety of shapes, composition, and optical characteristic. However, identifying and tailoring nanoparticles morphology to specific applications remains challenging and limits the development of efficient nanoplasmonic technologies. In this work, we report a strategy for the rational design of gold plasmonic nanoshells (AuNS) for the efficient ultrafast laser-based nanoscale bubble generation and cell membrane perforation, which constitute one of the most crucial challenges toward the development of effective gene therapy treatments. We design an in silico rational design framework that we use to tune AuNS morphology to simultaneously optimize for the reduction of the cavitation threshold while preserving the particle structural integrity. Our optimization procedure yields optimal AuNS that are slightly detuned compared to their plasmonic resonance conditions with an optical breakdown threshold 30% lower than randomly selected AuNS and 13% lower compared to similarly optimized gold nanoparticles (AuNP). This design strategy is validated using time-resolved bubble spectroscopy, shadowgraphy imaging and electron microscopy that confirm the particle structural integrity and a reduction of 51% of the cavitation threshold relative to optimal AuNP. Rationally designed AuNS are finally used to perforate cancer cells with an efficiency of 61%, using 33% less energy compared to AuNP, which demonstrate that our rational design framework is readily transferable to a cell environment

  6. Rational Design of Plasmonic Nanoparticles for Enhanced Cavitation and Cell Perforation.

    PubMed

    Lachaine, Rémi; Boutopoulos, Christos; Lajoie, Pierre-Yves; Boulais, Étienne; Meunier, Michel

    2016-05-11

    Metallic nanoparticles are routinely used as nanoscale antenna capable of absorbing and converting photon energy with subwavelength resolution. Many applications, notably in nanomedicine and nanobiotechnology, benefit from the enhanced optical properties of these materials, which can be exploited to image, damage, or destroy targeted cells and subcellular structures with unprecedented precision. Modern inorganic chemistry enables the synthesis of a large library of nanoparticles with an increasing variety of shapes, composition, and optical characteristic. However, identifying and tailoring nanoparticles morphology to specific applications remains challenging and limits the development of efficient nanoplasmonic technologies. In this work, we report a strategy for the rational design of gold plasmonic nanoshells (AuNS) for the efficient ultrafast laser-based nanoscale bubble generation and cell membrane perforation, which constitute one of the most crucial challenges toward the development of effective gene therapy treatments. We design an in silico rational design framework that we use to tune AuNS morphology to simultaneously optimize for the reduction of the cavitation threshold while preserving the particle structural integrity. Our optimization procedure yields optimal AuNS that are slightly detuned compared to their plasmonic resonance conditions with an optical breakdown threshold 30% lower than randomly selected AuNS and 13% lower compared to similarly optimized gold nanoparticles (AuNP). This design strategy is validated using time-resolved bubble spectroscopy, shadowgraphy imaging and electron microscopy that confirm the particle structural integrity and a reduction of 51% of the cavitation threshold relative to optimal AuNP. Rationally designed AuNS are finally used to perforate cancer cells with an efficiency of 61%, using 33% less energy compared to AuNP, which demonstrate that our rational design framework is readily transferable to a cell environment

  7. Rational design of metal oxide nanocomposite anodes for advanced lithium ion batteries

    NASA Astrophysics Data System (ADS)

    Li, Yong; Yu, Shenglan; Yuan, Tianzhi; Yan, Mi; Jiang, Yinzhu

    2015-05-01

    Metal-oxide anodes represent a significant future direction for advanced lithium ion batteries. However, their practical applications are still seriously hampered by electrode disintegration and capacity fading during cycling. Here, we report a rational design of 3D-staggered metal-oxide nanocomposite electrode directly fabricated by pulsed spray evaporation chemical vapor deposition, where various oxide nanocomponents are in a staggered distribution uniformly along three dimensions and across the whole electrode. Such a special design of nanoarchitecture combines the advantages of nanoscale materials in volume change and Li+/electron conduction as well as uniformly staggered and compact structure in atom migration during lithiation/delithiation, which exhibits high specific capacity, good cycling stability and excellent rate capability. The rational design of metal-oxide nanocomposite electrode opens up new possibilities for high performance lithium ion batteries.

  8. 50 CFR Table 3 to Part 226 - Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake River...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Habitat for Snake River Sockeye Salmon and Snake River Spring/Summer and Fall Chinook Salmon 3 Table 3 to... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT Pt. 226, Table 3 Table 3 to Part 226—Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake...

  9. 50 CFR Table 3 to Part 226 - Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake River...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Habitat for Snake River Sockeye Salmon and Snake River Spring/Summer and Fall Chinook Salmon 3 Table 3 to... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT Pt. 226, Table 3 Table 3 to Part 226—Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake...

  10. 50 CFR Table 3 to Part 226 - Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake River...

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Habitat for Snake River Sockeye Salmon and Snake River Spring/Summer and Fall Chinook Salmon 3 Table 3 to... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT Pt. 226, Table 3 Table 3 to Part 226—Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake...

  11. 50 CFR Table 3 to Part 226 - Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake River...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Habitat for Snake River Sockeye Salmon and Snake River Spring/Summer and Fall Chinook Salmon 3 Table 3 to... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT Pt. 226, Table 3 Table 3 to Part 226—Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake...

  12. 50 CFR Table 3 to Part 226 - Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake River...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Habitat for Snake River Sockeye Salmon and Snake River Spring/Summer and Fall Chinook Salmon 3 Table 3 to... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT Pt. 226, Table 3 Table 3 to Part 226—Hydrologic Units Containing Critical Habitat for Snake River Sockeye Salmon and Snake...

  13. Rational design of new electrolyte materials for electrochemical double layer capacitors

    NASA Astrophysics Data System (ADS)

    Schütter, Christoph; Husch, Tamara; Viswanathan, Venkatasubramanian; Passerini, Stefano; Balducci, Andrea; Korth, Martin

    2016-09-01

    The development of new electrolytes is a centerpiece of many strategies to improve electrochemical double layer capacitor (EDLC) devices. We present here a computational screening-based rational design approach to find new electrolyte materials. As an example application, the known chemical space of almost 70 million compounds is investigated in search of electrochemically more stable solvents. Cyano esters are identified as especially promising new compound class. Theoretical predictions are validated with subsequent experimental studies on a selected case. These studies show that based on theoretical predictions only, a previously untested, but very well performing compound class was identified. We thus find that our rational design strategy is indeed able to successfully identify completely new materials with substantially improved properties.

  14. Controlling the Spin Texture of Topological Insulators by Rational Design of Organic Molecules.

    PubMed

    Jakobs, Sebastian; Narayan, Awadhesh; Stadtmüller, Benjamin; Droghetti, Andrea; Rungger, Ivan; Hor, Yew S; Klyatskaya, Svetlana; Jungkenn, Dominik; Stöckl, Johannes; Laux, Martin; Monti, Oliver L A; Aeschlimann, Martin; Cava, Robert J; Ruben, Mario; Mathias, Stefan; Sanvito, Stefano; Cinchetti, Mirko

    2015-09-01

    We present a rational design approach to customize the spin texture of surface states of a topological insulator. This approach relies on the extreme multifunctionality of organic molecules that are used to functionalize the surface of the prototypical topological insulator (TI) Bi2Se3. For the rational design we use theoretical calculations to guide the choice and chemical synthesis of appropriate molecules that customize the spin texture of Bi2Se3. The theoretical predictions are then verified in angular-resolved photoemission experiments. We show that, by tuning the strength of molecule-TI interaction, the surface of the TI can be passivated, the Dirac point can energetically be shifted at will, and Rashba-split quantum-well interface states can be created. These tailored interface properties-passivation, spin-texture tuning, and creation of hybrid interface states-lay a solid foundation for interface-assisted molecular spintronics in spin-textured materials.

  15. Aggregation-induced emission rotors: rational design and tunable stimuli response.

    PubMed

    Li, Jie; Zhang, Yang; Mei, Ju; Lam, Jacky W Y; Hao, Jianhua; Tang, Ben Zhong

    2015-01-01

    A novel molecular design strategy is provided to rationally tune the stimuli response of luminescent materials with aggregation-induced emission (AIE) characteristics. A series of new AIE-active molecules (AIE rotors) are prepared by covalently linking different numbers of tetraphenylethene moieties together. Upon gradually increasing the number of rotatable phenyl rings, the sensitivity of the response of the AIE rotors to viscosity and temperature is significantly enhanced. Although the molecular size is further enlarged, the performance is only slightly improved due to slightly increased effective rotors, but with largely increased rotational barriers. Such molecular engineering and experimental results offer more in-depth insight into the AIE mechanism, namely, restriction of intramolecular rotations. Notably, through this rational design, the AIE rotor with the largest molecular size turns out to be the most viscosensitive luminogen with a viscosity factor of up to 0.98.

  16. Rationally designed multifunctional plasmonic nanostructures for surface-enhanced Raman spectroscopy: a review

    NASA Astrophysics Data System (ADS)

    Xie, Wei; Schlücker, Sebastian

    2014-11-01

    Rationally designed multifunctional plasmonic nanostructures efficiently integrate two or more functionalities into a single entity, for example, with both plasmonic and catalytic activity. This review article is focused on their synthesis and use in surface-enhanced Raman scattering (SERS) as a molecular spectroscopic technique with high sensitivity, fingerprint specificity, and surface selectivity. After a short tutorial on the fundamentals of Raman scattering and SERS in particular, applications ranging from chemistry (heterogeneous catalysis) to biology and medicine (diagnostics/imaging, therapy) are summarized.

  17. Tunable emission in lanthanide coordination polymer gels based on a rationally designed blue emissive gelator.

    PubMed

    Sutar, Papri; Suresh, Venkata M; Maji, Tapas Kumar

    2015-06-18

    Rational design and synthesis of a new low molecular weight gelator (LMWG) having 9,10-diphenylanthracene core and terminal terpyridine is reported. Tb(III) and Eu(III) ion coordination to a LMWG results in green and pink emissive coordination polymer gels, respectively, with coiled nanofiber morphology. Further, control over stoichiometry of LMWG:Tb(III):Eu(III) leads to yellow and white light emitting bimetallic gels. PMID:25995095

  18. A systems biology perspective on rational design of peptide vaccine against virus infections.

    PubMed

    Chen, Jiajia; Wang, Ying; Guo, Deyin; Shen, Bairong

    2012-01-01

    With the recent onset of influenza A (H1N1) pandemic, the need for improved vaccines against virus infections has become an international priority. Strategies for vaccine development have changed over time, from whole-virus to immunogenic proteins and further to antigenic viral peptides. Various algorithms and bioinformatics tools have been developed to predict immunogenic peptide regions in an antigenic protein sequence. Recent advances in next-generation sequencing technologies, as represented by real time DNA sequencing, provide increased throughput and yield of data on viral pathogens and host cells. This enables us to 'mine' the genomic sequence for putative vaccine candidates or targets, allowing a more rational approach to the peptide vaccine design. This review first describes current computational tools available for the rational design of peptide vaccines and then addresses recent attempts to define pathogenic peptides at '- omics' level. As there are interplay between antibody and T cells, as well as intersection between viruses and hosts, the vaccine-mediated immunity are orchestrated by multiple factors within an interaction network. Therefore, single viral peptide alone fails to provide optimal immunity. Systems biology offers a systems-level perspective of how the various arms of the immune response are integrated to give immune response, as well as how host and virus interact, thereby providing an integrated approach to select the most promising candidates for peptide vaccines development. We highlight in this article the system-level application of rational peptide vaccine design, which may be a general paradigm for future viral vaccine development.

  19. Rational design of carbon nitride photocatalysts by identification of cyanamide defects as catalytically relevant sites.

    PubMed

    Lau, Vincent Wing-Hei; Moudrakovski, Igor; Botari, Tiago; Weinberger, Simon; Mesch, Maria B; Duppel, Viola; Senker, Jürgen; Blum, Volker; Lotsch, Bettina V

    2016-01-01

    The heptazine-based polymer melon (also known as graphitic carbon nitride, g-C3N4) is a promising photocatalyst for hydrogen evolution. Nonetheless, attempts to improve its inherently low activity are rarely based on rational approaches because of a lack of fundamental understanding of its mechanistic operation. Here we employ molecular heptazine-based model catalysts to identify the cyanamide moiety as a photocatalytically relevant 'defect'. We exploit this knowledge for the rational design of a carbon nitride polymer populated with cyanamide groups, yielding a material with 12 and 16 times the hydrogen evolution rate and apparent quantum efficiency (400 nm), respectively, compared with the unmodified melon. Computational modelling and material characterization suggest that this moiety improves coordination (and, in turn, charge transfer kinetics) to the platinum co-catalyst and enhances the separation of the photogenerated charge carriers. The demonstrated knowledge transfer for rational catalyst design presented here provides the conceptual framework for engineering high-performance heptazine-based photocatalysts. PMID:27387536

  20. Rational design of carbon nitride photocatalysts by identification of cyanamide defects as catalytically relevant sites

    PubMed Central

    Lau, Vincent Wing-hei; Moudrakovski, Igor; Botari, Tiago; Weinberger, Simon; Mesch, Maria B.; Duppel, Viola; Senker, Jürgen; Blum, Volker; Lotsch, Bettina V.

    2016-01-01

    The heptazine-based polymer melon (also known as graphitic carbon nitride, g-C3N4) is a promising photocatalyst for hydrogen evolution. Nonetheless, attempts to improve its inherently low activity are rarely based on rational approaches because of a lack of fundamental understanding of its mechanistic operation. Here we employ molecular heptazine-based model catalysts to identify the cyanamide moiety as a photocatalytically relevant ‘defect'. We exploit this knowledge for the rational design of a carbon nitride polymer populated with cyanamide groups, yielding a material with 12 and 16 times the hydrogen evolution rate and apparent quantum efficiency (400 nm), respectively, compared with the unmodified melon. Computational modelling and material characterization suggest that this moiety improves coordination (and, in turn, charge transfer kinetics) to the platinum co-catalyst and enhances the separation of the photogenerated charge carriers. The demonstrated knowledge transfer for rational catalyst design presented here provides the conceptual framework for engineering high-performance heptazine-based photocatalysts. PMID:27387536

  1. Rational design of carbon nitride photocatalysts by identification of cyanamide defects as catalytically relevant sites.

    PubMed

    Lau, Vincent Wing-Hei; Moudrakovski, Igor; Botari, Tiago; Weinberger, Simon; Mesch, Maria B; Duppel, Viola; Senker, Jürgen; Blum, Volker; Lotsch, Bettina V

    2016-07-08

    The heptazine-based polymer melon (also known as graphitic carbon nitride, g-C3N4) is a promising photocatalyst for hydrogen evolution. Nonetheless, attempts to improve its inherently low activity are rarely based on rational approaches because of a lack of fundamental understanding of its mechanistic operation. Here we employ molecular heptazine-based model catalysts to identify the cyanamide moiety as a photocatalytically relevant 'defect'. We exploit this knowledge for the rational design of a carbon nitride polymer populated with cyanamide groups, yielding a material with 12 and 16 times the hydrogen evolution rate and apparent quantum efficiency (400 nm), respectively, compared with the unmodified melon. Computational modelling and material characterization suggest that this moiety improves coordination (and, in turn, charge transfer kinetics) to the platinum co-catalyst and enhances the separation of the photogenerated charge carriers. The demonstrated knowledge transfer for rational catalyst design presented here provides the conceptual framework for engineering high-performance heptazine-based photocatalysts.

  2. Rational design of carbon nitride photocatalysts by identification of cyanamide defects as catalytically relevant sites

    NASA Astrophysics Data System (ADS)

    Lau, Vincent Wing-Hei; Moudrakovski, Igor; Botari, Tiago; Weinberger, Simon; Mesch, Maria B.; Duppel, Viola; Senker, Jürgen; Blum, Volker; Lotsch, Bettina V.

    2016-07-01

    The heptazine-based polymer melon (also known as graphitic carbon nitride, g-C3N4) is a promising photocatalyst for hydrogen evolution. Nonetheless, attempts to improve its inherently low activity are rarely based on rational approaches because of a lack of fundamental understanding of its mechanistic operation. Here we employ molecular heptazine-based model catalysts to identify the cyanamide moiety as a photocatalytically relevant `defect'. We exploit this knowledge for the rational design of a carbon nitride polymer populated with cyanamide groups, yielding a material with 12 and 16 times the hydrogen evolution rate and apparent quantum efficiency (400 nm), respectively, compared with the unmodified melon. Computational modelling and material characterization suggest that this moiety improves coordination (and, in turn, charge transfer kinetics) to the platinum co-catalyst and enhances the separation of the photogenerated charge carriers. The demonstrated knowledge transfer for rational catalyst design presented here provides the conceptual framework for engineering high-performance heptazine-based photocatalysts.

  3. Inventing and improving ribozyme function: rational design versus iterative selection methods

    NASA Technical Reports Server (NTRS)

    Breaker, R. R.; Joyce, G. F.

    1994-01-01

    Two major strategies for generating novel biological catalysts exist. One relies on our knowledge of biopolymer structure and function to aid in the 'rational design' of new enzymes. The other, often called 'irrational design', aims to generate new catalysts, in the absence of detailed physicochemical knowledge, by using selection methods to search a library of molecules for functional variants. Both strategies have been applied, with considerable success, to the remodeling of existing ribozymes and the development of ribozymes with novel catalytic function. The two strategies are by no means mutually exclusive, and are best applied in a complementary fashion to obtain ribozymes with the desired catalytic properties.

  4. [Snake bites].

    PubMed

    Vincent, J L; Créteur, J

    1995-11-01

    Snake bites are a rare occurrence in Belgium. Nevertheless, all doctors should know how to react to this potentially very dangerous emergency. A snakebite does not necessarily result in poisoning: the effects can range from a little local discomfort to a severe systemic reaction with multiple organ failure. Therefore, all snake bites must be treated as serious and should receive adequate treatment. At the same time, hysterical over reaction must be avoided for this risks complications. This article reviews the principal elements of snake bite treatment: from the emergency stage through to stabilization in the hospital. Key points raised are the necessity to immobilize the affected region, to establish adequate perfusion and to anticipate infectious complications. Serum therapy indications are reviewed together with adjuvant interventions such as corticotherapy and heparin therapy. PMID:7501910

  5. Testing the limits of rational design by engineering pH sensitivity into membrane active peptides

    PubMed Central

    Wiedman, Gregory

    2015-01-01

    In this work, we sought to rationally design membrane active peptides that are triggered by low pH to form macromolecular-sized pores in lipid bilayers. Such peptides could have broad utility in biotechnology and in nanomedicine as cancer therapeutics or drug delivery vehicles that promote release of macromolecules from endosomes. Our approach to rational design was to combine the properties of a pH-independent peptide, MelP5, which forms large pores allowing passage of macromolecules, with the properties of two pH-dependent membrane active peptides, pHlip and GALA. We created two hybrid sequences, MelP5_Δ4 and MelP5_Δ6 by using the distribution of acidic residues on pHlip and GALA as a guide to insert acidic amino acids into the amphipathic helix of MelP5. We show that the new peptides bind to lipid bilayers and acquire secondary structure in a pH-dependent manner. The peptides also destabilize bilayers in a pH-dependent manner, such that lipid vesicles release the small molecules ANTS/DPX at low pH only. Thus, we were successful in designing pH-triggered pore-forming peptides. However, no macro-molecular release was observed under any conditions. Therefore, we abolished the unique macromolecular poration properties of MelP5 by introducing pH-sensitivity into its sequence. We conclude that the properties of pHlip, GALA and MelP5 are additive, but only partially so. We propose that this lack of additivity is a limitation in the rational design of novel membrane active peptides, and that high-throughput approaches to discovery will be critical for continued progress in the field. PMID:25572997

  6. Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design.

    PubMed

    Ehrt, Christiane; Brinkjost, Tobias; Koch, Oliver

    2016-05-12

    Modern rational drug design not only deals with the search for ligands binding to interesting and promising validated targets but also aims to identify the function and ligands of yet uncharacterized proteins having impact on different diseases. Additionally, it contributes to the design of inhibitors with distinct selectivity patterns and the prediction of possible off-target effects. The identification of similarities between binding sites of various proteins is a useful approach to cope with those challenges. The main scope of this perspective is to describe applications of different protein binding site comparison approaches to outline their applicability and impact on molecular design. The article deals with various substantial application domains and provides some outstanding examples to show how various binding site comparison methods can be applied to promote in silico drug design workflows. In addition, we will also briefly introduce the fundamental principles of different protein binding site comparison methods.

  7. Towards rational design of cannabinoid receptor 1 (CB1) antagonists for peripheral selectivity.

    PubMed

    Fulp, Alan; Bortoff, Katherine; Zhang, Yanan; Seltzman, Herbert; Snyder, Rodney; Maitra, Rangan

    2011-10-01

    CB1 receptor antagonists that are peripherally restricted were targeted. Compounds with permanent charge as well as compounds that have increased polar surface area were made and tested against CB1 for binding and activity. Sulfonamide and sulfamide with high polar surface area and good activity at CB1 were rationally designed and pharmacologically tested. Further optimization of these compounds and testing could lead to the development of a new class of therapeutics to treat disorders where the CB1 receptor system has been implicated. PMID:21875798

  8. Towards rational design of cannabinoid receptor 1 (CB1) antagonists for peripheral selectivity

    PubMed Central

    Fulp, Alan; Bortoff, Katherine; Zhang, Yanan; Seltzman, Herbert; Snyder, Rodney; Maitra, Rangan

    2011-01-01

    CB1 receptor antagonists that are peripherally restricted were targeted. Compounds with permanent charge as well as compounds that have increased polar surface area were made and tested against CB1 for binding and activity. Sulfonamide and sulfamide with high polar surface area and good activity at CB1 were rationally designed and pharmacologically tested. Further optimization of these compounds and testing could lead to the development of a new class of therapeutics to treat disorders where the CB1 receptor system has been implicated. PMID:21875798

  9. Control over Catenation in Metal−Organic Frameworks via Rational Design of the Organic Building Block

    SciTech Connect

    Farha, Omar K.; Malliakas, Christos D.; Kanatzidis, Mercouri G.; Hupp, Joseph T.

    2010-02-19

    Metal-organic frameworks (MOFs), a hybrid class of materials comprising inorganic nodes and organic struts, have potential application in many areas due to their high surface areas and uniform pores and channels. One of the key challenges to be overcome in MOF synthesis is the strong propensity for catenation (growth of multiple independent networks within a given crystal), as catenation reduces cavity sizes and diminishes porosity. Here we demonstrate that rational design of organic building blocks, which act as strut-impervious scaffolds, can be exploited to generate highly desired noncatenated materials in a controlled fashion.

  10. Recent advances in the rational design of silica-based nanoparticles for gene therapy.

    PubMed

    Niut, Yuting; Popatt, Amirali; Yu, Meihua; Karmakar, Surajit; Gu, Wenyi; Yu, Chengzhong

    2012-10-01

    Gene therapy has attracted much attention in modern society and provides a promising approach for treating genetic disorders, diseases and cancers. Safe and effective vectors are vital tools to deliver genetic molecules to cells. This review summarizes recent advances in the rational design of silica-based nanoparticles and their applications in gene therapy. An overview of different types of genetic agents available for gene therapy is provided. The engineering of various silica nanoparticles is described, which can be used as versatile complexation tools for genetic agents and advanced gene therapy. Several challenges are raised and future research directions in the area of gene therapy using silica-based nanoparticles are proposed.

  11. Crystals of Human Serum Albumin for Use in Genetic Engineering and Rational Drug Design

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C. (Inventor)

    1994-01-01

    This invention pertains to crystals of serum albumin and processes for growing them. The purpose of the invention is to provide crystals of serum albumin which can be studied to determine binding sites for drugs. Form 2 crystals grow in the monoclinic space P2(sub 1), and possesses the following unit cell constraints: a = 58.9 +/- 7, b = 88.3 +/- 7, c = 60.7 +/- 7, Beta = 101.0 +/- 2 degrees. One advantage of the invention is that it will allow rational drug design

  12. Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli.

    PubMed

    Nishio, Yousuke; Usuda, Yoshihiro; Matsui, Kazuhiko; Kurata, Hiroyuki

    2008-01-01

    The phosphotransferase system (PTS) is the sugar transportation machinery that is widely distributed in prokaryotes and is critical for enhanced production of useful metabolites. To increase the glucose uptake rate, we propose a rational strategy for designing the molecular architecture of the Escherichia coli glucose PTS by using a computer-aided design (CAD) system and verified the simulated results with biological experiments. CAD supports construction of a biochemical map, mathematical modeling, simulation, and system analysis. Assuming that the PTS aims at controlling the glucose uptake rate, the PTS was decomposed into hierarchical modules, functional and flux modules, and the effect of changes in gene expression on the glucose uptake rate was simulated to make a rational strategy of how the gene regulatory network is engineered. Such design and analysis predicted that the mlc knockout mutant with ptsI gene overexpression would greatly increase the specific glucose uptake rate. By using biological experiments, we validated the prediction and the presented strategy, thereby enhancing the specific glucose uptake rate.

  13. Simulating an Actomyosin in Vitro Motility Assay: Toward the Rational Design of Actomyosin-Based Microtransporters.

    PubMed

    Ishigure, Yuki; Nitta, Takahiro

    2015-09-01

    We present a simulation study of an actomyosin in vitro motility assay. In vitro motility assays have served as an essential element facilitating the application of actomyosin in nanotechnology; such applications include biosensors and biocomputation. Although actomyosin in vitro motility assays have been extensively investigated, some ambiguities remain, as a result of the limited spatio-temporal resolution and unavoidable uncertainties associated with the experimental process. These ambiguities hamper the rational design of nanodevices for practical applications. Here, with the aim of moving toward a rational design process, we developed a 3D computer simulation method of an actomyosin in vitro motility assay, based on a Brownian dynamics simulation. The simulation explicitly included the ATP hydrolysis cycle of myosin. The simulation was validated by the reproduction of previous experimental results. More importantly, the simulation provided new insights that are difficult to obtain experimentally, including data on the number of myosin motors actually binding to actin filaments, the mechanism responsible for the guiding of actin filaments by chemical edges, and the effect of the processivity of motor proteins on the guiding probabilities. The simulations presented here will be useful in interpreting experimental results, and also in designing future nanodevices integrated with myosin motors.

  14. Experimental and Theoretical Investigations of CB8-:Towards Rational Design of Hypercoordinated Planar Chemical Species

    SciTech Connect

    Averkiev, Boris B.; Wang, Leiming; Huang, Wei; Wang, Lai S.; Boldyrev, Alexander I.

    2009-11-01

    We demonstrated in our joint photoelectron spectroscopic and ab initio study that wheel-type structures with a boron ring are not appropriate for designing planar molecules with a hypercoordinate central carbon on the example of CB8, and CB8 clusters. According to our chemical bonding model, in the wheel type structures the central atom is involved in delocalized bonding, while peripheral atoms are involved in both delocalized bonding and 2c-2e -bonding. Since carbon is more electronegative than boron it favors peripheral positions where it can participate in 2c-2e -bonding. To design a chemical species with a central hypercoordinate carbon atom, one should consider electropositive ligands, which would have lone pairs instead of 2c-2e peripheral bonds. We presented a chemical bonding model capable of rationalizing and predicting structures either with a boron ring or a central planar carbon. This represents the first step toward rational design of nano- and subnano-structures with tailored properties.

  15. Rational Design of a Fusion Protein to Exhibit Disulfide-Mediated Logic Gate Behavior

    PubMed Central

    2015-01-01

    Synthetic cellular logic gates are primarily built from gene circuits owing to their inherent modularity. Single proteins can also possess logic gate functions and offer the potential to be simpler, quicker, and less dependent on cellular resources than gene circuits. However, the design of protein logic gates that are modular and integrate with other cellular components is a considerable challenge. As a step toward addressing this challenge, we describe the design, construction, and characterization of AND, ORN, and YES logic gates built by introducing disulfide bonds into RG13, a fusion of maltose binding protein and TEM-1 β-lactamase for which maltose is an allosteric activator of enzyme activity. We rationally designed these disulfide bonds to manipulate RG13’s allosteric regulation mechanism such that the gating had maltose and reducing agents as input signals, and the gates could be toggled between different gating functions using redox agents, although some gates performed suboptimally. PMID:25144732

  16. Rational design of mass diffusion metamaterial concentrators based on coordinate transformations

    NASA Astrophysics Data System (ADS)

    Restrepo-Flórez, Juan Manuel; Maldovan, Martin

    2016-08-01

    Recent advances in coordinate transformations of Fick's equation have paved the way for the design of metamaterial devices that can manipulate mass diffusion flux. The control of diffusion paths has a great potential for the design of novel catalytic and separation systems in chemical and biomolecular engineering. In order to explore these new applications, it is necessary to understand mass diffusion in coordinate transformation metamaterial devices. In this work, we present a comprehensive study on the impact of structure and material properties on the resultant physical properties of mass concentrator metamaterial shells. The concentration gradient at the core, the total mass flow rate towards the core, and the disturbance of the external concentration field are systematically examined in order to provide guidelines for the rational design and fabrication of metamaterial mass concentrators. A practical case is also presented where the concentration of oxygen diffusing in a polymeric system is studied.

  17. Rational design of nanofiber scaffolds for orthopedic tissue repair and regeneration

    PubMed Central

    Ma, Bing; Xie, Jingwei; Jiang, Jiang; Shuler, Franklin D; Bartlett, David E

    2013-01-01

    This article reviews recent significant advances in the design of nanofiber scaffolds for orthopedic tissue repair and regeneration. It begins with a brief introduction on the limitations of current approaches for orthopedic tissue repair and regeneration. It then illustrates that rationally designed scaffolds made up of electrospun nanofibers could be a promising solution to overcome the problems that current approaches encounter. The article also discusses the intriguing properties of electrospun nanofibers, including control of composition, structures, orders, alignments and mechanical properties, use as carriers for topical drug and/or gene sustained delivery, and serving as substrates for the regulation of cell behaviors, which could benefit musculoskeletal tissue repair and regeneration. It further highlights a few of the many recent applications of electrospun nanofiber scaffolds in repairing and regenerating various orthopedic tissues. Finally, the article concludes with perspectives on the challenges and future directions for better design, fabrication and utilization of nanofiber scaffolds for orthopedic tissue engineering. PMID:23987110

  18. Robust engineering design optimization with non-uniform rational B-splines-based metamodels

    NASA Astrophysics Data System (ADS)

    Steuben, John C.; Turner, Cameron J.; Crawford, Richard H.

    2013-07-01

    Non-uniform rational B-splines (NURBs) demonstrate properties that make them attractive as metamodels, or surrogate models, for engineering design purposes. Previous research has resulted in the development of algorithms capable of fitting NURBs-based metamodels to engineering design spaces, and optimizing these models. This article presents an approach to robust optimization that employs NURBs-based metamodels. This robust optimization technique exploits the unique structure of NURBs-based metamodels to derive a simple but effective robustness metric. An algorithm is demonstrated that uses this metric to weigh robustness against optimality, and visualizes the trade-offs between these metamodel properties. This approach is demonstrated with test problems of increasing dimensionality, including several practical design challenges.

  19. Rational design of the column of a heavy multipurpose machining center

    NASA Astrophysics Data System (ADS)

    Atapin, V. V.; Kurlaev, N. V.

    2016-04-01

    The main purpose in the design of supporting constructions of heavy multipurpose machining center is the reduction of mass at the given precision and productivity of machining. Accomplish these ends the technology of rational design of supporting constructions is offered. This technology is based on the decomposition method and the finite elements method in the combination with optimization methods. The technology has four stages: 1) calculation of external forces and loads, 2) as a result the boundary conditions (force, kinematics) for individual supporting constructions are formed, 3) a problem about final optimal distribution of a material by the individual supporting constructions with the real cross-section is solved; 4) dynamic analysis. By the example of design of the column of a heavy multipurpose machining center the main stages of rational design of the individual supporting constructions are shown. At a design stage of the carrying system consisting of load-bearing structures with simplified geometry, optimum overall dimensions of the column are identified. For the admitted system of preferences, it is necessary to accept the fact that the carrying system with the column with the sizes of cross section of 1.8 m (along х axis) and 2.6 m (along y axis) is the best. The analysis of the work of the column under the torsion condition with the use of method of mechanics shows that the column with square cross sections = 2.46·2.46 m which rigidity on torsion is 26 % higher in comparison with a production version is the best. The results of calculation show that a production-release design of the column with longitudinal and transverse edges of rigidity is 24 % heavier than the column with the edges located on a diagonally at equal rigidity.

  20. Rational design of the column of a heavy multipurpose machining center

    NASA Astrophysics Data System (ADS)

    Atapin, V. V.; Kurlaev, N. V.

    2016-04-01

    The main purpose in the design of supporting constructions of heavy multipurpose machining center is the reduction of mass at the given precision and productivity of machining. Accomplish these ends the technology of rational design of supporting constructions is offered. This technology is based on the decomposition method and the finite elements method in the combination with optimization methods. The technology has four stages: 1) calculation of external forces and loads, 2) as a result the boundary conditions (force, kinematics) for individual supporting constructions are formed, 3) a problem about final optimal distribution of a material by the individual supporting constructions with the real cross-section is solved; 4) dynamic analysis. By the example of design of the column of a heavy multipurpose machining center the main stages of rational design of the individual supporting constructions are shown. At a design stage of the carrying system consisting of load-bearing structures with simplified geometry, optimum overall dimensions of the column are identified. For the admitted system of preferences, it is necessary to accept the fact that the carrying system with the column with the sizes of cross section of 1.8 m (along x axis) and 2.6 m (along y axis) is the best. The analysis of the work of the column under the torsion condition with the use of method of mechanics shows that the column with square cross sections = 2.46·2.46 m which rigidity on torsion is 26 % higher in comparison with a production version is the best. The results of calculation show that a production-release design of the column with longitudinal and transverse edges of rigidity is 24 % heavier than the column with the edges located on a diagonally at equal rigidity.

  1. Rational Design of Chiral Nanostructures from Self-Assembly of a Ferrocene-Modified Dipeptide.

    PubMed

    Wang, Yuefei; Qi, Wei; Huang, Renliang; Yang, Xuejiao; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2015-06-24

    We report a new paradigm for the rational design of chiral nanostructures that is based on the hierarchical self-assembly of a ferrocene (Fc)-modified dipeptide, ferrocene-L-Phe-L-Phe-OH (Fc-FF). Compared to other chiral self-assembling systems, Fc-FF is unique because of its smaller size, biocompatibility, multiple functions (a redox center), and environmental responsiveness. X-ray and spectroscopic analyses showed that the incorporation of counterions during the hierarchical self-assembly of Fc-FF changed the conformations of the secondary structures from flat β sheets into twisted β sheets. This approach enables chiral self-assembly and the formation of well-defined chiral nanostructures composed of helical twisted β sheets. We identified two elementary forms for the helical twist of the β sheets, which allowed us to create a rich variety of rigid chiral nanostructures over a wide range of scales. Furthermore, through subtle modulations in the counterions, temperature, and solvent, we are able to precisely control the helical pitch, diameter, and handedness of the self-assembled chiral nanostructures. This unprecedented level of control not only offers insights into how rationally designed chiral nanostructures can be formed from simple molecular building blocks but also is of significant practical value for the use in chiroptics, templates, chiral sensing, and separations.

  2. Rational design of metal nitride redox materials for solar-driven ammonia synthesis.

    PubMed

    Michalsky, Ronald; Pfromm, Peter H; Steinfeld, Aldo

    2015-06-01

    Fixed nitrogen is an essential chemical building block for plant and animal protein, which makes ammonia (NH3) a central component of synthetic fertilizer for the global production of food and biofuels. A global project on artificial photosynthesis may foster the development of production technologies for renewable NH3 fertilizer, hydrogen carrier and combustion fuel. This article presents an alternative path for the production of NH3 from nitrogen, water and solar energy. The process is based on a thermochemical redox cycle driven by concentrated solar process heat at 700-1200°C that yields NH3 via the oxidation of a metal nitride with water. The metal nitride is recycled via solar-driven reduction of the oxidized redox material with nitrogen at atmospheric pressure. We employ electronic structure theory for the rational high-throughput design of novel metal nitride redox materials and to show how transition-metal doping controls the formation and consumption of nitrogen vacancies in metal nitrides. We confirm experimentally that iron doping of manganese nitride increases the concentration of nitrogen vacancies compared with no doping. The experiments are rationalized through the average energy of the dopant d-states, a descriptor for the theory-based design of advanced metal nitride redox materials to produce sustainable solar thermochemical ammonia.

  3. Rational design and synthesis of freestanding photoelectric nanodevices as highly efficient photocatalysts.

    PubMed

    Qu, Yongquan; Liao, Lei; Cheng, Rui; Wang, Yue; Lin, Yung-Chen; Huang, Yu; Duan, Xiangfeng

    2010-05-12

    Photocatalysts are of significant interest in solar energy harvesting and conversion into chemical energy. However, the photocatalysts available to date are limited by either poor efficiency in the visible light range or insufficient photoelectrochemical stability. Here we report the rational design of a new generation of freestanding photoelectric nanodevices as highly efficient and stable photocatalysts by integrating a nanoscale photodiode with two redox catalysts in a single nanowire heterostructure. We show that a platinum-silicon-silver nanowire heterostructure can be synthesized to integrate a nanoscale metal-semiconductor Schottky diode encased in a protective insulating shell with two exposed metal catalysts. We further demonstrated that the Schottky diodes exhibited a pronounced photovoltaic effect with nearly unity internal quantum efficiency and that the integrated nanowire heterostructures could be used as highly efficient photocatalysts for a wide range of thermodynamically downhill and uphill reactions including the photocatalytic degradation of organic dyes and the reduction of metal ions and carbon dioxide using visible light. Our studies for the first time demonstrated the integration of multiple distinct functional components into a single nanostructure to form a standalone active nanosystem and for the first time successfully realized a photoelectric nanodevice that is both highly efficient and highly stable throughout the entire solar spectrum. It thus opens a rational avenue to the design and synthesis of a new generation of photoelectric nanosystems with unprecedented efficiency and stability and will have a broad impact in areas including environmental remediation, artificial photosynthesis and solar fuel production.

  4. Rational Design and Synthesis of Freestanding Photoelectric Nanodevices as Highly Efficient Photocatalysts

    PubMed Central

    Qu, Yongquan; Liao, Lei; Cheng, Rui; Wang, Yue; Lin, Yung-chen; Huang, Yu; Duan, Xiangfeng

    2010-01-01

    Photocatalysts are of significant interest for solar energy harvesting and conversion into chemical energy. However, the photocatalysts available to date are limited by either poor efficiency in the visible light range or insufficient photoelectrochemical stability. Here we report the rational design of a new generation of freestanding photoelectric nanodevices as highly efficient and stable photocatalysts by integrating a nanoscale photodiode with two redox catalysts in a single nanowire heterostructure. We show that a platinum-silicon-silver nanowire heterostructure can be synthesized to integrate a nanoscale metal-semiconductor Schottky diode encased in a protective insulating shell with two exposed metal catalysts. We further demonstrated that the Schottky diodes exhibited pronounced photovoltaic effect with nearly unity internal quantum efficiency, and that the integrated nanowire heterostructures could be used as highly efficient photocatalysts for a wide range of thermodynamically downhill and uphill reactions including photocatalytic degradation of organic dyes, reduction of metal ions and carbon dioxide using visible light. Our studies for the first time demonstrated the integration of multiple distinct functional components into a single nanostructure to form a standalone active nanosystem, and for the first time successfully realized a photoelectric nanodevice that is both highly efficient and highly stable throughout the entire solar spectrum. It thus opens a rational avenue to design and synthesize a new generation of photoelectric nanosystems with unprecedented efficiency and stability, and will impact broadly in areas including environmental remediation and solar fuel production. PMID:20373781

  5. Rational design of metal nitride redox materials for solar-driven ammonia synthesis

    PubMed Central

    Michalsky, Ronald; Pfromm, Peter H.; Steinfeld, Aldo

    2015-01-01

    Fixed nitrogen is an essential chemical building block for plant and animal protein, which makes ammonia (NH3) a central component of synthetic fertilizer for the global production of food and biofuels. A global project on artificial photosynthesis may foster the development of production technologies for renewable NH3 fertilizer, hydrogen carrier and combustion fuel. This article presents an alternative path for the production of NH3 from nitrogen, water and solar energy. The process is based on a thermochemical redox cycle driven by concentrated solar process heat at 700–1200°C that yields NH3 via the oxidation of a metal nitride with water. The metal nitride is recycled via solar-driven reduction of the oxidized redox material with nitrogen at atmospheric pressure. We employ electronic structure theory for the rational high-throughput design of novel metal nitride redox materials and to show how transition-metal doping controls the formation and consumption of nitrogen vacancies in metal nitrides. We confirm experimentally that iron doping of manganese nitride increases the concentration of nitrogen vacancies compared with no doping. The experiments are rationalized through the average energy of the dopant d-states, a descriptor for the theory-based design of advanced metal nitride redox materials to produce sustainable solar thermochemical ammonia. PMID:26052421

  6. The Use of Drug Discovery Tools in Rational Organometallic Catalyst Design

    SciTech Connect

    Sumpter, Bobby G; Drummond, Michael L

    2007-01-01

    A computational procedure is detailed where techniques common in the drug discovery process - 2D- and 3D-Quantitative Structure-Activity Relationships (QSAR) - are applied to rationalize the catalytic activity of a synthetically flexible, Ti-N=P ethylene polymerization catalyst system. Once models relating molecular properties to catalyst activity are built with the two QSAR approaches, two database mining approaches are used to select a small number of ligands from a larger database that are likely to produce catalysts with high activity when grafted onto the Ti-N=P framework.. The software employed throughout this work is freely available, easy to use, and was applied in a "black box" approach, to highlight areas where the drug discovery tools, designed to address organic molecules, have difficulty in addressing issues arising from the presence of a metal atom. In general, 3D-QSAR offers an efficient way to screen new potential ligands and separate those likely to lead to poor catalysts from those that are likely to contribute to highly active catalysts. The results for 2D-QSAR appear to be quantitatively unreliable, likely due to the presence of a metal atom; nonetheless, there is evidence that qualitative predictions from different models may be reliable. Pitfalls in the database mining techniques are identified, none of which are insurmountable. The lessons learned about the potential uses and drawbacks of the techniques described herein are readily applicable to other catalyst frameworks, thereby enabling a rational approach to catalyst improvement and design.

  7. Rational design and application of responsive α-helical peptide hydrogels

    PubMed Central

    Banwell, Eleanor F.; Abelardo, Edgardo S.; Adams, Dave J.; Birchall, Martin A.; Corrigan, Adam; Donald, Athene M.; Kirkland, Mark; Serpell, Louise C.; Butler, Michael F.; Woolfson, Derek N.

    2009-01-01

    Biocompatible hydrogels have a wide variety of potential applications in biotechnology and medicine, such as the controlled delivery and release of cells, cosmetics and drugs; and as supports for cell growth and tissue engineering1. Rational peptide design and engineering are emerging as promising new routes to such functional biomaterials2-4. Here we present the first examples of rationally designed and fully characterized self-assembling hydrogels based on standard linear peptides with purely α-helical structures, which we call hydrogelating self-assembling fibres (hSAFs). These form spanning networks of α-helical fibrils that interact to give self-supporting physical hydrogels of >99% water content. The peptide sequences can be engineered to alter the underlying mechanism of gelation and, consequently, the hydrogel properties. Interestingly, for example, those with hydrogen-bonded networks melt upon heating, whereas those formed via hydrophobic interactions strengthen when warmed. The hSAFs are dual-peptide systems that only gel on mixing, which gives tight control over assembly5. These properties raise possibilities for using the hSAFs as substrates in cell culture. We have tested this in comparison with the widely used Matrigel substrate, and demonstrate that, like Matrigel, hSAFs support both growth and differentiation of rat adrenal pheochromocytoma cells for sustained periods in culture. PMID:19543314

  8. Rational design of metal nitride redox materials for solar-driven ammonia synthesis.

    PubMed

    Michalsky, Ronald; Pfromm, Peter H; Steinfeld, Aldo

    2015-06-01

    Fixed nitrogen is an essential chemical building block for plant and animal protein, which makes ammonia (NH3) a central component of synthetic fertilizer for the global production of food and biofuels. A global project on artificial photosynthesis may foster the development of production technologies for renewable NH3 fertilizer, hydrogen carrier and combustion fuel. This article presents an alternative path for the production of NH3 from nitrogen, water and solar energy. The process is based on a thermochemical redox cycle driven by concentrated solar process heat at 700-1200°C that yields NH3 via the oxidation of a metal nitride with water. The metal nitride is recycled via solar-driven reduction of the oxidized redox material with nitrogen at atmospheric pressure. We employ electronic structure theory for the rational high-throughput design of novel metal nitride redox materials and to show how transition-metal doping controls the formation and consumption of nitrogen vacancies in metal nitrides. We confirm experimentally that iron doping of manganese nitride increases the concentration of nitrogen vacancies compared with no doping. The experiments are rationalized through the average energy of the dopant d-states, a descriptor for the theory-based design of advanced metal nitride redox materials to produce sustainable solar thermochemical ammonia. PMID:26052421

  9. Rational Design of an Epstein-Barr Virus Vaccine Targeting the Receptor-Binding Site.

    PubMed

    Kanekiyo, Masaru; Bu, Wei; Joyce, M Gordon; Meng, Geng; Whittle, James R R; Baxa, Ulrich; Yamamoto, Takuya; Narpala, Sandeep; Todd, John-Paul; Rao, Srinivas S; McDermott, Adrian B; Koup, Richard A; Rossmann, Michael G; Mascola, John R; Graham, Barney S; Cohen, Jeffrey I; Nabel, Gary J

    2015-08-27

    Epstein-Barr virus (EBV) represents a major global health problem. Though it is associated with infectious mononucleosis and ∼200,000 cancers annually worldwide, a vaccine is not available. The major target of immunity is EBV glycoprotein 350/220 (gp350) that mediates attachment to B cells through complement receptor 2 (CR2/CD21). Here, we created self-assembling nanoparticles that displayed different domains of gp350 in a symmetric array. By focusing presentation of the CR2-binding domain on nanoparticles, potent neutralizing antibodies were elicited in mice and non-human primates. The structurally designed nanoparticle vaccine increased neutralization 10- to 100-fold compared to soluble gp350 by targeting a functionally conserved site of vulnerability, improving vaccine-induced protection in a mouse model. This rational approach to EBV vaccine design elicited potent neutralizing antibody responses by arrayed presentation of a conserved viral entry domain, a strategy that can be applied to other viruses.

  10. Capitalizing on knowledge of hepatitis C virus neutralizing epitopes for rational vaccine design.

    PubMed

    Kong, Leopold; Jackson, Kelli N; Wilson, Ian A; Law, Mansun

    2015-04-01

    Hepatitis C virus infects nearly 3% of the world's population and is often referred as a silent epidemic. It is a leading cause of liver cirrhosis and hepatocellular carcinoma in endemic countries. Although antiviral drugs are now available, they are not readily accessible to marginalized social groups and developing nations that are disproportionally impacted by HCV. To stop the HCV pandemic, a vaccine is needed. Recent advances in HCV research have provided new opportunities for studying HCV neutralizing antibodies and their subsequent use for rational vaccine design. It is now recognized that neutralizing antibodies to conserved antigenic sites of the virus can cross-neutralize diverse HCV genotypes and protect against infection in vivo. Structural characterization of the neutralizing epitopes has provided valuable information for design of candidate immunogens.

  11. Rational design of competitive electrocatalysts for the oxygen reduction reaction in hydrogen fuel cells

    NASA Astrophysics Data System (ADS)

    Stolbov, Sergey; Alcántara Ortigoza, Marisol

    2012-02-01

    The large-scale application of one of the most promising clean and renewable sources of energy, hydrogen fuel cells, still awaits efficient and cost-effective electrocatalysts for the oxygen reduction reaction (ORR) occurring on the cathode. We demonstrate that truly rational design renders electrocatalysts possessing both qualities. By unifying the knowledge on surface morphology, composition, electronic structure and reactivity, we solve that sandwich-like structures are an excellent choice for optimization. Their constituting species couple synergistically yielding reaction-environment stability, cost-effectiveness and tunable reactivity. This cooperative-action concept enabled us to predict two advantageous ORR electrocatalysts. Density functional theory calculations of the reaction free-energy diagrams confirm that these materials are more active toward ORR than the so far best Pt-based catalysts. Our designing concept advances also a general approach for engineering materials in heterogeneous catalysis.

  12. Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection

    PubMed Central

    Ke, Ruian; Loverdo, Claude; Qi, Hangfei; Sun, Ren; Lloyd-Smith, James O.

    2015-01-01

    Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensate when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design. PMID:26125950

  13. Rational design of crystalline supermicroporous covalent organic frameworks with triangular topologies

    NASA Astrophysics Data System (ADS)

    Dalapati, Sasanka; Addicoat, Matthew; Jin, Shangbin; Sakurai, Tsuneaki; Gao, Jia; Xu, Hong; Irle, Stephan; Seki, Shu; Jiang, Donglin

    2015-07-01

    Covalent organic frameworks (COFs) are an emerging class of highly ordered porous polymers with many potential applications. They are currently designed and synthesized through hexagonal and tetragonal topologies, limiting the access to and exploration of new structures and properties. Here, we report that a triangular topology can be developed for the rational design and synthesis of a new class of COFs. The triangular topology features small pore sizes down to 12 Å, which is among the smallest pores for COFs reported to date, and high π-column densities of up to 0.25 nm-2, which exceeds those of supramolecular columnar π-arrays and other COF materials. These crystalline COFs facilitate π-cloud delocalization and are highly conductive, with a hole mobility that is among the highest reported for COFs and polygraphitic ensembles.

  14. Rational design of a β-glycosidase with high regiospecificity for triterpenoid tailoring.

    PubMed

    Park, Sang Jin; Choi, Jung Min; Kyeong, Hyun-Ho; Kim, Song-Gun; Kim, Hak-Sung

    2015-03-23

    Triterpenoids with desired glycosylation patterns have attracted considerable attention as potential therapeutics for inflammatory diseases and various types of cancer. Sugar-hydrolyzing enzymes with high substrate specificity would be far more efficient than other methods for the synthesis of such specialty triterpenoids, but they are yet to be developed. Here we present a strategy to rationally design a β-glycosidase with high regiospecificity for triterpenoids. A β-glycosidase with broad substrate specificity was isolated, and its crystal structure was determined at 2.0 Å resolution. Based on the product profiles and substrate docking simulations, we modeled the substrate binding modes of the enzyme. From the model, the substrate binding cleft of the enzyme was redesigned in a manner that preferentially hydrolyzes glycans at specific glycosylation sites of triterpenoids. The designed mutants were shown to produce a variety of specialty triterpenoids with high purity.

  15. From G Protein-coupled Receptor Structure Resolution to Rational Drug Design*

    PubMed Central

    Jazayeri, Ali; Dias, Joao M.; Marshall, Fiona H.

    2015-01-01

    A number of recent technical solutions have led to significant advances in G protein-coupled receptor (GPCR) structural biology. Apart from a detailed mechanistic view of receptor activation, the new structures have revealed novel ligand binding sites. Together, these insights provide avenues for rational drug design to modulate the activities of these important drug targets. The application of structural data to GPCR drug discovery ushers in an exciting era with the potential to improve existing drugs and discover new ones. In this review, we focus on technical solutions that have accelerated GPCR crystallography as well as some of the salient findings from structures that are relevant to drug discovery. Finally, we outline some of the approaches used in GPCR structure based drug design. PMID:26100628

  16. Rational design of crystalline supermicroporous covalent organic frameworks with triangular topologies

    PubMed Central

    Dalapati, Sasanka; Addicoat, Matthew; Jin, Shangbin; Sakurai, Tsuneaki; Gao, Jia; Xu, Hong; Irle, Stephan; Seki, Shu; Jiang, Donglin

    2015-01-01

    Covalent organic frameworks (COFs) are an emerging class of highly ordered porous polymers with many potential applications. They are currently designed and synthesized through hexagonal and tetragonal topologies, limiting the access to and exploration of new structures and properties. Here, we report that a triangular topology can be developed for the rational design and synthesis of a new class of COFs. The triangular topology features small pore sizes down to 12 Å, which is among the smallest pores for COFs reported to date, and high π-column densities of up to 0.25 nm−2, which exceeds those of supramolecular columnar π-arrays and other COF materials. These crystalline COFs facilitate π-cloud delocalization and are highly conductive, with a hole mobility that is among the highest reported for COFs and polygraphitic ensembles. PMID:26178865

  17. Rationally designed axially chiral diarylethene switches with high helical twisting power.

    PubMed

    Li, Yannian; Wang, Mengfei; Wang, Hao; Urbas, Augustine; Li, Quan

    2014-12-01

    Three rationally designed axially chiral diarylethene switches were synthesized and their application as chiral dopants for phototunable cholesteric liquid crystal devices was investigated. Design of these molecules was based on the combination of photochromic dithienylcyclopentene core with bridged binaphthyl units as chiral precursors. Aromatic groups were introduced to the molecules at 6,6'-positions of binaphthyls through a Suzuki-Miyaura coupling reaction. Their helical twisting powers (HTPs) are significantly higher than those of the known chiral diarylethenes reported as chiral dopants so far. Photocyclization of these molecules upon light irradiation brought out dramatic variation in HTPs between different states. The primary colors, red, green, and blue, were obtained in reflection on light irradiation and with thermal stability. Moreover, a multi-switchable photodisplay was demonstrated using one of these chiral molecular switches.

  18. 20% PARTIAL SIBERIAN SNAKE IN THE AGS.

    SciTech Connect

    Huang, H; Bai, M; Brown, K A; Glenn, W; Luccio, A U; Mackay, W W; Montag, C; Ptitsyn, V; Roser, T; Tsoupas, N; Zeno, K; Ranjbar, V; Spinka, H; Underwood, D

    2002-11-06

    An 11.4% partial Siberian snake was used to successfully accelerate polarized proton through a strong intrinsic depolarizing spin resonance in the AGS. No noticeable depolarization was observed. This opens up the possibility of using a 20% to 30% partial Siberian snake in the AGS to overcome all weak and strong depolarizing spin resonances. Some design and operation issues of the new partial Siberian snake are discussed.

  19. Rational design of small molecule inhibitors targeting the Ras GEF, SOS1

    PubMed Central

    Evelyn, Chris R.; Duan, Xin; Biesiada, Jacek; Seibel, William L.; Meller, Jaroslaw; Zheng, Yi

    2014-01-01

    Summary Ras GTPases regulate intracellular signaling involved in cell proliferation. Elevated Ras signaling activity has been associated with human cancers. Ras activation is catalyzed by guanine-nucleotide exchange factors (GEFs), of which SOS1 is a major member that transduces receptor tyrosine kinase signaling to Ras. We have developed a rational approach coupling virtual screening with experimental screening in identifying small-molecule inhibitors targeting the catalytic site of SOS1 and SOS1-regulated Ras activity. A lead inhibitor, NSC-658497, is found to bind to SOS1, competitively suppresses SOS1-Ras interaction, and dose-dependently inhibits SOS1 GEF activity. Mutagenesis and structure-activity relationship studies map the NSC-658497 site of action to the SOS1 catalytic site, and define the chemical moieties in the inhibitor essential for the activity. NSC-658497 showed dose-dependent efficacy in inhibiting Ras, downstream signaling activities, and associated cell proliferation. These studies establish a proof of principle for rational design of small-molecule inhibitors targeting Ras GEF enzymatic activity. PMID:25455859

  20. Rational design of small molecule inhibitors targeting the Ras GEF, SOS1.

    PubMed

    Evelyn, Chris R; Duan, Xin; Biesiada, Jacek; Seibel, William L; Meller, Jaroslaw; Zheng, Yi

    2014-12-18

    Ras GTPases regulate intracellular signaling involved in cell proliferation. Elevated Ras signaling activity has been associated with human cancers. Ras activation is catalyzed by guanine nucleotide exchange factors (GEFs), of which SOS1 is a major member that transduces receptor tyrosine kinase signaling to Ras. We have developed a rational approach coupling virtual screening with experimental screening in identifying small-molecule inhibitors targeting the catalytic site of SOS1 and SOS1-regulated Ras activity. A lead inhibitor, NSC-658497, was found to bind to SOS1, competitively suppress SOS1-Ras interaction, and dose-dependently inhibit SOS1 GEF activity. Mutagenesis and structure-activity relationship studies map the NSC-658497 site of action to the SOS1 catalytic site, and define the chemical moieties in the inhibitor essential for the activity. NSC-658497 showed dose-dependent efficacy in inhibiting Ras, downstream signaling activities, and associated cell proliferation. These studies establish a proof of principle for rational design of small-molecule inhibitors targeting Ras GEF enzymatic activity.

  1. Rational design and optimization of downstream processes of virus particles for biopharmaceutical applications: current advances.

    PubMed

    Vicente, Tiago; Mota, José P B; Peixoto, Cristina; Alves, Paula M; Carrondo, Manuel J T

    2011-01-01

    The advent of advanced therapies in the pharmaceutical industry has moved the spotlight into virus-like particles and viral vectors produced in cell culture holding great promise in a myriad of clinical targets, including cancer prophylaxis and treatment. Even though a couple of cases have reached the clinic, these products have yet to overcome a number of biological and technological challenges before broad utilization. Concerning the manufacturing processes, there is significant research focusing on the optimization of current cell culture systems and, more recently, on developing scalable downstream processes to generate material for pre-clinical and clinical trials. We review the current options for downstream processing of these complex biopharmaceuticals and underline current advances on knowledge-based toolboxes proposed for rational optimization of their processing. Rational tools developed to increase the yet scarce knowledge on the purification processes of complex biologicals are discussed as alternative to empirical, "black-boxed" based strategies classically used for process development. Innovative methodologies based on surface plasmon resonance, dynamic light scattering, scale-down high-throughput screening and mathematical modeling for supporting ion-exchange chromatography show great potential for a more efficient and cost-effective process design, optimization and equipment prototyping.

  2. Toward Rational Fragment-Based Lead Design without 3D Structures

    PubMed Central

    2012-01-01

    Fragment-based lead discovery (FBLD) has become a prime component of the armamentarium of modern drug design programs. FBLD identifies low molecular weight ligands that weakly bind to important biological targets. Three-dimensional structural information about the binding mode is provided by X-ray crystallography or NMR spectroscopy and is subsequently used to improve the lead compounds. Despite tremendous success rates, FBLD relies on the availability of high-resolution structural information, still a bottleneck in drug discovery programs. To overcome these limitations, we recently demonstrated that the meta-structure approach provides an alternative route to rational lead identification in cases where no 3D structure information about the biological target is available. Combined with information-rich NMR data, this strategy provides valuable information for lead development programs. We demonstrate with several examples the feasibility of the combined NMR and meta-structure approach to devise a rational strategy for fragment evolution without resorting to highly resolved protein complex structures. PMID:22889313

  3. Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins

    PubMed Central

    Sormanni, Pietro; Aprile, Francesco A.; Vendruscolo, Michele

    2015-01-01

    Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions. PMID:26216991

  4. Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.

    PubMed

    Sormanni, Pietro; Aprile, Francesco A; Vendruscolo, Michele

    2015-08-11

    Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions.

  5. Applications of molecular physics 'biotechnology' to the rational design of an improved phenytoin analogue.

    PubMed

    Weaver, D F

    1992-12-01

    This study exploits molecular physics, in conjunction with a large scale computing environment, as a tool for understanding the clinical phenomenology of phenytoin (PHT) toxicology at a molecular level and for employing this understanding in an attempt to design improved drugs. The application of molecular physics techniques, such as quantum mechanics and molecular force field calculations, to the process of rational anticonvulsant drug design remains virtually unexplored. A 3-step strategy for applying these techniques to the design of an improved PHT molecule is presented. Step 1 employs quantitative structure-activity relationship calculations on 80 PHT analogues to ascertain the portion of the PHT molecule necessary for bioactivity (i.e. the 'bioactive face' of PHT); the N3-C4(O)-C5-R fragment of PHT was identified as the bioactive face. Step 2 employs molecular modelling studies to determine the portion of the PHT molecule necessary for the teratogenic, mutagenic and connective tissue toxicities of PHT (i.e. the 'biotoxic face'); the C2(O)-N3 fragment of PHT was identified as the biotoxic face. Step 3 experiments design an 'improved' PHT analogue, which maintains the bioactive face while eliminating the integrity of the biotoxic face; 2-deoxy-5,5-diphenylhydantoin was designed and synthesized as the improved PHT analogue. This compound had biological activity equivalent to PHT, but was unable to bind to nucleic acids or to chelate metals involved in connective tissue metabolism. PMID:1344772

  6. Applications of molecular physics 'biotechnology' to the rational design of an improved phenytoin analogue.

    PubMed

    Weaver, D F

    1992-12-01

    This study exploits molecular physics, in conjunction with a large scale computing environment, as a tool for understanding the clinical phenomenology of phenytoin (PHT) toxicology at a molecular level and for employing this understanding in an attempt to design improved drugs. The application of molecular physics techniques, such as quantum mechanics and molecular force field calculations, to the process of rational anticonvulsant drug design remains virtually unexplored. A 3-step strategy for applying these techniques to the design of an improved PHT molecule is presented. Step 1 employs quantitative structure-activity relationship calculations on 80 PHT analogues to ascertain the portion of the PHT molecule necessary for bioactivity (i.e. the 'bioactive face' of PHT); the N3-C4(O)-C5-R fragment of PHT was identified as the bioactive face. Step 2 employs molecular modelling studies to determine the portion of the PHT molecule necessary for the teratogenic, mutagenic and connective tissue toxicities of PHT (i.e. the 'biotoxic face'); the C2(O)-N3 fragment of PHT was identified as the biotoxic face. Step 3 experiments design an 'improved' PHT analogue, which maintains the bioactive face while eliminating the integrity of the biotoxic face; 2-deoxy-5,5-diphenylhydantoin was designed and synthesized as the improved PHT analogue. This compound had biological activity equivalent to PHT, but was unable to bind to nucleic acids or to chelate metals involved in connective tissue metabolism.

  7. Improving thermal and detergent stability of Bacillus stearothermophilus neopullulanase by rational enzyme design.

    PubMed

    Ece, Selin; Evran, Serap; Janda, Jan-Oliver; Merkl, Rainer; Sterner, Reinhard

    2015-06-01

    Neopullulanase, a glycosyl hydrolase from Bacillus stearothermophilus (bsNpl), is a potentially valuable enzyme for starch and detergent industries. However, as the protein is not active at elevated temperatures and high surfactant concentrations, we aimed to increase its stability by rational enzyme design. Nine potentially destabilizing cavities were identified in the crystal structure of the enzyme. Based on computational predictions, these cavities were filled by residues with bulkier side chains. The five Asp46Glu, Val239Leu, Val404Leu, Ser407Thr and Ala566Leu exchanges resulted in a drastic stabilization of bsNpl against inactivation by heat and detergents. The catalytic activity of the variants was identical to the wild-type enzyme.

  8. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

    PubMed Central

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-01-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria. PMID:27615705

  9. Phenolic melanin precursors provide a rational approach to the design of antitumor agents for melanoma

    SciTech Connect

    Jimbow, K.; Miura, T.; Ito, S.; Ishikawa, K.

    1989-01-01

    A unique biological property of the melanocyte, melanin synthesis may permit a rational approach to design agents for better management of malignant melanoma. This in vivo and in vitro study examined the selective melanocytotoxicity and antimelanoma effects of phenolic compounds, cysteinylphenol (CP), cysteaminylphenol (CAP), and related compounds, and found (1) that both 4-S-CP and 4-S-CAP are melanin precursors, (2) that 4-S-CAP possesses a marked depigmenting potency with selective destruction of melanocytes in black follicles, and (3) a significant inhibition in the protein synthesis and tumor growth of B16 melanoma. Importantly, a whole body autoradiography indicated that these phenolic melanin precursors are selectively incorporated into melanoma tissues after i.p. administration.

  10. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

    NASA Astrophysics Data System (ADS)

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-09-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.

  11. Basic principles for rational design of high-performance nanostructured silicon-based thermoelectric materials.

    PubMed

    Yang, Chun Cheng; Li, Sean

    2011-12-23

    Recently, nanostructured silicon-based thermoelectric materials have drawn great attention owing to their excellent thermoelectric performance in the temperature range around 450 °C, which is eminently applicable for concentrated solar thermal technology. In this work, a unified nanothermodynamic model is developed to investigate the predominant factors that determine the lattice thermal conductivity of nanocrystalline, nanoporous, and nanostructured bulk Si. A systematic study shows that the thermoelectric performance of these materials can be substantially enhanced by the following three basic principles: 1) artificial manipulation and optimization of roughness with surface/interface patterning/engineering; 2) grain-size reduction with innovative fabrication techniques in a controllable fashion; and 3) optimization of material parameters, such as bulk solid-vapor transition entropy, bulk vibrational entropy, dimensionality, and porosity, to decrease the lattice thermal conductivity. These principles may be used to rationally design novel nanostructured Si-based thermoelectric materials for renewable energy applications.

  12. In silico rational design of ionic liquids for the exfoliation and dispersion of boron nitride nanosheets.

    PubMed

    García, Gregorio; Atilhan, Mert; Aparicio, Santiago

    2016-01-14

    A requirement for exploiting most of the unique properties of boron-nitride (BN) nanosheets is their isolation from the bulk material. A rational design of task-specific ionic liquids (ILs) through DFT simulations is reported in this work. The applied computational protocol allowed the screening of large IL families, which was carried out bearing in mind the achievement of strong π-π stacking between the anions and BN nanosheets as well as a negative charge transfer from the anion to the surface. The selected ionic liquids yielded strong interaction energies with BN nanosheets and high charge transfer values, while the main features of the ionic liquid are not affected in the presence of nanosheets. DFT simulations provided a detailed picture of the interaction mechanism and useful structure-property relationships in the search of a new ionic liquid for BN exfoliation. PMID:26658819

  13. Fibrin-based biomaterials: Modulation of macroscopic properties through rational design at the molecular level

    PubMed Central

    Brown, Ashley C.; Barker, Thomas H.

    2013-01-01

    Fibrinogen is one of the primary components of the coagulation cascade and rapidly forms an insoluble matrix following tissue injury. In addition to its important role in hemostasis, fibrin acts as a scaffold for tissue repair and provides important cues for directing cell phenotype following injury. Because of these properties and the ease of polymerization of the material, fibrin has been widely utilized as a biomaterial for over a century. Modifying the macroscopic properties of fibrin, such as elasticity and porosity, has been somewhat elusive until recently, yet with a molecular-level rational design approach can now be somewhat easily modified through alterations of molecular interactions key to the protein’s polymerization process. This review outlines the biochemistry of fibrin and discusses methods for modification of molecular interactions and their application to fibrin based biomaterials. PMID:24056097

  14. Rational Design of Multi-Stimuli-Responsive Nanoparticles for Precise Cancer Therapy.

    PubMed

    An, Xiaonan; Zhu, Aijun; Luo, Huanhuan; Ke, Hengte; Chen, Huabing; Zhao, Youliang

    2016-06-28

    Stimuli-responsive nanoparticles with target capacity are of great interest in drug delivery for cancer therapy. However, the challenge is to achieve highly smart release with precise spatiotemporal control for cancer therapy. Herein, we report the preparation and properties of multi-stimuli-responsive nanoparticles through the co-assembly of a 3-arm star quaterpolymer with a near-infrared (NIR) photothermal agent and chemotherapeutic compound. The nanoparticles can exhibit NIR light/pH/reduction-responsive drug release and intracellular drug translocation in cancer cells, which further integrate photoinduced hyperthermia for synergistic anticancer efficiency, thereby leading to tumor ablation without tumor regrowth. Thus, this rational design of nanoparticles with multiple responsiveness represents a versatile strategy to provide smart drug delivery paradigms for cancer therapy. PMID:27285378

  15. Rational Design of Multi-Stimuli-Responsive Nanoparticles for Precise Cancer Therapy.

    PubMed

    An, Xiaonan; Zhu, Aijun; Luo, Huanhuan; Ke, Hengte; Chen, Huabing; Zhao, Youliang

    2016-06-28

    Stimuli-responsive nanoparticles with target capacity are of great interest in drug delivery for cancer therapy. However, the challenge is to achieve highly smart release with precise spatiotemporal control for cancer therapy. Herein, we report the preparation and properties of multi-stimuli-responsive nanoparticles through the co-assembly of a 3-arm star quaterpolymer with a near-infrared (NIR) photothermal agent and chemotherapeutic compound. The nanoparticles can exhibit NIR light/pH/reduction-responsive drug release and intracellular drug translocation in cancer cells, which further integrate photoinduced hyperthermia for synergistic anticancer efficiency, thereby leading to tumor ablation without tumor regrowth. Thus, this rational design of nanoparticles with multiple responsiveness represents a versatile strategy to provide smart drug delivery paradigms for cancer therapy.

  16. Rational design of metallic nanocavities for resonantly enhanced four-wave mixing

    PubMed Central

    Almeida, Euclides; Prior, Yehiam

    2015-01-01

    Optimizing the shape of nanostructures and nano-antennas for specific optical properties has evolved to be a very fruitful activity. With modern fabrication tools a large variety of possibilities is available for shaping both nanoparticles and nanocavities; in particular nanocavities in thin metal films have emerged as attractive candidates for new metamaterials and strong linear and nonlinear optical systems. Here we rationally design metallic nanocavities to boost their Four-Wave Mixing response by resonating the optical plasmonic resonances with the incoming and generated beams. The linear and nonlinear optical responses as well as the propagation of the electric fields inside the cavities are derived from the solution of Maxwell’s equations by using the 3D finite-differences time domain method. The observed conversion-efficiency of near-infrared to visible light equals or surpasses that of BBO of equivalent thickness. Implications to further optimization for efficient and broadband ultrathin nonlinear optical materials are discussed. PMID:25974175

  17. Rational design of a structure-switching DNA aptamer for potassium ions

    PubMed Central

    Catherine, Andrew T.; Shishido, Stephanie N.; Robbins-Welty, Gregg A.; Diegelman-Parente, Amy

    2014-01-01

    Structure-switching molecules provide a unique means for analyte detection, generating a response to analyte concentration through a binding-specific conformational change between non-binding and binding-competent states. While most ligand-binding molecules are not structure switching by default, many can be engineered to be so through the introduction of an alternative non-binding (and thus non-signalling) conformation. This population-shift mechanism is particularly effective with oligonucleotides and has led to the creation of structure-switching aptamers for many target ligands. Here, we report the rational design of structure-switching DNA aptamers, based on the thrombin binding aptamer (TBA), that bind potassium with affinities that bridge the gap between previously reported weak-binding and strong-binding aptamers. We also demonstrate a correlation between the free energy of the experimentally determined binding affinity for potassium and the computationally estimated free energy of the alternative (non-binding) structure. PMID:25352996

  18. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering

    PubMed Central

    Voigt, Franka; Wiedemann, Lisa; Zuliani, Cecilia; Querques, Irma; Sebe, Attila; Mátés, Lajos; Izsvák, Zsuzsanna; Ivics, Zoltán; Barabas, Orsolya

    2016-01-01

    Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases. PMID:27025571

  19. Engineering of isoamylase: improvement of protein stability and catalytic efficiency through semi-rational design.

    PubMed

    Li, Youran; Zhang, Liang; Ding, Zhongyang; Gu, Zhenghua; Shi, Guiyang

    2016-01-01

    Isoamylase catalyzes the hydrolysis of α-1,6-glycosidic linkages in glycogen, amylopectin and α/β-limit dextrins. A semi-rational design strategy was performed to improve catalytic properties of isoamylase from Bacillus lentus. Three residues in vicinity of the essential residues, Arg505, Asn513, and Gly608, were chosen as the mutation sites and were substituted by Ala, Pro, Glu, and Lys, respectively. Thermal stability of the mutant R505P and acidic stability of the mutant R505E were enhanced. The k cat /K m values of the mutant G608V have been promoted by 49%, and the specific activity increased by 33%. This work provides an effective strategy for improving the catalytic activity and stability of isoamylase, and the results obtained here may be useful for the improvement of catalytic properties of other α/β barrel enzymes.

  20. Understanding Amino Acid Mutations in Hepatitis B Virus Proteins for Rational Design of Vaccines and Drugs.

    PubMed

    Shen, Ke; Shen, Li; Wang, Jing; Jiang, Zhi; Shen, Bairong

    2015-01-01

    The hepatitis B virus (HBV) genome encodes four proteins, i.e., DNA polymerase, surface protein, X, and core proteins. HBV undergoes different selective pressures for drug resistance and immune/vaccine escape and mutations are common for the HBV proteins. We here collected all the reported amino acid mutations happened in these four HBV proteins and studied their patterns. The relationship between the mutations and epitopic functions are investigated with bioinformatics tools, based on their sequence information. Some interesting results are observed for the mutation patterns, such as we found the serine and threonine are both for frequently mutated residues and mutant residues, while the tryptophan and methionine have low mutability. The results provide important information for the understanding of the molecular mechanism of virus evolution and therefore will facilitate the future rational design of HBV vaccines or drugs.

  1. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering.

    PubMed

    Voigt, Franka; Wiedemann, Lisa; Zuliani, Cecilia; Querques, Irma; Sebe, Attila; Mátés, Lajos; Izsvák, Zsuzsanna; Ivics, Zoltán; Barabas, Orsolya

    2016-03-30

    Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases.

  2. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis.

    PubMed

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-01-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria. PMID:27615705

  3. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering.

    PubMed

    Voigt, Franka; Wiedemann, Lisa; Zuliani, Cecilia; Querques, Irma; Sebe, Attila; Mátés, Lajos; Izsvák, Zsuzsanna; Ivics, Zoltán; Barabas, Orsolya

    2016-01-01

    Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases. PMID:27025571

  4. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis.

    PubMed

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-01-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.

  5. From empiricism to rational design: a personal perspective of the evolution of vaccine development.

    PubMed

    De Gregorio, Ennio; Rappuoli, Rino

    2014-07-01

    Vaccination, which is the most effective medical intervention that has ever been introduced, originated from the observation that individuals who survived a plague or smallpox would not get the disease twice. To mimic the protective effects of natural infection, Jenner - and later Pasteur - inoculated individuals with attenuated or killed disease-causing agents. This empirical approach inspired a century of vaccine development and the effective prophylaxis of many infectious diseases. From the 1980s, several waves of new technologies have enabled the development of novel vaccines that would not have been possible using the empirical approach. The technological revolution in the field of vaccination is now continuing, and it is delivering novel and safer vaccines. In this Timeline article, we provide our views on the transition from empiricism to rational vaccine design.

  6. PoPMuSiC, rationally designing point mutations in protein structures.

    PubMed

    Kwasigroch, J M; Gilis, D; Dehouck, Y; Rooman, M

    2002-12-01

    PoPMuSiC is an efficient tool for rational computer-aided design of single-site mutations in proteins and peptides. Two types of queries can be submitted. The first option allows to estimate the changes in folding free energy for specific point mutations given by the user. In the second option, all possible point mutations in a given protein or protein region are performed and the most stabilizing or destabilizing mutations, or the neutral mutations with respect to thermodynamic stability, are selected. For each sequence position or secondary structure the deviation from the most stable sequence is moreover evaluated, which helps to identify the most suitable sites for the introduction of mutations.

  7. From empiricism to rational design: a personal perspective of the evolution of vaccine development.

    PubMed

    De Gregorio, Ennio; Rappuoli, Rino

    2014-07-01

    Vaccination, which is the most effective medical intervention that has ever been introduced, originated from the observation that individuals who survived a plague or smallpox would not get the disease twice. To mimic the protective effects of natural infection, Jenner - and later Pasteur - inoculated individuals with attenuated or killed disease-causing agents. This empirical approach inspired a century of vaccine development and the effective prophylaxis of many infectious diseases. From the 1980s, several waves of new technologies have enabled the development of novel vaccines that would not have been possible using the empirical approach. The technological revolution in the field of vaccination is now continuing, and it is delivering novel and safer vaccines. In this Timeline article, we provide our views on the transition from empiricism to rational vaccine design. PMID:24925139

  8. Improving thermal and detergent stability of Bacillus stearothermophilus neopullulanase by rational enzyme design.

    PubMed

    Ece, Selin; Evran, Serap; Janda, Jan-Oliver; Merkl, Rainer; Sterner, Reinhard

    2015-06-01

    Neopullulanase, a glycosyl hydrolase from Bacillus stearothermophilus (bsNpl), is a potentially valuable enzyme for starch and detergent industries. However, as the protein is not active at elevated temperatures and high surfactant concentrations, we aimed to increase its stability by rational enzyme design. Nine potentially destabilizing cavities were identified in the crystal structure of the enzyme. Based on computational predictions, these cavities were filled by residues with bulkier side chains. The five Asp46Glu, Val239Leu, Val404Leu, Ser407Thr and Ala566Leu exchanges resulted in a drastic stabilization of bsNpl against inactivation by heat and detergents. The catalytic activity of the variants was identical to the wild-type enzyme. PMID:25680359

  9. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis

    NASA Astrophysics Data System (ADS)

    Dhakal, Soma; Adendorff, Matthew R.; Liu, Minghui; Yan, Hao; Bathe, Mark; Walter, Nils G.

    2016-01-01

    The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies - incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies - incomplete closure upon actuation and conformational

  10. FRET-based small-molecule fluorescent probes: rational design and bioimaging applications.

    PubMed

    Yuan, Lin; Lin, Weiying; Zheng, Kaibo; Zhu, Sasa

    2013-07-16

    Fluorescence imaging has emerged as a powerful tool for monitoring biomolecules within the context of living systems with high spatial and temporal resolution. Researchers have constructed a large number of synthetic intensity-based fluorescent probes for bio-imaging. However, intensity-based fluorescent probes have some limitations: variations in probe concentration, probe environment, and excitation intensity may influence the fluorescence intensity measurements. In principle, the use of ratiometric fluorescent probes can alleviate this shortcoming. Förster resonance energy transfer (FRET) is one of the most widely used sensing mechanisms for ratiometric fluorescent probes. However, the development of synthetic FRET probes with favorable photophysical properties that are also suitable for biological imaging applications remains challenging. In this Account, we review the rational design and biological applications of synthetic FRET probes, focusing primarily on studies from our laboratory. To construct useful FRET probes, it is a pre-requisite to develop a FRET platform with favorable photophysical properties. The design criteria of a FRET platform include (1) well-resolved absorption spectra of the donor and acceptor, (2) well-separated emission spectra of the donor and acceptor, (3) donors and acceptors with comparable brightness, (4) rigid linkers, and (5) near-perfect efficiency in energy transfer. With an efficient FRET platform in hand, it is then necessary to modulate the donor-acceptor distance or spectral overlap integral in an analyte-dependent fashion for development of FRET probes. Herein, we emphasize our most recent progress on the development of FRET probes by spectral overlap integral, in particular by changing the molar absorption coefficient of the donor dyes such as rhodamine dyes, which undergo unique changes in the absorption profiles during the ring-opening and -closing processes. Although partial success has been obtained in design of

  11. Rational protein design: developing next-generation biological therapeutics and nanobiotechnological tools.

    PubMed

    Wilson, Corey J

    2015-01-01

    Proteins are the most functionally diverse macromolecules observed in nature, participating in a broad array of catalytic, biosensing, transport, scaffolding, and regulatory functions. Fittingly, proteins have become one of the most promising nanobiotechnological tools to date, and through the use of recombinant DNA and other laboratory methods we have produced a vast number of biological therapeutics derived from human genes. Our emerging ability to rationally design proteins (e.g., via computational methods) holds the promise of significantly expanding the number and diversity of protein therapies and has opened the gateway to realizing true and uncompromised personalized medicine. In the last decade computational protein design has been transformed from a set of fundamental strategies to stringently test our understanding of the protein structure-function relationship, to practical tools for developing useful biological processes, nano-devices, and novel therapeutics. As protein design strategies improve (i.e., in terms of accuracy and efficiency) clinicians will be able to leverage individual genetic data and biological metrics to develop and deliver personalized protein therapeutics with minimal delay.

  12. Cellular Uptake and Localization of Polymyxins in Renal Tubular Cells Using Rationally Designed Fluorescent Probes

    PubMed Central

    Yun, Bo; Azad, Mohammad A. K.; Nowell, Cameron J.; Nation, Roger L.; Thompson, Philip E.; Roberts, Kade D.

    2015-01-01

    Polymyxins are cyclic lipopeptide antibiotics that serve as a last line of defense against Gram-negative bacterial superbugs. However, the extensive accumulation of polymyxins in renal tubular cells can lead to nephrotoxicity, which is the major dose-limiting factor in clinical use. In order to gain further insights into the mechanism of polymyxin-induced nephrotoxicity, we have rationally designed novel fluorescent polymyxin probes to examine the localization of polymyxins in rat renal tubular (NRK-52E) cells. Our design strategy focused on incorporating a dansyl fluorophore at the hydrophobic centers of the polymyxin core structure. To this end, four novel regioselectively labeled monodansylated polymyxin B probes (MIPS-9541, MIPS-9542, MIPS-9543, and MIPS-9544) were designed, synthesized, and screened for their antimicrobial activities and apoptotic effects against rat kidney proximal tubular cells. On the basis of the assessment of antimicrobial activities, cellular uptake, and apoptotic effects on renal tubular cells, incorporation of a dansyl fluorophore at either position 6 or 7 (MIPS-9543 and MIPS-9544, respectively) of the polymyxin core structure appears to be an appropriate strategy for generating representative fluorescent polymyxin probes to be utilized in intracellular imaging and mechanistic studies. Furthermore, confocal imaging experiments utilizing these probes showed evidence of partial colocalization of the polymyxins with both the endoplasmic reticulum and mitochondria in rat renal tubular cells. Our results highlight the value of these new fluorescent polymyxin probes and provide further insights into the mechanism of polymyxin-induced nephrotoxicity. PMID:26392495

  13. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    PubMed Central

    2010-01-01

    Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR) and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. Conclusions This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts. PMID:21070658

  14. Rational Design of Peptide Vaccines Against Multiple Types of Human Papillomavirus.

    PubMed

    Dey, Sumanta; De, Antara; Nandy, Ashesh

    2016-01-01

    Human papillomavirus (HPV) occurs in many types, some of which cause cervical, genital, and other cancers. While vaccination is available against the major cancer-causing HPV types, many others are not covered by these preventive measures. Herein, we present a bioinformatics study for the designing of multivalent peptide vaccines against multiple HPV types as an alternative strategy to the virus-like particle vaccines being used now. Our technique of rational design of peptide vaccines is expected to ensure stability of the vaccine against many cycles of mutational changes, elicit immune response, and negate autoimmune possibilities. Using the L1 capsid protein sequences, we identified several peptides for potential vaccine design for HPV 16, 18, 33, 35, 45, and 11 types. Although there are concerns about the epitope-binding affinities for the peptides identified in this process, the technique indicates possibilities of multivalent, adjuvanted, peptide vaccines against a wider range of HPV types, and tailor-made different combinations of the peptides to address frequency variations of types over different population groups as required for prophylaxis and at lower cost than are in use at the present time.

  15. Theory and simulation of DNA-coated colloids: a guide for rational design

    NASA Astrophysics Data System (ADS)

    Angioletti-Uberti, Stefano; Mognetti, Bortolo M.; Frenkel, Daan

    By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the fact that a proper choice of the grafted DNA sequences yields fine control over the colloidal interactions. Theory and simulations have an important role to play in the optimal design of self- assembling DNACCs. At present, the powerful model-based design tools are not widely used, because the theoretical literature is fragmented and the connection between different theories is often not evident. In this Perspective, we aim to discuss the similarities and differences between the different models that have been described in the literature, their underlying assumptions, their strengths and their weaknesses. Using the tools described in the present Review, it should be possible to move towards a more rational design of novel self-assembling structures of DNACCs and, more generally, of systems where ligand-receptors bonds are used to control interactions.

  16. Rational Design of Peptide Vaccines Against Multiple Types of Human Papillomavirus

    PubMed Central

    Dey, Sumanta; De, Antara; Nandy, Ashesh

    2016-01-01

    Human papillomavirus (HPV) occurs in many types, some of which cause cervical, genital, and other cancers. While vaccination is available against the major cancer-causing HPV types, many others are not covered by these preventive measures. Herein, we present a bioinformatics study for the designing of multivalent peptide vaccines against multiple HPV types as an alternative strategy to the virus-like particle vaccines being used now. Our technique of rational design of peptide vaccines is expected to ensure stability of the vaccine against many cycles of mutational changes, elicit immune response, and negate autoimmune possibilities. Using the L1 capsid protein sequences, we identified several peptides for potential vaccine design for HPV 16, 18, 33, 35, 45, and 11 types. Although there are concerns about the epitope-binding affinities for the peptides identified in this process, the technique indicates possibilities of multivalent, adjuvanted, peptide vaccines against a wider range of HPV types, and tailor-made different combinations of the peptides to address frequency variations of types over different population groups as required for prophylaxis and at lower cost than are in use at the present time. PMID:27279731

  17. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis.

    PubMed

    Dhakal, Soma; Adendorff, Matthew R; Liu, Minghui; Yan, Hao; Bathe, Mark; Walter, Nils G

    2016-02-01

    The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies--incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.

  18. Theory and simulation of DNA-coated colloids: a guide for rational design.

    PubMed

    Angioletti-Uberti, Stefano; Mognetti, Bortolo M; Frenkel, Daan

    2016-03-01

    By exploiting the exquisite selectivity of DNA hybridization, DNA-coated colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the fact that a proper choice of the grafted DNA sequences yields fine control over the colloidal interactions. Theory and simulations have an important role to play in the optimal design of self assembling DNACCs. At present, the powerful model-based design tools are not widely used, because the theoretical literature is fragmented and the connection between different theories is often not evident. In this Perspective, we aim to discuss the similarities and differences between the different models that have been described in the literature, their underlying assumptions, their strengths and their weaknesses. Using the tools described in the present Review, it should be possible to move towards a more rational design of novel self-assembling structures of DNACCs and, more generally, of systems where ligand-receptor are used to control interactions.

  19. Theory and simulation of DNA-coated colloids: a guide for rational design.

    PubMed

    Angioletti-Uberti, Stefano; Mognetti, Bortolo M; Frenkel, Daan

    2016-03-01

    By exploiting the exquisite selectivity of DNA hybridization, DNA-coated colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the fact that a proper choice of the grafted DNA sequences yields fine control over the colloidal interactions. Theory and simulations have an important role to play in the optimal design of self assembling DNACCs. At present, the powerful model-based design tools are not widely used, because the theoretical literature is fragmented and the connection between different theories is often not evident. In this Perspective, we aim to discuss the similarities and differences between the different models that have been described in the literature, their underlying assumptions, their strengths and their weaknesses. Using the tools described in the present Review, it should be possible to move towards a more rational design of novel self-assembling structures of DNACCs and, more generally, of systems where ligand-receptor are used to control interactions. PMID:26862595

  20. Rational design of peptide-based building blocks for nanoscience and synthetic biology.

    PubMed

    Armstrong, Craig T; Boyle, Aimee L; Bromley, Elizabeth H C; Mahmoud, Zahra N; Smith, Lisa; Thomson, Andrew R; Woolfson, Derek N

    2009-01-01

    The rational design of peptides that fold to form discrete nanoscale objects, and/ or self-assemble into nanostructured materials is an exciting challenge. Such efforts test and extend our understanding of sequence-to-structure relationships in proteins, and potentially provide materials for applications in bionanotechnology. Over the past decade or so, rules for the folding and assembly of one particular protein-structure motif--the alpha-helical coiled coil have advanced sufficiently to allow the confident design of novel peptides that fold to prescribed structures. Coiled coils are based on interacting alpha-helices, and guide and cement many protein-protein interactions in nature. As such, they present excellent starting points for building complex objects and materials that span the nano-to-micron scales from the bottom up. Along with others, we have translated and extended our understanding of coiled-coil folding and assembly to develop novel peptide-based biomaterials. Herein, we outline briefly the rules for the folding and assembly of coiled-coil motifs, and describe how we have used them in de novo design of discrete nanoscale objects and soft synthetic biomaterials. Moreover, we describe how the approach can be extended to other small, independently folded protein motifs--such as zinc fingers and EF-hands--that could be incorporated into more complex, multi-component synthetic systems and new hybrid and responsive biomaterials.

  1. Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors

    PubMed Central

    Simon, Anna J.; Vallée-Bélisle, Alexis; Ricci, Francesco; Plaxco, Kevin W.

    2014-01-01

    Control over the sensitivity with which biomolecular receptors respond to small changes in the concentration of their target ligand is critical for the proper function of many cellular processes. Such control could likewise be of utility in artificial biotechnologies, such as biosensors, genetic logic gates, and “smart” materials, in which highly responsive behavior is of value. In nature, the control of molecular responsiveness is often achieved using “Hill-type” cooperativity, a mechanism in which sequential binding events on a multivalent receptor are coupled such that the first enhances the affinity of the next, producing a steep, higher-order dependence on target concentration. Here, we use an intrinsic-disorder–based mechanism that can be implemented without requiring detailed structural knowledge to rationally introduce this potentially useful property into several normally noncooperative biomolecules. To do so, we fabricate a tandem repeat of the receptor that is destabilized (unfolded) via the introduction of a long, unstructured loop. The first binding event requires the energetically unfavorable closing of this loop, reducing its affinity relative to that of the second binding event, which, in contrast occurs at a preformed site. Using this approach, we have rationally introduced cooperativity into three unrelated DNA aptamers, achieving in the best of these a Hill coefficient experimentally indistinguishable from the theoretically expected maximum. The extent of cooperativity and thus the steepness of the binding transition are, moreover, well modeled as simple functions of the energetic cost of binding-induced folding, speaking to the quantitative nature of this design strategy. PMID:25288724

  2. Snake Bite in South Asia: A Review

    PubMed Central

    Alirol, Emilie; Sharma, Sanjib Kumar; Bawaskar, Himmatrao Saluba; Kuch, Ulrich; Chappuis, François

    2010-01-01

    Snake bite is one of the most neglected public health issues in poor rural communities living in the tropics. Because of serious misreporting, the true worldwide burden of snake bite is not known. South Asia is the world's most heavily affected region, due to its high population density, widespread agricultural activities, numerous venomous snake species and lack of functional snake bite control programs. Despite increasing knowledge of snake venoms' composition and mode of action, good understanding of clinical features of envenoming and sufficient production of antivenom by Indian manufacturers, snake bite management remains unsatisfactory in this region. Field diagnostic tests for snake species identification do not exist and treatment mainly relies on the administration of antivenoms that do not cover all of the important venomous snakes of the region. Care-givers need better training and supervision, and national guidelines should be fed by evidence-based data generated by well-designed research studies. Poorly informed rural populations often apply inappropriate first-aid measures and vital time is lost before the victim is transported to a treatment centre, where cost of treatment can constitute an additional hurdle. The deficiency of snake bite management in South Asia is multi-causal and requires joint collaborative efforts from researchers, antivenom manufacturers, policy makers, public health authorities and international funders. PMID:20126271

  3. Adapting Rational Unified Process (RUP) approach in designing a secure e-Tendering model

    NASA Astrophysics Data System (ADS)

    Mohd, Haslina; Robie, Muhammad Afdhal Muhammad; Baharom, Fauziah; Darus, Norida Muhd; Saip, Mohamed Ali; Yasin, Azman

    2016-08-01

    e-Tendering is an electronic processing of the tender document via internet and allow tenderer to publish, communicate, access, receive and submit all tender related information and documentation via internet. This study aims to design the e-Tendering system using Rational Unified Process approach. RUP provides a disciplined approach on how to assign tasks and responsibilities within the software development process. RUP has four phases that can assist researchers to adjust the requirements of various projects with different scope, problem and the size of projects. RUP is characterized as a use case driven, architecture centered, iterative and incremental process model. However the scope of this study only focusing on Inception and Elaboration phases as step to develop the model and perform only three of nine workflows (business modeling, requirements, analysis and design). RUP has a strong focus on documents and the activities in the inception and elaboration phases mainly concern the creation of diagrams and writing of textual descriptions. The UML notation and the software program, Star UML are used to support the design of e-Tendering. The e-Tendering design based on the RUP approach can contribute to e-Tendering developers and researchers in e-Tendering domain. In addition, this study also shows that the RUP is one of the best system development methodology that can be used as one of the research methodology in Software Engineering domain related to secured design of any observed application. This methodology has been tested in various studies in certain domains, such as in Simulation-based Decision Support, Security Requirement Engineering, Business Modeling and Secure System Requirement, and so forth. As a conclusion, these studies showed that the RUP one of a good research methodology that can be adapted in any Software Engineering (SE) research domain that required a few artifacts to be generated such as use case modeling, misuse case modeling, activity

  4. Rational design of 5-aminolevulinic acid derivatives aimed at improving photodynamic therapy.

    PubMed

    Casas, Adriana; Batlle, Alcira

    2002-07-01

    5-aminolevulinic acid (ALA) is the first intermediate in heme biosynthesis and is therefore a precursor of protoporphyrin IX (PpIX). PpIX is used as an endogenous photosensitizer in photodynamic therapy (PDT). Several chemical modifications have been made, both on the amino and carboxyl groups of ALA to induce higher PpIX production and photosensitisation. Esterification of ALA with aliphatic lineal and cyclic alcohols was found to reduce the amount of ALA required for photosensitization. Esterification by aliphatic alcohols with carbohydrate chains equal or lower than C4 leads to porphyrin accumulation lower than ALA, whereas equal or longer than C6 chains leads to greater synthesis of porphyrin. A branch point in the alcohol located next to the site of ester cleavage limits access of the esters to the esterase active site, resulting in lower PpIX production. ALA esters of the polyethylenglycol family can induce high levels of PpIX, with some selectivity for endothelial cells toward tumor cells. On the basis of the differential expression of some aminopeptidases in tumor vasculature when compared to normal vasculature, some ALA-pseudopeptides were synthesized. In a rational design of ALA derivatives, the transport mechanism of these aminoacids into the cell is central. Due to the similar characteristics between ALA and GABA transport, a novel approach for designing new ALA derivatives which could penetrate more easily into tumoral cells, would be to take into account the structures of the inhibitors of GABA transport. PMID:12678731

  5. Construction of a rationally designed antibody platform for sequencing-assisted selection.

    PubMed

    Larman, H Benjamin; Xu, George Jing; Pavlova, Natalya N; Elledge, Stephen J

    2012-11-01

    Antibody discovery platforms have become an important source of both therapeutic biomolecules and research reagents. Massively parallel DNA sequencing can be used to assist antibody selection by comprehensively monitoring libraries during selection, thus greatly expanding the power of these systems. We have therefore constructed a rationally designed, fully defined single-chain variable fragment (scFv) library and analysis platform optimized for analysis with short-read deep sequencing. Sequence-defined oligonucleotide libraries encoding three complementarity-determining regions (L3 from the light chain, H2 and H3 from the heavy chain) were synthesized on a programmable microarray and combinatorially cloned into a single scFv framework for molecular display. Our unique complementarity-determining region sequence design optimizes for protein binding by utilizing a hidden Markov model that was trained on all antibody-antigen cocrystal structures in the Protein Data Bank. The resultant ~10(12)-member library was produced in ribosome-display format, and comprehensively analyzed over four rounds of antigen selections by multiplex paired-end Illumina sequencing. The hidden Markov model scFv library generated multiple binders against an emerging cancer antigen and is the basis for a next-generation antibody production platform. PMID:23064642

  6. Rational design and validation of a vanilloid-sensitive TRPV2 ion channel.

    PubMed

    Yang, Fan; Vu, Simon; Yarov-Yarovoy, Vladimir; Zheng, Jie

    2016-06-28

    Vanilloids activation of TRPV1 represents an excellent model system of ligand-gated ion channels. Recent studies using cryo-electron microcopy (cryo-EM), computational analysis, and functional quantification revealed the location of capsaicin-binding site and critical residues mediating ligand-binding and channel activation. Based on these new findings, here we have successfully introduced high-affinity binding of capsaicin and resiniferatoxin to the vanilloid-insensitive TRPV2 channel, using a rationally designed minimal set of four point mutations (F467S-S498F-L505T-Q525E, termed TRPV2_Quad). We found that binding of resiniferatoxin activates TRPV2_Quad but the ligand-induced open state is relatively unstable, whereas binding of capsaicin to TRPV2_Quad antagonizes resiniferatoxin-induced activation likely through competition for the same binding sites. Using Rosetta-based molecular docking, we observed a common structural mechanism underlying vanilloids activation of TRPV1 and TRPV2_Quad, where the ligand serves as molecular "glue" that bridges the S4-S5 linker to the S1-S4 domain to open these channels. Our analysis revealed that capsaicin failed to activate TRPV2_Quad likely due to structural constraints preventing such bridge formation. These results not only validate our current working model for capsaicin activation of TRPV1 but also should help guide the design of drug candidate compounds for this important pain sensor. PMID:27298359

  7. Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance

    PubMed Central

    Schoukroun-Barnes, Lauren R.; White, Ryan J.

    2015-01-01

    The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM). Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes. PMID:25835184

  8. Rational Design of Porous Conjugated Polymers and Roles of Residual Palladium for Photocatalytic Hydrogen Production.

    PubMed

    Li, Lianwei; Cai, Zhengxu; Wu, Qinghe; Lo, Wai-Yip; Zhang, Na; Chen, Lin X; Yu, Luping

    2016-06-22

    Developing highly efficient photocatalyts for water splitting is one of the grand challenges in solar energy conversion. Here, we report the rational design and synthesis of porous conjugated polymer (PCP) that photocatalytically generates hydrogen from water splitting. The design mimics natural photosynthetics systems with conjugated polymer component to harvest photons and the transition metal part to facilitate catalytic activities. A series of PCPs have been synthesized with different light harvesting chromophores and transition metal binding bipyridyl (bpy) sites. The photocatalytic activity of these bpy-containing PCPs can be greatly enhanced due to the improved light absorption, better wettability, local ordering structure, and the improved charge separation process. The PCP made of strong and fully conjugated donor chromophore DBD (M4) shows the highest hydrogen production rate at ∼33 μmol/h. The results indicate that copolymerization between a strong electron donor and weak electron acceptor into the same polymer chain is a useful strategy for developing efficient photocatalysts. This study also reveals that the residual palladium in the PCP networks plays a key role for the catalytic performance. The hydrogen generation activity of PCP photocatalyst can be further enhanced to 164 μmol/h with an apparent quantum yield of 1.8% at 350 nm by loading 2 wt % of extra platinum cocatalyst. PMID:27254306

  9. Towards a rational design of solid drug nanoparticles with optimised pharmacological properties

    PubMed Central

    Martin, Phillip; Smith, Darren; Curley, Paul; McDonald, Tom; Giardiello, Marco; Liptrott, Neill; Rannard, Steve; Owen, Andrew

    2016-01-01

    Abstract Solid drug nanoparticles (SDNs) are a nanotechnology with favourable characteristics to enhance drug delivery and improve the treatment of several diseases, showing benefit for improved oral bioavailability and injectable long‐acting medicines. The physicochemical properties and composition of nanoformulations can influence the absorption, distribution, and elimination of nanoparticles; consequently, the development of nanoparticles for drug delivery should consider the potential role of nanoparticle characteristics in the definition of pharmacokinetics. The aim of this study was to investigate the pharmacological behaviour of efavirenz SDNs and the identification of optimal nanoparticle properties and composition. Seventy‐seven efavirenz SDNs were included in the analysis. Cellular accumulation was evaluated in HepG2 (hepatic) and Caco‐2 (intestinal), CEM (lymphocyte), THP1 (monocyte), and A‐THP1 (macrophage) cell lines. Apparent intestinal permeability (Papp) was measured using a monolayer of Caco‐2 cells. The Papp values were used to evaluate the potential benefit on pharmacokinetics using a physiologically based pharmacokinetic model. The generated SDNs had an enhanced intestinal permeability and accumulation in different cell lines compared to the traditional formulation of efavirenz. Nanoparticle size and excipient choice influenced efavirenz apparent permeability and cellular accumulation, and this appeared to be cell line dependent. These findings represent a valuable platform for the design of SDNs, giving an empirical background for the selection of optimal nanoparticle characteristics and composition. Understanding how nanoparticle components and physicochemical properties influence pharmacological patterns will enable the rational design of SDNs with desirable pharmacokinetics. PMID:27774308

  10. Rational design and adaptive management of combination therapies for Hepatitis C virus infection

    SciTech Connect

    Ke, Ruian; Loverdo, Claude; Qi, Hangfei; Sun, Ren; Lloyd-Smith, James O.; Kouyos, Roger Dimitri

    2015-06-30

    Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensate when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design.

  11. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications.

    PubMed

    Yu, Yong; Mok, Beverly Y L; Loh, Xian Jun; Tan, Yen Nee

    2016-08-01

    Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents. PMID:27377035

  12. Rational design and adaptive management of combination therapies for Hepatitis C virus infection

    DOE PAGES

    Ke, Ruian; Loverdo, Claude; Qi, Hangfei; Sun, Ren; Lloyd-Smith, James O.; Kouyos, Roger Dimitri

    2015-06-30

    Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensatemore » when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design.« less

  13. Rationally designed particle preloading method to improve protein delivery performance of electrospun polyester nanofibers.

    PubMed

    Sun, Xue; Li, Ke; Chen, Sainan; Yao, Bing; Zhou, Yifa; Cui, Sisi; Hu, Junli; Liu, Yichun

    2016-10-15

    Particle preloading method by first loading proteins onto nano- or microparticles and then integrating these particles into electrospun polyester nanofibers has been widely used to encapsulate therapeutic proteins into polyester nanofibers. However, poor method design has resulted in unsatisfactory protein delivery performance. For example, the harsh conditions involved in preloading procedures damage the bioactivities of proteins, the improper integration leads to an uneven distribution of particles in nanofibers or insecure attachment of particles to nanofibers, producing uncontrolled protein release profiles. This study aimed to improve the protein delivery performance of polyester nanofibers by rationally designing a particle preloading method. Positively charged chitosan nanoparticles (CNPs) were used as carriers to adsorb negatively charged proteins in mild conditions and as primary barriers for protein release. The polar CNPs were then homogeneously dispersed in a polar polyester solution and subjected to electrospinning. Microscope observations indicated that CNPs were homogeneously embedded within polyester nanofibers. In vitro release behaviour and cell studies showed that proteins retained their bioactivity and could release from polyester nanofibers in a sustained manner for more than 4 weeks without any initial burst. Epidermal growth factor encapsulated in polyester nanofibers enhanced diabetic wound healing in vivo, demonstrating an application potential in biomedicine. Other properties of the nanofibers, including composition, wettability, cytotoxicity, and cell adhesion and spreading, were examined in detail as well. PMID:27568495

  14. Rational design and validation of a vanilloid-sensitive TRPV2 ion channel.

    PubMed

    Yang, Fan; Vu, Simon; Yarov-Yarovoy, Vladimir; Zheng, Jie

    2016-06-28

    Vanilloids activation of TRPV1 represents an excellent model system of ligand-gated ion channels. Recent studies using cryo-electron microcopy (cryo-EM), computational analysis, and functional quantification revealed the location of capsaicin-binding site and critical residues mediating ligand-binding and channel activation. Based on these new findings, here we have successfully introduced high-affinity binding of capsaicin and resiniferatoxin to the vanilloid-insensitive TRPV2 channel, using a rationally designed minimal set of four point mutations (F467S-S498F-L505T-Q525E, termed TRPV2_Quad). We found that binding of resiniferatoxin activates TRPV2_Quad but the ligand-induced open state is relatively unstable, whereas binding of capsaicin to TRPV2_Quad antagonizes resiniferatoxin-induced activation likely through competition for the same binding sites. Using Rosetta-based molecular docking, we observed a common structural mechanism underlying vanilloids activation of TRPV1 and TRPV2_Quad, where the ligand serves as molecular "glue" that bridges the S4-S5 linker to the S1-S4 domain to open these channels. Our analysis revealed that capsaicin failed to activate TRPV2_Quad likely due to structural constraints preventing such bridge formation. These results not only validate our current working model for capsaicin activation of TRPV1 but also should help guide the design of drug candidate compounds for this important pain sensor.

  15. Rational Design of Porous Conjugated Polymers and Roles of Residual Palladium for Photocatalytic Hydrogen Production.

    PubMed

    Li, Lianwei; Cai, Zhengxu; Wu, Qinghe; Lo, Wai-Yip; Zhang, Na; Chen, Lin X; Yu, Luping

    2016-06-22

    Developing highly efficient photocatalyts for water splitting is one of the grand challenges in solar energy conversion. Here, we report the rational design and synthesis of porous conjugated polymer (PCP) that photocatalytically generates hydrogen from water splitting. The design mimics natural photosynthetics systems with conjugated polymer component to harvest photons and the transition metal part to facilitate catalytic activities. A series of PCPs have been synthesized with different light harvesting chromophores and transition metal binding bipyridyl (bpy) sites. The photocatalytic activity of these bpy-containing PCPs can be greatly enhanced due to the improved light absorption, better wettability, local ordering structure, and the improved charge separation process. The PCP made of strong and fully conjugated donor chromophore DBD (M4) shows the highest hydrogen production rate at ∼33 μmol/h. The results indicate that copolymerization between a strong electron donor and weak electron acceptor into the same polymer chain is a useful strategy for developing efficient photocatalysts. This study also reveals that the residual palladium in the PCP networks plays a key role for the catalytic performance. The hydrogen generation activity of PCP photocatalyst can be further enhanced to 164 μmol/h with an apparent quantum yield of 1.8% at 350 nm by loading 2 wt % of extra platinum cocatalyst.

  16. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications.

    PubMed

    Yu, Yong; Mok, Beverly Y L; Loh, Xian Jun; Tan, Yen Nee

    2016-08-01

    Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents.

  17. Glycolipid-based TLR4 Modulators and Fluorescent Probes: Rational Design, Synthesis, and Biological Properties.

    PubMed

    Ciaramelli, Carlotta; Calabrese, Valentina; Sestito, Stefania E; Pérez-Regidor, Lucia; Klett, Javier; Oblak, Alja; Jerala, Roman; Piazza, Matteo; Martín-Santamaría, Sonsoles; Peri, Francesco

    2016-08-01

    The cationic glycolipid IAXO-102, a potent TLR4 antagonist targeting both MD-2 and CD14 co-receptors, has been used as scaffold to design new potential TLR4 modulators and fluorescent labels for the TLR4 receptor complex (membrane TLR4.MD-2 dimer and CD14). The primary amino group of IAXO-102, not involved in direct interaction with MD-2 and CD14 receptors, has been exploited to covalently attach a fluorescein (molecules 1 and 2) or to link two molecules of IAXO-102 through diamine and diammonium spacers, obtaining 'dimeric' molecules 3 and 4. The structure-based rational design of compounds 1-4 was guided by the optimization of MD-2 and CD14 binding. Compounds 1 and 2 inhibited TLR4 activation, in a concentration-dependent manner, and signaling in HEK-Blue TLR4 cells. The fluorescent labeling of murine macrophages by molecule 1 was inhibited by LPS and was also abrogated when cell surface proteins were digested by trypsin, thus suggesting an interaction of fluorescent probe 1 with membrane proteins of the TLR4 receptor system.

  18. Tuning Cellular Uptake of Molecular Probes by Rational Design of Their Assembly into Supramolecular Nanoprobes.

    PubMed

    Lock, Lye Lin; Reyes, Claudia D; Zhang, Pengcheng; Cui, Honggang

    2016-03-16

    Intracellular sensing of pathologically relevant biomolecules could provide essential information for accurate evaluation of disease staging and progression, yet the poor cellular uptake of water-soluble molecular probes limits their use as protease sensors. In other cases such as extracellular sensing, cellular uptake should be effectively inhibited. Self-assembly of molecular probes into supramolecular nanoprobes presents a potential strategy to alter their interaction mechanisms with cells to promote or reduce their cellular uptake. Here, we report on the design, synthesis, and assembly of peptide-based molecular beacons into supramolecular protease sensors of either spherical or filamentous shapes. We found that positively charged spherical nanobeacons demonstrate much higher cellular uptake efficiency than its monomeric form, thus making them most suitable for intracellular sensing of the lysosomal protease cathepsin B. Our results also suggest that assembly into filamentous nanobeacons significantly reduces their internalization by cancer cells, an important property that can be utilized for probing extracellular protease activities. These studies provide important guiding principles for rational design of supramolecular nanoprobes with tunable cellular uptake characteristics.

  19. Rational Design of an Epstein-Barr Virus Vaccine Targeting the Receptor-Binding Site.

    PubMed

    Kanekiyo, Masaru; Bu, Wei; Joyce, M Gordon; Meng, Geng; Whittle, James R R; Baxa, Ulrich; Yamamoto, Takuya; Narpala, Sandeep; Todd, John-Paul; Rao, Srinivas S; McDermott, Adrian B; Koup, Richard A; Rossmann, Michael G; Mascola, John R; Graham, Barney S; Cohen, Jeffrey I; Nabel, Gary J

    2015-08-27

    Epstein-Barr virus (EBV) represents a major global health problem. Though it is associated with infectious mononucleosis and ∼200,000 cancers annually worldwide, a vaccine is not available. The major target of immunity is EBV glycoprotein 350/220 (gp350) that mediates attachment to B cells through complement receptor 2 (CR2/CD21). Here, we created self-assembling nanoparticles that displayed different domains of gp350 in a symmetric array. By focusing presentation of the CR2-binding domain on nanoparticles, potent neutralizing antibodies were elicited in mice and non-human primates. The structurally designed nanoparticle vaccine increased neutralization 10- to 100-fold compared to soluble gp350 by targeting a functionally conserved site of vulnerability, improving vaccine-induced protection in a mouse model. This rational approach to EBV vaccine design elicited potent neutralizing antibody responses by arrayed presentation of a conserved viral entry domain, a strategy that can be applied to other viruses. PMID:26279189

  20. Rational design and optimization of plasmonic nanoarrays for surface enhanced infrared spectroscopy

    PubMed Central

    Liberman, Vladimir; Adato, Ronen; Jeys, Thomas H.; Saar, Brian G.; Erramilli, Shyamsunder; Altug, Hatice

    2012-01-01

    We present an approach for rational design and optimization of plasmonic arrays for ultrasensitive surface enhanced infrared absorption (SEIRA) spectroscopy of specific protein analytes. Motivated by our previous work that demonstrated sub-attomole detection of surface-bound silk fibroin [Proc. Natl. Acad. Sci. U.S.A. 106, 19227 (2009)], we introduce here a general framework that allows for the numerical optimization of metamaterial sensor designs in order to maximize the absorbance signal. A critical feature of our method is the explicit compensation for the perturbative effects of the analyte's refractive index which alters the resonance frequency and line-shape of the metamaterial response, thereby leading to spectral distortion in SEIRA signatures. As an example, we leverage our method to optimize the geometry of periodic arrays of plasmonic nanoparticles on both Si and CaF2 substrates. The optimal geometries result in a three-order of magnitude absorbance enhancement compared to an unstructured Au layer, with the CaF2 substrate offering an additional factor of three enhancement in absorbance over a traditional Si substrate. The latter improvement arises from increase of near-field intensity over the Au nanobar surface for the lower index substrate. Finally, we perform sensitivity analysis for our optimized arrays to predict the effects of fabrication imperfections. We find that <20% deviation from the optimized absorbance response is readily achievable over large areas with modern nanofabrication techniques. PMID:22714181

  1. Rational Design of Cathode Structure for High Rate Performance Lithium-Sulfur Batteries.

    PubMed

    Chen, Hongwei; Wang, Changhong; Dai, Yafei; Qiu, Shengqiang; Yang, Jinlong; Lu, Wei; Chen, Liwei

    2015-08-12

    Practical applications of Li-S batteries require not only high specific capacities and long cycle lifetimes but also high rate performance. We report a rationally designed Li-S cathode, which consists of a freestanding composite thin film assembled from S nanoparticles, reduced graphene oxide (rGO), and a multifunctional additive poly(anthraquinonyl sulfide) (PAQS). The S nanoparticles provide a high initial specific capacity, and the layered and porous rGO structure provides electron and ion transport paths and restricts polysulfide shuttling. PAQS is not only a highly efficient sulfide trapping agent but also an excellent Li(+) conductor, which benefits the battery reaction kinetics at a high rate. The resulting cathode exhibits an initial specific capacity of 1255 mAh g(-1) with a decay rate as low as 0.046% per cycles over 1200 cycles. Importantly, it displays a reversible capacity of 615 mAh g(-1) when discharged at a high rate of 8 C (13.744 A g(-1)). PMID:26148126

  2. Rational Design of Thermally Stable Novel Biocatalytic Nanomaterials: Enzyme Stability in Restricted Spatial Dimensions

    NASA Astrophysics Data System (ADS)

    Mudhivarthi, Vamsi K.

    Enzyme stability is of intense interest in bio-materials science as biocatalysts, and as sensing platforms. This is essentially because the unique properties of DNA, RNA, PAA can be coupled with the interesting and novel properties of proteins to produce systems with unprecedented control over their properties. In this article, the very first examples of enzyme/NA/inorganic hybrid nanomaterials and enzyme-Polyacrylic acid conjugates will be presented. The basic principles of design, synthesis and control of properties of these hybrid materials will be presented first, and this will be followed by a discussion of selected examples from our recent research findings. Data show that key properties of biological catalysts are improved by the inorganic framework especially when the catalyst is co-embedded with DNA. Several examples of such studies with various enzymes and proteins, including horseradish peroxidase (HRP), glucose oxidase (GO), cytochrome c (Cyt c), met-hemoglobin (Hb) and met-myoglobin (Mb) will be discussed. Additionally, key insights obtained by the standard methods of materials science including XRD, SEM and TEM as well as biochemical, calorimetric and spectroscopic methods will be discussed. Furthermore, improved structure and enhanced activities of the biocatalysts in specific cases will be demonstrated along with the potential stabilization mechanisms. Our hypothesis is that nucleic acids provide an excellent control over the enzyme-solid interactions as well as rational assembly of nanomaterials. These novel nanobiohybrid materials may aid in engineering more effective synthetic materials for gene-delivery, RNA-delivery and drug delivery applications.

  3. TSpred: a web server for the rational design of temperature-sensitive mutants.

    PubMed

    Tan, Kuan Pern; Khare, Shruti; Varadarajan, Raghavan; Madhusudhan, Mallur Srivatsan

    2014-07-01

    Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

  4. TSpred: a web server for the rational design of temperature-sensitive mutants

    PubMed Central

    Tan, Kuan Pern; Khare, Shruti; Varadarajan, Raghavan; Madhusudhan, Mallur Srivatsan

    2014-01-01

    Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes. PMID:24782523

  5. Relaxing the coenzyme specificity of 1,3-propanediol oxidoreductase from Klebsiella pneumoniae by rational design.

    PubMed

    Ma, Chengwei; Zhang, Le; Dai, Jianying; Xiu, Zhilong

    2010-04-15

    1,3-Propanediol has wide applications for large volume markets, particularly in the polymer business. Microbial production of 1,3-propanediol has been considered as a competitor to the traditional petrochemical routes. However, the formation of 1,3-propanediol is limited by the amount of NADH supplied by the oxidative pathway of glycerol dismutation. Previous metabolic flux analysis revealed that relaxation of the coenzyme specificity of 1,3-propanediol oxidoreductase for both NADH and NADPH would increase the production of 1,3-propanediol as well as maintaining the NADH-NAD(+) circle. This work tried to accomplish such a relaxation by rational protein design. Overall binding free energy indicated that the electrostatic energy was the major force discriminating NADH from NADPH. Computational alanine-scanning mutagenesis of the active site residues illustrated that Asp41 was the key residue responsible for the coenzyme specificity. Compared with Asp41Ala, Asp41Gly could further weaken the repulsion between Asp41 and the phosphate group esterified to the 2'-hydroxyl group of the ribose at the adenine end of NADPH. Site-directed mutagenesis was conducted and the relaxation was successfully realized.

  6. Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

    SciTech Connect

    Chen, Chunlong; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald; De Yoreo, James J.

    2014-09-05

    In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic interactions (EI) and hydrophobic interactions (HI), with HI playing the dominant role. While either strong EI or HI inhibit growth and suppress (104) face expression, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate EI allow peptoids to weakly adsorb while moderate HI cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of (104) faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.

  7. A density functional theory insight towards the rational design of ionic liquids for SO2 capture.

    PubMed

    García, Gregorio; Atilhan, Mert; Aparicio, Santiago

    2015-05-28

    A systematic density functional theory (DFT) analysis has been carried out to obtain information at the molecular level on the key parameters related to efficient SO2 capture by ionic liquids (ILs). A set of 55 ILs, for which high gas solubility is expected, has been selected. SO2 solubility of ILs was firstly predicted based on the COSMO-RS (Conductor-like Screening Model for Real Solvents) method, which provides a good prediction of gas solubility data in ILs without prior experimental knowledge of the compounds' features. Then, interactions between SO2 and ILs were deeply analyzed through DFT simulations. This work provides valuable information about required factors at the molecular level to provide high SO2 solubility in ILs, which is crucial for further implementation of these materials in the future. In our opinion, systematic research on ILs for SO2 capture increases our knowledge about those factors which could be controlled at the molecular level, providing an approach for the rational design of task-specific ILs.

  8. Rational design of transcranial current stimulation (TCS) through mechanistic insights into cortical network dynamics.

    PubMed

    Fröhlich, Flavio; Schmidt, Stephen L

    2013-01-01

    Transcranial current stimulation (TCS) is a promising method of non-invasive brain stimulation to modulate cortical network dynamics. Preliminary studies have demonstrated the ability of TCS to enhance cognition and reduce symptoms in both neurological and psychiatric illnesses. Despite the encouraging results of these studies, the mechanisms by which TCS and endogenous network dynamics interact remain poorly understood. Here, we propose that the development of the next generation of TCS paradigms with increased efficacy requires such mechanistic understanding of how weak electric fields (EFs) imposed by TCS interact with the nonlinear dynamics of large-scale cortical networks. We highlight key recent advances in the study of the interaction dynamics between TCS and cortical network activity. In particular, we illustrate an interdisciplinary approach that bridges neurobiology and electrical engineering. We discuss the use of (1) hybrid biological-electronic experimental approaches to disentangle feedback interactions; (2) large-scale computer simulations for the study of weak global perturbations imposed by TCS; and (3) optogenetic manipulations informed by dynamic systems theory to probe network dynamics. Together, we here provide the foundation for the use of rational design for the development of the next generation of TCS neurotherapeutics. PMID:24324427

  9. Rational design of CPP-based drug delivery systems: considerations from pharmacokinetics.

    PubMed

    Mickan, Arite; Sarko, Dikran; Haberkorn, Uwe; Mier, Walter

    2014-01-01

    Therapeutics are restricted from cellular internalization due to the biological barrier formed by the cell membrane. Especially for therapeutics with high molecular weight, strategies are required to enable delivery to intracellular targets. Cell-penetrating peptides (CPPs) represent a powerful tool to mediate the entry of large cargos such as proteins, siRNA and nanoparticles. The high diversity of CPPs is the prerequisite to use this class of carriers for various applications. However, therapies based on CPPs are hampered by their unfavorable pharmacokinetics, mainly dominated by their rapid renal clearance and their lack of specificity. Rational design is required to overcome these disadvantages and thereby exploits the actual potential of CPPs. We summarize and highlight the current state of knowledge with special emphasis on pharmacokinetics. The unclear internalization pathways of CPPs remain one of the main obstacles and therefore have been in the focus of research. In this review, several promising strategies such as the combination with targeting sequences, activatable CPPs and adjustment of the molecular weight are described. In addition, new absorption pathways such as nasal, pulmonary or transdermal uptake expand the applicability of CPPs and may be a promising prospect for clinical application.

  10. Targeting insulin amyloid assembly by small aromatic molecules: toward rational design of aggregation inhibitors.

    PubMed

    Levy-Sakin, Michal; Shreberk, Michal; Daniel, Yael; Gazit, Ehud

    2009-01-01

    Amyloid fibril formation is a common event in more than twenty human diseases and in some normal physiological processes. The mechanism of this ordered aggregation process and the molecular forces driving it are therefore of great importance. One of the strategies used in this field is targeting the fibrillization process by different factors, like, short peptides, organic molecules, etc. Here, we targeted insulin fibril formation by a range of small aromatic molecules, with different numbers of aromatic rings and various substituent groups. Using Thioflavin T fluorescence assay and transmission electron microscopy, we found that all dicyclic and tricyclic compounds in our screen were efficient inhibitors of insulin fibril formation. A common notion regarding amyloid inhibitors is that two functional groups are essentials for interfering with the amyloid formation process; a recognition motif and a bulky group for inducing a steric interference. However, here, we showed that some monocyclic compounds as small as toluene were also found to inhibit fibrillization. In addition, we found that substituent of benzene ring have a great influence on the inhibitory potency. Specifically, cyano, methyl and nitro groups increased the inhibitory potency. The results introduced here may contribute to future rational design of amyloid inhibitors.

  11. An Integrated Approach for the Rational Design of NanoVectors for Biomedical Imaging and Therapy

    PubMed Central

    Godin, Biana; Driessen, Wouter H.; Proneth, Bettina; Lee, Sei-Young; Srinivasan, Srimeenakshi; Rumbaut, Rolando; Arap, Wadih; Pasqualini, Renata; Ferrari, Mauro; Decuzzi, Paolo

    2013-01-01

    The use of nanoparticles for the early detection, cure and imaging of diseases has been proved already to have enormous potentials in different biomedical fields, as oncology and cardiology. A broad spectrum of nanoparticles are currently under development exhibiting differences in (i) size, ranging from few tens of nanometers to few microns; (ii) shape, from the classical spherical beads to discoidal, hemispherical, cylindrical and conical; (iii) surface functionalization, with a wide range of electrostatic charges and bio-molecule conjugations. Clearly, the library of nanoparticles generated by combining all possible sizes, shapes and surface physico-chemical properties is enormous. With such a complex scenario, an integrated approach is here proposed and described for the rational design of nanoparticle systems (nanovectors) for the intravascular delivery of therapeutic and imaging contrast agents. The proposed integrated approach combines multi-scale/multi-physics mathematical models with in-vitro assays and in-vivo intravital microscopy experiments and aims at identifying the optimal combination of size, shape and surface properties that maximize the nanovectors localization within the diseased microvasculature. PMID:20807601

  12. Phospholipid-based nonlamellar mesophases for delivery systems: bridging the gap between empirical and rational design.

    PubMed

    Martiel, Isabelle; Sagalowicz, Laurent; Mezzenga, Raffaele

    2014-07-01

    Phospholipids are ubiquitous cell membrane components and relatively well-accepted ingredients due to their natural origin. Phosphatidylcholine (PC) in particular offers a promising alternative to monoglycerides for lyotropic liquid crystalline (LLC) delivery system applications in the food, cosmetics and pharmaceutical industries, provided its strong tendency to form zero-mean curvature lamellar mesophases in water can be overcome. Higher negative curvatures are usually reached through the addition of a third lipid component, forming a ternary diagram phospholipid/water/oil. The initial part of this work summarizes the potential advantages and the challenges of phospholipid-based delivery system applications. In the next part, various ternary PC/water/oil systems are discussed, with a special emphasis on the PC/water/cyclohexane and PC/water/α-tocopherol systems. We report that R-(+)-limonene has a quantitatively similar effect as cyclohexane. The last part is devoted to the theoretical interpretation of the observed phase behaviors. A fruitful parallel is drawn with PC polymer-like reverse micelles, leading to a thermodynamic description in terms of interfacial bending energy. Investigations at the molecular level are reviewed to help in bridging the empirical and theoretical approaches. Predictive rules are finally derived from this wide-ranging overview, thereby opening the way to a future rational design of PC-based LLC delivery systems. PMID:24685272

  13. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design

    PubMed Central

    Foller Larsen, Anders; Dumat, Blaise; Wranne, Moa S.; Lawson, Christopher P.; Preus, Søren; Bood, Mattias; Gradén, Henrik; Marcus Wilhelmsson, L.; Grøtli, Morten

    2015-01-01

    Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs. PMID:26227585

  14. Rational design and controlled synthesis of Te/Bi2Te3 heterostructure nanostring composites

    NASA Astrophysics Data System (ADS)

    Zhang, Yuzhuo; Chen, Hong; Li, Zhiliang; Huang, Ting; Zheng, Shuqi

    2015-07-01

    Te/Bi2Te3 heterostructure nanostring composites composed of several Bi2Te3 nanoplates, which were perpendicularly strung together by Te nanorod, were rationally designed and synthesized via a facile solvothermal method on a large scale. The X-ray diffraction (XRD) characterization demonstrated that the Bi2Te3 nanoplates were rhombohedral phase and the Te nanorods were trigonal phase. The uniform nanostring morphologies were well characterized by scanning electron microscope (SEM) and transmission electron microscope (TEM). Detailed heterostructures were proved via energy dispersive spectrometer (EDS) and high-resolution transmission electron microscope (HRTEM). The morphology transformation from Bi2Te3 nanoplates to Te/Bi2Te3 heterostructure nanostrings could be controlled by adjusting the ratio of bismuth oxide to tellurium oxide. NaOH, serving as catalytic reduction agent and morphology controlling agent, played an important role in the synthesis of Te/Bi2Te3 heterostructure nanostrings. The reaction mechanism was also proposed to explain the formation process of the composites and the specific function of reagents in this reaction system.

  15. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design

    NASA Astrophysics Data System (ADS)

    Foller Larsen, Anders; Dumat, Blaise; Wranne, Moa S.; Lawson, Christopher P.; Preus, Søren; Bood, Mattias; Gradén, Henrik; Marcus Wilhelmsson, L.; Grøtli, Morten

    2015-07-01

    Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (ɛΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

  16. Tools for the rational design of bivalent microtubule-targeting drugs.

    PubMed

    Marangon, Jacopo; Christodoulou, Michael S; Casagrande, Fancesca V M; Tiana, Guido; Dalla Via, Lisa; Aliverti, Alessandro; Passarella, Daniele; Cappelletti, Graziella; Ricagno, Stefano

    2016-10-01

    Microtubule (MT) dynamic behaviour is an attractive drug target for chemotherapy, whose regulation by MT-stabilizing and destabilizing agents has been fruitfully applied in treating several types of cancers. MT-stabilizing agents are also emerging as potential remedies for neurodegenerative conditions, such as Alzheimer's and Parkinson's disease, although single-target drugs are not expected to fully cure these complex pathologies. Drug combination often displays enhanced efficacy with respect to mono-therapies. In particular, MT-targeting bivalent compounds (MTBCs) represent a promising class of molecules; however, surprisingly, the majority of MTBCs reported so far exhibit equal if not less efficacy than their building monomers. In order to shed light on MTBCs poor performance, we characterised through a set of complementary approaches thiocolchine (TH) and two bivalent TH-homodimers as prototype molecules. First, the binding affinities of these three molecules were assessed, then we obtained the crystallographic structure of a tubulin-TH complex. The binding affinities were interpreted in light of structural data and of molecular dynamics simulations. Finally, their effects on MT cytoskeleton and cell survival were validated on HeLa cells. The ensemble of these data provides chemical and structural considerations on how a successful rational design of MTBCs should be conceived.

  17. Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

    NASA Astrophysics Data System (ADS)

    Chen, Chun-Long; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald N.; Deyoreo, James J.

    2014-09-01

    In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic and hydrophobic interactions, with hydrophobic interactions playing the dominant role. While either strong electrostatic or hydrophobic interactions inhibit growth and reduces expression of the {104} faces, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate electrostatic interactions allow peptoids to weakly adsorb while moderate hydrophobic interactions cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of the {104} faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.

  18. Engineering of genetic control tools in Synechocystis sp. PCC 6803 using rational design techniques.

    PubMed

    Albers, Stevan C; Gallegos, Victor A; Peebles, Christie A M

    2015-12-20

    Cyanobacteria show promise as photosynthetic microbial factories capable of harnessing sunlight and CO2 to produce valuable end products, but few genetic control tools have been characterized and utilized in these organisms. To develop a suite of control elements capable of gene control at a variety of expression strengths, a library of 10 promoter-constructs were developed and built via rational design techniques by adding individual nucleotides in a step-wise manner within the -10 and -35 cis-acting regions of the tac promoter. This suite produced a dynamic range of expression strength, exhibiting a 78 fold change between the lowest expressing promoter, Psca8- and the highest expressing promoter, Psca3-2 when tested within Synechocystis sp. PCC 6803. Additionally, this study details the construction of a chemically inducible construct for use in Synechocystis that is based on the tac repressor system most commonly used in Escherichia coli. This research demonstrates the construction of a highly expressed inducible promoter that is also capable of high levels of gene repression. Upon chemical induction with IPTG, this same mutant strain was capable of exhibiting an average 24X increase in GFP expression over that of the repressed state.

  19. Rational design of novel cathode materials in solid oxide fuel cells using first-principles simulations

    NASA Astrophysics Data System (ADS)

    Choi, YongMan; Lin, M. C.; Liu, Meilin

    The search for clean and renewable sources of energy represents one of the most vital challenges facing us today. Solid oxide fuel cells (SOFCs) are among the most promising technologies for a clean and secure energy future due to their high energy efficiency and excellent fuel flexibility (e.g., direct utilization of hydrocarbons or renewable fuels). To make SOFCs economically competitive, however, development of new materials for low-temperature operation is essential. Here we report our results on a computational study to achieve rational design of SOFC cathodes with fast oxygen reduction kinetics and rapid ionic transport. Results suggest that surface catalytic properties are strongly correlated with the bulk transport properties in several material systems with the formula of La 0.5Sr 0.5BO 2.75 (where B = Cr, Mn, Fe, or Co). The predictions seem to agree qualitatively with available experimental results on these materials. This computational screening technique may guide us to search for high-efficiency cathode materials for a new generation of SOFCs.

  20. Surface Termination of M1 Phase and Rational Design of Propane Ammoxidation Catalysts

    SciTech Connect

    Guliants, Vadim

    2015-02-16

    This final report describes major accomplishments in this research project which has demonstrated that the M1 phase is the only crystalline phase required for propane ammoxidation to acrylonitrile and that a surface monolayer terminating the ab planes of the M1 phase is responsible for their activity and selectivity in this reaction. Fundamental studies of the topmost surface chemistry and mechanism of propane ammoxidation over the Mo-V-(Te,Sb)-(Nb,Ta)-O M1 and M2 phases resulted in the development of quantitative understanding of the surface molecular structure – reactivity relationships for this unique catalytic system. These oxides possess unique catalytic properties among mixed metal oxides, because they selectively catalyze three alkane transformation reactions, namely propane ammoxidation to acrylonitrile, propane oxidation to acrylic acid and ethane oxidative dehydrogenation, all of considerable economic significance. Therefore, the larger goal of this research was to expand this catalysis to other alkanes of commercial interest, and more broadly, demonstrate successful approaches to rational design of improved catalysts that can be applied to other selective (amm)oxidation processes.

  1. Engineering of genetic control tools in Synechocystis sp. PCC 6803 using rational design techniques.

    PubMed

    Albers, Stevan C; Gallegos, Victor A; Peebles, Christie A M

    2015-12-20

    Cyanobacteria show promise as photosynthetic microbial factories capable of harnessing sunlight and CO2 to produce valuable end products, but few genetic control tools have been characterized and utilized in these organisms. To develop a suite of control elements capable of gene control at a variety of expression strengths, a library of 10 promoter-constructs were developed and built via rational design techniques by adding individual nucleotides in a step-wise manner within the -10 and -35 cis-acting regions of the tac promoter. This suite produced a dynamic range of expression strength, exhibiting a 78 fold change between the lowest expressing promoter, Psca8- and the highest expressing promoter, Psca3-2 when tested within Synechocystis sp. PCC 6803. Additionally, this study details the construction of a chemically inducible construct for use in Synechocystis that is based on the tac repressor system most commonly used in Escherichia coli. This research demonstrates the construction of a highly expressed inducible promoter that is also capable of high levels of gene repression. Upon chemical induction with IPTG, this same mutant strain was capable of exhibiting an average 24X increase in GFP expression over that of the repressed state. PMID:26450561

  2. Strongly hyperpolarized gas from parahydrogen by rational design of ligand-capped nanoparticles

    PubMed Central

    Sharma, Ramesh; Bouchard, Louis-S

    2012-01-01

    The production of hyperpolarized fluids in continuous mode would broaden substantially the range of applications in chemistry, materials science, and biomedicine. Here we show that the rational design of a heterogeneous catalyst based on a judicious choice of metal type, nanoparticle size and surface decoration with appropriate ligands leads to highly efficient pairwise addition of dihydrogen across an unsaturated bond. This is demonstrated in a parahydrogen-induced polarization (PHIP) experiment by a 508-fold enhancement (±78) of a CH3 proton signal and a corresponding 1219-fold enhancement (±187) of a CH2 proton signal using nuclear magnetic resonance (1H-NMR). In contrast, bulk metal catalyst does not show this effect due to randomization of reacting dihydrogen. Our approach results in the largest gas-phase NMR signal enhancement by PHIP known to date. Sensitivity-enhanced NMR with this technique could be used to image microfluidic reactions in-situ, to probe nonequilibrium thermodynamics or for the study of metabolic reactions. PMID:22355789

  3. Tumor suppression by a rationally designed reversible inhibitor of methionine aminopeptidase-2.

    PubMed

    Wang, Jieyi; Sheppard, George S; Lou, Pingping; Kawai, Megumi; BaMaung, Nwe; Erickson, Scott A; Tucker-Garcia, Lora; Park, Chang; Bouska, Jennifer; Wang, Yi-Chun; Frost, David; Tapang, Paul; Albert, Daniel H; Morgan, Sherry J; Morowitz, Michael; Shusterman, Suzanne; Maris, John M; Lesniewski, Rick; Henkin, Jack

    2003-11-15

    Methionine aminopeptidase (MetAP)-2 has been suggested as a novel target for cancer therapy because the anticancer agent TNP-470 irreversibly inactivates the catalytic activity of this enzyme. However, the importance of MetAP2 in cell growth and tumor progression was uncertain because previous data were based on the chemically reactive TNP-470. Here we show that a rationally designed reversible MetAP2 inhibitor, A-357300, suppresses tumor growth preclinically without the toxicities observed with TNP-470. We have synthesized this bestatin-type MetAP2 inhibitor with the aid of crystal structures of the enzyme-inhibitor complexes and parallel synthesis. A-357300 induces cytostasis by cell cycle arrest at the G(1) phase selectively in endothelial cells and in a subset of tumor cells, but not in most primary cells of nonendothelial type. A-357300 inhibits angiogenesis both in vitro and in vivo and shows potent antitumor efficacy in carcinoma, sarcoma, and neuroblastoma murine models. These data affirm that MetAP2 plays a pivotal role in cell growth and establish that reversible MetAP2 inhibitors are promising novel cancer therapeutic agents.

  4. Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers

    PubMed Central

    Araya-Durán, Ingrid; Varas-Concha, Ignacio; Almonacid, Daniel Eduardo; González-Nilo, Fernando Danilo

    2015-01-01

    Biomimetics, or the use of principles of Nature for developing new materials, is a paradigm that could help Nanomedicine tremendously. One of the current challenges in Nanomedicine is the rational design of new efficient and safer gene carriers. Poly(amidoamine) (PAMAM) dendrimers are a well-known class of nanoparticles, extensively used as non-viral nucleic acid carriers, due to their positively charged end-groups. Yet, there are still several aspects that can be improved for their successful application in in vitro and in vivo systems, including their affinity for nucleic acids as well as lowering their cytotoxicity. In the search of new functional groups that could be used as new dendrimer-reactive groups, we followed a biomimetic approach to determine the amino acids with highest prevalence in protein-DNA interactions. Then we introduced them individually as terminal groups of dendrimers, generating a new class of nanoparticles. Molecular dynamics studies of two systems: PAMAM-Arg and PAMAM-Lys were also performed in order to describe the formation of complexes with DNA. Results confirmed that the introduction of amino acids as terminal groups in a dendrimer increases their affinity for DNA and the interactions in the complexes were characterized at atomic level. We end up by briefly discussing additional modifications that can be made to PAMAM dendrimers to turned them into promising new gene carriers. PMID:26382062

  5. 25th Anniversary Article: Rational Design and Applications of Hydrogels in Regenerative Medicine

    PubMed Central

    Annabi, Nasim; Tamayol, Ali; Uquillas, Jorge Alfredo; Akbari, Mohsen; Bertassoni, Luiz E.; Cha, Chaenyung; Camci-Unal, Gulden; Dokmeci, Mehmet R.

    2014-01-01

    Hydrogels are hydrophilic polymer-based materials with high water content and physical characteristics that resemble the native extracellular matrix. Because of their remarkable properties, hydrogel systems are used for a wide range of biomedical applications, such as three-dimensional (3D) matrices for tissue engineering, drug-delivery vehicles, composite biomaterials, and as injectable fillers in minimally invasive surgeries. In addition, the rational design of hydrogels with controlled physical and biological properties can be used to modulate cellular functionality and tissue morphogenesis. Here, the development of advanced hydrogels with tunable physiochemical properties is highlighted, with particular emphasis on elastomeric, light-sensitive, composite, and shape-memory hydrogels. Emerging technologies developed over the past decade to control hydrogel architecture are also discussed and a number of potential applications and challenges in the utilization of hydrogels in regenerative medicine are reviewed. It is anticipated that the continued development of sophisticated hydrogels will result in clinical applications that will improve patient care and quality of life. PMID:24741694

  6. Rational design of metal-organic electronic devices: A computational perspective

    NASA Astrophysics Data System (ADS)

    Chilukuri, Bhaskar

    engineers to choose the appropriate metal electrodes considering the chemical interactions at the interface. Additionally, the calculations performed on the interfaces provided valuable insight into binding energies, charge redistribution, change in the energy levels, dipole formation, etc., which are important parameters to consider while fabricating an electronic device. The research described in this dissertation highlights the application of unique computational modeling methods at different levels of theory to guide the experimental chemists and device engineers toward a rational design of transition metal based electronic devices with low cost and high performance.

  7. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes.

    PubMed

    Pollock, Jonathan; Borkin, Dmitry; Lund, George; Purohit, Trupta; Dyguda-Kazimierowicz, Edyta; Grembecka, Jolanta; Cierpicki, Tomasz

    2015-09-24

    Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein-ligand complexes. Such fluorine-backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin-MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes with menin. We found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin-MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine-backbone interactions in protein-ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin-MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine-backbone interactions may represent a particularly attractive approach to improve inhibitors of protein-protein interactions.

  8. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes

    PubMed Central

    2015-01-01

    Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein–ligand complexes. Such fluorine–backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin–MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes with menin. We found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin–MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine–backbone interactions in protein–ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin–MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine–backbone interactions may represent a particularly attractive approach to improve inhibitors of protein–protein interactions. PMID:26288158

  9. Rational design of allosteric-inhibition sites in classical protein tyrosine phosphatases

    PubMed Central

    Chio, Cynthia M.; Yu, Xiaoling; Bishop, Anthony C.

    2015-01-01

    Protein tyrosine phosphatases (PTPs), which catalyze the dephosphorylation of phosphotyrosine in protein substrates, are critical regulators of metazoan cell signaling and have emerged as potential drug targets for a range of human diseases. Strategies for chemically targeting the function of individual PTPs selectively could serve to elucidate the signaling roles of these enzymes and would potentially expedite validation of the therapeutic promise of PTP inhibitors. Here we report a novel strategy for the design of non-natural allosteric-inhibition sites in PTPs; these sites, which can be introduced into target PTPs through protein engineering, serve to sensitize target PTPs to potent and selective inhibition by a biarsenical small molecule. Building on the recent discovery of a naturally occurring cryptic allosteric site in wild-type Src-homology-2 domain containing PTP (Shp2) that can be targeted by biarsenical compounds, we hypothesized that Shp2’s unusual sensitivity to biarsenicals could be strengthened through rational design and that the Shp2-specific site could serve as a blueprint for the introduction of non-natural inhibitor sensitivity in other PTPs. Indeed, we show here that the strategic introduction of a cysteine residue at a position removed from the Shp2 active site can serve to increase the potency and selectivity of the interaction between Shp2’s allosteric site and the biarsenical inhibitor. Moreover, we find that “Shp2-like” allosteric sites can be installed de novo in PTP enzymes that do not possess naturally occurring sensitivity to biarsenical compounds. Using primary-sequence alignments to guide our enzyme engineering, we have successfully introduced allosteric-inhibition sites in four classical PTPs—PTP1B, PTPH-1, FAP-1, and HePTP—from four different PTP subfamilies, suggesting that our sensitization approach can likely be applied widely across the classical PTP family to generate biarsenical-responsive PTPs. PMID:25828055

  10. Rational design of a minimal size sensor array for metal ion detection.

    PubMed

    Palacios, Manuel A; Wang, Zhuo; Montes, Victor A; Zyryanov, Grigory V; Anzenbacher, Pavel

    2008-08-01

    The focus of this study was to demonstrate that, in the luminescent sensors, the signal transduction may possibly be the most important part in the sensing process. Rational design of fluorescent sensor arrays for cations utilizing extended conjugated chromophores attached to 8-hydroxyquinoline is reported. All of the optical sensors utilized in the arrays comprise the same 8-hydroxyquinoline (8-HQ) receptor and various conjugated chromophores to yield a different response to various metal cations. This is because the conjugated chromophores attached to the receptor are partially quenched in their resting state, and upon the cation coordination by the 8-HQ, the resulting metalloquinolinolate complex displays a change in fluorescence. A delicate balance of conjugation, fluorescence enhancement, energy transfer, and a heavy metal quenching effect results in a fingerprint-like pattern of responses for each sensor-cation complex. Principal component analysis (PCA) and linear discriminant analysis (LDA) are used to demonstrate the contribution of individual sensors within the array, information that may be used to design sensor arrays with the smallest number of sensor elements. This approach allows discriminating between 10 cations by as few as two or even one sensor element. Examples of arrays comprising various numbers of sensor elements and their utility in qualitative identification of Ca(2+), Mg(2+), Cd(2+), Hg(2+), Co(2+), Zn(2+), Cu(2+), Ni(2+), Al(3+), and Ga(3+) ions are presented. A two-member array was found to identify 11 analytes with 100% accuracy. Also the best two of the sensors were tested alone and both were found to be able to discriminate among the samples with 99% and 96% accuracy, respectively. To illustrate the utility of this approach to a real-world application, identification of enhanced soft drinks based on their Ca(2+), Mg(2+), and Zn(2+) cation content was performed. The same approach to reducing array elements was used to construct three

  11. Intensive mutagenesis of the nisin hinge leads to the rational design of enhanced derivatives.

    PubMed

    Healy, Brian; Field, Des; O'Connor, Paula M; Hill, Colin; Cotter, Paul D; Ross, R Paul

    2013-01-01

    Nisin A is the most extensively studied lantibiotic and has been used as a preservative by the food industry since 1953. This 34 amino acid peptide contains three dehydrated amino acids and five thioether rings. These rings, resulting from one lanthionine and four methyllanthionine bridges, confer the peptide with its unique structure. Nisin A has two mechanisms of action, with the N-terminal domain of the peptide inhibiting cell wall synthesis through lipid II binding and the C-terminal domain responsible for pore-formation. The focus of this study is the three amino acid 'hinge' region (N 20, M 21 and K 22) which separates these two domains and allows for conformational flexibility. As all lantibiotics are gene encoded, novel variants can be generated through manipulation of the corresponding gene. A number of derivatives in which the hinge region was altered have previously been shown to possess enhanced antimicrobial activity. Here we take this approach further by employing simultaneous, indiscriminate site-saturation mutagenesis of all three hinge residues to create a novel bank of nisin derivative producers. Screening of this bank revealed that producers of peptides with hinge regions consisting of AAK, NAI and SLS displayed enhanced bioactivity against a variety of targets. These and other results suggested a preference for small, chiral amino acids within the hinge region, leading to the design and creation of producers of peptides with hinges consisting of AAA and SAA. These producers, and the corresponding peptides, exhibited enhanced bioactivity against Lactococcus lactis HP, Streptococcus agalactiae ATCC 13813, Mycobacterium smegmatis MC2155 and Staphylococcus aureus RF122 and thus represent the first example of nisin derivatives that possess enhanced activity as a consequence of rational design. PMID:24244524

  12. The management of snake bite.

    PubMed

    Reid, H A; Theakston, R D

    1983-01-01

    The present article reviews current knowledge on the epidemiology, pathophysiology, and treatment of snake bite, with particular reference to the situation in developing countries. There is little reliable information on the incidence of snake bite in many parts of the world, and epidemiological studies are needed, using enzyme-linked immunosorbent assay to identify and quantify serum levels of venom antigen and antibody. The pathophysiology and clinical features of envenoming by medically important snakes are discussed. Antivenom, if used correctly, can reverse systemic poisoning even if given days after the bite. It is therefore wise to wait for the appearance of signs of systemic poisoning before administering antivenom, rather than using it routinely. WHO has designated the Liverpool School of Tropical Medicine as a Collaborating Centre for the Control of Antivenoms, and this Centre now holds a collection of reference venoms from several important snake species. Characterization of these and of standard antivenoms should significantly improve the management of snake bite throughout the world. PMID:6609008

  13. Rational design of surface/interface chemistry for quantitative in vivo monitoring of brain chemistry.

    PubMed

    Zhang, Meining; Yu, Ping; Mao, Lanqun

    2012-04-17

    To understand the molecular basis of brain functions, researchers would like to be able to quantitatively monitor the levels of neurochemicals in the extracellular fluid in vivo. However, the chemical and physiological complexity of the central nervous system (CNS) presents challenges for the development of these analytical methods. This Account describes the rational design and careful construction of electrodes and nanoparticles with specific surface/interface chemistry for quantitative in vivo monitoring of brain chemistry. We used the redox nature of neurochemicals at the electrode/electrolyte interface to establish a basis for monitoring specific neurochemicals. Carbon nanotubes provide an electrode/electrolyte interface for the selective oxidation of ascorbate, and we have developed both in vivo voltammetry and an online electrochemical detecting system for continuously monitoring this molecule in the CNS. Although Ca(2+) and Mg(2+) are involved in a number of neurochemical signaling processes, they are still difficult to detect in the CNS. These divalent cations can enhance electrocatalytic oxidation of NADH at an electrode modified with toluidine blue O. We used this property to develop online electrochemical detection systems for simultaneous measurements of Ca(2+) and Mg(2+) and for continuous selective monitoring of Mg(2+) in the CNS. We have also harnessed biological schemes for neurosensing in the brain to design other monitoring systems. By taking advantage of the distinct reaction properties of dopamine (DA), we have developed a nonoxidative mechanism for DA sensing and a system that can potentially be used for continuously sensing of DA release. Using "artificial peroxidase" (Prussian blue) to replace a natural peroxidase (horseradish peroxidase, HRP), our online system can simultaneously detect basal levels of glucose and lactate. By substituting oxidases with dehydrogenases, we have used enzyme-based biosensing schemes to develop a physiologically

  14. Rational design, synthesis, and evaluation of tetrahydroxamic acid chelators for stable complexation of zirconium(IV).

    PubMed

    Guérard, François; Lee, Yong-Sok; Brechbiel, Martin W

    2014-05-01

    Metals of interest for biomedical applications often need to be complexed and associated in a stable manner with a targeting agent before use. Whereas the fundamentals of most transition-metal complexation processes have been thoroughly studied, the complexation of Zr(IV) has been somewhat neglected. This metal has received growing attention in recent years, especially in nuclear medicine, with the use of (89) Zr, which a β(+) -emitter with near ideal characteristics for cancer imaging. However, the best chelating agent known for this radionuclide is the trishydroxamate desferrioxamine B (DFB), the Zr(IV) complex of which exhibits suboptimal stability, resulting in the progressive release of (89) Zr in vivo. Based on a recent report demonstrating the higher thermodynamic stability of the tetrahydroxamate complexes of Zr(IV) compared with the trishydroxamate complexes analogues to DFB, we designed a series of tetrahydroxamic acids of varying geometries for improved complexation of this metal. Three macrocycles differing in their cavity size (28 to 36-membered rings) were synthesized by using a ring-closing metathesis strategy, as well as their acyclic analogues. A solution study with (89) Zr showed the complexation to be more effective with increasing cavity size. Evaluation of the kinetic inertness of these new complexes in ethylenediaminetetraacetic acid (EDTA) solution showed significantly improved stabilities of the larger chelates compared with (89) Zr-DFB, whereas the smaller complexes suffered from insufficient stabilities. These results were rationalized by a quantum chemical study. The lower stability of the smaller chelates was attributed to ring strain, whereas the better stability of the larger cyclic complexes was explained by the macrocyclic effect and by the structural rigidity. Overall, these new chelating agents open new perspectives for the safe and efficient use of (89) Zr in nuclear imaging, with the best chelators providing dramatically

  15. Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction.

    PubMed

    Endoh, Tamaki; Sugimoto, Naoki

    2015-08-01

    Conformational transitions of biomolecules in response to specific stimuli control many biological processes. In natural functional RNA switches, often called riboswitches, a particular RNA structure that has a suppressive or facilitative effect on gene expression transitions to an alternative structure with the opposite effect upon binding of a specific metabolite to the aptamer region. Stability of RNA secondary structure (-ΔG°) can be predicted based on thermodynamic parameters and is easily tuned by changes in nucleobases. We envisioned that tuning of a functional RNA switch that causes an allosteric interaction between an RNA and a peptide would be possible based on a predicted switching energy (ΔΔG°) that corresponds to the energy difference between the RNA secondary structure before (-ΔG°before) and after (-ΔG°after) the RNA conformational transition. We first selected functional RNA switches responsive to neomycin with predicted ΔΔG° values ranging from 5.6 to 12.2 kcal mol(-1). We then demonstrated a simple strategy to rationally convert the functional RNA switch to switches responsive to natural metabolites thiamine pyrophosphate, S-adenosyl methionine, and adenine based on the predicted ΔΔG° values. The ΔΔG° values of the designed RNA switches proportionally correlated with interaction energy (ΔG°interaction) between the RNA and peptide, and we were able to tune the sensitivity of the RNA switches for the trigger molecule. The strategy demonstrated here will be generally applicable for construction of functional RNA switches and biosensors in which mechanisms are based on conformational transition of nucleic acids.

  16. Improving the Thermostability of Acidic Pullulanase from Bacillus naganoensis by Rational Design

    PubMed Central

    Lv, Jinzhi; Li, Qingbin; Tian, Jian; Wu, Ningfeng

    2016-01-01

    Pullulanase (EC 3.2.1.41) plays an important role in the specific hydrolysis of branch points in amylopectin. Enhancing its thermostability is required for its industrial application. In this study, rational protein design was used to improve the thermostability of PulB from Bacillus naganoensis (AB231790.1), which has strong enzymatic properties. Three positive single-site mutants (PulB-D328H, PulB-N387D, and PulB-A414P) were selected from six mutants. After incubation at 65°C for 5 min, the residual activities of PulB-D328H, PulB-N387D, and PulB-A414P were 4.5-, 1.7-, and 1.47-fold higher than PulB-WT, and their Tm values (the temperature at which half protein molecule denature) were 1.8°C, 0.4°C, and 0.9°C higher than PulB-WT, respectively. Then the final combined mutant PulB-328/387/414 was constructed. The t1/2 of it was 12.9-fold longer than that of PulB-WT at 65°C and the total increase in Tm of it (5.0°C) was almost 60% greater than the sum of individual increases (3.1°C). In addition, kinetic studies revealed that the kcat and the kcat/Km of PulB-328/387/414 increased by 38.8% and 12.9%. The remarkable improvement in thermostability and the high catalytic efficiency of PulB-328/387/414 make it suitable for industrial applications. PMID:27764201

  17. A rationally designed tyrosine hydroxylase DNA vaccine induces specific antineuroblastoma immunity.

    PubMed

    Huebener, Nicole; Fest, Stefan; Strandsby, Anne; Michalsky, Elke; Preissner, Robert; Zeng, Yan; Gaedicke, Gerhard; Lode, Holger N

    2008-07-01

    Therapeutic vaccination against tumor antigens without induction of autoimmunity remains a major challenge in cancer immunotherapy. Here, we show for the first time effective therapeutic vaccination followed by suppression of established spontaneous neuroblastoma metastases using a tyrosine hydroxylase (TH) DNA minigene vaccine. We identified three novel mouse TH (mTH3) derived peptides with high predicted binding affinity to MHC class I antigen H2-K(k) according to the prediction program SYFPEITHI and computer modeling of epitopes into the MHC class I antigen binding groove. Subsequently, a DNA minigene vaccine was generated based on the expression vector pCMV-F3Ub encoding mutated ubiquitin (Gly(76) to Ala(76)) and mTH3. Prophylactic and therapeutic efficacies of this vaccine were established following oral delivery with attenuated Salmonella typhimurium SL7207. Only mice immunized with mTH3 were free of spontaneous liver metastases. This effect was clearly dependent on ubiquitin and high affinity of the mTH epitopes to MHC class I antigens. Specifically, we showed a crucial role for minigene expression as a stable ubiquitin-Ala(76) fusion peptide for vaccine efficacy. The immune response following the mTH3 DNA minigene vaccination was mediated by CD8(+) T cells as indicated by infiltration of primary tumors and TH-specific cytolytic activity in vitro. Importantly, no cell infiltration was detectable in TH-expressing adrenal medulla, indicating the absence of autoimmunity. In summary, we show effective therapeutic vaccination against neuroblastoma with a novel rationally designed TH minigene vaccine without induction of autoimmunity providing an important baseline for future clinical application of this strategy.

  18. Towards Rational Design of a Toxoid Vaccine against the Heat-Stable Toxin of Escherichia coli.

    PubMed

    Taxt, Arne M; Diaz, Yuleima; Aasland, Rein; Clements, John D; Nataro, James P; Sommerfelt, Halvor; Puntervoll, Pål

    2016-04-01

    Enterotoxigenic Escherichia coli(ETEC) is an important cause of diarrheal disease and death in children <5 years old. ETEC strains that express the heat-stable toxin (ST), with or without the heat-labile toxin, are among the four most important diarrhea-causing pathogens. This makes ST an attractive target for an ETEC vaccine. An ST vaccine should be nontoxic and elicit an immune response that neutralizes native ST without cross-reacting with the human endogenous guanylate cyclase C receptor ligands. To identify variants of ST with no or low toxicity, we screened a library of all 361 possible single-amino-acid mutant forms of ST by using the T84 cell assay. Moreover, we identified mutant variants with intact epitopes by screening for the ability to bind neutralizing anti-ST antibodies. ST mutant forms with no or low toxicity and intact epitopes are termed toxoid candidates, and the top 30 candidates all had mutations of residues A14, N12, and L9. The identification of nontoxic variants of L9 strongly suggests that it is a novel receptor-interacting residue, in addition to the previously identified N12, P13, and A14 residues. The screens also allowed us to map the epitopes of three neutralizing monoclonal antibodies, one of which cross-reacts with the human ligand uroguanylin. The common dominant epitope residue for all non-cross-reacting antibodies was Y19. Our results suggest that it should be possible to rationally design ST toxoids that elicit neutralizing immune responses against ST with minimal risk of immunological cross-reactivity.

  19. Rational design of on-chip refractive index sensors based on lattice plasmon resonances (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Lin, Linhan; Zheng, Yuebing

    2015-08-01

    Lattice plasmon resonances (LPRs), which originate from the plasmonic-photonic coupling in gold or silver nanoparticle arrays, possess ultra-narrow linewidth by suppressing the radiative damping and provide the possibility to develop the plasmonic sensors with high figure of merit (FOM). However, the plasmonic-photonic coupling is greatly suppressed when the nanoparticles are immobilized on substrates because the diffraction orders are cut off at the nanoparticle-substrate interfaces. Here, we develop the rational design of LPR structures for the high-performance, on-chip plasmonic sensors based on both orthogonal and parallel coupling. Our finite-difference time-domain simulations in the core/shell SiO2/Au nanocylinder arrays (NCAs) reveal that new modes of localized surface plasmon resonances (LSPRs) show up when the aspect ratio of the NCAs is increased. The height-induced LSPRs couple with the superstrate diffraction orders to generate the robust LPRs in asymmetric environment. The high wavelength sensitivity and narrow linewidth in these LPRs lead to the plasmonic sensors with high FOM and high signal-to-noise ratio (SNR). Wide working wavelengths from visible to near-infrared are also achieved by tuning the parameters of the NCAs. Moreover, the wide detection range of refractive index is obtained in the parallel LPR structure. The electromagnetic field distributions in the NCAs demonstrate the height-enabled tunability of the plasmonic "hot spots" at the sub-nanoparticles resolution and the coupling between these "hot spots" with the superstrate diffraction waves, which are responsible for the high performance LPRs-based on-chip refractive index sensors.

  20. Towards Rational Design of a Toxoid Vaccine against the Heat-Stable Toxin of Escherichia coli

    PubMed Central

    Taxt, Arne M.; Diaz, Yuleima; Aasland, Rein; Clements, John D.; Nataro, James P.; Sommerfelt, Halvor

    2016-01-01

    Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrheal disease and death in children <5 years old. ETEC strains that express the heat-stable toxin (ST), with or without the heat-labile toxin, are among the four most important diarrhea-causing pathogens. This makes ST an attractive target for an ETEC vaccine. An ST vaccine should be nontoxic and elicit an immune response that neutralizes native ST without cross-reacting with the human endogenous guanylate cyclase C receptor ligands. To identify variants of ST with no or low toxicity, we screened a library of all 361 possible single-amino-acid mutant forms of ST by using the T84 cell assay. Moreover, we identified mutant variants with intact epitopes by screening for the ability to bind neutralizing anti-ST antibodies. ST mutant forms with no or low toxicity and intact epitopes are termed toxoid candidates, and the top 30 candidates all had mutations of residues A14, N12, and L9. The identification of nontoxic variants of L9 strongly suggests that it is a novel receptor-interacting residue, in addition to the previously identified N12, P13, and A14 residues. The screens also allowed us to map the epitopes of three neutralizing monoclonal antibodies, one of which cross-reacts with the human ligand uroguanylin. The common dominant epitope residue for all non-cross-reacting antibodies was Y19. Our results suggest that it should be possible to rationally design ST toxoids that elicit neutralizing immune responses against ST with minimal risk of immunological cross-reactivity. PMID:26883587

  1. Light-driven coordination-induced spin-state switching: rational design of photodissociable ligands.

    PubMed

    Thies, Steffen; Sell, Hanno; Bornholdt, Claudia; Schütt, Christian; Köhler, Felix; Tuczek, Felix; Herges, Rainer

    2012-12-14

    The bistability of spin states (e.g., spin crossover) in bulk materials is well investigated and understood. We recently extended spin-state switching to isolated molecules at room temperature (light-driven coordination-induced spin-state switching, or LD-CISSS). Whereas bistability and hysteresis in conventional spin-crossover materials are caused by cooperative effects in the crystal lattice, spin switching in LD-CISSS is achieved by reversibly changing the coordination number of a metal complex by means of a photochromic ligand that binds in one configuration but dissociates in the other form. We present mathematical proof that the maximum efficiency in property switching by such a photodissociable ligand (PDL) is only dependent on the ratio of the association constants of both configurations. Rational design by using DFT calculations was applied to develop a photoswitchable ligand with a high switching efficiency. The starting point was a nickel-porphyrin as the transition-metal complex and 3-phenylazopyridine as the photodissociable ligand. Calculations and experiments were performed in two iterative steps to find a substitution pattern at the phenylazopyridine ligand that provided optimum performance. Following this strategy, we synthesized an improved photodissociable ligand that binds to the Ni-porphyrin with an association constant that is 5.36 times higher in its trans form than in the cis form. The switching efficiency between the diamagnetic and paramagnetic state is efficient as well (72% paramagnetic Ni-porphyrin after irradiation at 365 nm, 32% paramagnetic species after irradiation at 440 nm). Potential applications arise from the fact that the LD-CISSS approach for the first time allows reversible switching of the magnetic susceptibility of a homogeneous solution. Photoswitchable contrast agents for magnetic resonance imaging and light-controlled magnetic levitation are conceivable applications. PMID:23090862

  2. Rational design and applications of a Rac GTPase-specific small molecule inhibitor.

    PubMed

    Akbar, Huzoor; Cancelas, Jose; Williams, David A; Zheng, Jie; Zheng, Yi

    2006-01-01

    Rac GTPases are involved in the regulation of multiple cell functions and have been implicated in the pathology of certain human diseases. Dominant negative mutants of Rac have been the tool of choice in studying Rac function in cells. Given the difficulty of introducing high concentrations of the Rac mutants into primary cells and nonspecific effects of the mutants on Rho guanine nucleotide exchange factor (GEF) activities, it is desirable to develop small molecule inhibitors that could specifically inhibit Rac activities. Here we describe the rational design, characterization, and applications of a first-generation Rac-specific small molecule inhibitor. On the basis of the structure-function information of Rac interaction with GEFs, in a computer-based virtual screening we have identified NSC23766, a highly soluble and membrane permeable compound, as a specific inhibitor of a subset of GEF binding to Rac and, therefore, Rac activation by these GEFs. In fibroblast cells, NSC23766 inhibited Rac1 GTP-loading without affecting Cdc42 or RhoA activity and suppressed cell proliferation induced by a Rac GEF Tiam1. It has little effect on cell growth induced by a constitutively active Rac1 mutant. In addition, NSC23766 inhibited: (1) the anchorage-independent growth and invasion phenotypes of human prostate cancer PC-3 cells; (2) Rac activation and Rac-dependent aggregation of platelets stimulated by thrombin; and (3) Rac1 and Rac2 activities of hematopoietic stem/progenitor cells and induced their mobilization from mouse bone marrow to peripheral blood. Thus, NSC23766 is a lead small molecule inhibitor of Rac activity and could be useful for studying Rac-mediated cellular functions and for modulating pathological conditions in which Rac-deregulation may play a role.

  3. Dangerous snakes, deadly snakes and medically important snakes

    PubMed Central

    2013-01-01

    This correspondence argues that the dangerousness of a venomous snake species is not solely determined by the venom characteristics or the lethality of the snake, and recognizes that medical importance comprises a key variable as well. The medical importance of a snake is determined by several factors – including frequency of medical attention after a bite, local or systemic envenomation provoked by the bite, fatal bites, long term consequences, availability of antivenom therapy as well as the size of the population at risk – that may vary from one region to another. PMID:24099013

  4. Rational design of a minimal size sensor array for metal ion detection.

    PubMed

    Palacios, Manuel A; Wang, Zhuo; Montes, Victor A; Zyryanov, Grigory V; Anzenbacher, Pavel

    2008-08-01

    The focus of this study was to demonstrate that, in the luminescent sensors, the signal transduction may possibly be the most important part in the sensing process. Rational design of fluorescent sensor arrays for cations utilizing extended conjugated chromophores attached to 8-hydroxyquinoline is reported. All of the optical sensors utilized in the arrays comprise the same 8-hydroxyquinoline (8-HQ) receptor and various conjugated chromophores to yield a different response to various metal cations. This is because the conjugated chromophores attached to the receptor are partially quenched in their resting state, and upon the cation coordination by the 8-HQ, the resulting metalloquinolinolate complex displays a change in fluorescence. A delicate balance of conjugation, fluorescence enhancement, energy transfer, and a heavy metal quenching effect results in a fingerprint-like pattern of responses for each sensor-cation complex. Principal component analysis (PCA) and linear discriminant analysis (LDA) are used to demonstrate the contribution of individual sensors within the array, information that may be used to design sensor arrays with the smallest number of sensor elements. This approach allows discriminating between 10 cations by as few as two or even one sensor element. Examples of arrays comprising various numbers of sensor elements and their utility in qualitative identification of Ca(2+), Mg(2+), Cd(2+), Hg(2+), Co(2+), Zn(2+), Cu(2+), Ni(2+), Al(3+), and Ga(3+) ions are presented. A two-member array was found to identify 11 analytes with 100% accuracy. Also the best two of the sensors were tested alone and both were found to be able to discriminate among the samples with 99% and 96% accuracy, respectively. To illustrate the utility of this approach to a real-world application, identification of enhanced soft drinks based on their Ca(2+), Mg(2+), and Zn(2+) cation content was performed. The same approach to reducing array elements was used to construct three

  5. Rational Ligand Design for U(VI) and Pu(IV)

    SciTech Connect

    Szigethy, Geza

    2009-08-12

    Nuclear power is an attractive alternative to hydrocarbon-based energy production at a time when moving away from carbon-producing processes is widely accepted as a significant developmental need. Hence, the radioactive actinide power sources for this industry are necessarily becoming more widespread, which is accompanied by the increased risk of exposure to both biological and environmental systems. This, in turn, requires the development of technology designed to remove such radioactive threats efficiently and selectively from contaminated material, whether that be contained nuclear waste streams or the human body. Raymond and coworkers (University of California, Berkeley) have for decades investigated the interaction of biologically-inspired, hard Lewis-base ligands with high-valent, early-actinide cations. It has been established that such ligands bind strongly to the hard Lewis-acidic early actinides, and many poly-bidentate ligands have been developed and shown to be effective chelators of actinide contaminants in vivo. Work reported herein explores the effect of ligand geometry on the linear U(IV) dioxo dication (uranyl, UO2 2+). The goal is to utilize rational ligand design to develop ligands that exhibit shape selectivity towards linear dioxo cations and provides thermodynamically favorable binding interactions. The uranyl complexes with a series of tetradentate 3-hydroxy-pyridin-2-one (3,2-HOPO) ligands were studied in both the crystalline state as well as in solution. Despite significant geometric differences, the uranyl affinities of these ligands vary only slightly but are better than DTPA, the only FDA-approved chelation therapy for actinide contamination. The terepthalamide (TAM) moiety was combined into tris-beidentate ligands with 1,2- and 3,2-HOPO moieties were combined into hexadentate ligands whose structural preferences and solution thermodynamics were measured with the uranyl cation. In addition to achieving coordinative

  6. Asymmetric Homoenolate Additions to Acyl Phosphonates through Rational Design of a Tailored N-Heterocyclic Carbene Catalyst

    PubMed Central

    Jang, Ki Po; Hutson, Gerri E.; Johnston, Ryne C.; McCusker, Elizabeth O.; Cheong, Paul H.-Y.; Scheidt, Karl A.

    2014-01-01

    A highly selective NHC-catalyzed synthesis of γ-butyrolactones from the fusion of enals and α-ketophosphonates has been developed. Computational modeling of competing transition states was employed to guide a rational design strategy and achieve enhanced levels of enantioselectivity with a new tailored C1-symmetric biaryl saturated imidazolium-derived NHC catalyst. This new annulation is compatible with a wide range of acyl phosphonates and α,β-unsaturated aldehydes. PMID:24299299

  7. A multi-factors rational design strategy for enhancing the thermostability of Escherichia coli AppA phytase.

    PubMed

    Fei, Baojin; Xu, Hui; Cao, Yu; Ma, Shuhan; Guo, Hongxiu; Song, Tao; Qiao, Dairong; Cao, Yi

    2013-05-01

    Despite recent advances in our understanding of the importance of protein surface properties for protein thermostability,there are seldom studies on multi-factors rational design strategy, so a more scientific, simple and effective rational strategy is urgent for protein engineering. Here, we first attempted to use a three-factors rational design strategy combining three common structural features, protein flexibility, protein surface, and salt bridges. Escherichia coli AppA phytase was used as a model enzyme to improve its thermostability. Moreover, the structure and enzyme features of the thermostable mutants designed by our strategy were analyzed roundly. For the single mutants, two (Q206E and Y311K), in five exhibited thermostable property with a higher success rate of prediction (40 %). For the multiple mutants, the themostable sites were combined with another site, I427L, we obtained by directed evolution, Q206E/I427L, Y311K/I427L, and Q206E/Y311K/I427L, all exhibited thermostable property. The Y311K/I427L doubled thermostability (61.7 %, and was compared to 30.97 % after being heated at 80 °C for 10 min) and catalytic efficiency (4.46 was compared to 2.37) improved more than the wild-type AppA phytase almost without hampering catalytic activity. These multi-factors of rational design strategy can be applied practically as a thermostabilization strategy instead of the conventional single-factor approach.

  8. SNAKE CALIBRATION IN RHIC.

    SciTech Connect

    RANJBAR,V.; BAI,M.; LUCCIO,A.; MACKAY,W.W.; ROSER,T.; LEET,S.Y.

    2002-06-02

    A proper understanding of the response of the spin orientation due to the currents in the four helices which make up each snake is necessary to control spin tune, avoid snake resonances and facilitate the operation of the RHIC spin flipper. The effect of the helical dipole snakes in RHIC is to rotate the spin orientation an angle {mu} about an axis at an angle {phi} in the horizontal plane. With two snakes the combined effect gives rise to a spin precession frequency which is determined by the {mu} and {phi} angles at each snake. Depolarization or spin flipping can occur when this spin tune is near an external driving frequency. We employed the RHIC spin flipper in this way to determine the spin tune and thus verify spin tune predictions based upon previous field measurements of the snake. We also considered the response of snake resonances locations to spin tune as another way of verifying spin tune predictions.

  9. Intimate organic-inorganic nanocomposites via rationally designed conjugated polymer-grafted precursors.

    PubMed

    Jung, Jaehan; Yoon, Young Jun; Lin, Zhiqun

    2016-09-28

    Semiconducting organic-inorganic nanocomposites comprising the conjugated polymer poly(3-hexylthiophene) (P3HT) in intimate contact with CdSe nanocrystals were crafted by exploiting rationally designed P3HT-grafted cadmium precursors (i.e., Cd-P3HT complexes). The bifunctional ligand 4-bromobenzyl phosphonic acid (BPA-Br) that possesses two terminal functional groups at each end was employed, enabling the coordination of BPA-Br with Cd first to yield Cd-phosphonic acid complexes (Cd-BPA-Br) followed by the subsequent substitution of the bromide moiety into the azide (N3) group to form N3-functionalized Cd-phosphonic acid complexes (Cd-BPA-N3). Cd-P3HT complexes were then synthesized via a click reaction between Cd-BPA-N3 and ethynyl-terminated P3HT (P3HT-[triple bond, length as m-dash]). The success of the click reaction was confirmed by spectroscopic measurements. The morphology of CdSe nanocrystals (i.e., quantum dot and multi-branched) in P3HT-CdSe nanocrystal nanocomposites can be altered by tuning the concentration of Cd-P3HT complexes and the addition of excess Cd-BPA-Br (i.e., Cd-P3HT solely for the synthesis of CdSe quantum dots, and Cd-P3HT and Cd-BPA-Br at the ratio Cd-P3HT : Cd-BPA-Br = 1 : 1 for the synthesis of multi-branched CdSe nanocrystals). The photophysical properties of the resulting P3HT-CdSe nanocomposites were examined via absorption and photoluminescence studies. In comparison with P3HT-[triple bond, length as m-dash], the significant emission quenching of nanocomposites suggested the efficient charge transfer at the P3HT/CdSe interface. It is noteworthy that the implementation of judiciously synthesized Cd-P3HT complexes as precursors rendered the in situ synthesis of P3HT-CdSe nanocrystal nanocomposites, dispensing with the need for the use of insulating aliphatic ligands and tedious ligand exchange procedures for the preparation of functional polymer-tethered nanocrystals. PMID:27604874

  10. P-glycoprotein recognition of substrates and circumvention through rational drug design.

    PubMed

    Raub, Thomas J

    2006-01-01

    It is now well recognized that membrane efflux transporters, especially P-glycoprotein (P-gp; ABCB1), play a role in determining the absorption, distribution, metabolism, excretion, and toxicology behaviors of some drugs and molecules in development. An investment in screening structure-activity relationship (SAR) is warranted in early discovery when exposure and/or target activity in an in vivo efficacy model is not achieved and P-gp efflux is identified as a rate-limiting factor. However, the amount of investment in SAR must be placed into perspective by assessing the risks associated with the intended therapeutic target, the potency and margin of safety of the compound, the intended patient population(s), and the market competition. The task of rationally designing a chemistry strategy for circumventing a limiting P-gp interaction can be daunting. The necessity of retaining biological potency and metabolic stability places restrictions on what can be done, and the factors for P-gp recognition of substrates are complicated and poorly understood. The parameters within the assays that affect overall pump efficiency or net efflux, such as passive diffusion, membrane partitioning, and molecular interaction between pump and substrate, should be understood when interpreting data sets associated with chemistry around a scaffold. No single, functional group alone is often the cause, but one group can accentuate the recognition points existing within a scaffold. This can be likened to a rheostat, rather than an on/off switch, where addition or removal of a key group can increase or decrease the pumping efficiency. The most practical approach to de-emphasize the limiting effects of P-gp on a particular scaffold is to increase passive diffusion. Efflux pumping efficiency may be overcome when passive diffusion is fast enough. Eliminating, or substituting with fewer, groups that solvate in water, or decreasing their hydrogen bonding capacity, and adding halogen groups can

  11. Rational design of therapeutic mAbs against aggregation through protein engineering and incorporation of glycosylation motifs applied to bevacizumab

    PubMed Central

    Courtois, Fabienne; Agrawal, Neeraj J; Lauer, Timothy M; Trout, Bernhardt L

    2016-01-01

    The aggregation of biotherapeutics is a major hindrance to the development of successful drug candidates; however, the propensity to aggregate is often identified too late in the development phase to permit modification to the protein's sequence. Incorporating rational design for the stability of proteins in early discovery has numerous benefits. We engineered out aggregation-prone regions on the Fab domain of a therapeutic monoclonal antibody, bevacizumab, to rationally design a biobetter drug candidate. With the purpose of stabilizing bevacizumab with respect to aggregation, 2 strategies were undertaken: single point mutations of aggregation-prone residues and engineering a glycosylation site near aggregation-prone residues to mask these residues with a carbohydrate moiety. Both of these approaches lead to comparable decreases in aggregation, with an up to 4-fold reduction in monomer loss. These single mutations and the new glycosylation pattern of the Fab domain do not modify binding to the target. Biobetters with increased stability against aggregation can therefore be generated in a rational manner, by either removing or masking the aggregation-prone region or crowding out protein-protein interactions. PMID:26514585

  12. Rational design of therapeutic mAbs against aggregation through protein engineering and incorporation of glycosylation motifs applied to bevacizumab.

    PubMed

    Courtois, Fabienne; Agrawal, Neeraj J; Lauer, Timothy M; Trout, Bernhardt L

    2016-01-01

    The aggregation of biotherapeutics is a major hindrance to the development of successful drug candidates; however, the propensity to aggregate is often identified too late in the development phase to permit modification to the protein's sequence. Incorporating rational design for the stability of proteins in early discovery has numerous benefits. We engineered out aggregation-prone regions on the Fab domain of a therapeutic monoclonal antibody, bevacizumab, to rationally design a biobetter drug candidate. With the purpose of stabilizing bevacizumab with respect to aggregation, 2 strategies were undertaken: single point mutations of aggregation-prone residues and engineering a glycosylation site near aggregation-prone residues to mask these residues with a carbohydrate moiety. Both of these approaches lead to comparable decreases in aggregation, with an up to 4-fold reduction in monomer loss. These single mutations and the new glycosylation pattern of the Fab domain do not modify binding to the target. Biobetters with increased stability against aggregation can therefore be generated in a rational manner, by either removing or masking the aggregation-prone region or crowding out protein-protein interactions.

  13. Rational design of therapeutic mAbs against aggregation through protein engineering and incorporation of glycosylation motifs applied to bevacizumab.

    PubMed

    Courtois, Fabienne; Agrawal, Neeraj J; Lauer, Timothy M; Trout, Bernhardt L

    2016-01-01

    The aggregation of biotherapeutics is a major hindrance to the development of successful drug candidates; however, the propensity to aggregate is often identified too late in the development phase to permit modification to the protein's sequence. Incorporating rational design for the stability of proteins in early discovery has numerous benefits. We engineered out aggregation-prone regions on the Fab domain of a therapeutic monoclonal antibody, bevacizumab, to rationally design a biobetter drug candidate. With the purpose of stabilizing bevacizumab with respect to aggregation, 2 strategies were undertaken: single point mutations of aggregation-prone residues and engineering a glycosylation site near aggregation-prone residues to mask these residues with a carbohydrate moiety. Both of these approaches lead to comparable decreases in aggregation, with an up to 4-fold reduction in monomer loss. These single mutations and the new glycosylation pattern of the Fab domain do not modify binding to the target. Biobetters with increased stability against aggregation can therefore be generated in a rational manner, by either removing or masking the aggregation-prone region or crowding out protein-protein interactions. PMID:26514585

  14. Testing the limits of rational design by engineering pH sensitivity into membrane-active peptides.

    PubMed

    Wiedman, Gregory; Wimley, William C; Hristova, Kalina

    2015-04-01

    In this work, we sought to rationally design membrane-active peptides that are triggered by low pH to form macromolecular-sized pores in lipid bilayers. Such peptides could have broad utility in biotechnology and in nanomedicine as cancer therapeutics or drug delivery vehicles that promote release of macromolecules from endosomes. Our approach to rational design was to combine the properties of a pH-independent peptide, MelP5, which forms large pores allowing passage of macromolecules, with the properties of two pH-dependent membrane-active peptides, pHlip and GALA. We created two hybrid sequences, MelP5_Δ4 and MelP5_Δ6, by using the distribution of acidic residues on pHlip and GALA as a guide to insert acidic amino acids into the amphipathic helix of MelP5. We show that the new peptides bind to lipid bilayers and acquire secondary structure in a pH-dependent manner. The peptides also destabilize bilayers in a pH-dependent manner, such that lipid vesicles release the small molecules ANTS/DPX at low pH only. Thus, we were successful in designing pH-triggered pore-forming peptides. However, no macromolecular release was observed under any conditions. Therefore, we abolished the unique macromolecular poration properties of MelP5 by introducing pH sensitivity into its sequence. We conclude that the properties of pHlip, GALA, and MelP5 are additive, but only partially so. We propose that this lack of additivity is a limitation in the rational design of novel membrane-active peptides, and that high-throughput approaches to discovery will be critical for continued progress in the field.

  15. A rational design for the nanoencapsulation of poisonous animal venoms in liposomes prepared with natural phospholipids.

    PubMed

    da Costa, Maria Helena Bueno; Sant'Anna, Osvaldo A; Quintilio, Wagner; Schwendener, Reto Albert; de Araujo, Pedro Soares

    2012-11-01

    Liposomes have been used since the 1970's to encapsulate drugs envisaging enhancement in efficacy and therapeutic index, avoidance of side effects and increase in the encapsulated agent stability. The major problem when encapsulating snake venoms is the liposomal membrane instability caused by venom phospholipases. Here the results obtained encapsulating Crotalus durissimus terrificus and a pool of Bothropic venoms within liposomes (LC and LB, respectively) used to produce anti-venom sera are presented. The strategy was to modify the immunization protocol to enhance antibody production and to minimize toxic effects by encapsulating inactivated venoms within stabilized liposomes. Chemically modified venoms were solubilized in a buffer containing an inhibitor and a chelating agent. The structures of the venoms were analyzed by UV, CD spectroscopy and ELISA. In spite of the differences in the helical content between natural and modified venoms, they were recognized by horse anti-sera. To maintain long-term stability, mannitol was used as a cryoprotectant. The encapsulation efficiencies were 59 % (LB) and 99 % (LC), as followed by filtration on Sephacryl S1000. Light scattering measurements led us to conclude that both, LB (119 ±47 nm) and LC (147±56 nm) were stable for 22 days at 4 °C, even after lyophilization. Genetically selected mice and mixed breed horses were immunized with these formulations. The animals did not show clinical symptoms of venom toxicity. Both, LB and LC enhanced by at least 30 % the antibody titers 25 days after injection and total IgG titers remained high 91 days after immunization. The liposomal formulation clearly exhibited adjuvant properties.

  16. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics

    PubMed Central

    Philipp, Jenny; Künze, Georg; Wodtke, Robert; Löser, Reik; Fahmy, Karim; Pisabarro, M. Teresa

    2016-01-01

    Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands. PMID:27123592

  17. Rational Suicide?

    ERIC Educational Resources Information Center

    Mayo, David J.

    1998-01-01

    The rational suicide paradigm is contrasted with the traditional view of the mental health professions. Historical background on suicide in western civilization is supplied and the concept of rationality elucidated. Parallels between the questions of refusing life-prolonging therapy and rational suicide are discussed, as are reasons for suicide.…

  18. A Rational Design Strategy for the Selective Activity Enhancement of a Molecular Chaperone toward a Target Substrate.

    PubMed

    Aprile, Francesco A; Sormanni, Pietro; Vendruscolo, Michele

    2015-08-18

    Molecular chaperones facilitate the folding and assembly of proteins and inhibit their aberrant aggregation. They thus offer several opportunities for biomedical and biotechnological applications, as for example they can often prevent protein aggregation more effectively than other therapeutic molecules, including small molecules and antibodies. Here we present a method of designing molecular chaperones with enhanced activity against specific amyloidogenic substrates while leaving unaltered their functions toward other substrates. The method consists of grafting onto a molecular chaperone a peptide designed to bind specifically an epitope in the target substrate. We illustrate this strategy by describing Hsp70 variants with increased affinities for α-synuclein and Aβ42 but otherwise unaltered affinities for other substrates. These designed variants inhibit protein aggregation and disaggregate preformed fibrils significantly more effectively than wild-type Hsp70 indicating that the strategy presented here provides a possible route for tailoring rationally molecular chaperones for specific purposes.

  19. [Hygienic characteristics of daily ration, designed for military servicemen doing call-up military service].

    PubMed

    Smagulov, N K; Mukhametzhanov, A M

    2016-01-01

    The article gives the hygienic characteristics of the daily diet of soldiers doing call-up military service. The object of study--military servicemen aged 18-22 years doing call-up military service. The material of the study data was obtained from a continuous cross-sectional study of dietary intake among military personnel. Investigation pointed out that consumption of nutrients and energy value of the surveyed military personnel was broadly in accordance with recommended physiological requirements for nutrients and energy for this age group. However; despite the adequacy of energy supply, showed signs of imbalance on the nutrients of rations provided in the military establishment. Structure of consumption of products is not in full compliance with the existing recommendations of the Kazakh academy of Nutrition. PMID:27120954

  20. Rational design and evolutional fine tuning of Saccharomyces cerevisiae for biomass breakdown.

    PubMed

    Hasunuma, Tomohisa; Ishii, Jun; Kondo, Akihiko

    2015-12-01

    Conferring biomass hydrolysis activity on yeast through genetic engineering has paved the way for the development of groundbreaking processes for producing liquid fuels and commodity chemicals from lignocellulosic biomass. However, the overproduction and misfolding of heterologous and endogenous proteins can trigger cellular stress, increasing the metabolic burden and retarding growth. Improving the efficiency of lignocellulosic breakdown requires engineering of yeast secretory pathway based on system-wide metabolic analysis as well as DNA constructs for enhanced cellulase gene expression with advanced molecular biology tools. Also, yeast is subjected to severe stress due to toxic compounds generated during lignocellulose pretreatment in consolidated saccharification and fermentation processes. The prospect for development of robust yeast strains makes combining evolutionary and rational engineering strategies.

  1. A Rationally Designed Connector for Assembly of Protein-Functionalized DNA Nanostructures.

    PubMed

    Koßmann, Katja J; Ziegler, Cornelia; Angelin, Alessandro; Meyer, Rebecca; Skoupi, Marc; Rabe, Kersten S; Niemeyer, Christof M

    2016-06-16

    We report on the rational engineering of the binding interface of the self-ligating HaloTag protein to generate an optimized linker for DNA nanostructures. Five amino acids positioned around the active-site entry channel for the chlorohexyl ligand (CH) of the HaloTag protein were exchanged for positively charged lysine amino acids to produce the HOB (halo-based oligonucleotide binder) protein. HOB was genetically fused with the enzyme cytochrome P450 BM3, as well as with BMR, the separated reductase domain of BM3. The resulting HOB-fusion proteins revealed significantly improved rates in ligation with CH-modified oligonucleotides and DNA origami nanostructures. These results suggest that the efficient self-assembly of protein-decorated DNA structures can be greatly improved by fine-tuning of the electrostatic interactions between proteins and the negatively charged nucleic acid nanostructures. PMID:26972311

  2. Rational Design of a Colorimetric pH Sensor from a Soluble Retinoic Acid Chaperone

    PubMed Central

    Berbasova, Tetyana; Nosrati, Meisam; Vasileiou, Chrysoula; Wang, Wenjing; Lee, Kin Sing Stephen; Yapici, Ipek; Geiger, James H.; Borhan, Babak

    2014-01-01

    Reengineering of cellular retinoic acid binding protein II (CRABPII) to be capable of binding retinal as a protonated Schiff base is described. Through rational alterations of the binding pocket, electrostatic perturbations of the embedded retinylidene chromophore that favor delocalization of the iminium charge lead to exquisite control in the regulation of chromophoric absorption properties, spanning the visible spectrum (474–640 nm). The pKa of the retinylidene protonated Schiff base was modulated from 2.4 to 8.1, giving rise to a set of proteins of varying colors and pH sensitivities. These proteins were used to demonstrate a concentration-independent, ratiometric pH sensor. PMID:24059243

  3. Converting bulk sugars into prebiotics: semi-rational design of a transglucosylase with controlled selectivity.

    PubMed

    Verhaeghe, Tom; De Winter, Karel; Berland, Magali; De Vreese, Rob; D'hooghe, Matthias; Offmann, Bernard; Desmet, Tom

    2016-03-01

    Despite the growing importance of prebiotics in nutrition and gastroenterology, their structural variety is currently still very limited. The lack of straightforward procedures to gain new products in sufficient amounts often hampers application testing and further development. Although the enzyme sucrose phosphorylase can be used to produce the rare disaccharide kojibiose (α-1,2-glucobiose) from the bulk sugars sucrose and glucose, the target compound is only a side product that is difficult to isolate. Accordingly, for this biocatalyst to become economically attractive, the formation of other glucobioses should be avoided and therefore we applied semi-rational mutagenesis and low-throughput screening, which resulted in a double mutant (L341I_Q345S) with a selectivity of 95% for kojibiose. That way, an efficient and scalable production process with a yield of 74% could be established, and with a simple yeast treatment and crystallization step over a hundred grams of highly pure kojibiose (>99.5%) was obtained.

  4. Rational design of a colorimetric pH sensor from a soluble retinoic acid chaperone.

    PubMed

    Berbasova, Tetyana; Nosrati, Meisam; Vasileiou, Chrysoula; Wang, Wenjing; Lee, Kin Sing Stephen; Yapici, Ipek; Geiger, James H; Borhan, Babak

    2013-10-30

    Reengineering of cellular retinoic acid binding protein II (CRABPII) to be capable of binding retinal as a protonated Schiff base is described. Through rational alterations of the binding pocket, electrostatic perturbations of the embedded retinylidene chromophore that favor delocalization of the iminium charge lead to exquisite control in the regulation of chromophoric absorption properties, spanning the visible spectrum (474-640 nm). The pKa of the retinylidene protonated Schiff base was modulated from 2.4 to 8.1, giving rise to a set of proteins of varying colors and pH sensitivities. These proteins were used to demonstrate a concentration-independent, ratiometric pH sensor. PMID:24059243

  5. A Rationally Designed Connector for Assembly of Protein-Functionalized DNA Nanostructures.

    PubMed

    Koßmann, Katja J; Ziegler, Cornelia; Angelin, Alessandro; Meyer, Rebecca; Skoupi, Marc; Rabe, Kersten S; Niemeyer, Christof M

    2016-06-16

    We report on the rational engineering of the binding interface of the self-ligating HaloTag protein to generate an optimized linker for DNA nanostructures. Five amino acids positioned around the active-site entry channel for the chlorohexyl ligand (CH) of the HaloTag protein were exchanged for positively charged lysine amino acids to produce the HOB (halo-based oligonucleotide binder) protein. HOB was genetically fused with the enzyme cytochrome P450 BM3, as well as with BMR, the separated reductase domain of BM3. The resulting HOB-fusion proteins revealed significantly improved rates in ligation with CH-modified oligonucleotides and DNA origami nanostructures. These results suggest that the efficient self-assembly of protein-decorated DNA structures can be greatly improved by fine-tuning of the electrostatic interactions between proteins and the negatively charged nucleic acid nanostructures.

  6. [Hygienic characteristics of daily ration, designed for military servicemen doing call-up military service].

    PubMed

    Smagulov, N K; Mukhametzhanov, A M

    2016-01-01

    The article gives the hygienic characteristics of the daily diet of soldiers doing call-up military service. The object of study--military servicemen aged 18-22 years doing call-up military service. The material of the study data was obtained from a continuous cross-sectional study of dietary intake among military personnel. Investigation pointed out that consumption of nutrients and energy value of the surveyed military personnel was broadly in accordance with recommended physiological requirements for nutrients and energy for this age group. However; despite the adequacy of energy supply, showed signs of imbalance on the nutrients of rations provided in the military establishment. Structure of consumption of products is not in full compliance with the existing recommendations of the Kazakh academy of Nutrition.

  7. Protein engineering of Bacillus acidopullulyticus pullulanase for enhanced thermostability using in silico data driven rational design methods.

    PubMed

    Chen, Ana; Li, Yamei; Nie, Jianqi; McNeil, Brian; Jeffrey, Laura; Yang, Yankun; Bai, Zhonghu

    2015-10-01

    Thermostability has been considered as a requirement in the starch processing industry to maintain high catalytic activity of pullulanase under high temperatures. Four data driven rational design methods (B-FITTER, proline theory, PoPMuSiC-2.1, and sequence consensus approach) were adopted to identify the key residue potential links with thermostability, and 39 residues of Bacillus acidopullulyticus pullulanase were chosen as mutagenesis targets. Single mutagenesis followed by combined mutagenesis resulted in the best mutant E518I-S662R-Q706P, which exhibited an 11-fold half-life improvement at 60 °C and a 9.5 °C increase in Tm. The optimum temperature of the mutant increased from 60 to 65 °C. Fluorescence spectroscopy results demonstrated that the tertiary structure of the mutant enzyme was more compact than that of the wild-type (WT) enzyme. Structural change analysis revealed that the increase in thermostability was most probably caused by a combination of lower stability free-energy and higher hydrophobicity of E518I, more hydrogen bonds of S662R, and higher rigidity of Q706P compared with the WT. The findings demonstrated the effectiveness of combined data-driven rational design approaches in engineering an industrial enzyme to improve thermostability.

  8. Snaking through Science.

    ERIC Educational Resources Information Center

    Chattin, Sam S.

    1983-01-01

    Suggestions are provided for using animals (particularly snakes) as the focus of studies and activities in the science classroom. For example, cages with animals can serve as a learning center on various aspects of the animal. A list of suggestions for the care and feeding of snakes is provided. (JN)

  9. The Web-Based DNA Vaccine Database DNAVaxDB and Its Usage for Rational DNA Vaccine Design.

    PubMed

    Racz, Rebecca; He, Yongqun

    2016-01-01

    A DNA vaccine is a vaccine that uses a mammalian expression vector to express one or more protein antigens and is administered in vivo to induce an adaptive immune response. Since the 1990s, a significant amount of research has been performed on DNA vaccines and the mechanisms behind them. To meet the needs of the DNA vaccine research community, we created DNAVaxDB ( http://www.violinet.org/dnavaxdb ), the first Web-based database and analysis resource of experimentally verified DNA vaccines. All the data in DNAVaxDB, which includes plasmids, antigens, vaccines, and sources, is manually curated and experimentally verified. This chapter goes over the detail of DNAVaxDB system and shows how the DNA vaccine database, combined with the Vaxign vaccine design tool, can be used for rational design of a DNA vaccine against a pathogen, such as Mycobacterium bovis.

  10. Line width roughness reduction by rational design of photoacid generator for sub-millisecond laser post-exposure bake

    NASA Astrophysics Data System (ADS)

    Jiang, Jing; Thompson, Michael O.; Ober, Christopher K.

    2014-03-01

    Sub-millisecond laser post-exposure bake (PEB) is an alternative technology to address the excessive acid diffusion for chemically amplified photoresist systems. By rationally designing the resist, laser post-exposure bake is able to improve the resolution and reduce the line width roughness (LWR) compared to patterns exposed under the same conditions but using conventional hotplate PEB. It was found that only the resist with high deprotection activation energy and low diffusion activation energy showed improved performance using laser PEB. Accordingly, a PAG was designed to have low acid diffusivity by binding the counter ions to a molecular glass core while keeping photophysical properties and processing conditions similar to a conventional PAG. By reducing the diffusivity of the counter ions, the PAG was able to further reduce LWR by 60% using laser PEB.

  11. Rational design of a binary metal alloy for chemical vapour deposition growth of uniform single-layer graphene.

    PubMed

    Dai, Boya; Fu, Lei; Zou, Zhiyu; Wang, Min; Xu, Haitao; Wang, Sheng; Liu, Zhongfan

    2011-01-01

    Controlled growth of high-quality graphene is still the bottleneck of practical applications. The widely used chemical vapour deposition process generally suffers from an uncontrollable carbon precipitation effect that leads to inhomogeneous growth and strong correlation to the growth conditions. Here we report the rational design of a binary metal alloy that effectively suppresses the carbon precipitation process and activates a self-limited growth mechanism for homogeneous monolayer graphene. As demonstrated by an Ni-Mo alloy, the designed binary alloy contains an active catalyst component for carbon source decomposition and graphene growth and a black hole counterpart for trapping the dissolved carbons and forming stable metal carbides. This type of process engineering has been used to grow strictly single-layer graphene with 100% surface coverage and excellent tolerance to variations in growth conditions. With simplicity, scalability and a very large growth window, the presented approach may facilitate graphene research and industrial applications. PMID:22045001

  12. Rational design for multifunctional non-liposomal lipid-based nanocarriers for cancer management: theory to practice

    PubMed Central

    2013-01-01

    Nanomedicines have gained more and more attention in cancer therapy thanks to their ability to enhance the tumour accumulation and the intracellular uptake of drugs while reducing their inactivation and toxicity. In parallel, nanocarriers have been successfully employed as diagnostic tools increasing imaging resolution holding great promises both in preclinical research and in clinical settings. Lipid-based nanocarriers are a class of biocompatible and biodegradable vehicles that provide advanced delivery of therapeutic and imaging agents, improving pharmacokinetic profile and safety. One of most promising engineering challenges is the design of innovative and versatile multifunctional targeted nanotechnologies for cancer treatment and diagnosis. This review aims to highlight rational approaches to design multifunctional non liposomal lipid-based nanocarriers providing an update of literature in this field. PMID:24564841

  13. Homicidal Snake Bite in Children.

    PubMed

    Paulis, Melad G; Faheem, Ayman L

    2016-03-01

    Snake bites are common in many regions of the world. Snake envenomation is relatively uncommon in Egypt; such unfortunate events usually attract much publicity. Snake bite is almost only accidental, occurring in urban areas and desert. Few cases were reported to commit suicide by snake. Homicidal snake poisoning is so rare. It was known in ancient world by executing capital punishment by throwing the victim into a pit full of snakes. Another way was to ask the victim to put his hand inside a small basket harboring a deadly snake. Killing a victim by direct snake bite is so rare. There was one reported case where an old couple was killed by snake bite. Here is the first reported case of killing three children by snake bite. It appeared that the diagnosis of such cases is so difficult and depended mainly on the circumstantial evidences.

  14. Homicidal Snake Bite in Children.

    PubMed

    Paulis, Melad G; Faheem, Ayman L

    2016-03-01

    Snake bites are common in many regions of the world. Snake envenomation is relatively uncommon in Egypt; such unfortunate events usually attract much publicity. Snake bite is almost only accidental, occurring in urban areas and desert. Few cases were reported to commit suicide by snake. Homicidal snake poisoning is so rare. It was known in ancient world by executing capital punishment by throwing the victim into a pit full of snakes. Another way was to ask the victim to put his hand inside a small basket harboring a deadly snake. Killing a victim by direct snake bite is so rare. There was one reported case where an old couple was killed by snake bite. Here is the first reported case of killing three children by snake bite. It appeared that the diagnosis of such cases is so difficult and depended mainly on the circumstantial evidences. PMID:27404632

  15. Reviewing Ligand-Based Rational Drug Design: The Search for an ATP Synthase Inhibitor

    PubMed Central

    Lee, Chia-Hsien; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2011-01-01

    Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design process. In this paper, by describing the search for an ATP synthase inhibitor, we review two frequently used approaches in ligand-based drug design: The pharmacophore model and the quantitative structure-activity relationship (QSAR) method. Moreover, since ATP synthase ligands are potentially useful drugs in cancer therapy, pharmacophore models were constructed to pave the way for novel inhibitor designs. PMID:21954360

  16. Cardiac troponin I: a case study in rational antibody design for human diagnostics.

    PubMed

    Conroy, P J; O'Kennedy, R J; Hearty, S

    2012-06-01

    In vitro diagnostic (IVD) platforms provide rapid and accurate determination of disease status. The clinical performance of antibody-based diagnostic platforms is paramount as the information provided often informs the medical intervention taken and, ultimately, the patient's outcome. Breaking down such an immuno-IVD device into its component elements, the biorecognition entity is key to the analytical specificity of the test. Furthermore, tailored optimisation of the antibody is often necessary to impart the desired biophysical properties for the specific application. This tailoring is now widely facilitated by advances in combinatorial approaches to antibody generation, molecular evolution strategies and the availability of truly high-throughput (HT), refined surface plasmon resonance-based screening tools. In this paper, we demonstrate a rational, knowledge-driven approach to the generation of epitope-specific antibodies for the early detection of cardiovascular disease, discuss the merits of the approaches taken and offer a perspective on HT strategies to mining large antibody libraries. These results highlight the expedience of such methodologies for the development of truly superior cardiovascular disease biorecognition elements. PMID:22509048

  17. Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model.

    PubMed

    Jiang, Yang; Zhang, Haiyang; Tan, Tianwei

    2016-07-12

    A nonbonded dummy model for metal ions is highly imperative for the computation of complex biological systems with for instance multiple metal centers. Here we present nonbonded dummy parameters of 11 divalent metallic cations, namely, Mg(2+), V(2+), Cr(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), Sn(2+), and Hg(2+), that are optimized to be compatible with three widely used water models (TIP3P, SPC/E, and TIP4P-EW). The three sets of metal parameters reproduce simultaneously the solvation free energies (ΔGsol), the ion-oxygen distance in the first solvation shell (IOD), and coordination numbers (CN) in explicit water with a relative error less than 1%. The main sources of errors to ΔGsol that arise from the boundary conditions and treatment of electrostatic interactions are corrected rationally, which ensures the independence of the proposed parameters on the methodology used in the calculation. This work will be of great value for the computational study of metal-containing biological systems. PMID:27182744

  18. Physics of icing and rational design of surfaces with extraordinary icephobicity.

    PubMed

    Schutzius, Thomas M; Jung, Stefan; Maitra, Tanmoy; Eberle, Patric; Antonini, Carlo; Stamatopoulos, Christos; Poulikakos, Dimos

    2015-05-01

    Icing of surfaces is commonplace in nature and technology, affecting everyday life and sometimes causing catastrophic events. Understanding (and counteracting) surface icing brings with it significant scientific challenges that requires interdisciplinary knowledge from diverse scientific fields such as nucleation thermodynamics and heat transfer, fluid dynamics, surface chemistry, and surface nanoengineering. Here we discuss key aspects and findings related to the physics of ice formation on surfaces and show how such knowledge could be employed to rationally develop surfaces with extreme resistance to icing (extraordinary icephobicity). Although superhydrophobic surfaces with micro-, nano-, or (often biomimetic) hierarchical roughnesses have shown in laboratory settings (under certain conditions) excellent repellency and low adhesion to water down to temperatures near or below the freezing point, extreme icephobicity necessitates additional important functionalities. Other approaches, such as lubricant-impregnated surfaces, exhibit both advantages and serious limitations with respect to icing. In all, a clear path toward passive surfaces with extreme resistance to ice formation remains a challenge, but it is one well worth undertaking. Equally important to potential applications is scalable surface manufacturing and the ability of icephobic surfaces to perform reliably and sustainably outside the laboratory under adverse conditions. Surfaces should possess mechanical and chemical stability, and they should be thermally resilient. Such issues and related research directions are also addressed in this article.

  19. Designing of skull defect implants using C1 rational cubic Bezier and offset curves

    NASA Astrophysics Data System (ADS)

    Mohamed, Najihah; Majid, Ahmad Abd; Piah, Abd Rahni Mt; Rajion, Zainul Ahmad

    2015-05-01

    Some of the reasons to construct skull implant are due to head trauma after an accident or an injury or an infection or because of tumor invasion or when autogenous bone is not suitable for replacement after a decompressive craniectomy (DC). The main objective of our study is to develop a simple method to redesign missing parts of the skull. The procedure begins with segmentation, data approximation, and estimation process of the outer wall by a C1 continuous curve. Its offset curve is used to generate the inner wall. A metaheuristic algorithm, called harmony search (HS) is a derivative-free real parameter optimization algorithm inspired from the musical improvisation process of searching for a perfect state of harmony. In this study, data approximation by a rational cubic Bézier function uses HS to optimize position of middle points and value of the weights. All the phases contribute significantly in making our proposed technique automated. Graphical examples of several postoperative skulls are displayed to show the effectiveness of our proposed method.

  20. Disentangling electron tunneling and protein dynamics of cytochrome c through a rationally designed surface mutation.

    PubMed

    Alvarez-Paggi, Damián; Meister, Wiebke; Kuhlmann, Uwe; Weidinger, Inez; Tenger, Katalin; Zimányi, László; Rákhely, Gábor; Hildebrandt, Peter; Murgida, Daniel H

    2013-05-23

    Nonexponential distance dependence of the apparent electron-transfer (ET) rate has been reported for a variety of redox proteins immobilized on biocompatible electrodes, thus posing a physicochemical challenge of possible physiological relevance. We have recently proposed that this behavior may arise not only from the structural and dynamical complexity of the redox proteins but also from their interplay with strong electric fields present in the experimental setups and in vivo (J. Am Chem. Soc. 2010, 132, 5769-5778). Therefore, protein dynamics are finely controlled by the energetics of both specific contacts and the interaction between the protein's dipole moment and the interfacial electric fields. In turn, protein dynamics may govern electron-transfer kinetics through reorientation from low to high donor-acceptor electronic coupling orientations. Here we present a combined computational and experimental study of WT cytochrome c and the surface mutant K87C adsorbed on electrodes coated with self-assembled monolayers (SAMs) of varying thickness (i.e., variable strength of the interfacial electric field). Replacement of the positively charged K87 by a neutral amino acid allowed us to disentangle protein dynamics and electron tunneling from the reaction kinetics and to rationalize the anomalous distance dependence in terms of (at least) two populations of distinct average electronic couplings. Thus, it was possible to recover the exponential distance dependence expected from ET theory. These results pave the way for gaining further insight into the parameters that control protein electron transfer.

  1. Physics of icing and rational design of surfaces with extraordinary icephobicity.

    PubMed

    Schutzius, Thomas M; Jung, Stefan; Maitra, Tanmoy; Eberle, Patric; Antonini, Carlo; Stamatopoulos, Christos; Poulikakos, Dimos

    2015-05-01

    Icing of surfaces is commonplace in nature and technology, affecting everyday life and sometimes causing catastrophic events. Understanding (and counteracting) surface icing brings with it significant scientific challenges that requires interdisciplinary knowledge from diverse scientific fields such as nucleation thermodynamics and heat transfer, fluid dynamics, surface chemistry, and surface nanoengineering. Here we discuss key aspects and findings related to the physics of ice formation on surfaces and show how such knowledge could be employed to rationally develop surfaces with extreme resistance to icing (extraordinary icephobicity). Although superhydrophobic surfaces with micro-, nano-, or (often biomimetic) hierarchical roughnesses have shown in laboratory settings (under certain conditions) excellent repellency and low adhesion to water down to temperatures near or below the freezing point, extreme icephobicity necessitates additional important functionalities. Other approaches, such as lubricant-impregnated surfaces, exhibit both advantages and serious limitations with respect to icing. In all, a clear path toward passive surfaces with extreme resistance to ice formation remains a challenge, but it is one well worth undertaking. Equally important to potential applications is scalable surface manufacturing and the ability of icephobic surfaces to perform reliably and sustainably outside the laboratory under adverse conditions. Surfaces should possess mechanical and chemical stability, and they should be thermally resilient. Such issues and related research directions are also addressed in this article. PMID:25346213

  2. Rational design of MgB2 conductors toward practical applications

    NASA Astrophysics Data System (ADS)

    Patel, Dipak; Hossain, Md Shahriar Al; Motaman, Ashkan; Barua, Shaon; Shahabuddin, Mohammed; Kim, Jung Ho

    2014-09-01

    We report the research progress that has been made on developing rational MgB2 superconducting conductors toward practical applications. Owing to the poor performance of the critical current density (Jc) of bare MgB2, various techniques have been developed to overcome this obstacle. Among these, chemical doping has proved to be the most effective way to enhance the superconducting properties, such as Jc and the irreversibility field (Birr). More than a hundred different forms of dopants have been investigated over the past 13 years. Among these, the most effective dopants have been identified to be silicon carbide, carbon, and malic acid. The best results, Birr of 22 T and Jc of 40,000 A cm-2 at 4.2 K and 10 T, have been reported for malic acid treated MgB2 conductors, which have matched the benchmark performance of commercial low temperature superconductor wire such as Nb-Ti. This work will review and discuss the progress on MgB2 conductor development over the past few years at the University of Wollongong and Hyper Tech Research, Inc.

  3. Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model.

    PubMed

    Jiang, Yang; Zhang, Haiyang; Tan, Tianwei

    2016-07-12

    A nonbonded dummy model for metal ions is highly imperative for the computation of complex biological systems with for instance multiple metal centers. Here we present nonbonded dummy parameters of 11 divalent metallic cations, namely, Mg(2+), V(2+), Cr(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), Sn(2+), and Hg(2+), that are optimized to be compatible with three widely used water models (TIP3P, SPC/E, and TIP4P-EW). The three sets of metal parameters reproduce simultaneously the solvation free energies (ΔGsol), the ion-oxygen distance in the first solvation shell (IOD), and coordination numbers (CN) in explicit water with a relative error less than 1%. The main sources of errors to ΔGsol that arise from the boundary conditions and treatment of electrostatic interactions are corrected rationally, which ensures the independence of the proposed parameters on the methodology used in the calculation. This work will be of great value for the computational study of metal-containing biological systems.

  4. Activity improvement of a Kluyveromyces lactis aldo-keto reductase KlAKR via rational design.

    PubMed

    Luo, Xi; Wang, Ya-Jun; Shen, Wei; Zheng, Yu-Guo

    2016-04-20

    Optically pure t-butyl 6-cyano-(3R, 5R)-dihydroxyhexanoate ((R)-1b) is the key chiral precursor for atorvastatin calcium, the most widely used cholesterol-lowering drug. Wild-type aldo-keto reductase KlAKR from Kluyveromyces lactis has ideal diastereoselectivity toward t-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate (1a, dep>99.5%) but poor activity. A rational engineering was used to improve the KlAKR activity. Based on homology modeling and molecular docking, two amino acid residues (295 and 296) were selected as mutation sites, and two rounds of site-saturation mutagenesis were performed. Among the mutants, KlAKR-Y295W/W296L exhibited the highest catalytic efficiency (kcat/Km) toward 1a up to 12.37s(-1)mM(-1), which was 11.25-fold higher than that of wild-type KlAKR. Moreover, the majority of mutations have no negative impact on stereoselectivity. Using KlAKR-Y295W/W296L coupled with Exiguobacterium sibiricum glucose dehydrogenase (EsGDH) for cofactor regeneration, (R)-1b was accumulated up to 162.7mM with dep value above 99.5%. KlAKR-Y295W/W296L represents a robust tool for (R)-1b synthesis.

  5. Rational design of vaccines: learning from immune evasion mechanisms of persistent viruses and tumors.

    PubMed

    Arens, Ramon

    2012-01-01

    The induction of adaptive immunity and prevention of tolerance is a critical component of vaccination and immunotherapy in order to prevent pathogen-related diseases and to eradicate malignant cells. Although many acute infections can be controlled by vaccination, the development of prophylactic and therapeutic vaccines against persistent viruses and tumors remains challenging. The diverse immune evasion strategies used by persistent DNA viruses such as herpesviruses contribute directly to their persistence and escape from immune control. Intriguingly, many tumors have also developed escape mechanisms to dismantle similar aspects of the host's immune system. Analogous targets of immune evasion mechanisms comprise suppression of antigen presentation and T cell costimulatory pathways, induction of immunosuppressive cytokines, and obstruction of interferon and chemokine functions, which emphasizes them not only as critical elements of T cell activation pathways but also as the potential "Achilles' heels" of the host immune system. The insight that immune evasion by viruses and tumors targets analogous host immune pathways might lead to cross-pollination of the viral and tumor immunology research fields, which could lead to new perspectives and appreciation of the intricacies and subtleties that arise from the merging of these fields. Accordingly, a rational and combinatorial manipulation of immune evasion pathways and their targets should aid in the development of safer and more effective vaccine strategies and immunotherapies for a wide range of infections and malignancies.

  6. Rational Design of a Lanthanide-Based Complex Featuring Different Single-Molecule Magnets.

    PubMed

    Pointillart, F; Guizouarn, T; Lefeuvre, B; Golhen, S; Cador, O; Ouahab, L

    2015-11-16

    The rational synthesis of the 2-{1-methylpyridine-N-oxide-4,5-[4,5-bis(propylthio)tetrathiafulvalenyl]-1H-benzimidazol-2-yl}pyridine ligand (L) is described. It led to the tetranuclear complex [Dy4(tta)12(L)2] (Dy-Dy2-Dy) after coordination reaction with the precursor Dy(tta)3⋅2 H2O (tta(-) = 2-thenoyltrifluoroacetonate). The X-ray structure of Dy-Dy2-Dy can be described as two terminal mononuclear units bridged by a central antiferromagnetically coupled dinuclear complex. The terminal N2O6 and central O8 environments are described as distorted square antiprisms. The ac magnetism measurements revealed a strong out-of-phase signal of the magnetic susceptibility with two distinct sets of data. The high- and low-frequency components were attributed to the two terminal mononuclear single-molecule magnets (SMMs) and the central dinuclear SMM, respectively. A magnetic hysteresis loop was detected at very low temperature. From both structural and magnetic points of view, the tetranuclear SMM Dy-Dy2-Dy is a self-assembly of two known mononuclear SMMs bridged by a known dinuclear SMM.

  7. Rational screening of antibodies and design of sandwich enzyme linked immunosorbant assay on the basis of a kinetic model.

    PubMed

    Choi, Dong Hwan; Katakura, Yoshio; Ninomiya, Kazuaki; Shioya, Suteaki

    2008-03-01

    A rational strategy for the rapid establishment of a sensitive sandwich enzyme linked immunosorbant assay was developed. The kinetic properties required for the solid-phase and enzyme-conjugated antibodies of sandwich ELISA were determined rationally on the basis of a kinetic model describing antibody-antigen interaction. Some antibodies possessing the required kinetic properties against a model antigen, C-reactive protein (CRP), were successfully isolated from a phage antibody library under the screening conditions that were designed on the basis of simulation results. The best combination of solid-phase and enzyme-conjugated antibodies that gives the most sensitive sandwich ELISA was determined by simulation on the basis of the apparent association and dissociation rate constants of the isolated antibodies. It was confirmed by experiment that the sandwich ELISA using the best combination of antibodies was actually the most sensitive one. Our strategy would be useful for the rapid establishment of sensitive sandwich ELISAs compared with the traditional hybridoma method in which the best condition is determined by trial and error.

  8. Rational design of thermostable vaccines by engineered peptide-induced virus self-biomineralization under physiological conditions.

    PubMed

    Wang, Guangchuan; Cao, Rui-Yuan; Chen, Rong; Mo, Lijuan; Han, Jian-Feng; Wang, Xiaoyu; Xu, Xurong; Jiang, Tao; Deng, Yong-Qiang; Lyu, Ke; Zhu, Shun-Ya; Qin, E-De; Tang, Ruikang; Qin, Cheng-Feng

    2013-05-01

    The development of vaccines against infectious diseases represents one of the most important contributions to medical science. However, vaccine-preventable diseases still cause millions of deaths each year due to the thermal instability and poor efficacy of vaccines. Using the human enterovirus type 71 vaccine strain as a model, we suggest a combined, rational design approach to improve the thermostability and immunogenicity of live vaccines by self-biomineralization. The biomimetic nucleating peptides are rationally integrated onto the capsid of enterovirus type 71 by reverse genetics so that calcium phosphate mineralization can be biologically induced onto vaccine surfaces under physiological conditions, generating a mineral exterior. This engineered self-biomineralized virus was characterized in detail for its unique structural, virological, and chemical properties. Analogous to many exteriors, the mineral coating confers some new properties on enclosed vaccines. The self-biomineralized vaccine can be stored at 26 °C for more than 9 d and at 37 °C for approximately 1 wk. Both in vitro and in vivo experiments demonstrate that this engineered vaccine can be used efficiently after heat treatment or ambient temperature storage, which reduces the dependence on a cold chain. Such a combination of genetic technology and biomineralization provides an economic solution for current vaccination programs, especially in developing countries that lack expensive refrigeration infrastructures. PMID:23589862

  9. Rational design and validation of an anti-protein kinase C active-state specific antibody based on conformational changes

    PubMed Central

    Pena, Darlene Aparecida; Andrade, Victor Piana de; Silva, Gabriela Ávila Fernandes; Neves, José Ivanildo; Oliveira, Paulo Sergio Lopes de; Alves, Maria Julia Manso; Devi, Lakshmi A.; Schechtman, Deborah

    2016-01-01

    Protein kinase C (PKC) plays a regulatory role in key pathways in cancer. However, since phosphorylation is a step for classical PKC (cPKC) maturation and does not correlate with activation, there is a lack of tools to detect active PKC in tissue samples. Here, a structure-based rational approach was used to select a peptide to generate an antibody that distinguishes active from inactive cPKC. A peptide conserved in all cPKCs, C2Cat, was chosen since modeling studies based on a crystal structure of PKCβ showed that it is localized at the interface between the C2 and catalytic domains of cPKCs in an inactive kinase. Anti-C2Cat recognizes active cPKCs at least two-fold better than inactive kinase in ELISA and immunoprecipitation assays, and detects the temporal dynamics of cPKC activation upon receptor or phorbol stimulation. Furthermore, the antibody is able to detect active PKC in human tissue. Higher levels of active cPKC were observed in the more aggressive triple negative breast cancer tumors as compared to the less aggressive estrogen receptor positive tumors. Thus, this antibody represents a reliable, hitherto unavailable and a valuable tool to study PKC activation in cells and tissues. Similar structure-based rational design strategies can be broadly applied to obtain active-state specific antibodies for other signal transduction molecules. PMID:26911897

  10. Rational design and validation of an anti-protein kinase C active-state specific antibody based on conformational changes.

    PubMed

    Pena, Darlene Aparecida; Andrade, Victor Piana de; Silva, Gabriela Ávila Fernandes; Neves, José Ivanildo; Oliveira, Paulo Sergio Lopes de; Alves, Maria Julia Manso; Devi, Lakshmi A; Schechtman, Deborah

    2016-02-25

    Protein kinase C (PKC) plays a regulatory role in key pathways in cancer. However, since phosphorylation is a step for classical PKC (cPKC) maturation and does not correlate with activation, there is a lack of tools to detect active PKC in tissue samples. Here, a structure-based rational approach was used to select a peptide to generate an antibody that distinguishes active from inactive cPKC. A peptide conserved in all cPKCs, C2Cat, was chosen since modeling studies based on a crystal structure of PKCβ showed that it is localized at the interface between the C2 and catalytic domains of cPKCs in an inactive kinase. Anti-C2Cat recognizes active cPKCs at least two-fold better than inactive kinase in ELISA and immunoprecipitation assays, and detects the temporal dynamics of cPKC activation upon receptor or phorbol stimulation. Furthermore, the antibody is able to detect active PKC in human tissue. Higher levels of active cPKC were observed in the more aggressive triple negative breast cancer tumors as compared to the less aggressive estrogen receptor positive tumors. Thus, this antibody represents a reliable, hitherto unavailable and a valuable tool to study PKC activation in cells and tissues. Similar structure-based rational design strategies can be broadly applied to obtain active-state specific antibodies for other signal transduction molecules.

  11. A retrospective study of use of polyvalent anti-snake venom and risk factors for mortality from snake bite in a tertiary care setting

    PubMed Central

    Pore, Shraddha M.; Ramanand, Sunita J.; Patil, Praveenkumar T.; Gore, Alka D.; Pawar, Mayur P.; Gaidhankar, Smita L.; Ghanghas, Ravi R.

    2015-01-01

    Aims: Envenomation with poisonous snakes is associated with considerable morbidity and mortality. The present study was undertaken with the objectives of assessing anti-snake venom (ASV) use, early adverse reactions to ASV, premedication and clinical outcomes in snake bite patients. Association of various risk factors (age, gender, dose of ASV, time gap between snake bite and ASV administration, use of mechanical ventilation and type of snake bite) with mortality was also assessed. Settings and Design: This retrospective study was conducted at two Tertiary Care Teaching Hospitals. Subjects and Methods: The medical records of 176 patients of snake bite with documented use of ASV were retrospectively analyzed to retrieve relevant data. Statistical Analysis: Descriptive statistics was used to express results about ASV use, early adverse reactions to ASV, premedication and clinical outcomes. Univariate and multivariate analysis was performed to find out significant risk factors associated with mortality. Results: The main indication for ASV was vasculotoxic snake bite (75%) followed by neurotoxic snake bite (16%). Mean dose of ASV was 18.63 ± 14.52 vials. Prophylactic premedication with corticosteroids alone or in combination with antihistaminic was used in more than 70% patients. Early adverse reactions to ASV were seen in 4% patients. Neurotoxic snake bite was a significant risk factor associated with mortality in multivariate analysis. Conclusions: Neurotoxic snake bite is an independent predictor of mortality in snake bite patients. Currently used polyvalent ASV may be less effective in treating neurotoxic snake bite. PMID:26069363

  12. The Promiscuity of [beta]-Strand Pairing Allows for Rational Design of [beta]-Sheet Face Inversion

    SciTech Connect

    Makabe, Koki; Koide, Shohei

    2009-06-17

    Recent studies suggest the dominant role of main-chain H-bond formation in specifying {beta}-sheet topology. Its essentially sequence-independent nature implies a large degree of freedom in designing {beta}-sheet-based nanomaterials. Here we show rational design of {beta}-sheet face inversions by incremental deletions of {beta}-strands from the single-layer {beta}-sheet of Borrelia outer surface protein A. We show that a {beta}-sheet structure can be maintained when a large number of native contacts are removed and that one can design large-scale conformational transitions of a {beta}-sheet such as face inversion by exploiting the promiscuity of strand-strand interactions. High-resolution X-ray crystal structures confirmed the success of the design and supported the importance of main-chain H-bonds in determining {beta}-sheet topology. This work suggests a simple but effective strategy for designing and controlling nanomaterials based on {beta}-rich peptide self-assemblies.

  13. Rational Design Synthesis and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases

    SciTech Connect

    R Daher; M Coincon; M Fonvielle; P Gest; M Guerin; M Jackson; J Sygusch; M Therisod

    2011-12-31

    We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows Ki against class II Fbas from various pathogens in the nM range, with very high selectivity (up to 105). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.

  14. Kinetic control over pathway complexity in supramolecular polymerization through modulating the energy landscape by rational molecular design.

    PubMed

    Ogi, Soichiro; Fukui, Tomoya; Jue, Melinda L; Takeuchi, Masayuki; Sugiyasu, Kazunori

    2014-12-22

    Far-from-equilibrium thermodynamic systems that are established as a consequence of coupled equilibria are the origin of the complex behavior of biological systems. Therefore, research in supramolecular chemistry has recently been shifting emphasis from a thermodynamic standpoint to a kinetic one; however, control over the complex kinetic processes is still in its infancy. Herein, we report our attempt to control the time evolution of supramolecular assembly in a process in which the supramolecular assembly transforms from a J-aggregate to an H-aggregate over time. The transformation proceeds through a delicate interplay of these two aggregation pathways. We have succeeded in modulating the energy landscape of the respective aggregates by a rational molecular design. On the basis of this understanding of the energy landscape, programming of the time evolution was achieved through adjusting the balance between the coupled equilibria.

  15. Rational designed bipolar, conjugated polymer-DNA composite beacon for the sensitive detection of proteins and ions.

    PubMed

    Jia, Yongmei; Zuo, Xiaolei; Lou, Xiaoding; Miao, Mao; Cheng, Yong; Min, Xuehong; Li, Xinchun; Xia, Fan

    2015-04-01

    Nature owns remarkable capabilities in sensing target molecules, while the artificial biosensor lags far behind nature. Inspired by nature, we devise a new sensing platform that can specifically bind the molecules and synchronously initiate a specific signal response. We rationally designed a type of bipolar probe that is comprised of a hydrophilic DNA part and a hydrophobic conjugated polymer (CP) unit. In aqueous solution, they can form micelles with a hydrophobic CP core and a hydrophilic DNA shell. The aggregation-caused quenching suppresses the fluorescence of CP. Adding telomerase, the hydropathical profile of the bipolar probes is drastically regulated that results in the collapse of micelles and liberates fluorescence simultaneously. The probe has been used in both mimic systems and real urine samples (38 samples). We achieve sensitive and specific detection of telomerase and obtain clearly classification for normal people and cancer patients. It can also be used in a signal off sensor that is used to detect mercury ions.

  16. Rational Design of an α-Ketoamide-Based Near-Infrared Fluorescent Probe Specific for Hydrogen Peroxide in Living Systems.

    PubMed

    Xie, Xilei; Yang, Xiu'e; Wu, Tianhong; Li, Yong; Li, Mengmeng; Tan, Qi; Wang, Xu; Tang, Bo

    2016-08-16

    Hydrogen peroxide, an important biomolecule, receives earnest attention because of its physiological and pathological functions. In this Article, we present the rational design, characterization, and biological application of a mitochondria-targetable NIR fluorescent sensor, Mito-NIRHP, for hydrogen peroxide visualization. Mito-NIRHP utilizes a unique reaction switch, α-ketoamide moiety, to turn on a highly specific, sensitive, and rapid fluorescence response toward hydrogen peroxide coupled with the intramolecular charge transfer strategy. Mito-NIRHP is competent to track endogenously produced hydrogen peroxide in both living cells and living animals. In addition, utilizing Mito-NIRHP, overgeneration of hydrogen peroxide during ischemia-reperfusion injury was directly visualized at both cell and organ levels.

  17. Structure-Based Rational Design of Prodrugs To Enable Their Combination with Polymeric Nanoparticle Delivery Platforms for Enhanced Antitumor Efficacy**

    PubMed Central

    Wang, Hangxiang; Xie, Haiyang; Wu, Jiaping; Wei, Xuyong; Zhou, Lin; Xu, Xiao; Zheng, Shusen

    2014-01-01

    Drug-loaded nanoparticles (NPs) are of particular interest for efficient cancer therapy due to their improved drug delivery and therapeutic index in various types of cancer. However, the encapsulation of many chemotherapeutics into delivery NPs is often hampered by their unfavorable physicochemical properties. Here, we employed a drug reform strategy to construct a small library of SN-38 (7-ethyl-10-hydroxycamptothecin)-derived prodrugs, in which the phenolate group was modified with a variety of hydrophobic moieties. This esterification fine-tuned the polarity of the SN-38 molecule and enhanced the lipophilicity of the formed prodrugs, thereby inducing their self-assembly into biodegradable poly(ethylene glycol)-block-poly(d,l-lactic acid) (PEG-PLA) nanoparticulate structures. Our strategy combining the rational engineering of prodrugs with the pre-eminent features of conventionally used polymeric materials should open new avenues for designing more potent drug delivery systems as a therapeutic modality. PMID:25196427

  18. Rational design of a protein that binds integrin αvβ3 outside the ligand binding site

    PubMed Central

    Turaga, Ravi Chakra; Yin, Lu; Yang, Jenny J.; Lee, Hsiauwei; Ivanov, Ivaylo; Yan, Chunli; Yang, Hua; Grossniklaus, Hans E.; Wang, Siming; Ma, Cheng; Sun, Li; Liu, Zhi-Ren

    2016-01-01

    Integrin αvβ3 expression is altered in various diseases and has been proposed as a drug target. Here we use a rational design approach to develop a therapeutic protein, which we call ProAgio, that binds to integrin αvβ3 outside the classical ligand-binding site. We show ProAgio induces apoptosis of integrin αvβ3-expressing cells by recruiting and activating caspase 8 to the cytoplasmic domain of integrin αvβ3. ProAgio also has anti-angiogenic activity and strongly inhibits growth of tumour xenografts, but does not affect the established vasculature. Toxicity analyses demonstrate that ProAgio is not toxic to mice. Our study reports a new integrin-targeting agent with a unique mechanism of action, and provides a template for the development of integrin-targeting therapeutics. PMID:27241473

  19. Controlling resistant bacteria with a novel class of β-lactamase inhibitor peptides: from rational design to in vivo analyses

    PubMed Central

    Mandal, Santi M.; Migliolo, Ludovico; Silva, Osmar N.; Fensterseifer, Isabel C. M.; Faria-Junior, Celio; Dias, Simoni C.; Basak, Amit; Hazra, Tapas K.; Franco, Octávio L.

    2014-01-01

    Peptide rational design was used here to guide the creation of two novel short β-lactamase inhibitors, here named dBLIP-1 and -2, with length of five amino acid residues. Molecular modeling associated with peptide synthesis improved bactericidal efficacy in addition to amoxicillin, ampicillin and cefotaxime. Docked structures were consistent with calorimetric analyses against bacterial β-lactamases. These two compounds were further tested in mice. Whereas commercial antibiotics alone failed to cure mice infected with Staphylococcus aureus and Escherichia coli expressing β-lactamases, infection was cleared when treated with antibiotics in combination with dBLIPs, clearly suggesting that peptides were able to neutralize bacterial resistance. Moreover, immunological assays were also performed showing that dBLIPs were unable to modify mammalian immune response in both models, reducing the risks of collateral effects. In summary, the unusual peptides here described provide leads to overcome β-lactamase-based resistance, a remarkable clinical challenge. PMID:25109311

  20. Rational design of organophosphorus hydrolase with high catalytic efficiency for detoxifying a V-type nerve agent.

    PubMed

    Jeong, Young-Su; Choi, Jung Min; Kyeong, Hyun-Ho; Choi, Jae-Youl; Kim, Eui-Joong; Kim, Hak-Sung

    2014-07-01

    V-type nerve agents, known as VX, are organophosphate (OP) compounds, and show extremely toxic effects on human and animals by causing cholinergic overstimulation of synapses. The bacterial organophosphorus hydrolase (OPH) has attracted much attention for detoxifying V-type agents through hydrolysis of the P-S bond. However, low catalytic efficiency of OPH has limited the practical use of the enzyme. Here we present rational design of OPH with high catalytic efficiency for a V-type nerve agent. Based on the model structure of the enzyme and substrate docking simulation, we predicted the key residues that appear to enhance the access of the substrate to the active site of the enzyme, and constructed numerous OPH mutants. Of them, double mutant, L271/Y309A, was shown to exhibit a 150-fold higher catalytic efficiency for VX than the wild-type.

  1. Rational design of a protein that binds integrin αvβ3 outside the ligand binding site.

    PubMed

    Turaga, Ravi Chakra; Yin, Lu; Yang, Jenny J; Lee, Hsiauwei; Ivanov, Ivaylo; Yan, Chunli; Yang, Hua; Grossniklaus, Hans E; Wang, Siming; Ma, Cheng; Sun, Li; Liu, Zhi-Ren

    2016-05-31

    Integrin αvβ3 expression is altered in various diseases and has been proposed as a drug target. Here we use a rational design approach to develop a therapeutic protein, which we call ProAgio, that binds to integrin αvβ3 outside the classical ligand-binding site. We show ProAgio induces apoptosis of integrin αvβ3-expressing cells by recruiting and activating caspase 8 to the cytoplasmic domain of integrin αvβ3. ProAgio also has anti-angiogenic activity and strongly inhibits growth of tumour xenografts, but does not affect the established vasculature. Toxicity analyses demonstrate that ProAgio is not toxic to mice. Our study reports a new integrin-targeting agent with a unique mechanism of action, and provides a template for the development of integrin-targeting therapeutics.

  2. One-pot synthesis of MWW zeolite nanosheets using a rationally designed organic structure-directing agent

    PubMed Central

    Luo, Helen Y.; Michaelis, Vladimir K.; Hodges, Sydney; Griffin, Robert G.

    2015-01-01

    A new material MIT-1 comprised of delaminated MWW zeolite nanosheets is synthesized in one-pot using a rationally designed organic structure-directing agent (OSDA). The OSDA is comprised of a hydrophilic head segment that resembles the OSDA used to synthesize the zeolite precursor MCM22(P), a hydrophobic tail segment that resembles the swelling agent used to swell MCM22(P), and a di-quaternary ammonium linker that connects both segments. MIT-1 features high crystallinity and surface areas exceeding 500 m2g−1, and can be synthesized over a wide synthesis window that includes Si/Al ratios ranging from 13 to 67. Characterization data reveal high mesoporosity and acid strength with no detectable amorphous silica phases. Compared to MCM-22 and MCM-56, MIT-1 shows a three-fold increase in catalytic activity for the Friedel-Crafts alkylation of benzene with benzyl alcohol. PMID:26478803

  3. Joint Experimental, in Silico, and NMR Studies toward the Rational Design of Iminium-Based Organocatalyst Derived from Renewable Sources.

    PubMed

    Gerosa, Gabriela G; Spanevello, Rolando A; Suárez, Alejandra G; Sarotti, Ariel M

    2015-08-01

    An efficient organocatalyst for iminium-ion based asymmetric Diels-Alder (DA) reactions has been rationally designed. The most influential structure-activity relationships were determined experimentally, while DFT calculations and NMR studies provided further mechanistic insight. This knowledge guided an in silico screening of 62 different catalysts using an ONIOM(B3LYP/6-31G*:AM1) transition-state modeling, which showed good correlation between theory and experiment. The top-scored compound was easily synthesized from levoglucosenone, a biomass-derived chiral enone, and evaluated in the DA reaction between (E)-cinnamaldehyde and cyclopentadiene. In line with the computational finding, excellent results (up to 97% ee) were obtained. In addition, the catalyst could be easily recovered and reused with no loss in its catalytic activity.

  4. Rational Design of a Dephosphorylation-Resistant Reporter Enables Single-Cell Measurement of Tyrosine Kinase Activity.

    PubMed

    Turner, Abigail H; Lebhar, Michael S; Proctor, Angela; Wang, Qunzhao; Lawrence, David S; Allbritton, Nancy L

    2016-02-19

    Although peptide-based reporters of protein tyrosine kinase (PTK) activity have been used to study PTK enzymology in vitro, the application of these reporters to intracellular conditions is compromised by their dephosphorylation, preventing PTK activity measurements. Nonproteinogenic amino acids may be utilized to rationally design selective peptidic ligands by accessing greater chemical and structural diversity than is available using the native amino acids. We describe a peptidic reporter that, upon phosphorylation by the epidermal growth factor receptor (EGFR), is resistant to dephosphorylation both in vitro and in cellulo. The reporter contains a conformationally constrained phosphorylatable moiety (7-(S)-hydroxy-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) in the place of L-tyrosine and is efficiently phosphorylated in A431 epidermoid carcinoma cells. Dephosphorylation of the reporter occurs 3 orders of magnitude more slowly compared with that of the conventional tyrosine-containing reporter.

  5. Rational Design of Diketopyrrolopyrrole-Based Small Molecules as Donating Materials for Organic Solar Cells

    PubMed Central

    Jin, Ruifa; Wang, Kai

    2015-01-01

    A series of diketopyrrolopyrrole-based small molecules have been designed to explore their optical, electronic, and charge transport properties as organic solar cell (OSCs) materials. The calculation results showed that the designed molecules can lower the band gap and extend the absorption spectrum towards longer wavelengths. The designed molecules own the large longest wavelength of absorption spectra, the oscillator strength, and absorption region values. The optical, electronic, and charge transport properties of the designed molecules are affected by the introduction of different π-bridges and end groups. We have also predicted the mobility of the designed molecule with the lowest total energies. Our results reveal that the designed molecules are expected to be promising candidates for OSC materials. Additionally, the designed molecules are expected to be promising candidates for electron and/or hole transport materials. On the basis of our results, we suggest that molecules under investigation are suitable donors for [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and its derivatives as acceptors of OSCs. PMID:26343640

  6. Rational Design of Diketopyrrolopyrrole-Based Small Moleculesas Donating Materials for Organic Solar Cells.

    PubMed

    Jin, Ruifa; Wang, Kai

    2015-01-01

    A series of diketopyrrolopyrrole-based small molecules have been designed to explore their optical, electronic, and charge transport properties as organic solar cell(OSCs) materials. The calculation results showed that the designed molecules can lower the band gap and extend the absorption spectrum towards longer wavelengths.The designed molecules own the large longest wavelength of absorption spectra,the oscillator strength, and absorption region values. The optical, electronic, and charge transport properties of the designed molecules are affected by the introduction of different π-bridges and end groups. We have also predicted the mobility of the designed molecule with the lowest total energies. Our results reveal that the designed molecules are expected to be promising candidates for OSC materials. Additionally, the designed molecules are expected to be promising candidates for electron and/or hole transport materials. On the basis of our results, we suggest that molecules under investigation are suitable donors for[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and its derivatives as acceptors of OSCs. PMID:26343640

  7. Rational Design of Diketopyrrolopyrrole-Based Small Moleculesas Donating Materials for Organic Solar Cells.

    PubMed

    Jin, Ruifa; Wang, Kai

    2015-08-27

    A series of diketopyrrolopyrrole-based small molecules have been designed to explore their optical, electronic, and charge transport properties as organic solar cell(OSCs) materials. The calculation results showed that the designed molecules can lower the band gap and extend the absorption spectrum towards longer wavelengths.The designed molecules own the large longest wavelength of absorption spectra,the oscillator strength, and absorption region values. The optical, electronic, and charge transport properties of the designed molecules are affected by the introduction of different π-bridges and end groups. We have also predicted the mobility of the designed molecule with the lowest total energies. Our results reveal that the designed molecules are expected to be promising candidates for OSC materials. Additionally, the designed molecules are expected to be promising candidates for electron and/or hole transport materials. On the basis of our results, we suggest that molecules under investigation are suitable donors for[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and its derivatives as acceptors of OSCs.

  8. Rational Design of Bioelectrochemically Multifunctional Film with Oxidase, Ferrocene, and Graphene Oxide for Development of in Vivo Electrochemical Biosensors.

    PubMed

    Wang, Xiuyun; Li, Qian; Xu, Jingjing; Wu, Shuo; Xiao, Tongfang; Hao, Jie; Yu, Ping; Mao, Lanqun

    2016-06-01

    This study demonstrates a new strategy to develop in vivo electrochemical biosensors through rational design and simple formation of bioelectrochemically multifunctional film (BMF). The BMF is rationally designed by first efficiently incorporating oxidase, ferrocene mediator, and graphene oxide into polymaleimidostyrene/polystyrene (PMS/PS) matrix to form a homogeneous mixture and then simply formed by drop-coating the mixture onto solid conducting substrate. By using the as-formed BMF, electrochemical biosensors could be constructed with a technical simplicity and high reproducibility. To illustrate the BMF-based biosensors for in vivo applications, we directly couple the biosensors to in vivo microdialysis to establish an online electrochemical system (OECS) for in vivo monitoring of glucose in rat auditory cortex during salicylate-induced tinnitus model. The OECS with the BMF-based biosensor as the detector shows a linear response toward glucose within a concentration range from 50 to 500 μM with a detection limit of 10 μM (S/N = 3). Additionally, the OECS is stable and does not suffer from the interference from the electroactive species endogenously coexisting in the brain microdialysate. With the BMF-based OECS, the basal level of glucose in the microdialysate continuously sampled from rat auditory cortex is determined to be 120 ± 10 μM (n = 5). After the rats were administrated with salicylate to induce transient tinnitus, the microdialysate glucose concentration in the rat auditory cortex remarkably increased to 433 ± 190 μM (n = 5) at the time point of 1.5 h. This study essentially offers a new, technically simple and reproducible approach to development of in vivo electrochemical biosensors, which is envisaged to be relatively useful for understanding of the molecular basis of brain functions. PMID:27146343

  9. Rational Design of Bioelectrochemically Multifunctional Film with Oxidase, Ferrocene, and Graphene Oxide for Development of in Vivo Electrochemical Biosensors.

    PubMed

    Wang, Xiuyun; Li, Qian; Xu, Jingjing; Wu, Shuo; Xiao, Tongfang; Hao, Jie; Yu, Ping; Mao, Lanqun

    2016-06-01

    This study demonstrates a new strategy to develop in vivo electrochemical biosensors through rational design and simple formation of bioelectrochemically multifunctional film (BMF). The BMF is rationally designed by first efficiently incorporating oxidase, ferrocene mediator, and graphene oxide into polymaleimidostyrene/polystyrene (PMS/PS) matrix to form a homogeneous mixture and then simply formed by drop-coating the mixture onto solid conducting substrate. By using the as-formed BMF, electrochemical biosensors could be constructed with a technical simplicity and high reproducibility. To illustrate the BMF-based biosensors for in vivo applications, we directly couple the biosensors to in vivo microdialysis to establish an online electrochemical system (OECS) for in vivo monitoring of glucose in rat auditory cortex during salicylate-induced tinnitus model. The OECS with the BMF-based biosensor as the detector shows a linear response toward glucose within a concentration range from 50 to 500 μM with a detection limit of 10 μM (S/N = 3). Additionally, the OECS is stable and does not suffer from the interference from the electroactive species endogenously coexisting in the brain microdialysate. With the BMF-based OECS, the basal level of glucose in the microdialysate continuously sampled from rat auditory cortex is determined to be 120 ± 10 μM (n = 5). After the rats were administrated with salicylate to induce transient tinnitus, the microdialysate glucose concentration in the rat auditory cortex remarkably increased to 433 ± 190 μM (n = 5) at the time point of 1.5 h. This study essentially offers a new, technically simple and reproducible approach to development of in vivo electrochemical biosensors, which is envisaged to be relatively useful for understanding of the molecular basis of brain functions.

  10. Improving the specific activity of β-mannanase from Aspergillus niger BK01 by structure-based rational design.

    PubMed

    Huang, Jian-Wen; Chen, Chun-Chi; Huang, Chun-Hsiang; Huang, Ting-Yung; Wu, Tzu-Hui; Cheng, Ya-Shan; Ko, Tzu-Ping; Lin, Cheng-Yen; Liu, Je-Ruei; Guo, Rey-Ting

    2014-03-01

    β-Mannanase has found various biotechnological applications because it is capable of degrading mannans into smaller sugar components. A highly potent example is the thermophilic β-mannanase from Aspergillus niger BK01 (ManBK), which can be efficiently expressed in industrial yeast strains and is thus an attractive candidate for commercial utilizations. In order to understand the molecular mechanism, which helps in strategies to improve the enzyme's performance that would meet industrial demands, 3D-structural information is a great asset. Here, we present the 1.57Å crystal structure of ManBK. The protein adopts a typical (β/α)8 fold that resembles the other GH5 family members. Polysaccharides were subsequently modeled into the substrate binding groove to identify the residues and structural features that may be involved in the catalytic reaction. Based on the structure, rational design was conducted to engineer ManBK in an attempt to enhance its enzymatic activity. Among the 23 mutants that we constructed, the most promising Y216W showed an 18±2.7% increase in specific activity by comparison with the wild type enzyme. The optimal temperature and heat tolerance profiles of Y216W were similar to those of the wild type, manifesting a preserved thermostability. Kinetic studies showed that Y216W has higher kcat values than the wild type enzyme, suggesting a faster turnover rate of catalysis. In this study we applied rational design to ManBK by using its crystal structure as a basis and identified the Y216W mutant that shows great potentials in industrial applications.

  11. Model-based rational feedback controller design for closed-loop deep brain stimulation of Parkinson's disease

    NASA Astrophysics Data System (ADS)

    Gorzelic, P.; Schiff, S. J.; Sinha, A.

    2013-04-01

    Objective. To explore the use of classical feedback control methods to achieve an improved deep brain stimulation (DBS) algorithm for application to Parkinson's disease (PD). Approach. A computational model of PD dynamics was employed to develop model-based rational feedback controller design. The restoration of thalamocortical relay capabilities to patients suffering from PD is formulated as a feedback control problem with the DBS waveform serving as the control input. Two high-level control strategies are tested: one that is driven by an online estimate of thalamic reliability, and another that acts to eliminate substantial decreases in the inhibition from the globus pallidus interna (GPi) to the thalamus. Control laws inspired by traditional proportional-integral-derivative (PID) methodology are prescribed for each strategy and simulated on this computational model of the basal ganglia network. Main Results. For control based upon thalamic reliability, a strategy of frequency proportional control with proportional bias delivered the optimal control achieved for a given energy expenditure. In comparison, control based upon synaptic inhibitory output from the GPi performed very well in comparison with those of reliability-based control, with considerable further reduction in energy expenditure relative to that of open-loop DBS. The best controller performance was amplitude proportional with derivative control and integral bias, which is full PID control. We demonstrated how optimizing the three components of PID control is feasible in this setting, although the complexity of these optimization functions argues for adaptive methods in implementation. Significance. Our findings point to the potential value of model-based rational design of feedback controllers for Parkinson's disease.

  12. A crystal structure-guided rational design switching non-carbohydrate inhibitors' specificity between two β-GlcNAcase homologs

    PubMed Central

    Liu, Tian; Guo, Peng; Zhou, Yong; Wang, Jing; Chen, Lei; Yang, Huibin; Qian, Xuhong; Yang, Qing

    2014-01-01

    Selective inhibition of function-specific β-GlcNAcase has great potential in terms of drug design and biological research. The symmetrical bis-naphthalimide M-31850 was previously obtained by screening for specificity against human glycoconjugate-lytic β-GlcNAcase. Using protein-ligand co-crystallization and molecular docking, we designed an unsymmetrical dyad of naphthalimide and thiadiazole, Q2, that changes naphthalimide specificity from against a human glycoconjugate-lytic β-GlcNAcase to against insect and bacterial chitinolytic β-GlcNAcases. The crystallographic and in silico studies reveal that the naphthalimide ring can be utilized to bind different parts of these enzyme homologs, providing a new starting point to design specific inhibitors. Moreover, Q2-induced closure of the substrate binding pocket is the structural basis for its 13-fold increment in inhibitory potency. Q2 is the first non-carbohydrate inhibitor against chitinolytic β-GlcNAcases. This study provides a useful example of structure-based rationally designed inhibitors as potential pharmaceuticals or pesticides. PMID:25155420

  13. Insights into the Rational Design of Multi-Functional Fullerene Systems for Application in Blended Heterojunction Organic Solar Cells

    NASA Astrophysics Data System (ADS)

    Cowart, John S., Jr.

    Elucidating the structure-function relationships of organic semiconductors has been central to the advancement of organic photovoltaics (OPVs). In particular, enhancing the performance of p-type materials in disordered heterojunctions is broadly acknowledged as the principal factor leading to current trends of improved power conversion efficiencies (PCEs). However, two additional factors are crucially important for the next step forward in improving PCEs. First, investigating the influence, design and synthesis of new n-type materials, specifically fullerene acceptors, is of high importance. Second, because fullerene performance is often compromised by the morphological disorder of bulk heterojunctions, developing fullerenes systems that retain fidelity within disordered blends is also of broad interest. In light of these challenges, the field has witnessed a notable shift towards developing a comprehensive understanding of the design rules needed to advance the performance of fullerene acceptors in bulk heterojunctions. This work spotlights two multi-functional fullerene systems designed for blended heterojunctions. First, the synthesis of several novel fullerene-dye adducts with enhanced photon absorption will be presented. The ability of these adducts to absorb visible light in their pure state was evaluated and systematically examined versus their capacity to complement the absorption of low band gap donors and mediate charge transport in bulk heterojunctions. Second, mixed fullerene ternary blends were introduced as a strategy to stabilize the morphology in bulk heterojunctions and prolong operational lifetimes of OPV devices. Combined, these two systems offer unique insight into the rational design of fullerenes for their application in blended systems.

  14. A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins.

    PubMed

    Zhou, Zhaojuan; Xiao, Lu; Xiang, Yu; Zhou, Jun; Tong, Aijun

    2015-08-19

    DNA aptazymes are allosteric DNAzymes activated by the targets of DNA aptamers. They take the advantages of both aptamers and DNAzymes, which can recognize specific targets with high selectivity and catalyze multiple-turnover reactions for signal amplification, respectively, and have shown their great promise in many analytical applications. So far, however, the available examples of DNA aptazyme sensors are still limited in utilizing only several DNAzymes and DNA aptamers, most likely due to the lack of a general and simple approach for rational design. Herein, we have developed such a general approach for designing fluorescent DNA aptazyme sensors. In this approach, aptamers and DNAzymes are connected at the ends to avoid any change in their original sequences, therefore enabling the general use of different aptamers and DNAzymes in the design. Upon activation of the aptazymes by the targets of interest, the rate of fluorescence enhancement via the cleavage of a dually labeled substrate by the active aptazymes is then monitored for target quantification. Two DNAzymes and two aptamers are used as examples for the design of three fluorescent aptazyme sensors, and they all show high selectivity and sensitivity for the detection of their targets. More DNA aptazyme sensors for a broader range of targets could be developed by this general approach as long as suitable DNAzymes and aptamers are used.

  15. A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins.

    PubMed

    Zhou, Zhaojuan; Xiao, Lu; Xiang, Yu; Zhou, Jun; Tong, Aijun

    2015-08-19

    DNA aptazymes are allosteric DNAzymes activated by the targets of DNA aptamers. They take the advantages of both aptamers and DNAzymes, which can recognize specific targets with high selectivity and catalyze multiple-turnover reactions for signal amplification, respectively, and have shown their great promise in many analytical applications. So far, however, the available examples of DNA aptazyme sensors are still limited in utilizing only several DNAzymes and DNA aptamers, most likely due to the lack of a general and simple approach for rational design. Herein, we have developed such a general approach for designing fluorescent DNA aptazyme sensors. In this approach, aptamers and DNAzymes are connected at the ends to avoid any change in their original sequences, therefore enabling the general use of different aptamers and DNAzymes in the design. Upon activation of the aptazymes by the targets of interest, the rate of fluorescence enhancement via the cleavage of a dually labeled substrate by the active aptazymes is then monitored for target quantification. Two DNAzymes and two aptamers are used as examples for the design of three fluorescent aptazyme sensors, and they all show high selectivity and sensitivity for the detection of their targets. More DNA aptazyme sensors for a broader range of targets could be developed by this general approach as long as suitable DNAzymes and aptamers are used. PMID:26343441

  16. Rational Design of Fluorescent Phthalazinone Derivatives for One- and Two-Photon Imaging.

    PubMed

    Yang, Lingfei; Zhu, Yuanjun; Shui, Mengyang; Zhou, Tongliang; Cai, Yuanbo; Wang, Wei; Xu, Fengrong; Niu, Yan; Wang, Chao; Zhang, Jun-Long; Xu, Ping; Yuan, Lan; Liang, Lei

    2016-08-22

    Phthalazinone derivatives were designed as optical probes for one- and two-photon fluorescence microscopy imaging. The design strategy involves stepwise extension and modification of pyridazinone by 1) expansion of pyridazinone to phthalazinone, a larger conjugated system, as the electron acceptor, 2) coupling of electron-donating aromatic groups such as N,N-diethylaminophenyl, thienyl, naphthyl, and quinolyl to the phthalazinone, and 3) anchoring of an alkyl chain to the phthalazinone with various terminal substituents such as triphenylphosphonio, morpholino, triethylammonio, N-methylimidazolio, pyrrolidino, and piperidino. Theoretical calculations were utilized to verify the initial design. The desired fluorescent probes were synthesized by two different routes in considerable yields. Twenty-two phthalazinone derivatives were synthesized and their photophysical properties were measured. Selected compounds were applied in cell imaging, and valuable information was obtained. Furthermore, the designed compounds showed excellent performance in two-photon microscopic imaging of mouse brain slices.

  17. Rational Mutagenesis to Support Structure-based Drug Design: MAPKAP Kinase 2 as a Case Study

    SciTech Connect

    M Argiriadi; S Sousa; D Banach; D Marcotte; T Xiang; M Tomlinson; M Demers; C Harris; S Kwak; et al.

    2011-12-31

    Structure-based drug design (SBDD) can provide valuable guidance to drug discovery programs. Robust construct design and expression, protein purification and characterization, protein crystallization, and high-resolution diffraction are all needed for rapid, iterative inhibitor design. We describe here robust methods to support SBDD on an oral anti-cytokine drug target, human MAPKAP kinase 2 (MK2). Our goal was to obtain useful diffraction data with a large number of chemically diverse lead compounds. Although MK2 structures and structural methods have been reported previously, reproducibility was low and improved methods were needed. Our construct design strategy had four tactics: N- and C-terminal variations; entropy-reducing surface mutations; activation loop deletions; and pseudoactivation mutations. Generic, high-throughput methods for cloning and expression were coupled with automated liquid dispensing for the rapid testing of crystallization conditions with minimal sample requirements. Initial results led to development of a novel, customized robotic crystallization screen that yielded MK2/inhibitor complex crystals under many conditions in seven crystal forms. In all, 44 MK2 constructs were generated, {approx}500 crystals were tested for diffraction, and {approx}30 structures were determined, delivering high-impact structural data to support our MK2 drug design effort. Key lessons included setting reasonable criteria for construct performance and prioritization, a willingness to design and use customized crystallization screens, and, crucially, initiation of high-throughput construct exploration very early in the drug discovery process.

  18. Combined Bioinformatic and Rational Design Approach To Develop Antimicrobial Peptides against Mycobacterium tuberculosis

    PubMed Central

    Pearson, C. Seth; Kloos, Zachary; Murray, Brian; Tabe, Ebot; Gupta, Monica; Kwak, Jun Ha; Karande, Pankaj

    2016-01-01

    Drug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens is Mycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity against M. tuberculosis using a combination of “database filtering” bioinformatics, protein engineering, and de novo design. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) against M. tuberculosis and also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of the M. tuberculosis membrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created. PMID:26902758

  19. Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering

    PubMed Central

    Lakin, Matthew R.; Brown, Carl W.; Horwitz, Eli K.; Fanning, M. Leigh; West, Hannah E.; Stefanovic, Darko; Graves, Steven W.

    2014-01-01

    The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics. PMID:25347066

  20. Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.

    PubMed

    Lakin, Matthew R; Brown, Carl W; Horwitz, Eli K; Fanning, M Leigh; West, Hannah E; Stefanovic, Darko; Graves, Steven W

    2014-01-01

    The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics.

  1. Combined Bioinformatic and Rational Design Approach To Develop Antimicrobial Peptides against Mycobacterium tuberculosis.

    PubMed

    Pearson, C Seth; Kloos, Zachary; Murray, Brian; Tabe, Ebot; Gupta, Monica; Kwak, Jun Ha; Karande, Pankaj; McDonough, Kathleen A; Belfort, Georges

    2016-05-01

    Drug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens is Mycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity against M. tuberculosis using a combination of "database filtering" bioinformatics, protein engineering, and de novo design. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) against M. tuberculosis and also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of the M. tuberculosis membrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created.

  2. Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin

    SciTech Connect

    Lin, Y.W.; Robinson, H.; Yeung, N.; Gao, Y.-G.; Miner, K. D.; Tian, S.; Lu, Y.

    2010-05-11

    A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu has a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.

  3. Roles of Glutamates and Metal ions in a Rationally Designed Nitric Oxide Reductase Based on Myoglobin

    SciTech Connect

    Y Lin; N Yeung; Y Gao; K Miner; S Tian; H Robinson; Y Lu

    2011-12-31

    A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu has a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.

  4. Snake Filament Eruption

    NASA Video Gallery

    A very long solar filament that had been snaking around the Sun erupted on Dec. 6, 2010 with a flourish. NASA's Solar Dynamics Observatory (SDO) caught the action in dramatic detail in extreme ultr...

  5. Standby Gasoline Rationing Plan

    SciTech Connect

    1980-06-01

    The final rules adopted by the President for a Standby Gasoline Rationing Plan are presented. The plan provides that eligibility for ration allotments will be determined primarily on the basis of motor vehicle registrations, taking into account historical differences in the use of gasoline among states. The regulations also provide authority for supplemental allotments to firms so that their allotment will equal a specified percentage of gasoline use during a base period. Priority classifications, i.e., agriculture, defense, etc., are established to assure adequate gasoline supplies for designated essential services. Ration rights must be provided by end-users to their suppliers for each gallon sold. DOE will regulate the distribution of gasoline at the wholesale level according to the transfer by suppliers of redeemed ration rights and the gasoline allocation regulations. Ration rights are transferable. A ration banking system is created to facilitate transfers of ration rights. Each state will be provided with a reserve of ration rights to provide for hardship needs and to alleviate inequities. (DC)

  6. Rational design of a DNA wire possessing an extremely high hole transport ability.

    PubMed

    Okamoto, Akimitsu; Tanaka, Kazuo; Saito, Isao

    2003-04-30

    DNA is a promising conductive biopolymer. However, there are problems that need to be solved to realize real DNA wires. These include the low efficiency of hole transport and the serious oxidative damage that can occur during hole transport. We have demonstrated a protocol for the design of a DNA wire that can effectively mediate hole transport that is not adversely affected by oxidation during hole transport through the DNA duplex. We have synthesized a stable and effective DNA wire by incorporating a designer nucleobase, benzodeazaadenine derivatives, which have lower oxidation potentials and wider stacking areas but are not decomposed during hole transport.

  7. Pulmonoscopy of Snakes.

    PubMed

    Knotek, Zdenek; Jekl, Vladimir

    2015-09-01

    Pulmonoscopy is a practical diagnostic tool for investigating respiratory diseases in snakes. Two different approaches exist for pulmonoscopy, tracheal and transcutaneous. The access to the proximal or distal lung is limited by the length and diameter of the endoscope when using the tracheal approach. The transcutaneous approach allows direct evaluation of the lung and distal trachea through the air sac. Both of the methods are safe, and specific contraindications for pulmonoscopy in snakes are not known except for any anesthesia contraindication.

  8. Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding.

    PubMed

    He, Linling; Cheng, Yushao; Kong, Leopold; Azadnia, Parisa; Giang, Erick; Kim, Justin; Wood, Malcolm R; Wilson, Ian A; Law, Mansun; Zhu, Jiang

    2015-08-04

    Development of a prophylactic vaccine against hepatitis C virus (HCV) has been hampered by the extraordinary viral diversity and the poor host immune response. Scaffolding, by grafting an epitope onto a heterologous protein scaffold, offers a possible solution to epitope vaccine design. In this study, we designed and characterized epitope vaccine antigens for the antigenic sites of HCV envelope glycoproteins E1 (residues 314-324) and E2 (residues 412-423), for which neutralizing antibody-bound structures are available. We first combined six structural alignment algorithms in a "scaffolding meta-server" to search for diverse scaffolds that can structurally accommodate the HCV epitopes. For each antigenic site, ten scaffolds were selected for computational design, and the resulting epitope scaffolds were analyzed using structure-scoring functions and molecular dynamics simulation. We experimentally confirmed that three E1 and five E2 epitope scaffolds bound to their respective neutralizing antibodies, but with different kinetics. We then investigated a "multivalent scaffolding" approach by displaying 24 copies of an epitope scaffold on a self-assembling nanoparticle, which markedly increased the avidity of antibody binding. Our study thus demonstrates the utility of a multi-scale scaffolding strategy in epitope vaccine design and provides promising HCV immunogens for further assessment in vivo.

  9. Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution

    PubMed Central

    Barrozo, Alexandre; Borstnar, Rok; Marloie, Gaël; Kamerlin, Shina Caroline Lynn

    2012-01-01

    Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies. PMID:23202907

  10. Peer Mentoring in Long-Term Care: Rational, Design, and Retention

    ERIC Educational Resources Information Center

    Hegeman, Carol; Hoskinson, Debi; Munro, Heather; Maiden, Patricia; Pillemer, Karl

    2007-01-01

    This article describes two successful peer-mentoring programs designed to improve the quality of care in nursing homes and retention rates among direct care staff. The first program, "Growing Strong Roots," examined CNA retention rates and the second program, "Peer Mentoring for Long Term Charge Nurses," examined RN and LPN retention rates. These…

  11. Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding

    NASA Astrophysics Data System (ADS)

    He, Linling; Cheng, Yushao; Kong, Leopold; Azadnia, Parisa; Giang, Erick; Kim, Justin; Wood, Malcolm R.; Wilson, Ian A.; Law, Mansun; Zhu, Jiang

    2015-08-01

    Development of a prophylactic vaccine against hepatitis C virus (HCV) has been hampered by the extraordinary viral diversity and the poor host immune response. Scaffolding, by grafting an epitope onto a heterologous protein scaffold, offers a possible solution to epitope vaccine design. In this study, we designed and characterized epitope vaccine antigens for the antigenic sites of HCV envelope glycoproteins E1 (residues 314-324) and E2 (residues 412-423), for which neutralizing antibody-bound structures are available. We first combined six structural alignment algorithms in a “scaffolding meta-server” to search for diverse scaffolds that can structurally accommodate the HCV epitopes. For each antigenic site, ten scaffolds were selected for computational design, and the resulting epitope scaffolds were analyzed using structure-scoring functions and molecular dynamics simulation. We experimentally confirmed that three E1 and five E2 epitope scaffolds bound to their respective neutralizing antibodies, but with different kinetics. We then investigated a “multivalent scaffolding” approach by displaying 24 copies of an epitope scaffold on a self-assembling nanoparticle, which markedly increased the avidity of antibody binding. Our study thus demonstrates the utility of a multi-scale scaffolding strategy in epitope vaccine design and provides promising HCV immunogens for further assessment in vivo.

  12. Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding

    PubMed Central

    He, Linling; Cheng, Yushao; Kong, Leopold; Azadnia, Parisa; Giang, Erick; Kim, Justin; Wood, Malcolm R.; Wilson, Ian A.; Law, Mansun; Zhu, Jiang

    2015-01-01

    Development of a prophylactic vaccine against hepatitis C virus (HCV) has been hampered by the extraordinary viral diversity and the poor host immune response. Scaffolding, by grafting an epitope onto a heterologous protein scaffold, offers a possible solution to epitope vaccine design. In this study, we designed and characterized epitope vaccine antigens for the antigenic sites of HCV envelope glycoproteins E1 (residues 314–324) and E2 (residues 412–423), for which neutralizing antibody-bound structures are available. We first combined six structural alignment algorithms in a “scaffolding meta-server” to search for diverse scaffolds that can structurally accommodate the HCV epitopes. For each antigenic site, ten scaffolds were selected for computational design, and the resulting epitope scaffolds were analyzed using structure-scoring functions and molecular dynamics simulation. We experimentally confirmed that three E1 and five E2 epitope scaffolds bound to their respective neutralizing antibodies, but with different kinetics. We then investigated a “multivalent scaffolding” approach by displaying 24 copies of an epitope scaffold on a self-assembling nanoparticle, which markedly increased the avidity of antibody binding. Our study thus demonstrates the utility of a multi-scale scaffolding strategy in epitope vaccine design and provides promising HCV immunogens for further assessment in vivo. PMID:26238798

  13. Rational design of ultrastable and reversibly photoswitchable fluorescent proteins for super-resolution imaging of the bacterial periplasm

    PubMed Central

    El Khatib, Mariam; Martins, Alexandre; Bourgeois, Dominique; Colletier, Jacques-Philippe; Adam, Virgile

    2016-01-01

    Phototransformable fluorescent proteins are central to several nanoscopy approaches. As yet however, there is no available variant allowing super-resolution imaging in cell compartments that maintain oxidative conditions. Here, we report the rational design of two reversibly switchable fluorescent proteins able to fold and photoswitch in the bacterial periplasm, rsFolder and rsFolder2. rsFolder was designed by hybridisation of Superfolder-GFP with rsEGFP2, and inherited the fast folding properties of the former together with the rapid switching of the latter, but at the cost of a reduced switching contrast. Structural characterisation of the switching mechanisms of rsFolder and rsEGFP2 revealed different scenarios for chromophore cis-trans isomerisation and allowed designing rsFolder2, a variant of rsFolder that exhibits improved switching contrast and is amenable to RESOLFT nanoscopy. The rsFolders can be efficiently expressed in the E. coli periplasm, opening the door to the nanoscale investigation of proteins localised in hitherto non-observable cellular compartments. PMID:26732634

  14. Rational design of alpha-helical tandem repeat proteins with closed architectures

    PubMed Central

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L.; Bradley, Philip

    2015-01-01

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials1,2. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks3,4. The overall architecture of tandem repeat protein structures – which is dictated by the internal geometry and local packing of the repeat building blocks – is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners5–9, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis10. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid11 repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering12–20, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that – to our knowledge – is not yet present in the protein structure database21. PMID:26675735

  15. Rational design of α-helical tandem repeat proteins with closed architectures.

    PubMed

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L; Bradley, Philip

    2015-12-24

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.

  16. A rational design for the separation of metallic and semiconducting single-walled carbon nanotubes using a magnetic field

    NASA Astrophysics Data System (ADS)

    Luo, Chengzhi; Wan, Da; Jia, Junji; Li, Delong; Pan, Chunxu; Liao, Lei

    2016-06-01

    The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm2 V-1 s-1 and an on/off ratio of 106. We also established a model to quantitatively calculate the percentage of m-SWNTs on the substrate and this model shows a good match with the experimental data. Furthermore, our rational design also provides a new avenue for the growth of SWNTs with specific chirality and manipulated arrangement due to the difference of magnetic susceptibilities between different diameters, chiralities, and types.The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm2 V-1 s-1 and an on/off ratio of 106. We also established a model to quantitatively calculate the percentage of m

  17. Rationally designed fluorescently labeled sulfate-binding protein mutants: evaluation in the development of a sensing system for sulfate

    NASA Technical Reports Server (NTRS)

    Shrestha, Suresh; Salins, Lyndon L E.; Mark Ensor, C.; Daunert, Sylvia

    2002-01-01

    Periplasmic binding proteins from E. coli undergo large conformational changes upon binding their respective ligands. By attaching a fluorescent probe at rationally selected unique sites on the protein, these conformational changes in the protein can be monitored by measuring the changes in fluorescence intensity of the probe which allow the development of reagentless sensing systems for their corresponding ligands. In this work, we evaluated several sites on bacterial periplasmic sulfate-binding protein (SBP) for attachment of a fluorescent probe and rationally designed a reagentless sensing system for sulfate. Eight different mutants of SBP were prepared by employing the polymerase chain reaction (PCR) to introduce a unique cysteine residue at a specific location on the protein. The sites Gly55, Ser90, Ser129, Ala140, Leu145, Ser171, Val181, and Gly186 were chosen for mutagenesis by studying the three-dimensional X-ray crystal structure of SBP. An environment-sensitive fluorescent probe (MDCC) was then attached site-specifically to the protein through the sulfhydryl group of the unique cysteine residue introduced. Each fluorescent probe-conjugated SBP mutant was characterized in terms of its fluorescence properties and Ser171 was determined to be the best site for the attachment of the fluorescent probe that would allow for the development of a reagentless sensing system for sulfate. Three different environment-sensitive fluorescent probes (1,5-IAEDANS, MDCC, and acylodan) were studied with the SBP171 mutant protein. A calibration curve for sulfate was constructed using the labeled protein and relating the change in the fluorescence intensity with the amount of sulfate present in the sample. The detection limit for sulfate was found to be in the submicromolar range using this system. The selectivity of the sensing system was demonstrated by evaluating its response to other anions. A fast and selective sensing system with detection limits for sulfate in the

  18. A unique peptide deformylase platform to rationally design and challenge novel active compounds

    PubMed Central

    Fieulaine, Sonia; Alves de Sousa, Rodolphe; Maigre, Laure; Hamiche, Karim; Alimi, Mickael; Bolla, Jean-Michel; Taleb, Abbass; Denis, Alexis; Pagès, Jean-Marie; Artaud, Isabelle; Meinnel, Thierry; Giglione, Carmela

    2016-01-01

    Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae PDF could be used as PDF prototype as it allowed to get complete sets of 3-dimensional, biophysical and kinetic data with virtually any inhibitor compound. Structure-activity relationship analysis with this single reference system allowed us to reveal distinct binding modes for different PDF inhibitors and the key role of a hydrogen bond in potentiating the interaction between ligand and target. We propose this protein as an irreplaceable tool, allowing easy and relevant fine comparisons between series, to design, challenge and validate novel series of inhibitors. As proof-of-concept, we report here the design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug resistant clinical isolate. PMID:27762275

  19. Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design.

    PubMed

    Ferguson, Andrew L; Mann, Jaclyn K; Omarjee, Saleha; Ndung'u, Thumbi; Walker, Bruce D; Chakraborty, Arup K

    2013-03-21

    A prophylactic or therapeutic vaccine offers the best hope to curb the HIV-AIDS epidemic gripping sub-Saharan Africa, but it remains elusive. A major challenge is the extreme viral sequence variability among strains. Systematic means to guide immunogen design for highly variable pathogens like HIV are not available. Using computational models, we have developed an approach to translate available viral sequence data into quantitative landscapes of viral fitness as a function of the amino acid sequences of its constituent proteins. Predictions emerging from our computationally defined landscapes for the proteins of HIV-1 clade B Gag were positively tested against new in vitro fitness measurements and were consistent with previously defined in vitro measurements and clinical observations. These landscapes chart the peaks and valleys of viral fitness as protein sequences change and inform the design of immunogens and therapies that can target regions of the virus most vulnerable to selection pressure.

  20. Rational Design of a Bisphenol A Aptamer Selective Surface-Enhanced Raman Scattering Nanoprobe

    PubMed Central

    2015-01-01

    Surface-enhanced Raman scattering (SERS) optical nanoprobes offer a number of advantages for ultrasensitive analyte detection. These functionalized colloidal nanoparticles are a multifunctional assay component. providing a platform for conjugation to spectral tags, stabilizing polymers, and biorecognition elements such as aptamers or antibodies. We demonstrate the design and characterization of a SERS-active nanoprobe and investigate the nanoparticles’ biorecognition capabilities for use in a competitive binding assay. Specifically, the nanoprobe is designed for the quantification of bisphenol A (BPA) levels in the blood after human exposure to the toxin in food and beverage plastic packaging. The nanoprobes demonstrated specific affinity to a BPA aptamer with a dissociation constant Kd of 54 nM, and provided a dose-dependent SERS spectra with a limit of detection of 3 nM. Our conjugation approach shows the versatility of colloidal nanoparticles in assay development, acting as detectable spectral tagging elements and biologically active ligands concurrently. PMID:25329684

  1. Rational design of dynamic ammonium salt catalysts towards more flexible and selective function

    PubMed Central

    Ishihara, Kazuaki

    2009-01-01

    This review focuses on the development of dynamic ammonium salt catalysis for selective organic transformations conducted in our laboratory since 2002. Several important concepts in designing of catalysts are described with some examples. In particular, the practial synthesis of chiral 1,1′-binaphthyl-2,2′-disulfonic acid (BINSA) and its application in chiral ammonium salt catalysis for the enantioselective direct Mannich-type reaction are described. PMID:19838010

  2. Rational design of orally-active, pyrrolidine-based progesterone receptor partial agonists

    SciTech Connect

    Thompson, Scott K.; Washburn, David G.; Frazee, James S.; Madauss, Kevin P.; Hoang, Tram H.; Lapinski, Leahann; Grygielko, Eugene T.; Glace, Lindsay E.; Trizna, Walter; Williams, Shawn P.; Duraiswami, Chaya; Bray, Jeffrey D.; Laping, Nicholas J.

    2010-09-03

    Using the X-ray crystal structure of an amide-based progesterone receptor (PR) partial agonist bound to the PR ligand binding domain, a novel PR partial agonist class containing a pyrrolidine ring was designed. Members of this class of N-alkylpyrrolidines demonstrate potent and highly selective partial agonism of the progesterone receptor, and one of these analogs was shown to be efficacious upon oral dosing in the OVX rat model of estrogen opposition.

  3. Rational design of microRNA-siRNA chimeras for multifunctional target suppression.

    PubMed

    Jiang, Zhou; Liu, Weijun; Wang, Yuhui; Gao, Zhen; Gao, Ge; Wang, Xiaowei

    2013-12-01

    MicroRNAs (miRNAs) are involved in a variety of human diseases by simultaneously suppressing many gene targets. Thus, the therapeutic value of miRNAs has been intensely studied. However, there are potential limitations with miRNA-based therapeutics such as a relatively moderate impact on gene target regulation and cellular phenotypic control. To address these issues, we proposed to design new chimeric small RNAs (aiRNAs) by incorporating sequences from both miRNAs and siRNAs. These aiRNAs not only inherited functions from natural miRNAs, but also gained new functions of gene knockdown in an siRNA-like fashion. The improved efficacy of multifunctional aiRNAs was demonstrated in our study by design and testing of an aiRNA that inherited the functions of both miR-200a and an AKT1-targeting siRNA for simultaneous suppression of cancer cell motility and proliferation. The general principles of aiRNA design were further validated by engineering new aiRNAs mimicking another miRNA, miR-9. By regulating multiple cellular functions, aiRNAs could be used as an improved tool over miRNAs to target disease-related genes, thus alleviating our dependency on a limited number of miRNAs for the development of RNAi-based therapeutics.

  4. Computer-aided rational design of novel EBF analogues with an aromatic ring.

    PubMed

    Wang, Shanshan; Sun, Yufeng; Du, Shaoqing; Qin, Yaoguo; Duan, Hongxia; Yang, Xinling

    2016-06-01

    Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode between AgamOBP7 and novel (E)-β-farnesene (EBF) analogues with an aromatic ring. The ligand-binding cavity in OBP7 was found to be mostly hydrophobic due to the presence of several nonpolar residues. The interactions between the EBF analogues and the hydrophobic residues in the binding cavity increased in strength as the distance between them decreased. The EBF analogues with an N-methyl formamide or ester linkage had higher docking scores than those with an amide linkage. Moreover, delocalized π-π and electrostatic interactions were found to contribute significantly to the binding between the ligand benzene ring and nearby protein residues. To design new compounds with higher activity, four EBF analogues D1-D4 with a benzene ring were synthesized and evaluated based on their docking scores and binding affinities. D2, which had an N-methyl formamide group linkage, exhibited stronger binding than D1, which had an amide linkage. D4 exhibited particularly strong binding due to multiple hydrophobic interactions with the protein. This study provides crucial foundations for designing novel EBF analogues based on the OBP structure. Graphical abstract The design strategy of new EBF analogues based on the OBP7 structure. PMID:27251400

  5. Rational design and synthesis of an orally bioavailable peptide guided by NMR amide temperature coefficients

    PubMed Central

    Wang, Conan K.; Northfield, Susan E.; Colless, Barbara; Chaousis, Stephanie; Hamernig, Ingrid; Lohman, Rink-Jan; Nielsen, Daniel S.; Schroeder, Christina I.; Liras, Spiros; Price, David A.; Fairlie, David P.; Craik, David J.

    2014-01-01

    Enhancing the oral bioavailability of peptide drug leads is a major challenge in drug design. As such, methods to address this challenge are highly sought after by the pharmaceutical industry. Here, we propose a strategy to identify appropriate amides for N-methylation using temperature coefficients measured by NMR to identify exposed amides in cyclic peptides. N-methylation effectively caps these amides, modifying the overall solvation properties of the peptides and making them more membrane permeable. The approach for identifying sites for N-methylation is a rapid alternative to the elucidation of 3D structures of peptide drug leads, which has been a commonly used structure-guided approach in the past. Five leucine-rich peptide scaffolds are reported with selectively designed N-methylated derivatives. In vitro membrane permeability was assessed by parallel artificial membrane permeability assay and Caco-2 assay. The most promising N-methylated peptide was then tested in vivo. Here we report a novel peptide (15), which displayed an oral bioavailability of 33% in a rat model, thus validating the design approach. We show that this approach can also be used to explain the notable increase in oral bioavailability of a somatostatin analog. PMID:25416591

  6. Cancer Drug Delivery: Considerations in the Rational Design of Nanosized Bioconjugates

    PubMed Central

    2015-01-01

    In order to efficiently deliver anticancer agents to tumors, biocompatible nanoparticles or bioconjugates, including antibody–drug conjugates (ADCs), have recently been designed, synthesized, and tested, some even in clinical trials. Controlled delivery can be enhanced by changing specific design characteristics of the bioconjugate such as its size, the nature of the payload, and the surface features. The delivery of macromolecular drugs to cancers largely relies on the leaky nature of the tumor vasculature compared with healthy vessels in normal organs. When administered intravenously, macromolecular bioconjugates and nanosized agents tend to circulate for prolonged times, unless they are small enough to be excreted by the kidney or stealthy enough to evade the macrophage phagocytic system (MPS), formerly the reticulo-endothelial system (RES). Therefore, macromolecular bioconjugates and nanosized agents with long circulation times leak preferentially into tumor tissue through permeable tumor vessels and are then retained in the tumor bed due to reduced lymphatic drainage. This process is known as the enhanced permeability and retention (EPR) effect. However, success of cancer drug delivery only relying on the EPR effect is still limited. To cure cancer patients, further improvement of drug delivery is required by both designing superior agents and enhancing EPR effects. In this Review, we describe the basis of macromolecular or nanosized bioconjugate delivery into cancer tissue and discuss current diagnostic methods for evaluating leakiness of the tumor vasculature. Then, we discuss methods to augment conventional “permeability and retention” effects for macromolecular or nanosized bioconjugates in cancer tissue. PMID:25385142

  7. Computer-aided rational design of novel EBF analogues with an aromatic ring.

    PubMed

    Wang, Shanshan; Sun, Yufeng; Du, Shaoqing; Qin, Yaoguo; Duan, Hongxia; Yang, Xinling

    2016-06-01

    Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode between AgamOBP7 and novel (E)-β-farnesene (EBF) analogues with an aromatic ring. The ligand-binding cavity in OBP7 was found to be mostly hydrophobic due to the presence of several nonpolar residues. The interactions between the EBF analogues and the hydrophobic residues in the binding cavity increased in strength as the distance between them decreased. The EBF analogues with an N-methyl formamide or ester linkage had higher docking scores than those with an amide linkage. Moreover, delocalized π-π and electrostatic interactions were found to contribute significantly to the binding between the ligand benzene ring and nearby protein residues. To design new compounds with higher activity, four EBF analogues D1-D4 with a benzene ring were synthesized and evaluated based on their docking scores and binding affinities. D2, which had an N-methyl formamide group linkage, exhibited stronger binding than D1, which had an amide linkage. D4 exhibited particularly strong binding due to multiple hydrophobic interactions with the protein. This study provides crucial foundations for designing novel EBF analogues based on the OBP structure. Graphical abstract The design strategy of new EBF analogues based on the OBP7 structure.

  8. Toward rational protein crystallization: A Web server for the design of crystallizable protein variants

    PubMed Central

    Goldschmidt, Lukasz; Cooper, David R.; Derewenda, Zygmunt S.; Eisenberg, David

    2007-01-01

    Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for “stubborn crystallizers” is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss of conformational entropy upon crystallization and renders crystallization thermodynamically favorable. The method has been successfully used to crystallize more than 15 novel proteins, all stubborn crystallizers. But the choice of suitable sites for mutagenesis is not trivial. Herein, we announce a Web server, the surface entropy reduction prediction server (SERp server), designed to identify mutations that may facilitate crystallization. Suggested mutations are predicted based on an algorithm incorporating a conformational entropy profile, a secondary structure prediction, and sequence conservation. Minor considerations include the nature of flanking residues and gaps between mutation candidates. While designed to be used with default values, the server has many user-controlled parameters allowing for considerable flexibility. Within, we discuss (1) the methodology of the server, (2) how to interpret the results, and (3) factors that must be considered when selecting mutations. We also attempt to benchmark the server by comparing the server's predictions with successful SER structures. In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER. PMID:17656576

  9. Rational primer design greatly improves differential display-PCR (DD-PCR).

    PubMed Central

    Graf, D; Fisher, A G; Merkenschlager, M

    1997-01-01

    Since its conception in 1992, differential display PCR (DD-PCR) has attracted widespread interest. Theoretically an attractive cloning approach, it combines the comparative analysis of several samples with the sensitivity of PCR. Although a large number of studies embracing this technology have been initiated, few novel genes of interest have been identified, suggesting that the method has not realised its potential. The present report shows that by modifying primer design, sampling of differentially expressed genes can be greatly enhanced and relevant genes can be isolated. Using our modified conditions DD-PCR efficiently screens a wide range of gene expression levels, in which differences are represented on a linear scale. PMID:9153330

  10. Rational Design, Synthesis and Evaluation of Coumarin Derivatives as Protein-protein Interaction Inhibitors.

    PubMed

    De Luca, Laura; Agharbaoui, Fatima E; Gitto, Rosaria; Buemi, Maria Rosa; Christ, Frauke; Debyser, Zeger; Ferro, Stefania

    2016-09-01

    Herein we describe the design and synthesis of a new series of coumarin derivatives searching for novel HIV-1 integrase (IN) allosteric inhibitors. All new obtained compounds were tested in order to evaluate their ability to inhibit the interaction between the HIV-1 IN enzyme and the nuclear protein lens epithelium growth factor LEDGF/p75. A combined approach of docking and molecular dynamic simulations has been applied to clarify the activity of the new compounds. Specifically, the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA) was calculated, whereas hydrogen bond occupancies were monitored throughout simulations methods.

  11. Rational Design, Synthesis and Evaluation of Coumarin Derivatives as Protein-protein Interaction Inhibitors.

    PubMed

    De Luca, Laura; Agharbaoui, Fatima E; Gitto, Rosaria; Buemi, Maria Rosa; Christ, Frauke; Debyser, Zeger; Ferro, Stefania

    2016-09-01

    Herein we describe the design and synthesis of a new series of coumarin derivatives searching for novel HIV-1 integrase (IN) allosteric inhibitors. All new obtained compounds were tested in order to evaluate their ability to inhibit the interaction between the HIV-1 IN enzyme and the nuclear protein lens epithelium growth factor LEDGF/p75. A combined approach of docking and molecular dynamic simulations has been applied to clarify the activity of the new compounds. Specifically, the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA) was calculated, whereas hydrogen bond occupancies were monitored throughout simulations methods. PMID:27546050

  12. Research on Snake-Like Robot with Controllable Scales

    NASA Astrophysics Data System (ADS)

    Chen, Kailin; Zhao, Yuting; Chen, Shuping

    The purpose of this paper is to propose a new structure for a snake-like robot. This type of snake-like robot is different from the normal snake-like robot because it has lots of controllable scales which have a large role in helping moving. Besides, a new form of robot gait named as linear motion mode is developed based on theoretical analysis for the new mechanical structure. Through simulation and analysis in simmechanics of matlab, we proved the validity of theories about the motion mode of snake-like robot. The proposed machine construction and control method for the designed motion is verified experimentally by the independent developed snake robot.

  13. Multi-terrain locomotor interactions in flying snakes

    NASA Astrophysics Data System (ADS)

    Yeaton, Isaac; Baumgardner, Grant; Ross, Shane; Socha, John

    Arboreal snakes of the genus Chrysopelea are the only known snakes to glide. To execute aerial locomotion, a snake uses one of several stereotyped jumps from a tree into the air, while simultaneously flattening its body into an aerodynamically favorable shape. Large amplitude traveling waves are propagated posteriorly during the stable glide, while landing involves body wrapping, passive body compression, and energy absorption through compliance in the landing substrate to dissipate the accumulated kinetic energy from the glide. In all of these locomotor events, from interacting with cylindrical branches, falling through the air, grasping compliant tree branches and leaves, to landing on solid ground, snakes appropriate the same body morphology and perhaps the same basic neural mechanisms. Here we discuss our use of computational models and animal experiments to understand how flying snakes interact with and locomote on and through multiple media, potentially providing principles for legless locomotor designs. Supported by NSF 1351322.

  14. Observation of snake resonances at Relativistic Heavy Ion Collider

    SciTech Connect

    Bai, M.; Ahrens, L.; Alekseev, I.G.; Alessi, J.; et al

    2010-09-27

    The Siberian snakes are powerful tools in preserving polarization in high energy accelerators has been demonstrated at the Brookhaven Relativistic Heavy Ion Collider (RHIC). Equipped with two full Siberian snakes in each ring, polarization is preserved during acceleration from injection to 100 GeV. However, the Siberian snakes also introduce a new set of depolarization resonances, i.e. snake resonances as first discovered by Lee and Tepikian. The intrinsic spin resonances above 100 GeV are about a factor of two stronger than those below 100 GeV which raises the challenge to preserve the polarization up to 250 GeV. In 2009, polarized protons collided for the first time at the RHIC design store energy of 250 GeV. This paper presents the experimental measurements of snake resonances at RHIC. The plan for avoiding these resonances is also presented.

  15. Hairpin Ribozyme Genes Curtail Alcohol Drinking: from Rational Design to in vivo Effects in the Rat.

    PubMed

    Sapag, Amalia; Irrazábal, Thergiory; Lobos-González, Lorena; Muñoz-Brauning, Carlos R; Quintanilla, María Elena; Tampier, Lutske

    2016-01-01

    Ribozyme genes were designed to reduce voluntary alcohol drinking in a rat model of alcohol dependence. Acetaldehyde generated from alcohol in the liver is metabolized by the mitochondrial aldehyde dehydrogenase (ALDH2) such that diminishing ALDH2 activity leads to the aversive effects of blood acetaldehyde upon alcohol intake. A stepwise approach was followed to design genes encoding ribozymes targeted to the rat ALDH2 mRNA. In vitro studies of accessibility to oligonucleotides identified suitable target sites in the mRNA, one of which fulfilled hammerhead and hairpin ribozyme requirements (CGGUC). Ribozyme genes delivered in plasmid constructs were tested in rat cells in culture. While the hairpin ribozyme reduced ALDH2 activity 56% by cleavage and blockade (P < 0.0001), the hammerhead ribozyme elicited minor effects by blockade. The hairpin ribozyme was tested in vivo by adenoviral gene delivery to UChB alcohol drinker rats. Ethanol intake was curtailed 47% for 34 days (P < 0.0001), while blood acetaldehyde more than doubled upon ethanol administration and ALDH2 activity dropped 25% in liver homogenates, not affecting other ALDH isoforms. Thus, hairpin ribozymes targeted to 16 nt in the ALDH2 mRNA provide durable and specific effects in vivo, representing an improvement on previous work and encouraging development of gene therapy for alcoholism. PMID:27404720

  16. Rational Design of Potent and Selective Inhibitors of an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa.

    PubMed

    Kitamura, Seiya; Hvorecny, Kelli L; Niu, Jun; Hammock, Bruce D; Madden, Dean R; Morisseau, Christophe

    2016-05-26

    The virulence factor cystic fibrosis transmembrane conductance regulator (CFTR) inhibitory factor (Cif) is secreted by Pseudomonas aeruginosa and is the founding member of a distinct class of epoxide hydrolases (EHs) that triggers the catalysis-dependent degradation of the CFTR. We describe here the development of a series of potent and selective Cif inhibitors by structure-based drug design. Initial screening revealed 1a (KB2115), a thyroid hormone analog, as a lead compound with low micromolar potency. Structural requirements for potency were systematically probed, and interactions between Cif and 1a were characterized by X-ray crystallography. On the basis of these data, new compounds were designed to yield additional hydrogen bonding with residues of the Cif active site. From this effort, three compounds were identified that are 10-fold more potent toward Cif than our first-generation inhibitors and have no detectable thyroid hormone-like activity. These inhibitors will be useful tools to study the pathological role of Cif and have the potential for clinical application. PMID:27120257

  17. Use of Organosilicon Compounds towards the Rational Design of Antiparasitic and Antiviral Drugs

    PubMed Central

    Déléris, Gérard

    1995-01-01

    One of the major problems met for the conception of antiviral or antiparasitic drugs is to reach a high level of selectivity towards the pathogenic agent versus the host. We shall describe two synthetic approaches where main group organometallics have been used towards this goal. A series of nucleoside sila-analogues was synthesized as potential therapeutic agents designed to inhibit HIV Reverse Transcriptase. In a second approach novel organosilicon derivatives have been synthesized as mimics of antisense oligonucleotides. Infectious agents, namely viruses or parasites, more or less use cellular machinery. Therefore therapeutic agents must interfere with biochemical mechanisms or possess high affinity towards specific molecular cellular components, to reach selectivity. We thought that main group organometallics could show many advantages for designing biologically active molecules in this field. They allow a high synthetic flexibility for the modulations of physico-chemical properties and they show a mechanistic behaviour which may be close to the one of several heteroelements present in living organisms such as sulfur or phosphorus. We tried to use this approach towards two directions involving the synthesis of organosilicon derivatives i.e: -the synthesis of organosilicon derivatives as inhibitors of HIV Reverse Transcriptase, -the synthesis of organosilicon precursors of modified antisense oligonucleotides. PMID:18472760

  18. Rational design of an estrogen receptor mutant with altered DNA-binding specificity

    PubMed Central

    Nguyen, Denis; Bail, Martine; Pesant, Genevieve; Dupont, Virginie N.; Rouault, Étienne; Deschênes, Julie; Rocha, Walter; Melançon, Geneviève; Steinberg, Sergey V.; Mader, Sylvie

    2007-01-01

    Although artificial C2-H2 zinc fingers can be designed to recognize specific DNA sequences, it remains unclear to which extent nuclear receptor C4 zinc fingers can be tailored to bind novel DNA elements. Steroid receptors bind as dimers to palindromic response elements differing in the two central base pairs of repeated motifs. Predictions based on one amino acid—one base-pair relationships may not apply to estrogen receptors (ERs), which recognize the two central base pairs of estrogen response elements (EREs) via two charged amino acids, each contacting two bases on opposite DNA strands. Mutagenesis of these residues, E203 and K210 in ERα, indicated that both contribute to ERE binding. Removal of the electric charge and steric constraints associated with K210 was required for full loss of parental DNA-binding specificity and recognition of novel sequences by E203 mutants. Although some of the new binding profiles did not match predictions, the double mutation E203R-K210A generated as predicted a mutant ER that was transcriptionally active on palindromes of PuGCTCA motifs, but not on consensus EREs. This study demonstrates the feasibility of designing C4 zinc finger mutants with novel DNA-binding specificity, but also uncovers limitations of this approach. PMID:17478511

  19. Spectromicroscopic insights for rational design of redox-based memristive devices

    PubMed Central

    Baeumer, Christoph; Schmitz, Christoph; Ramadan, Amr H. H.; Du, Hongchu; Skaja, Katharina; Feyer, Vitaliy; Müller, Philipp; Arndt, Benedikt; Jia, Chun-Lin; Mayer, Joachim; De Souza, Roger A.; Michael Schneider, Claus; Waser, Rainer; Dittmann, Regina

    2015-01-01

    The demand for highly scalable, low-power devices for data storage and logic operations is strongly stimulating research into resistive switching as a novel concept for future non-volatile memory devices. To meet technological requirements, it is imperative to have a set of material design rules based on fundamental material physics, but deriving such rules is proving challenging. Here, we elucidate both switching mechanism and failure mechanism in the valence-change model material SrTiO3, and on this basis we derive a design rule for failure-resistant devices. Spectromicroscopy reveals that the resistance change during device operation and failure is indeed caused by nanoscale oxygen migration resulting in localized valence changes between Ti4+ and Ti3+. While fast reoxidation typically results in retention failure in SrTiO3, local phase separation within the switching filament stabilizes the retention. Mimicking this phase separation by intentionally introducing retention-stabilization layers with slow oxygen transport improves retention times considerably. PMID:26477940

  20. Rational Design of a Hierarchical Tin Dendrite Electrode for Efficient Electrochemical Reduction of CO2.

    PubMed

    Won, Da Hye; Choi, Chang Hyuck; Chung, Jaehoon; Chung, Min Wook; Kim, Eun-Hee; Woo, Seong Ihl

    2015-09-21

    Catalysis is a key technology for the synthesis of renewable fuels through electrochemical reduction of CO2 . However, successful CO2 reduction still suffers from the lack of affordable catalyst design and understanding the factors governing catalysis. Herein, we demonstrate that the CO2 conversion selectivity on Sn (or SnOx /Sn) electrodes is correlated to the native oxygen content at the subsurface. Electrochemical analyses show that the reduced Sn electrode with abundant oxygen species effectively stabilizes a CO2 (.-) intermediate rather than the clean Sn surface, and consequently results in enhanced formate production in the CO2 reduction. Based on this design strategy, a hierarchical Sn dendrite electrode with high oxygen content, consisting of a multi-branched conifer-like structure with an enlarged surface area, was synthesized. The electrode exhibits a superior formate production rate (228.6 μmol h(-1)  cm(-2) ) at -1.36 VRHE without any considerable catalytic degradation over 18 h of operation. PMID:26219092

  1. Hairpin Ribozyme Genes Curtail Alcohol Drinking: from Rational Design to in vivo Effects in the Rat.

    PubMed

    Sapag, Amalia; Irrazábal, Thergiory; Lobos-González, Lorena; Muñoz-Brauning, Carlos R; Quintanilla, María Elena; Tampier, Lutske

    2016-07-12

    Ribozyme genes were designed to reduce voluntary alcohol drinking in a rat model of alcohol dependence. Acetaldehyde generated from alcohol in the liver is metabolized by the mitochondrial aldehyde dehydrogenase (ALDH2) such that diminishing ALDH2 activity leads to the aversive effects of blood acetaldehyde upon alcohol intake. A stepwise approach was followed to design genes encoding ribozymes targeted to the rat ALDH2 mRNA. In vitro studies of accessibility to oligonucleotides identified suitable target sites in the mRNA, one of which fulfilled hammerhead and hairpin ribozyme requirements (CGGUC). Ribozyme genes delivered in plasmid constructs were tested in rat cells in culture. While the hairpin ribozyme reduced ALDH2 activity 56% by cleavage and blockade (P < 0.0001), the hammerhead ribozyme elicited minor effects by blockade. The hairpin ribozyme was tested in vivo by adenoviral gene delivery to UChB alcohol drinker rats. Ethanol intake was curtailed 47% for 34 days (P < 0.0001), while blood acetaldehyde more than doubled upon ethanol administration and ALDH2 activity dropped 25% in liver homogenates, not affecting other ALDH isoforms. Thus, hairpin ribozymes targeted to 16 nt in the ALDH2 mRNA provide durable and specific effects in vivo, representing an improvement on previous work and encouraging development of gene therapy for alcoholism.

  2. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation

    PubMed Central

    Doench, John G.; Hartenian, Ella; Graham, Daniel B.; Tothova, Zuzana; Hegde, Mudra; Smith, Ian; Sullender, Meagan; Ebert, Benjamin L.; Xavier, Ramnik J.; Root, David E.

    2014-01-01

    Components of the prokaryotic clustered regularly interspersed palindromic repeat (CRISPR) loci have recently been repurposed for use in mammalian cells1–6. The Cas9 protein can be programmed with a single guide RNA (sgRNA) to generate site-specific DNA breaks, but there are few known rules governing on-target efficacy of this system7,8. We created a pool of sgRNAs, tiling across all possible target sites of a panel of six endogenous mouse and three endogenous human genes and quantitatively assessed their ability to produce null alleles of their target gene by antibody staining and flow cytometry. We discovered sequence features that improved activity, including a further optimization of the proto-spacer adjacent motif (PAM) of Streptococcus pyogenes Cas9. The results from 1,841 sgRNAs were used to construct a predictive model of sgRNA activity to improve sgRNA design for gene editing and genetic screens. We provide an online tool for the design of highly active sgRNAs for any gene of interest. PMID:25184501

  3. Rational design of self-assembly pathways for complex multicomponent structures

    PubMed Central

    Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan

    2015-01-01

    The field of complex self-assembly is moving toward the design of multiparticle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such “addressable complexity,” we need to understand the factors that optimize the yield and the kinetics of self-assembly. Here we use a simple theoretical method to explain the key features responsible for the unexpected success of DNA-brick experiments, which are currently the only demonstration of reliable self-assembly with such a large number of components. Simulations confirm that our theory accurately predicts the narrow temperature window in which error-free assembly can occur. Even more strikingly, our theory predicts that correct assembly of the complete structure may require a time-dependent experimental protocol. Furthermore, we predict that low coordination numbers result in nonclassical nucleation behavior, which we find to be essential for achieving optimal nucleation kinetics under mild growth conditions. We also show that, rather surprisingly, the use of heterogeneous bond energies improves the nucleation kinetics and in fact appears to be necessary for assembling certain intricate 3D structures. This observation makes it possible to sculpt nucleation pathways by tuning the distribution of interaction strengths. These insights not only suggest how to improve the design of structures based on DNA bricks, but also point the way toward the creation of a much wider class of chemical or colloidal structures with addressable complexity. PMID:25941388

  4. Spectromicroscopic insights for rational design of redox-based memristive devices

    NASA Astrophysics Data System (ADS)

    Baeumer, Christoph; Schmitz, Christoph; Ramadan, Amr H. H.; Du, Hongchu; Skaja, Katharina; Feyer, Vitaliy; Müller, Philipp; Arndt, Benedikt; Jia, Chun-Lin; Mayer, Joachim; de Souza, Roger A.; Michael Schneider, Claus; Waser, Rainer; Dittmann, Regina

    2015-10-01

    The demand for highly scalable, low-power devices for data storage and logic operations is strongly stimulating research into resistive switching as a novel concept for future non-volatile memory devices. To meet technological requirements, it is imperative to have a set of material design rules based on fundamental material physics, but deriving such rules is proving challenging. Here, we elucidate both switching mechanism and failure mechanism in the valence-change model material SrTiO3, and on this basis we derive a design rule for failure-resistant devices. Spectromicroscopy reveals that the resistance change during device operation and failure is indeed caused by nanoscale oxygen migration resulting in localized valence changes between Ti4+ and Ti3+. While fast reoxidation typically results in retention failure in SrTiO3, local phase separation within the switching filament stabilizes the retention. Mimicking this phase separation by intentionally introducing retention-stabilization layers with slow oxygen transport improves retention times considerably.

  5. Functionalized Single-Walled Carbon Nanotubes as Rationally Designed Vehicles for Tumor-Targeted Drug Delivery

    SciTech Connect

    Chen,J.; Wong,S.; Chen, S.; Zhao, X.; Kuznetsova, L.V.; and Ojima, I.

    2008-11-14

    A novel single-walled carbon nanotube (SWNT)-based tumor-targeted drug delivery system (DDS) has been developed, which consists of a functionalized SWNT linked to tumor-targeting modules as well as prodrug modules. There are three key features of this nanoscale DDS: (a) use of functionalized SWNTs as a biocompatible platform for the delivery of therapeutic drugs or diagnostics, (b) conjugation of prodrug modules of an anticancer agent (taxoid with a cleavable linker) that is activated to its cytotoxic form inside the tumor cells upon internalization and in situ drug release, and (c) attachment of tumor-recognition modules (biotin and a spacer) to the nanotube surface. To prove the efficacy of this DDS, three fluorescent and fluorogenic molecular probes were designed, synthesized, characterized, and subjected to the analysis of the receptor-mediated endocytosis and drug release inside the cancer cells (L1210FR leukemia cell line) by means of confocal fluorescence microscopy. The specificity and cytotoxicity of the conjugate have also been assessed and compared with L1210 and human noncancerous cell lines. Then, it has unambiguously been proven that this tumor-targeting DDS works exactly as designed and shows high potency toward specific cancer cell lines, thereby forming a solid foundation for further development.

  6. Engineering phage materials with desired peptide display: rational design sustained through natural selection.

    PubMed

    Merzlyak, Anna; Lee, Seung-Wuk

    2009-12-01

    Genetic engineering of phage provides novel opportunities to build various nanomaterials by displaying functional peptide motifs on its surface coat protein. However, any genetic modifications of phage coat proteins must be able to accommodate their many biological roles in the phage replication process. To express functional but inherently unfavorable peptide motifs on major coat protein pVIII, we devised a novel genetic conjugation method to circumvent bacterial biological censorship. Constraining the designed peptides among the degenerate flanking residues, we obtained a pVIII library of phage that retained the desired sequences yet could navigate through the phage replication process due to the naturally selected flanking residues. Further, we systematically analyzed the biochemical and size-related compensation mechanisms of the pVIII expressed peptides by constructing four chemically diverse (His, Trp, Glu, Lys) partial library series. Described genetic conjugation methodology can serve to improve the design of engineered phage and allow further exploitation of these particles as functional nanobiomaterials for various applications. PMID:19842621

  7. Rational Design of a Hierarchical Tin Dendrite Electrode for Efficient Electrochemical Reduction of CO2.

    PubMed

    Won, Da Hye; Choi, Chang Hyuck; Chung, Jaehoon; Chung, Min Wook; Kim, Eun-Hee; Woo, Seong Ihl

    2015-09-21

    Catalysis is a key technology for the synthesis of renewable fuels through electrochemical reduction of CO2 . However, successful CO2 reduction still suffers from the lack of affordable catalyst design and understanding the factors governing catalysis. Herein, we demonstrate that the CO2 conversion selectivity on Sn (or SnOx /Sn) electrodes is correlated to the native oxygen content at the subsurface. Electrochemical analyses show that the reduced Sn electrode with abundant oxygen species effectively stabilizes a CO2 (.-) intermediate rather than the clean Sn surface, and consequently results in enhanced formate production in the CO2 reduction. Based on this design strategy, a hierarchical Sn dendrite electrode with high oxygen content, consisting of a multi-branched conifer-like structure with an enlarged surface area, was synthesized. The electrode exhibits a superior formate production rate (228.6 μmol h(-1)  cm(-2) ) at -1.36 VRHE without any considerable catalytic degradation over 18 h of operation.

  8. Rational Design of Multiamphiphilic Polymer Compatibilizers: Versatile Solubility and Hybridization of Noncovalently Functionalized CNT Nanocomposites.

    PubMed

    Cho, Kie Yong; Yeom, Yong Sik; Seo, Heun Young; Park, Young Hun; Jang, Ha Na; Baek, Kyung-Youl; Yoon, Ho Gyu

    2015-05-13

    The design of amphiphilic polymer compatibilizers for solubility manipulation of CNT composites was systematically generalized in this study. Structurally tailored multiamphiphilic compatibilizer were designed and synthesized by applying simple, high-yield reactions. This multiamphiphilic compatibilizer was applied for noncovalent functionalization of CNTs as well as provided CNTs with outstanding dispersion stability, manipulation of solubility, and hybridization with Ag nanoparticles (NPs). With regard to the dispersion properties, superior records in maximum concentration (2.88-3.10 mg/mL in chloroform), and mass ratio of the compatibilizer for good CNT dispersion (36 wt %) were achieved by MWCNTs functionalized with a multiamphiphilic block copolymer compatibilizer. In particular, the solubility limitations of MWCNT dispersion in solvents ranging from toluene (nonpolar) to aqueous solution (polar) are surprisingly resolved by introducing this multiamphiphilic polymer compatibilizer. Furthermore, this polymer compatibilizer allowed the synthesis of the hybrid CNT nanocomposites with Ag nanoparticles by an in situ nucleation process. As such, the multiamphiphilic compatibilizer candidate as a new concept for the noncovalent functionalization of CNTs can extend their use for a wide range of applications. PMID:25875313

  9. Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery

    PubMed Central

    Lounnas, Valère; Ritschel, Tina; Kelder, Jan; McGuire, Ross; Bywater, Robert P.; Foloppe, Nicolas

    2013-01-01

    The past decade has witnessed a paradigm shift in preclinical drug discovery with structure-based drug design (SBDD) making a comeback while high-throughput screening (HTS) methods have continued to generate disappointing results. There is a deficit of information between identified hits and the many criteria that must be fulfilled in parallel to convert them into preclinical candidates that have a real chance to become a drug. This gap can be bridged by investigating the interactions between the ligands and their receptors. Accurate calculations of the free energy of binding are still elusive; however progresses were made with respect to how one may deal with the versatile role of water. A corpus of knowledge combining X-ray structures, bioinformatics and molecular modeling techniques now allows drug designers to routinely produce receptor homology models of increasing quality. These models serve as a basis to establish and validate efficient rationales used to tailor and/or screen virtual libraries with enhanced chances of obtaining hits. Many case reports of successful SBDD show how synergy can be gained from the combined use of several techniques. The role of SBDD with respect to two different classes of widely investigated pharmaceutical targets: (a) protein kinases (PK) and (b) G-protein coupled receptors (GPCR) is discussed. Throughout these examples prototypical situations covering the current possibilities and limitations of SBDD are presented. PMID:24688704

  10. 50 CFR 226.205 - Critical habitat for Snake River sockeye salmon, Snake River fall chinook salmon, and Snake River...

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of the USGS publication and maps may be... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Critical habitat for Snake River sockeye... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT § 226.205 Critical habitat...

  11. 50 CFR 226.205 - Critical habitat for Snake River sockeye salmon, Snake River fall chinook salmon, and Snake River...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of the USGS publication and maps may be... 50 Wildlife and Fisheries 10 2013-10-01 2013-10-01 false Critical habitat for Snake River sockeye... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT § 226.205 Critical habitat...

  12. 50 CFR 226.205 - Critical habitat for Snake River sockeye salmon, Snake River fall chinook salmon, and Snake River...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of the USGS publication and maps may be... 50 Wildlife and Fisheries 10 2012-10-01 2012-10-01 false Critical habitat for Snake River sockeye... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT § 226.205 Critical habitat...

  13. 50 CFR 226.205 - Critical habitat for Snake River sockeye salmon, Snake River fall chinook salmon, and Snake River...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of the USGS publication and maps may be... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Critical habitat for Snake River sockeye... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT § 226.205 Critical habitat...

  14. 50 CFR 226.205 - Critical habitat for Snake River sockeye salmon, Snake River fall chinook salmon, and Snake River...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of the USGS publication and maps may be... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Critical habitat for Snake River sockeye... ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS DESIGNATED CRITICAL HABITAT § 226.205 Critical habitat...

  15. Rational design, synthesis and biological evaluation of modular fluorogenic substrates with high affinity and selectivity for PTP1B.

    PubMed

    Sanchini, Silvano; Perruccio, Francesca; Piizzi, Grazia

    2014-05-01

    Protein-tyrosine phosphatase 1B (PTP1B) is a key regulatory enzyme in several signal transduction pathways, and its upregulation has been associated with type-2 diabetes, obesity and cancer. Selective determination of the functional significance of PTP1B remains a major challenge because the activity of this crucial enzyme is currently evaluated through the use of fluorescent probes that lack selectivity and are limited to biochemical assays. Here we describe the rational design, synthesis and biological evaluation of new modular PTP1B fluorogenic substrates. The self-immolative 4-hydroxybenzyl alcohol has been used as a key component for the design of phosphotyrosine mimics linked to a latent chromophore, which is released through an enzyme-initiated domino reaction. Preliminary biological investigations showed that, by optimising the stereoelectronic properties and the binding interactions at the enzyme active site, it is possible to achieve substrates with high affinity and promising selectivity. Due to their modular nature, the synthesised fluorogenic probes represent versatile tools; customisation of the different subunits could widen the scope of these probes to a broader range of in vitro assays. Finally, these studies elucidate the critical role played by Asp181 in the PTP1B-catalysed dephosphorylation mechanism: disruption of the native conformation of this key amino acid residue on the WDP loop yields fluorogenic inhibitors, rather than substrates. For this reason, our studies also represent a step forward for the development of improved PTP1B noncovalent inhibitors. PMID:24719298

  16. Rational drug design and synthesis of molecules targeting the angiotensin II type 1 and type 2 receptors.

    PubMed

    Kellici, Tahsin F; Tzakos, Andreas G; Mavromoustakos, Thomas

    2015-03-02

    The angiotensin II (Ang II) type 1 and type 2 receptors (AT1R and AT2R) orchestrate an array of biological processes that regulate human health. Aberrant function of these receptors triggers pathophysiological responses that can ultimately lead to death. Therefore, it is important to design and synthesize compounds that affect beneficially these two receptors. Cardiovascular disease, which is attributed to the overactivation of the vasoactive peptide hormone Αng II, can now be treated with commercial AT1R antagonists. Herein, recent achievements in rational drug design and synthesis of molecules acting on the two AT receptors are reviewed. Quantitative structure activity relationships (QSAR) and molecular modeling on the two receptors aim to assist the search for new active compounds. As AT1R and AT2R are GPCRs and drug action is localized in the transmembrane region the role of membrane bilayers is exploited. The future perspectives in this field are outlined. Tremendous progress in the field is expected if the two receptors are crystallized, as this will assist the structure based screening of the chemical space and lead to new potent therapeutic agents in cardiovascular and other diseases.

  17. Rational design of efficient electrode–electrolyte interfaces for solid-state energy storage using ion soft landing

    DOE PAGES

    Prabhakaran, Venkateshkumar; Mehdi, B. Layla; Ditto, Jeffrey J.; Engelhard, Mark H.; Wang, Bingbing; Gunaratne, K. Don D.; Johnson, David C.; Browning, Nigel D.; Johnson, Grant E.; Laskin, Julia

    2016-04-21

    Here, the rational design of improved electrode-electrolyte interfaces (EEI) for energy storage is critically dependent on a molecular-level understanding of ionic interactions and nanoscale phenomena. The presence of non-redox active species at EEI has been shown to strongly influence Faradaic efficiency and long-term operational stability during energy storage processes. Herein, we achieve substantially higher performance and long-term stability of EEI prepared with highly-dispersed discrete redox-active cluster anions (50 ng of pure ~0.7 nm size molybdenum polyoxometalate anions (POM) anions on 25 mg (≈ 0.2 wt%) carbon nanotube (CNT) electrodes) by complete elimination of strongly coordinating non-redox species through ion soft-landingmore » (SL). For the first time, electron microscopy provides atomically-resolved images of individual POM species directly on complex technologically relevant CNT electrodes. In this context, SL is established as a versatile approach for the controlled design of novel surfaces for both fundamental and applied research in energy storage.« less

  18. Rational design of efficient electrode-electrolyte interfaces for solid-state energy storage using ion soft landing

    NASA Astrophysics Data System (ADS)

    Prabhakaran, Venkateshkumar; Mehdi, B. Layla; Ditto, Jeffrey J.; Engelhard, Mark H.; Wang, Bingbing; Gunaratne, K. Don D.; Johnson, David C.; Browning, Nigel D.; Johnson, Grant E.; Laskin, Julia

    2016-04-01

    The rational design of improved electrode-electrolyte interfaces (EEI) for energy storage is critically dependent on a molecular-level understanding of ionic interactions and nanoscale phenomena. The presence of non-redox active species at EEI has been shown to strongly influence Faradaic efficiency and long-term operational stability during energy storage processes. Herein, we achieve substantially higher performance and long-term stability of EEI prepared with highly dispersed discrete redox-active cluster anions (50 ng of pure ~0.75 nm size molybdenum polyoxometalate (POM) anions on 25 μg (~0.2 wt%) carbon nanotube (CNT) electrodes) by complete elimination of strongly coordinating non-redox species through ion soft landing (SL). Electron microscopy provides atomically resolved images of a uniform distribution of individual POM species soft landed directly on complex technologically relevant CNT electrodes. In this context, SL is established as a versatile approach for the controlled design of novel surfaces for both fundamental and applied research in energy storage.

  19. Semi-Rational Design of Geobacillus stearothermophilus L-Lactate Dehydrogenase to Access Various Chiral α-Hydroxy Acids.

    PubMed

    Aslan, Aşkın Sevinç; Birmingham, William R; Karagüler, Nevin Gül; Turner, Nicholas J; Binay, Barış

    2016-06-01

    Chiral α-hydroxy acids (AHAs) are rapidly becoming important synthetic building blocks, in particular for the production of pharmaceuticals and other fine chemicals. Chiral compounds of a variety of functionalities are now often derived using enzymes, and L-lactate dehydrogenase from the thermophilic organism Geobacillus stearothermophilus (bsLDH) has the potential to be employed for the industrial synthesis of chiral α-hydroxy acids. Despite the thorough characterization of this enzyme, generation of variants with high activity on non-natural substrates has remained difficult and therefore limits the use of bsLDH in industry. Here, we present the engineering of bsLDH using semi-rational design as a method of focusing screening in a small and smart library for novel biocatalysts. In this study, six mutant libraries were designed in an effort to expand the substrate range of bsLDH. The eight variants identified as having enhanced activity toward the selected α-keto acids belonged to the same library, which targeted two positions simultaneously. These new variants now may be useful biocatalysts for chiral synthesis of α-hydroxy acids.

  20. Rational design of efficient electrode–electrolyte interfaces for solid-state energy storage using ion soft landing

    PubMed Central

    Prabhakaran, Venkateshkumar; Mehdi, B. Layla; Ditto, Jeffrey J.; Engelhard, Mark H.; Wang, Bingbing; Gunaratne, K. Don D.; Johnson, David C.; Browning, Nigel D.; Johnson, Grant E.; Laskin, Julia

    2016-01-01

    The rational design of improved electrode–electrolyte interfaces (EEI) for energy storage is critically dependent on a molecular-level understanding of ionic interactions and nanoscale phenomena. The presence of non-redox active species at EEI has been shown to strongly influence Faradaic efficiency and long-term operational stability during energy storage processes. Herein, we achieve substantially higher performance and long-term stability of EEI prepared with highly dispersed discrete redox-active cluster anions (50 ng of pure ∼0.75 nm size molybdenum polyoxometalate (POM) anions on 25 μg (∼0.2 wt%) carbon nanotube (CNT) electrodes) by complete elimination of strongly coordinating non-redox species through ion soft landing (SL). Electron microscopy provides atomically resolved images of a uniform distribution of individual POM species soft landed directly on complex technologically relevant CNT electrodes. In this context, SL is established as a versatile approach for the controlled design of novel surfaces for both fundamental and applied research in energy storage. PMID:27097686

  1. A rational design for the separation of metallic and semiconducting single-walled carbon nanotubes using a magnetic field.

    PubMed

    Luo, Chengzhi; Wan, Da; Jia, Junji; Li, Delong; Pan, Chunxu; Liao, Lei

    2016-07-14

    The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm(2) V(-1) s(-1) and an on/off ratio of 10(6). We also established a model to quantitatively calculate the percentage of m-SWNTs on the substrate and this model shows a good match with the experimental data. Furthermore, our rational design also provides a new avenue for the growth of SWNTs with specific chirality and manipulated arrangement due to the difference of magnetic susceptibilities between different diameters, chiralities, and types.

  2. Rational design of efficient electrode-electrolyte interfaces for solid-state energy storage using ion soft landing.

    PubMed

    Prabhakaran, Venkateshkumar; Mehdi, B Layla; Ditto, Jeffrey J; Engelhard, Mark H; Wang, Bingbing; Gunaratne, K Don D; Johnson, David C; Browning, Nigel D; Johnson, Grant E; Laskin, Julia

    2016-04-21

    The rational design of improved electrode-electrolyte interfaces (EEI) for energy storage is critically dependent on a molecular-level understanding of ionic interactions and nanoscale phenomena. The presence of non-redox active species at EEI has been shown to strongly influence Faradaic efficiency and long-term operational stability during energy storage processes. Herein, we achieve substantially higher performance and long-term stability of EEI prepared with highly dispersed discrete redox-active cluster anions (50 ng of pure ∼0.75 nm size molybdenum polyoxometalate (POM) anions on 25 μg (∼0.2 wt%) carbon nanotube (CNT) electrodes) by complete elimination of strongly coordinating non-redox species through ion soft landing (SL). Electron microscopy provides atomically resolved images of a uniform distribution of individual POM species soft landed directly on complex technologically relevant CNT electrodes. In this context, SL is established as a versatile approach for the controlled design of novel surfaces for both fundamental and applied research in energy storage.

  3. Rational design of a low-affinity peptide for the detection of cystatin C in a fast homogeneous immunoassay.

    PubMed

    Dobslaff, Kristin; Zscharnack, Kristin; Kreisig, Thomas; Zuchner, Thole

    2016-02-01

    Immunoassays play an essential role in current research and diagnostics resulting in a variety of detection principles. Thereby, homogeneous assays are often used for a fast signal response as demanded for example in point-of-care diagnostics. These systems often rely on a competitive assay design where the sample analyte and the corresponding dye-labeled substance are competing for binding sites on an antibody present in limited amounts. Due to the similar affinities of the antibody towards the sample analyte and the competitor, both sensitivity and assay time are limited. As a consequence, a competitor with a slightly reduced affinity towards the antibody can potentially overcome these drawbacks. Here, we present the rational design of a low-affinity peptide (donor peptide) as a specific analyte competitor for a FRET-based homogeneous immunoassay for the analysis of the protein cystatin C. Thereby, the strategy of peptide-induced antibody generation was combined with the selective variation of the immunization sequence in order to achieve a lower affinity towards the antibody. We could show that shortened donor peptides improved the resulting quenching efficiency in the immunoassay. In addition, the substitution of small hydrophobic amino acids by those with a higher steric demand appeared to be the most promising strategy providing a fast assay response for cystatin C of only 90 s.

  4. Semi-Rational Design of Geobacillus stearothermophilus L-Lactate Dehydrogenase to Access Various Chiral α-Hydroxy Acids.

    PubMed

    Aslan, Aşkın Sevinç; Birmingham, William R; Karagüler, Nevin Gül; Turner, Nicholas J; Binay, Barış

    2016-06-01

    Chiral α-hydroxy acids (AHAs) are rapidly becoming important synthetic building blocks, in particular for the production of pharmaceuticals and other fine chemicals. Chiral compounds of a variety of functionalities are now often derived using enzymes, and L-lactate dehydrogenase from the thermophilic organism Geobacillus stearothermophilus (bsLDH) has the potential to be employed for the industrial synthesis of chiral α-hydroxy acids. Despite the thorough characterization of this enzyme, generation of variants with high activity on non-natural substrates has remained difficult and therefore limits the use of bsLDH in industry. Here, we present the engineering of bsLDH using semi-rational design as a method of focusing screening in a small and smart library for novel biocatalysts. In this study, six mutant libraries were designed in an effort to expand the substrate range of bsLDH. The eight variants identified as having enhanced activity toward the selected α-keto acids belonged to the same library, which targeted two positions simultaneously. These new variants now may be useful biocatalysts for chiral synthesis of α-hydroxy acids. PMID:26852025

  5. A rational design for the separation of metallic and semiconducting single-walled carbon nanotubes using a magnetic field.

    PubMed

    Luo, Chengzhi; Wan, Da; Jia, Junji; Li, Delong; Pan, Chunxu; Liao, Lei

    2016-07-14

    The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm(2) V(-1) s(-1) and an on/off ratio of 10(6). We also established a model to quantitatively calculate the percentage of m-SWNTs on the substrate and this model shows a good match with the experimental data. Furthermore, our rational design also provides a new avenue for the growth of SWNTs with specific chirality and manipulated arrangement due to the difference of magnetic susceptibilities between different diameters, chiralities, and types. PMID:27315328

  6. The rational design of a peptide-based hydrogel responsive to H2S.

    PubMed

    Peltier, Raoul; Chen, Ganchao; Lei, Haipeng; Zhang, Mei; Gao, Liqian; Lee, Su Seong; Wang, Zuankai; Sun, Hongyan

    2015-12-18

    The development of hydrogels that are responsive to external stimuli in a well-controlled manner is important for numerous biomedical applications. Herein we reported the first example of a hydrogel responsive to hydrogen sulphide (H2S). H2S is an important gasotransmitter whose deregulation has been associated with a number of pathological conditions. Our hydrogel design is based on the functionalization of an ultrashort hydrogelating peptide sequence with an azidobenzyl moiety, which was reported to react with H2S selectively under physiological conditions. The resulting peptide was able to produce hydrogels at a concentration as low as 0.1 wt%. It could then be fully degraded in the presence of excess H2S. We envision that the novel hydrogel developed in this study may provide useful tools for biomedical research. PMID:26463661

  7. Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors.

    PubMed

    Schirmeister, Tanja; Kesselring, Jochen; Jung, Sascha; Schneider, Thomas H; Weickert, Anastasia; Becker, Johannes; Lee, Wook; Bamberger, Denise; Wich, Peter R; Distler, Ute; Tenzer, Stefan; Johé, Patrick; Hellmich, Ute A; Engels, Bernd

    2016-07-13

    We propose a structure-based protocol for the development of customized covalent inhibitors. Starting from a known inhibitor, in the first and second steps appropriate substituents of the warhead are selected on the basis of quantum mechanical (QM) computations and hybrid approaches combining QM with molecular mechanics (QM/MM). In the third step the recognition unit is optimized using docking approaches for the noncovalent complex. These predictions are finally verified by QM/MM or molecular dynamic simulations. The applicability of our approach is successfully demonstrated by the design of reversible covalent vinylsulfone-based inhibitors for rhodesain. The examples show that our approach is sufficiently accurate to identify compounds with the desired properties but also to exclude nonpromising ones.

  8. Rational Design of Push-Pull Fluorene Dyes: Synthesis and Structure-Photophysics Relationship.

    PubMed

    Shaya, Janah; Fontaine-Vive, Fabien; Michel, Benoît Y; Burger, Alain

    2016-07-18

    Our work surveyed experimental and theoretical investigations to construct highly emissive D-π-A (D=donor, A=acceptor) fluorenes. The synthetic routes were optimised to be concise and gram-scalable. The molecular design was first rationalised by varying the electron-withdrawing group from an aldehyde, ketotriazole or succinyl to methylenemalonitrile or benzothiadiazole. The electron-donating group was next varied from aliphatic or aromatic amines to saturated cyclic amines ranging from aziridine to azepane. Spectroscopic studies correlated with TD-DFT calculations provided the optimised structures. The selected push-pull dyes exhibited visible absorptions, significant brightness, important solvatofluorochromism, mega-Stokes shifts (>250 nm) and dramatic shifts in emission to the near-infrared. The current library includes the comprehensive characterization of 16 prospective dyes for fluorescence applications. Among them, several fluorene derivatives bearing different conjugation anchors were tested for coupling and demonstrated to preserve the photophysical responses once further bound.

  9. Selective ablation of β-galactosidase-expressing cells with a rationally designed activatable photosensitizer.

    PubMed

    Ichikawa, Yuki; Kamiya, Mako; Obata, Fumiaki; Miura, Masayuki; Terai, Takuya; Komatsu, Toru; Ueno, Tasuku; Hanaoka, Kenjiro; Nagano, Tetsuo; Urano, Yasuteru

    2014-06-23

    We have developed an activatable photosensitizer capable of specifically inducing the death of β-galactosidase-expressing cells in response to photoirradiation. By using a selenium-substituted rhodol scaffold bearing β-galactoside as a targeting substituent, we designed and synthesized HMDESeR-βGal, which has a non-phototoxic spirocyclic structure owing to the presence of the galactoside moiety. However, β-galactosidase efficiently converted HMDESeR-βGal into phototoxic HMDESeR, which exists predominantly in the open xanthene form. This structural change resulted in drastic recovery of visible-wavelength absorption and the ability to generate singlet oxygen ((1)O2). When HMDESeR-βGal was applied to larval Drosophila melanogaster wing disks, which express β-galactosidase only in the posterior region, photoirradiation induced cell death in the β-galactosidase-expressing region with high specificity.

  10. Biobased building blocks for the rational design of renewable block polymers.

    PubMed

    Holmberg, Angela L; Reno, Kaleigh H; Wool, Richard P; Epps, Thomas H

    2014-10-14

    Block polymers (BPs) derived from biomass (biobased) are necessary components of a sustainable future that relies minimally on petroleum-based plastics for applications ranging from thermoplastic elastomers and pressure-sensitive adhesives to blend compatibilizers. To facilitate their adoption, renewable BPs must be affordable, durable, processable, versatile, and reasonably benign. Their desirability further depends on the relative sustainability of the renewable resources and the methods employed in the monomer and polymer syntheses. Various strategies allow these BPs' characteristics to be tuned and enhanced for commercial applications, and many of these techniques also can be applied to manipulate the wide-ranging mechanical and thermal properties of biobased and self-assembling block polymers. From feedstock to application, this review article highlights promising renewable BPs, plus their material and assembly properties, in support of de novo design strategies that could revolutionize material sustainability.

  11. Rational Design of Glycomimetic Compounds Targeting the Saccharomyces cerevisiae Transglycosylase Gas2.

    PubMed

    Delso, Ignacio; Valero-González, Jessika; Marca, Eduardo; Tejero, Tomás; Hurtado-Guerrero, Ramón; Merino, Pedro

    2016-02-01

    The transglycosylase Saccharomyces cerevisiae Gas2 (ScGas2) belongs to a large family of enzymes that are key players in yeast cell wall remodeling. Despite its biologic importance, no studies on the synthesis of substrate-based compounds as potential inhibitors have been reported. We have synthesized a series of docking-guided glycomimetics that were evaluated by fluorescence spectroscopy and saturation-transfer difference (STD) NMR experiments, revealing that a minimum of three glucose units linked via a β-(1,3) linkage are required for achieving molecular recognition at the binding donor site. The binding mode of our compounds is further supported by STD-NMR experiments using the active site-mutants Y107Q and Y244Q. Our results are important for both understanding of ScGas2-substrate interactions and setting up the basis for future design of glycomimetics as new antifungal agents.

  12. Rational design of alpha-helical antimicrobial peptides: do's and don'ts.

    PubMed

    Uggerhøj, Lars Erik; Poulsen, Tanja Juul; Munk, Jens Kristian; Fredborg, Marlene; Sondergaard, Teis Esben; Frimodt-Moller, Niels; Hansen, Paul Robert; Wimmer, Reinhard

    2015-01-19

    Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure-activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin (GLLKRIKTLL-NH2 ) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic activity can be achieved through subtle increases in the hydrophobicity of the hydrophobic face or through subtle increases in the polarity of the hydrophilic face of the helix, or-most efficiently-a combination of both. A set of guidelines based on the results is given, for assistance in how to modify cationic α-helical AMPs in order to control activity and selectivity. The guidelines are finally tested on a different peptide.

  13. The Molecular Mechanisms and Rational Design of Anti-Diabetic Vanadium Compounds.

    PubMed

    Niu, Xia; Xiao, Ruyue; Wang, Na; Wang, Ziwei; Zhang, Yue; Xia, Qing; Yang, Xiaoda

    2016-01-01

    Vanadium compounds are promising anti-diabetic agents. Although BEOV was not able to succeed in phase II clinical trial, great progresses have been made in the past three decades on the discovery and development of anti-diabetic vanadium compounds. A vast of knowledge has been obtained on the molecular mechanisms of both the pharmacological and toxicological effects of vanadium complexes. It has been revealed that vanadium compounds exert insulin enhancement effects and cell protection via a multiple mechanism involving inhibition of PTP1B, activation of PPARs- AMPK signaling, regulation of unfolded protein responses (UPRs), and stimulation of antioxidant enzymes, while vanadium-induced oxidative stress and inflammatory response could primarily be attributed to vanadium toxicity. Based on the present results concerning the relationship between structures, biological activities and biochemical properties, the rationale for future design of anti-diabetic vanadium compounds has been discussed.

  14. Rational Design of Glycomimetic Compounds Targeting the Saccharomyces cerevisiae Transglycosylase Gas2.

    PubMed

    Delso, Ignacio; Valero-González, Jessika; Marca, Eduardo; Tejero, Tomás; Hurtado-Guerrero, Ramón; Merino, Pedro

    2016-02-01

    The transglycosylase Saccharomyces cerevisiae Gas2 (ScGas2) belongs to a large family of enzymes that are key players in yeast cell wall remodeling. Despite its biologic importance, no studies on the synthesis of substrate-based compounds as potential inhibitors have been reported. We have synthesized a series of docking-guided glycomimetics that were evaluated by fluorescence spectroscopy and saturation-transfer difference (STD) NMR experiments, revealing that a minimum of three glucose units linked via a β-(1,3) linkage are required for achieving molecular recognition at the binding donor site. The binding mode of our compounds is further supported by STD-NMR experiments using the active site-mutants Y107Q and Y244Q. Our results are important for both understanding of ScGas2-substrate interactions and setting up the basis for future design of glycomimetics as new antifungal agents. PMID:26280762

  15. Rational design of fluorescent membrane probes for apoptosis based on 3-hydroxyflavone

    NASA Astrophysics Data System (ADS)

    Darwich, Zeinab; Kucherak, Oleksandr A.; Kreder, Rémy; Richert, Ludovic; Vauchelles, Romain; Mély, Yves; Klymchenko, Andrey S.

    2013-06-01

    Environment-sensitive probes constitute powerful tools for monitoring changes in the physico-chemical properties of cell plasma membranes. Among these probes, 3-hydroxyflavone probes are of great interest due to their dual emission and ratiometric response. Here, three probes derived from the parent F2N12S were designed, characterized and applied to monitor the membrane changes occurring during apoptosis. These three probes were designed to orient the dye vertically in the membrane. They differ by the length of their alkyl chains (from 4 to 8 carbons), which were included to optimize their affinity to the lipid membranes. Among these three probes, the one with medium chain length (hexyl) showed the best affinity to model and cell membranes, while the one with the longest alkyl chains (octyl) did not efficiently stain the membranes, probably due to aggregation. The new probes were found to be more sensitive than F2N12S to both the lipid phase and surface charge in lipid vesicles and to loss of lipid order in cell plasma membranes after cholesterol extraction. The one with the shortest (butyl) chains was found to be the most sensitive to apoptosis, while the one with medium-length (hexyl) chains was the brightest. Interestingly, apoptosis induced by different agents led to similar spectroscopic effects to those produced by the loss of lipid order and change in the surface charge, confirming that apoptosis decreases the lipid order and increases the negative surface charge in the outer leaflet of cell membranes. In conclusion, these studies report the relationship between the probe structures and their sensitivity to lipid order, surface charge and apoptosis and propose new probes for membrane research.

  16. Rationally designed hierarchical MnO2-shell/ZnO-nanowire/carbon-fabric for high-performance supercapacitor electrodes

    NASA Astrophysics Data System (ADS)

    Yang, Q.; Zhang, X. T.; Zhang, M. Y.; Gao, Y.; Gao, H.; Liu, X. C.; Liu, H.; Wong, K. W.; Lau, W. M.

    2014-12-01

    High-performance supercapacitor electrodes with a novel hierarchical structure of MnO2/ZnO/carbon-fabric were rationally designed, and prepared by a simple three-step-solution method. The design comprises ZnO nanowires radially grown on each micron-size fiber of a carbon-fabric electrode, with a thin MnO2 shell on each ZnO nano-core. This multi-scale hierarchical structure yields: (a) high specific area of pseudo-capacitive MnO2 to maximize specific capacitance; (b) effective MnO2-electrolyte interface to facilitate fast charging/discharging; and (c) conductive MnO2-ZnO-electrode path to reduce energy loss. In addition, the overall capacitor performance is optimized by choosing proper thickness of MnO2 shell and aspect ratio of ZnO nano-core. The design was realized and validated with the development of a simple three-step-solution method: (a) radial deposition of nano-ZnO on carbon fabric; (b) coating ZnO by a thin layer of carbon; and (c) reduction of MnO4- and replacement of this carbon overlayer by MnO2. With this design and method, high specific capacitance of 886 F g-1 was found from electrodes with 5 nm MnO2 on ZnO having an average diameter of 50 nm and aspect ratio of 30. These samples showed specific energy of 16 Wh kg-1 and specific power of 27 kW kg-1 at current density of 20 mA cm-2, and good long-term cycling stability.

  17. Rational Catalyst Design of Titanium-Silica Materials Aided by Site-Specific Titration Tools

    NASA Astrophysics Data System (ADS)

    Eaton, Todd Robert

    between particle and crystal size, as obtained from XRD. In the course of establishing these relationships we've gained the knowledge of how to control TiO x structure, which enables the design of new and better catalysts. Understanding the synthesis-structure-function relationships allow for the design of a tandem photo/thermocatalytic reaction system for producing and consuming H2O2. By partially overcoating a TiO 2 photocatalyst with a ˜2 nm silica layer we observe a 56-fold rate improvement compared to bare-TiO2 for H2O2 synthesis from the proton-assisted reduction of O2. Addition of metal-SiO2 thermocatalysts (metal=Ti, Nb, or Ta) with sites needed for H2O2 activation creates a tandem system wherein the H2O2 produced in situ is utilized for alkene epoxidation. Compared to a thermocatalytic-only system, the tandem system accelerates epoxidation for cis-cyclooctene(11x faster), styrene(20x) and 1-octene(30x). This approach demonstrates a means for epoxidation with O2 that avoids H2O2 purification and transport, simplifies the total process, provides new opportunities for control by independent H2O2 production and consumption in the same reactor, and enhances rates relative to thermocatalytic-only epoxidation by intimately coupling H2O2 generation and consumption. Critically, establishment of titanium-silica synthesis-structure-function relationships enables the design of new catalysts and systems that are less energy- and material-intensive, leading towards more sustainable chemistry.

  18. Electromagnetic modelling and rational design of GLAD thin films for optical applications

    NASA Astrophysics Data System (ADS)

    Leontyev, Viktor A.

    This thesis presents a theoretical study of columnar films, fabricated by glancing angle deposition (GLAD), as photonic bandgap structures and metamaterials with predictable dielectric and magnetic response. Glancing angle deposition (GLAD) employs extremely oblique vapour incidence and computerized substrate motion to produce nanocolumns with a variety of shapes. Columns grow in random or periodic arrays and may be periodic in one, two, or three dimensions. The films' optical properties were studied using finite-difference time-domain and finite-difference frequency-domain methods, as well as effective medium theories, with support from experimental research. A large part of the thesis is devoted to column arrays with subwavelength intercolumnar distance and periodically modulated column shape. Among them, s-shaped columns were designed as polarizers for linearly polarized light. Simulations have shown a competitive effect from two structural anisotropy sources, causing a band gap suppression for one of two linear polarizations, and high polarizing ability. Simulations were compared to the measurements with a very good agreement in spectral response. Subwavelength column arrays were further explored as anisotropic interference mirrors with omnidirectional reflection bands. Index graded vertical post films were designed, having up to four times wider reflection bands than in the isotropic analogs. Band gap properties of 3D periodic GLAD columns were studied on the example of square-spiral photonic crystals. A significant influence of column cross-section was shown, that currently prevents fabrication of square spirals with a 3D band gap in the visible range. Inverted square-spiral films have better performance, which is further improved by material redistribution along the spiral. Lastly, this work studies the effective dielectric response of porous columnar films with metal particles. Characteristic matrix formalism was combined with finite-difference modelling to

  19. Rational design and study on recognition property of paracetamol-imprinted polymer.

    PubMed

    Liu, Ying; Wang, Fang; Tan, Tianwei; Lei, Ming

    2010-01-01

    The design and study on recognition of paracetamol-imprinted polymer for application in quantification of drugs was reported. Base on our previous work, the promising monomer, itaconic acid (IA), was computationally selected rapidly from the virtual library using the interaction energy (DeltaE) between a paracetamol (PR) molecule and four monomer molecules as a measure of their interaction. The possible conformation of PR interacting with IA displayed the nature of the interaction between PR and IA; hydrogen bonds (hbs) mainly contribute to this interaction. UV spectra analysis confirmed the occurrence of the hbs interaction between PR and IA at the polymerization stage. The optimal solvents for porogen and eluant were determined by the strength of hbs interaction between PR and the solvents, which were calculated employing density functional theory. The corresponding molecularly imprinted polymers (MIPs) and non-imprinted polymers were prepared and evaluated. The experimental results were consistent with those calculated, which confirmed the validity of the above-related calculation believed to facilitate the selection of monomers and solvents for the synthesis of MIP at molecular level. PMID:18769881

  20. Switching the Regioselectivity of a Cyclohexanone Monooxygenase toward (+)-trans-Dihydrocarvone by Rational Protein Design.

    PubMed

    Balke, Kathleen; Schmidt, Sandy; Genz, Maika; Bornscheuer, Uwe T

    2016-01-15

    The regioselectivity of the Baeyer-Villiger monooxygenase-catalyzed oxidation is governed mostly by electronic effects leading to the migration of the higher substituted residue. However, in some cases, substrate binding occurs in a way that the less substituted residue lies in an antiperiplanar orientation to the peroxy bond in the Criegee intermediate yielding in the formation of the "abnormal" lactone product. We are the first to demonstrate a complete switch in the regioselectivity of the BVMO from Arthrobacter sp. (CHMOArthro) as exemplified for (+)-trans-dihydrocarvone by redesigning the active site of the enzyme. In the designed triple mutant, the substrate binds in an inverted orientation leading to a ratio of 99:1 in favor of the normal lactone instead of exclusive formation of the abnormal lactone in case of the wild type enzyme. In order to validate our computational study, the beneficial mutations were successfully transferred to the CHMO from Acinetobacter sp. (CHMOAcineto), again yielding in a complete switch of regioselectivity.

  1. Rationally designed peptidomimetic modulators of aβ toxicity in Alzheimer's disease.

    PubMed

    Rajasekhar, K; Suresh, S N; Manjithaya, Ravi; Govindaraju, T

    2015-01-01

    Alzheimer's disease is one of the devastating illnesses mankind is facing in the 21st century. The main pathogenic event in Alzheimer's disease is believed to be the aggregation of the β-amyloid (Aβ) peptides into toxic aggregates. Molecules that interfere with this process may act as therapeutic agents for the treatment of the disease. Use of recognition unit based peptidomimetics as inhibitors are a promising approach, as they exhibit greater protease stability compared to natural peptides. Here, we present peptidomimetic inhibitors of Aβ aggregation designed based on the KLVFF (P1) sequence that is known to bind Aβ aggregates. We improved inhibition efficiency of P1 by introducing multiple hydrogen bond donor-acceptor moieties (thymine/barbiturate) at the N-terminal (P2 and P3), and blood serum stability by modifying the backbone by incorporating sarcosine (N-methylglycine) units at alternate positions (P4 and P5). The peptidomimetics showed moderate to good activity in both inhibition and dissolution of Aβ aggregates as depicted by thioflavin assay, circular dichroism (CD) measurements and microscopy (TEM). The activity of P4 and P5 were studied in a yeast cell model showing Aβ toxicity. P4 and P5 could rescue yeast cells from Aβ toxicity and Aβ aggregates were cleared by the process of autophagy. PMID:25633824

  2. Rationally designed molecularly imprinted polymers for selective extraction of methocarbamol from human plasma.

    PubMed

    Gholivand, Mohammad Bagher; Khodadadian, Mehdi

    2011-09-15

    Molecularly imprinted polymers (MIPs) with high selectivity toward methocarbamol have been computationally designed and synthesized based on the general non-covalent molecular imprinting approach. A virtual library consisting of 18 functional monomers was built and possible interactions between the template and functional monomers were investigated using a semiempirical approach. The monomers with the highest binding scores were then considered for additional calculations using a more accurate quantum mechanical (QM) calculation exploiting the density functional theory (DFT) at B3LYP/6-31G(d,p) level. The cosmo polarizable continuum model (CPCM) was also used to simulate the polymerization solvent. On the basis of computational results, acrylic acid (AA) and tetrahydrofuran (THF) were found to be the best choices of functional monomer and polymerization solvent, respectively. MIPs were then synthesized by the precipitation polymerization method and used as selective adsorbents to develop a molecularly imprinted solid-phase extraction (MISPE) procedure before quantitative analysis. After MISPE the drug could be determined either by differential pulse voltammetry (DPV), on a glassy carbon electrode modified with multiwalled-carbon nanotubes (GC/MWNT), or high performance chromatography (HPLC) with UV detection. A comparative study between MISPE-DPV and MISPE-HPLC-UV was performed. The MISPE-DPV was more sensitive but both techniques showed similar accuracy and precision. PMID:21807239

  3. Rational design of dendrimer/lipid nanoassemblies in drug delivery for cancer chemotherapy

    NASA Astrophysics Data System (ADS)

    Sun, Qihang

    Nanocarriers can minimize the side effects and improve therapeutic efficacy of anticancer drugs. Although some success has been achieved via active or passive drug delivery to tumor cells, the known nanocarriers are far from satisfying therapeutic efficacy expectations. This is because they usually fail in one of the four crucial requirements, that is, to retain drug in blood circulation but release it reliably in tumor cells and to be stealthy in transport in circulation and tumor tissue but sticky upon arrival at the tumor cell. Therefore, the goal of this work is to fabricate nanoassemblies of dendrimers and lipids to address all these challenges. Particularly, nanoassemblies designed and prepared in this work are illustrated to improve the tumor tissue penetration. Examples of dendrimers synthesized in this work are water-insoluble, pH-dependent water-insoluble and water-soluble biodegradable polyester dendrimers. These dendrimers are shown to be encapsulated by commonly used fusogenic and long-circulating lipids to form reliable nanoassemblies. The dendrimer/lipid nanocarriers are used to demonstrate a cascade drug delivery. They are expected to be stable in circulation, due to their appropriately large size, but to release the drug-loaded dendrimers in tumor tissue. The released dendrimers carrying drugs are much smaller and hence expected to have a much deeper penetration throughout the tumor tissue.

  4. Rational Design of Berberine-Based FtsZ Inhibitors with Broad-Spectrum Antibacterial Activity

    PubMed Central

    Sun, Ning; Chan, Fung-Yi; Lu, Yu-Jing; Neves, Marco A. C.; Lui, Hok-Kiu; Wang, Yong; Chow, Ka-Yan; Chan, Kin-Fai; Yan, Siu-Cheong; Leung, Yun-Chung; Abagyan, Ruben; Chan, Tak-Hang; Wong, Kwok-Yin

    2014-01-01

    Inhibition of the functional activity of Filamenting temperature-sensitive mutant Z (FtsZ) protein, an essential and highly conserved bacterial cytokinesis protein, is a promising approach for the development of a new class of antibacterial agents. Berberine, a benzylisoquinoline alkaloid widely used in traditional Chinese and native American medicines for its antimicrobial properties, has been recently reported to inhibit FtsZ. Using a combination of in silico structure-based design and in vitro biological assays, 9-phenoxyalkyl berberine derivatives were identified as potent FtsZ inhibitors. Compared to the parent compound berberine, the derivatives showed a significant enhancement of antibacterial activity against clinically relevant bacteria, and an improved potency against the GTPase activity and polymerization of FtsZ. The most potent compound 2 strongly inhibited the proliferation of Gram-positive bacteria, including methicillin-resistant S. aureus and vancomycin-resistant E. faecium, with MIC values between 2 and 4 µg/mL, and was active against the Gram-negative E. coli and K. pneumoniae, with MIC values of 32 and 64 µg/mL respectively. The compound perturbed the formation of cytokinetic Z-ring in E. coli. Also, the compound interfered with in vitro polymerization of S. aureus FtsZ. Taken together, the chemical modification of berberine with 9-phenoxyalkyl substituent groups greatly improved the antibacterial activity via targeting FtsZ. PMID:24824618

  5. Rationally designed porous polystyrene encapsulated zirconium phosphate nanocomposite for highly efficient fluoride uptake in waters

    PubMed Central

    Zhang, Qingrui; Du, Qing; Jiao, Tifeng; Zhang, Zhaoxiang; Wang, Sufeng; Sun, Qina; Gao, Faming

    2013-01-01

    Fluoride pollution in waters has engulfed worldwide regions and an excess of fluoride intake always causes skeletal fluorosis. Herein, a novel hybrid nanomaterial ZrP-MPN was fabricated for fluoride retention by encapsulating nano-ZrP onto macroporous polystyrene materials modified with quaternary ammonium groups. The as-obtained materials exhibited favorable removal of fluoride ions from aqueous solution in presence of common anions (SO42−/NO3−/Cl−) at high contents. Moreover outstanding sorption properties were also detected by involving series of commercial adsorbents (AA/magnetite/GFH/manganese sands) as references. Such satisfactory performances might be ascribed to the structural design of nanocomposite. (1) the CH2N+(CH3)3Cl groups enhances sorption diffusion and preconcentration in sorbent phase theoretically based on Donnan membrane principle; (2) the embedded ZrP nanoparticles also devotes to the efficient adsorption capacities due to its size-dependent specific properties. Additionally, the exhausted ZrP-MPN could be regenerated readily by alkaline solution. Thus, ZrP-MPN was a promising material for fluoride retention in waters. PMID:23989688

  6. Rational design and validation of a Tip60 histone acetyltransferase inhibitor

    NASA Astrophysics Data System (ADS)

    Gao, Chunxia; Bourke, Emer; Scobie, Martin; Famme, Melina Arcos; Koolmeister, Tobias; Helleday, Thomas; Eriksson, Leif A.; Lowndes, Noel F.; Brown, James A. L.

    2014-06-01

    Histone acetylation is required for many aspects of gene regulation, genome maintenance and metabolism and dysfunctional acetylation is implicated in numerous diseases, including cancer. Acetylation is regulated by histone acetyltransferases (HATs) and histone deacetylases and currently, few general HAT inhibitors have been described. We identified the HAT Tip60 as an excellent candidate for targeted drug development, as Tip60 is a key mediator of the DNA damage response and transcriptional co-activator. Our modeling of Tip60 indicated that the active binding pocket possesses opposite charges at each end, with the positive charges attributed to two specific side chains. We used structure based drug design to develop a novel Tip60 inhibitor, TH1834, to fit this specific pocket. We demonstrate that TH1834 significantly inhibits Tip60 activity in vitro and treating cells with TH1834 results in apoptosis and increased unrepaired DNA damage (following ionizing radiation treatment) in breast cancer but not control cell lines. Furthermore, TH1834 did not affect the activity of related HAT MOF, as indicated by H4K16Ac, demonstrating specificity. The modeling and validation of the small molecule inhibitor TH1834 represents a first step towards developing additional specific, targeted inhibitors of Tip60 that may lead to further improvements in the treatment of breast cancer.

  7. Rationally designed porous polystyrene encapsulated zirconium phosphate nanocomposite for highly efficient fluoride uptake in waters

    NASA Astrophysics Data System (ADS)

    Zhang, Qingrui; Du, Qing; Jiao, Tifeng; Zhang, Zhaoxiang; Wang, Sufeng; Sun, Qina; Gao, Faming

    2013-08-01

    Fluoride pollution in waters has engulfed worldwide regions and an excess of fluoride intake always causes skeletal fluorosis. Herein, a novel hybrid nanomaterial ZrP-MPN was fabricated for fluoride retention by encapsulating nano-ZrP onto macroporous polystyrene materials modified with quaternary ammonium groups. The as-obtained materials exhibited favorable removal of fluoride ions from aqueous solution in presence of common anions (SO42-/NO3-/Cl-) at high contents. Moreover outstanding sorption properties were also detected by involving series of commercial adsorbents (AA/magnetite/GFH/manganese sands) as references. Such satisfactory performances might be ascribed to the structural design of nanocomposite. (1) the CH2N+(CH3)3Cl groups enhances sorption diffusion and preconcentration in sorbent phase theoretically based on Donnan membrane principle; (2) the embedded ZrP nanoparticles also devotes to the efficient adsorption capacities due to its size-dependent specific properties. Additionally, the exhausted ZrP-MPN could be regenerated readily by alkaline solution. Thus, ZrP-MPN was a promising material for fluoride retention in waters.

  8. Improvements in Rational Design Strategies of Inulin Derivative Polycation for siRNA Delivery.

    PubMed

    Sardo, Carla; Craparo, Emanuela Fabiola; Porsio, Barbara; Giammona, Gaetano; Cavallaro, Gennara

    2016-07-11

    The advances of short interfering RNA (siRNA)-mediated therapy provide a powerful option for the treatment of many diseases, including cancer, by silencing the expression of targeted genes involved in the progression of the pathology. On this regard, a new pH-responsive polycation derived from inulin, Inulin-g-imidazole-g-diethylenetriamine (INU-IMI-DETA), was designed and employed to produce INU-IMI-DETA/siRNA "Inulin COmplex Nanoaggregates" (ICONs). The experimental results showed that INU-IMI-DETA exhibited strong cationic characteristics and high solubility in the pH range 3-5 and self-aggregation triggered by pH increase and physiological salt concentration. INU-IMI-DETA showed as well a high buffering capacity in the endosomal pH range of 7.4-5.1. In the concentration range between 25 and 1000 μg/mL INU-IMI-DETA had no cytotoxic effect on breast cancer cells (MCF-7) and no lytic effect on human red blood cells. ICONs were prepared by two-step procedure involving complexation and precipitation into DPBS buffer (pH 7.4) to produce siRNA-loaded nanoaggregates with minimized surface charge and suitable size for parenteral administration. Bafilomycin A1 inhibited transfection on MCF-7 cells, indicating that the protonation of the imidazole groups in the endolysosome pathway favors the escape of the system from endolysosomal compartment, increasing the amount of siRNA that can reach the cytoplasm.

  9. Rational design of redox mediators for advanced Li-O2 batteries

    NASA Astrophysics Data System (ADS)

    Lim, Hee-Dae; Lee, Byungju; Zheng, Yongping; Hong, Jihyun; Kim, Jinsoo; Gwon, Hyeokjo; Ko, Youngmin; Lee, Minah; Cho, Kyeongjae; Kang, Kisuk

    2016-06-01

    The discovery of effective catalysts is an important step towards achieving Li-O2 batteries with long cycle life and high round-trip efficiency. Soluble-type catalysts or redox mediators (RMs) possess great advantages over conventional solid catalysts, generally exhibiting much higher efficiency. Here, we select a series of organic RM candidates as a model system to identify the key descriptor in determining the catalytic activities and stabilities in Li-O2 cells. It is revealed that the level of ionization energies, readily available parameters from a database of the molecules, can serve such a role when comparing with the formation energy of Li2O2 and the highest occupied molecular orbital energy of the electrolyte. It is demonstrated that they are critical in reducing the overpotential and improving the stability of Li-O2 cells, respectively. Accordingly, we propose a general principle for designing feasible catalysts and report a RM, dimethylphenazine, with a remarkably low overpotential and high stability.

  10. Rationally designed porous polystyrene encapsulated zirconium phosphate nanocomposite for highly efficient fluoride uptake in waters.

    PubMed

    Zhang, Qingrui; Du, Qing; Jiao, Tifeng; Zhang, Zhaoxiang; Wang, Sufeng; Sun, Qina; Gao, Faming

    2013-01-01

    Fluoride pollution in waters has engulfed worldwide regions and an excess of fluoride intake always causes skeletal fluorosis. Herein, a novel hybrid nanomaterial ZrP-MPN was fabricated for fluoride retention by encapsulating nano-ZrP onto macroporous polystyrene materials modified with quaternary ammonium groups. The as-obtained materials exhibited favorable removal of fluoride ions from aqueous solution in presence of common anions (SO4(2-)/NO3(-)/Cl(-)) at high contents. Moreover outstanding sorption properties were also detected by involving series of commercial adsorbents (AA/magnetite/GFH/manganese sands) as references. Such satisfactory performances might be ascribed to the structural design of nanocomposite. (1) the CH2N(+)(CH3)3Cl groups enhances sorption diffusion and preconcentration in sorbent phase theoretically based on Donnan membrane principle; (2) the embedded ZrP nanoparticles also devotes to the efficient adsorption capacities due to its size-dependent specific properties. Additionally, the exhausted ZrP-MPN could be regenerated readily by alkaline solution. Thus, ZrP-MPN was a promising material for fluoride retention in waters. PMID:23989688

  11. Rational Design of Potent Antagonists to the Human Growth Hormone Receptor

    NASA Astrophysics Data System (ADS)

    Fuh, Germaine; Cunningham, Brian C.; Fukunaga, Rikiro; Nagata, Shigekazu; Goeddel, David V.; Wells, James A.

    1992-06-01

    A hybrid receptor was constructed that contained the extracellular binding domain of the human growth hormone (hGH) receptor linked to the transmembrane and intracellular domains of the murine granulocyte colony-stimulating factor receptor. Addition of hGH to a myeloid leukemia cell line (FDC-P1) that expressed the hybrid receptor caused proliferation of these cells. The mechanism for signal transduction of the hybrid receptor required dimerization because monoclonal antibodies to the hGH receptor were agonists whereas their monovalent fragments were not. Receptor dimerization occurs sequentially-a receptor binds to site 1 on hGH, and then a second receptor molecule binds to site 2 on hGH. On the basis of this sequential mechanism, which may occur in many other cytokine receptors, inactive hGH analogs were designed that were potent antagonists to hGH-induced cell proliferation. Such antagonists could be useful for treating clinical conditions of hGH excess, such as acromegaly.

  12. Protein-Support Interactions for Rationally Designed Bilirubin Oxidase Based Cathode: A Computational Study.

    PubMed

    Matanovic, Ivana; Babanova, Sofia; Chavez, Madelaine Seow; Atanassov, Plamen

    2016-04-21

    An example of biocathode based on bilirubin oxidase (BOx) was used to demonstrate how density functional theory can be combined with docking simulations in order to study the interface interactions between the enzyme and specifically designed electrode surface. The electrode surface was modified through the adsorption of bilirubin, the natural substrate for BOx, and the prepared electrode was electrochemically characterized using potentiostatic measurements. The experimentally determined current densities showed that the presence of bilirubin led to significant improvement of the cathode operation. On the basis of the computationally calculated binding energies of bilirubin to the graphene support and BOx and the analysis of the positioning of bilirubin relative to the support and T1 Cu atom of the enzyme, we hypothesize that the bilirubin serves as a geometric and electronic extension of the support. The computational results further confirm that the modification of the electrode surface with bilirubin provides an optimal orientation of BOx toward the support but also show that bilirubin facilitates the interfacial electron transfer by decreasing the distance between the electrode surface and the T1 Cu atom. PMID:27015361

  13. Rationally designed porous polystyrene encapsulated zirconium phosphate nanocomposite for highly efficient fluoride uptake in waters.

    PubMed

    Zhang, Qingrui; Du, Qing; Jiao, Tifeng; Zhang, Zhaoxiang; Wang, Sufeng; Sun, Qina; Gao, Faming

    2013-01-01

    Fluoride pollution in waters has engulfed worldwide regions and an excess of fluoride intake always causes skeletal fluorosis. Herein, a novel hybrid nanomaterial ZrP-MPN was fabricated for fluoride retention by encapsulating nano-ZrP onto macroporous polystyrene materials modified with quaternary ammonium groups. The as-obtained materials exhibited favorable removal of fluoride ions from aqueous solution in presence of common anions (SO4(2-)/NO3(-)/Cl(-)) at high contents. Moreover outstanding sorption properties were also detected by involving series of commercial adsorbents (AA/magnetite/GFH/manganese sands) as references. Such satisfactory performances might be ascribed to the structural design of nanocomposite. (1) the CH2N(+)(CH3)3Cl groups enhances sorption diffusion and preconcentration in sorbent phase theoretically based on Donnan membrane principle; (2) the embedded ZrP nanoparticles also devotes to the efficient adsorption capacities due to its size-dependent specific properties. Additionally, the exhausted ZrP-MPN could be regenerated readily by alkaline solution. Thus, ZrP-MPN was a promising material for fluoride retention in waters.

  14. Rational design of allosteric regulation of homoserine dehydrogenase by a nonnatural inhibitor L-lysine.

    PubMed

    Chen, Zhen; Rappert, Sugima; Zeng, An-Ping

    2015-02-20

    Allosteric proteins, which can sense different signals, are interesting biological parts for synthetic biology. In particular, the design of an artificial allosteric enzyme to sense an unnatural signal is both challenging and highly desired, for example, for a precise and dynamical control of fluxes of growth-essential but byproduct pathways in metabolic engineering of industrial microorganisms. In this work, we used homoserine dehydrogenase (HSDH) of Corynebacterium glutamicum, which is naturally allosterically regulated by threonine and isoleucine, as an example to demonstrate the feasibility of reengineering an allosteric enzyme to respond to an unnatural inhibitor L-lysine. For this purpose, the natural threonine binding sites of HSD were first predicted and verified by mutagenesis experiments. The threonine binding sites were then engineered to a lysine binding pocket. The reengineered HSD only responds to lysine inhibition but not to threonine. This is a significant step toward the construction of artificial molecular circuits for dynamic control of growth-essential byproduct formation pathway for lysine biosynthesis. PMID:24344690

  15. Rational design of stable and functional hirudin III mutants with lower antigenicity.

    PubMed

    Asgari, Saeme; Mirzahoseini, Hasan; Karimipour, Morteza; Rahimi, Hamze; Ebrahim-Habibi, Azadeh

    2015-11-01

    Hirudin is an inhibitor of thrombin and used as an effective anticoagulant, but has a potential to develop unacceptable immune responses. In this study, two computational tools were used to predict T-cell epitopes within Hirudin variant III (HVIII) sequence, and design mutations that would lessen its antigenicity. Homology models of native and mutant HVIII proteins (T4K, S9G, V21G, and V21K) were generated, and further used to assess their interactions with thrombin. The docking experiment showed that all mutants had a suitable pattern of interactions, with similar or lower interaction energies compared with the native protein. These complexes were subsequently subjected to molecular dynamics simulation. All mutants complexes had overall stable structures over simulation time, with RMSD, gyration radius, hydrogen bonds numbers, and accessible surface areas patterns that were comparable with the native HVIII over time. Interestingly, in all mutants, a shorter length was observed for the two salt bridges Arg73-Asp55 and Arg77-Glu57, which are suggested to be important in Hirudin-thrombin complex formation. Best selected mutants expressed in Escherichia coli BL21(DE3), subsequently SDS-PAGE and Western blot analysis confirmed the successful same expression of Hirudin and mutants. In conclusion, we believe that this computational approach could identify potentially safer proteins with preserved or even improved functionality. PMID:26321653

  16. A rational approach towards the design of chitosan-based nanoparticles obtained by ionotropic gelation.

    PubMed

    Kleine-Brueggeney, H; Zorzi, G K; Fecker, T; El Gueddari, N E; Moerschbacher, B M; Goycoolea, F M

    2015-11-01

    Chitosan is a linear aminopolysaccharide that has been widely used for the formation of chitosan-based nanoparticles by ionic gelation with sodium tripolyphosphate (TPP). Often, the experimental design used to obtain these systems does not take into consideration important variables, such as the degree of acetylation (DA) and the molecular weight (Mw) of chitosan. In this work, we studied the formation of chitosan-TPP nanoparticles with chitosan samples of varying DA and Mw (DA0 ∼ 0-47% and Mw ∼ 2.5-282 kDa). We addressed the influence the degree of space occupancy and the degree of crosslinking on the physical properties of chitosan-TPP nanoparticles. Nanoparticles that comprised chitosan of DA ∼ 0-21.7% behaved differently than those made of chitosan of DA ∼ 34.7-47%. We attributed these differences to the polymer conformation and chain flexibility of the distinct chitosans in solution. Moreover, chitosan of high Mw were found to have a stronger preference for incorporating into the formed nanoparticles than do low-Mw ones, as determined by SEC-HPLC. These results open new perspectives to understand the formation of chitosan nanoparticles by the ionic gelation technique.

  17. Rationally designed coiled-coil DNA looping peptides control DNA topology.

    PubMed

    Gowetski, Daniel B; Kodis, Erin J; Kahn, Jason D

    2013-09-01

    Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein-DNA nanostructures.

  18. New mimetic peptides inhibitors of Αβ aggregation. Molecular guidance for rational drug design.

    PubMed

    Barrera Guisasola, Exequiel E; Andujar, Sebastián A; Hubin, Ellen; Broersen, Kerensa; Kraan, Ivonne M; Méndez, Luciana; Delpiccolo, Carina M L; Masman, Marcelo F; Rodríguez, Ana M; Enriz, Ricardo D

    2015-05-01

    A new series of mimetic peptides possessing a significant Aβ aggregation modulating effect was reported here. These compounds were obtained based on a molecular modelling study which allowed us to perform a structural-based virtual selection. Monitoring Aβ aggregation by thioflavin T fluorescence and transmission electron microscopy revealed that fibril formation was significantly decreased upon prolonged incubation in presence of the active compounds. Dot blot analysis suggested a decrease of soluble oligomers strongly associated with cognitive decline in Alzheimer's disease. For the molecular dynamics simulations, we used an Aβ42 pentameric model where the compounds were docked using a blind docking technique. To analyze the dynamic behaviour of the complexes, extensive molecular dynamics simulations were carried out in explicit water. We also measured parameters or descriptors that allowed us to quantify the effect of these compounds as potential inhibitors of Aβ aggregation. Thus, significant alterations in the structure of our Aβ42 protofibril model were identified. Among others we observed the destruction of the regular helical twist, the loss of a stabilizing salt bridge and the loss of a stabilizing hydrophobic interaction in the β1 region. Our results may be helpful in the structural identification and understanding of the minimum structural requirements for these molecules and might provide a guide in the design of new aggregation modulating ligands.

  19. A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies.

    PubMed

    Henry, Kevin A; Sulea, Traian; van Faassen, Henk; Hussack, Greg; Purisima, Enrico O; MacKenzie, C Roger; Arbabi-Ghahroudi, Mehdi

    2016-01-01

    Staphylococcal protein A (SpA) and streptococcal protein G (SpG) affinity chromatography are the gold standards for purifying monoclonal antibodies (mAbs) in therapeutic applications. However, camelid VHH single-domain Abs (sdAbs or VHHs) are not bound by SpG and only sporadically bound by SpA. Currently, VHHs require affinity tag-based purification, which limits their therapeutic potential and adds considerable complexity and cost to their production. Here we describe a simple and rapid mutagenesis-based approach designed to confer SpA binding upon a priori non-SpA-binding VHHs. We show that SpA binding of VHHs is determined primarily by the same set of residues as in human mAbs, albeit with an unexpected degree of tolerance to substitutions at certain core and non-core positions and some limited dependence on at least one residue outside the SpA interface, and that SpA binding could be successfully introduced into five VHHs against three different targets with no adverse effects on expression yield or antigen binding. Next-generation sequencing of llama, alpaca and dromedary VHH repertoires suggested that species differences in SpA binding may result from frequency variation in specific deleterious polymorphisms, especially Ile57. Thus, the SpA binding phenotype of camelid VHHs can be easily modulated to take advantage of tag-less purification techniques, although the frequency with which this is required may depend on the source species. PMID:27631624

  20. Improvements in Rational Design Strategies of Inulin Derivative Polycation for siRNA Delivery.

    PubMed

    Sardo, Carla; Craparo, Emanuela Fabiola; Porsio, Barbara; Giammona, Gaetano; Cavallaro, Gennara

    2016-07-11

    The advances of short interfering RNA (siRNA)-mediated therapy provide a powerful option for the treatment of many diseases, including cancer, by silencing the expression of targeted genes involved in the progression of the pathology. On this regard, a new pH-responsive polycation derived from inulin, Inulin-g-imidazole-g-diethylenetriamine (INU-IMI-DETA), was designed and employed to produce INU-IMI-DETA/siRNA "Inulin COmplex Nanoaggregates" (ICONs). The experimental results showed that INU-IMI-DETA exhibited strong cationic characteristics and high solubility in the pH range 3-5 and self-aggregation triggered by pH increase and physiological salt concentration. INU-IMI-DETA showed as well a high buffering capacity in the endosomal pH range of 7.4-5.1. In the concentration range between 25 and 1000 μg/mL INU-IMI-DETA had no cytotoxic effect on breast cancer cells (MCF-7) and no lytic effect on human red blood cells. ICONs were prepared by two-step procedure involving complexation and precipitation into DPBS buffer (pH 7.4) to produce siRNA-loaded nanoaggregates with minimized surface charge and suitable size for parenteral administration. Bafilomycin A1 inhibited transfection on MCF-7 cells, indicating that the protonation of the imidazole groups in the endolysosome pathway favors the escape of the system from endolysosomal compartment, increasing the amount of siRNA that can reach the cytoplasm. PMID:27238382

  1. Computational ligand-based rational design: Role of conformational sampling and force fields in model development

    PubMed Central

    Shim, Jihyun; MacKerell, Alexander D.

    2011-01-01

    A significant number of drug discovery efforts are based on natural products or high throughput screens from which compounds showing potential therapeutic effects are identified without knowledge of the target molecule or its 3D structure. In such cases computational ligand-based drug design (LBDD) can accelerate the drug discovery processes. LBDD is a general approach to elucidate the relationship of a compound's structure and physicochemical attributes to its biological activity. The resulting structure-activity relationship (SAR) may then act as the basis for the prediction of compounds with improved biological attributes. LBDD methods range from pharmacophore models identifying essential features of ligands responsible for their activity, quantitative structure-activity relationships (QSAR) yielding quantitative estimates of activities based on physiochemical properties, and to similarity searching, which explores compounds with similar properties as well as various combinations of the above. A number of recent LBDD approaches involve the use of multiple conformations of the ligands being studied. One of the basic components to generate multiple conformations in LBDD is molecular mechanics (MM), which apply an empirical energy function to relate conformation to energies and forces. The collection of conformations for ligands is then combined with functional data using methods ranging from regression analysis to neural networks, from which the SAR is determined. Accordingly, for effective application of LBDD for SAR determinations it is important that the compounds be accurately modelled such that the appropriate range of conformations accessible to the ligands is identified. Such accurate modelling is largely based on use of the appropriate empirical force field for the molecules being investigated and the approaches used to generate the conformations. The present chapter includes a brief overview of currently used SAR methods in LBDD followed by a more

  2. A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies

    PubMed Central

    Henry, Kevin A.; Sulea, Traian; van Faassen, Henk; Hussack, Greg; Purisima, Enrico O.; MacKenzie, C. Roger; Arbabi-Ghahroudi, Mehdi

    2016-01-01

    Staphylococcal protein A (SpA) and streptococcal protein G (SpG) affinity chromatography are the gold standards for purifying monoclonal antibodies (mAbs) in therapeutic applications. However, camelid VHH single-domain Abs (sdAbs or VHHs) are not bound by SpG and only sporadically bound by SpA. Currently, VHHs require affinity tag-based purification, which limits their therapeutic potential and adds considerable complexity and cost to their production. Here we describe a simple and rapid mutagenesis-based approach designed to confer SpA binding upon a priori non-SpA-binding VHHs. We show that SpA binding of VHHs is determined primarily by the same set of residues as in human mAbs, albeit with an unexpected degree of tolerance to substitutions at certain core and non-core positions and some limited dependence on at least one residue outside the SpA interface, and that SpA binding could be successfully introduced into five VHHs against three different targets with no adverse effects on expression yield or antigen binding. Next-generation sequencing of llama, alpaca and dromedary VHH repertoires suggested that species differences in SpA binding may result from frequency variation in specific deleterious polymorphisms, especially Ile57. Thus, the SpA binding phenotype of camelid VHHs can be easily modulated to take advantage of tag-less purification techniques, although the frequency with which this is required may depend on the source species. PMID:27631624

  3. Towards the rational design of organic/inorganic interface for solid supported CO2 capture

    NASA Astrophysics Data System (ADS)

    He, Feng

    Monoethanolamine (MEA, HO(CH2)2NH2) aqueous solution based CO2 capture is the current technology used to mitigate power plants' green house gas emission. Solid based CO2 capture technique is regarded as a promising alternative, because it is more cost-effective and environmentally friendly than the solution based technique. Recently, solid-supported CO2 capture on MEA modified TiO 2 powders has been demonstrated [1]. It is believed that the main reaction pathway involved in solid-supported amine based CO2 capture is similar to the reaction in the amine solution, where the amine group reacts with CO2 to form carbamate (--NHCOO--). From the previous work on the MEA/TiO2 (110) system [2], it is found that MEA covered rutile TiO2 (110) did not capture CO 2. The main reaction pathway in this system was blocked because the amine group attached to the surface. In order to design a functional system, we proposed two possible mechanisms to free --NH2 from rutile TiO2 (110) surface. In this work, we investigated one of our six candidates, the 3-Amino-1-propanol (3AP, HO(CH2) 3NH2) molecule. The classical reactive force field (ReaxFF) [3] method has been employed to investigate the 3AP/TiO2 (110) system with emphasis on binding configurations and binding energies. We found that the amine group of 3AP did not attach to the rutile TiO2 (110) surface, indicating the CO2 capture capability of the 3AP/TiO 2 (110) system, which was confirmed by our experimental collaborators [4].

  4. Rational design of an auxin antagonist of the SCF(TIR1) auxin receptor complex.

    PubMed

    Hayashi, Ken-ichiro; Neve, Joshua; Hirose, Masakazu; Kuboki, Atsuhito; Shimada, Yukihisa; Kepinski, Stefan; Nozaki, Hiroshi

    2012-03-16

    The plant hormone auxin is a master regulator of plant growth and development. By regulating rates of cell division and elongation and triggering specific patterning events, indole 3-acetic acid (IAA) regulates almost every aspect of plant development. The perception of auxin involves the formation of a ternary complex consisting of an F-box protein of the TIR1/AFB family of auxin receptors, the auxin molecule, and a member the Aux/IAA family of co-repressor proteins. In this study, we identified a potent auxin antagonist, α-(phenylethyl-2-oxo)-IAA, as a lead compound for TIR1/AFB receptors by in silico virtual screening. This molecule was used as the basis for the development of a more potent TIR1 antagonist, auxinole (α-[2,4-dimethylphenylethyl-2-oxo]-IAA), using a structure-based drug design approach. Auxinole binds TIR1 to block the formation of the TIR1-IAA-Aux/IAA complex and so inhibits auxin-responsive gene expression. Molecular docking analysis indicates that the phenyl ring in auxinole would strongly interact with Phe82 of TIR1, a residue that is crucial for Aux/IAA recognition. Consistent with this predicted mode of action, auxinole competitively inhibits various auxin responses in planta. Additionally, auxinole blocks auxin responses of the moss Physcomitrella patens, suggesting activity over a broad range of species. Our works not only substantiates the utility of chemical tools for plant biology but also demonstrates a new class of small molecule inhibitor of protein-protein interactions common to mechanisms of perception of other plant hormones, such as jasmonate, gibberellin, and abscisic acid.

  5. Snakes: An Integrated Unit Plan.

    ERIC Educational Resources Information Center

    Lawrence, Lisa

    This document presents an integrated unit plan on snakes targeting second grade students. Objectives of the unit include developing concepts of living things, understanding the contribution and importance of snakes to the environment, and making connections between different disciplines. The unit integrates the topic of snakes into the areas of…

  6. Rational design and preparation of organic semiconductors for use in field effect transistors and photovoltaic cells

    NASA Astrophysics Data System (ADS)

    Mauldin, Clayton Edward

    The goal of this research was to develop methods to control the material properties of organic semiconductors, like solubility, stability, charge mobility, and self-assembly, through structural design. Investigations of structure-property relationships were conducted to optimize the properties of organic semiconductors for applications in organic field effect transistors (OFETs) and organic photovoltaics (OPVs). Chapter 1 gives an introduction to charge transport in organic semiconductors, and describes how the structure of conjugated molecules can affect their electrical performance and facilitate facile solution deposition. Furthermore, factors that can affect the stability of organic semiconductors to ambient conditions are discussed. Also, the device characteristics of OFETs and OPVs are summarized as a reference for subsequent chapters. Chapter 2 discusses the investigation of the air stability of distyryl oligothiophenes in OFETs. This work made use of thermally labile solubilizing groups to facilitate solution deposition of the oligothiophenes. In addition to device characterization, an extensive analysis of the thin film morphology using AFM, NEXAFS and GIXD is presented. This work revealed the general stability of distyryl oligothiophenes to oxidative degradation, and the high degree of crystallinity in our thin films. In Chapter 3, the charge transporting properties of pentathiophene monolayer islands is analyzed using current sensing AFM. The pentathiophenes were prepared with carboxylic acid moieties for self assembly, and the sub-monolayer films were transferred onto conductive substrates using the Langmuir-Blodgett technique. The morphology of the monolayers was observed to be sensitive to the alkyl substitution pattern of the pentathiophenes, which in turn affected charge transport. Hierarchical supramolecular assemblies of oligothiophenes and block copolymers are studied in Chapter 4. The structure of the assemblies is studied by TEM and small angle

  7. Rational Design of Iron Oxide Nanoparticles as Targeted Nanomedicines for Cancer Therapy

    NASA Astrophysics Data System (ADS)

    Kievit, Forrest M.

    2011-07-01

    Nanotechnology provides a flexible platform for the development of effective therapeutic nanomaterials that can interact specifically with a target in a biological system and provoke a desired biological response. Of the nanomaterials studied, superparamagnetic iron oxide nanoparticles (SPIONs) have emerged as one of top candidates for cancer therapy due to their intrinsic superparamagnetism that enables non-invasive magnetic resonance imaging (MRI) and biodegradability favorable for in vivo application. This dissertation is aimed at development of SPION-based nanomedicines to overcome the current limitations in cancer therapy. These limitations include non-specificity of therapy which can harm healthy tissue, the difficulty in delivering nucleic acids for gene therapy, the formation of drug resistance, and the inability to detect and treat micrometastases. First, a SPION-based non-viral gene delivery vehicle was developed through functionalization of the SPION core with a co-polymer designed to provide stable binding of DNA and low toxicity which showed excellent gene delivery in vitro and in vivo. This SPION-based non-viral gene delivery vehicle was then activated with a targeting agent to improve gene delivery throughout a xenograft tumor of brain cancer. It was found that targeting did not promote the accumulation of SPIONs at the tumor site, but rather improved the distribution of SPIONs throughout the tumor so a higher proportion of cells received treatment. Next, the high surface area of SPIONs was utilized for loading large amounts of drug which was shown to overcome the multidrug resistance acquired by many cancer cells. Drug bound to SPIONs showed significantly higher multidrug resistant cell uptake as compared to free drug which translated into improved cell kill. Also, an antibody activated SPION was developed and was shown to be able to target micrometastases in a transgenic animal model of metastatic breast cancer. These SPION-based nanomedicines

  8. Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors.

    PubMed

    Figueiredo, Ana C; Clement, Cristina C; Zakia, Sheuli; Gingold, Julian; Philipp, Manfred; Pereira, Pedro J B

    2012-01-01

    The tremendous social and economic impact of thrombotic disorders, together with the considerable risks associated to the currently available therapies, prompt for the development of more efficient and safer anticoagulants. Novel peptide-based thrombin inhibitors were identified using in silico structure-based design and further validated in vitro. The best candidate compounds contained both L- and D-amino acids, with the general sequence D-Phe(P3)-Pro(P2)-D-Arg(P1)-P1'-CONH₂. The P1' position was scanned with L- and D-isomers of natural or unnatural amino acids, covering the major chemical classes. The most potent non-covalent and proteolysis-resistant inhibitors contain small hydrophobic or polar amino acids (Gly, Ala, Ser, Cys, Thr) at the P1' position. The lead tetrapeptide, D-Phe-Pro-D-Arg-D-Thr-CONH₂, competitively inhibits α-thrombin's cleavage of the S2238 chromogenic substrate with a K(i) of 0.92 µM. In order to understand the molecular details of their inhibitory action, the three-dimensional structure of three peptides (with P1' L-isoleucine (fPrI), L-cysteine (fPrC) or D-threonine (fPrt)) in complex with human α-thrombin were determined by X-ray crystallography. All the inhibitors bind in a substrate-like orientation to the active site of the enzyme. The contacts established between the D-Arg residue in position P1 and thrombin are similar to those observed for the L-isomer in other substrates and inhibitors. However, fPrC and fPrt disrupt the active site His57-Ser195 hydrogen bond, while the combination of a P1 D-Arg and a bulkier P1' residue in fPrI induce an unfavorable geometry for the nucleophilic attack of the scissile bond by the catalytic serine. The experimental models explain the observed relative potency of the inhibitors, as well as their stability to proteolysis. Moreover, the newly identified direct thrombin inhibitors provide a novel pharmacophore platform for developing antithrombotic agents by exploring the conformational

  9. The dementia and disability project in Thai elderly: rational, design, methodology and early results

    PubMed Central

    2013-01-01

    were free of chronic diseases. Treatment gap (indicating those who have untreated or inadequate treatment) of diabetes mellitus and hypertension in Thai elders in this study was 37% and 55.5% respectively. 62.6% of Thai elders have ApoE3E3 allele. Prevalence of positive ApoE4 gene in this study is 22.85%. 38.6% of Thai elders who had MRI brain study have moderate to severe white matter lesions. Conclusion The large and comprehensive set of measurements in DDP allows a wide-ranging explanation of the functional and clinical features to be investigated in relation to white matter lesions or cortical atrophy of the brain in Thai elderly population. An almost 2 year follow up was made available to those with MCI and dementia and some of the cognitively normal elderly. The longitudinal design will provide great understanding of the possible contributors to disability in the elderly and to the progression of cognitive decline in Thai elders. PMID:23305293

  10. Rational optimization of culture conditions for the most efficient ethanol production in Scheffersomyces stipitis using design of experiments.

    PubMed

    Unrean, Pornkamol; Nguyen, Nhung H A

    2012-01-01

    Optimization of culture parameters for achieving the most efficient ethanol fermentation is challenging due to multiple variables involved. Here we presented a rationalized methodology for multi-variables optimization through the design of experiments DoE approach. Three critical parameters, pH, temperature, and agitation speed, affecting ethanol fermentation in S. stipitis was investigated. A predictive model showed that agitation speed significantly affected ethanol synthesis. Reducing pH and temperature also improved ethanol production. The model identified the optimum culture conditions for the most efficient ethanol production with the yield and productivity of 0.46 g/g and 0.28 g/l h, respectively, which is consistent with experimental observation. The results also indicated the scalability of the model from shake flask to bioreactor. Thus, DoE is a promising tool permitting the rapid establishment of culture conditions for the most efficient ethanol fermentation in S. stipitis. The approach could be useful to reduce process development time in lignocellulosic ethanol industry.

  11. Structure-Based Rational Design to Enhance the Solubility and Thermostability of a Bacterial Laccase Lac15

    PubMed Central

    Fang, Zemin; Zhou, Peng; Chang, Fei; Yin, Qiang; Fang, Wei; Yuan, Jing; Zhang, Xuecheng; Xiao, Yazhong

    2014-01-01

    Bacterial laccases are ideal alternatives of fungal laccases for specific industrial applications due to specific characteristics such as alkalescence dependence and high chloride tolerance. However, some bacterial laccases presented as inclusion bodies when expressing in Escherichia coli and showed thermal instability. In this study, rational design was employed to enhance the solubility and the thermostablity of the bacterial laccase Lac15-His6 based on the crystal structure obtained previously. After deletion of His-tag and residues323–332, the obtained Lac15D was completely expressed in soluble form even at a higher temperature of 28°C, compared to only 50% of Lac15-His6 expressed solubly at 16°C. It showed a two-time higher activity at temperatures lower than 35°C and a half-life increasing from 72 min to 150 min at 45°C. When used in chromogenic reactions, Lac15D showed constant activity toward dye precursors and their combinations under alkaline conditions, demonstrating its application potential in hair coloring biotechnology. PMID:25036001

  12. Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo.

    PubMed

    Yu, Dan; Dong, Zhiqiang; Gustafson, William Clay; Ruiz-González, Rubén; Signor, Luca; Marzocca, Fanny; Borel, Franck; Klassen, Matthew P; Makhijani, Kalpana; Royant, Antoine; Jan, Yuh-Nung; Weiss, William A; Guo, Su; Shu, Xiaokun

    2016-02-01

    Fluorescent proteins (FPs) are powerful tools for cell and molecular biology. Here based on structural analysis, a blue-shifted mutant of a recently engineered monomeric infrared fluorescent protein (mIFP) has been rationally designed. This variant, named iBlueberry, bears a single mutation that shifts both excitation and emission spectra by approximately 40 nm. Furthermore, iBlueberry is four times more photostable than mIFP, rendering it more advantageous for imaging protein dynamics. By tagging iBlueberry to centrin, it has been demonstrated that the fusion protein labels the centrosome in the developing zebrafish embryo. Together with GFP-labeled nucleus and tdTomato-labeled plasma membrane, time-lapse imaging to visualize the dynamics of centrosomes in radial glia neural progenitors in the intact zebrafish brain has been demonstrated. It is further shown that iBlueberry can be used together with mIFP in two-color protein labeling in living cells and in two-color tumor labeling in mice.

  13. A kinetic study on the reduction of CO2 by frustrated Lewis pairs: from understanding to rational design.

    PubMed

    Liu, Lei; Vankova, Nina; Heine, Thomas

    2016-02-01

    Carbon dioxide (CO2) is known as one of the major reasons for global warming. On the other hand, CO2 is considered as an abundant carbon source. Therefore, transformation of CO2 into target chemicals nowadays is of great interest. Recently, a concept of so-called "frustrated Lewis pairs" (FLPs) has been proposed. Such FLPs show unusual reactivity, such as hydrogen activation and the reduction of CO2. In this study, by means of density functional theory (DFT) and ab initio calculations, we conduct a kinetic survey on the reduction of CO2 by a series of FLPs. We investigate the relationship between the electronic structures and kinetic properties. The kinetic properties include: (1) reaction energy barriers, (2) the structural properties of the associated transition states (TSs), and (3) the natural charge population in these TSs. Our results indicate that there is a systematic relationship between the electronic structures and the kinetic properties, and, as a rule of thumb, similar activation barriers for both individual reactions are needed for best performance. The derived relationship can be used not only to rationalize the published experimental results, but also to assist the future design of more efficient Lewis acid-base pairs as metal-free catalysts for the reduction of CO2.

  14. Rational design of translational pausing without altering the amino acid sequence dramatically promotes soluble protein expression: a strategic demonstration.

    PubMed

    Chen, Wei; Jin, Jingjie; Gu, Wei; Wei, Bo; Lei, Yun; Xiong, Sheng; Zhang, Gong

    2014-11-10

    The production of many pharmaceutical and industrial proteins in prokaryotic hosts is hindered by the insolubility of industrial expression products resulting from misfolding. Even with a correct primary sequence, an improper translation elongation rate in a heterologous expression system is an important cause of misfolding. In silico analysis revealed that most of the endogenous Escherichia coli genes display translational pausing sites that promote correct folding, and almost 1/5 genes have pausing sites at the 3'-termini of their coding sequence. Therefore, we established a novel strategy to efficiently promote the expression of soluble and active proteins without altering the amino acid sequence or expression conditions. This strategy uses the rational design of translational pausing based on structural information solely through synonymous substitutions, i.e. no change on the amino acids sequence. We demonstrated this strategy on a promising antiviral candidate, Cyanovirin-N (CVN), which could not be efficiently expressed in any previously reported system. By introducing silent mutations, we increased the soluble expression level in E. coli by 2000-fold without altering the CVN protein sequence, and the specific activity was slightly higher for the optimized CVN than for the wild-type variant. This strategy introduces new possibilities for the production of bioactive recombinant proteins.

  15. Rational Design of Sulfonated A3 Adenosine Receptor-Selective Nucleosides as Pharmacological Tools to Study Chronic Neuropathic Pain

    PubMed Central

    Paoletta, Silvia; Tosh, Dilip K.; Finley, Amanda; Gizewski, Elizabeth T.; Moss, Steven M.; Gao, Zhan-Guo; Auchampach, John A.; Salvemini, Daniela; Jacobson, Kenneth A.

    2013-01-01

    (N)-Methanocarba (bicyclo[3.1.0]hexane)-adenosine derivatives were probed for sites of charged sulfonate substitution, which precludes diffusion across biological membranes, e.g. blood brain barrier. Molecular modeling predicted that sulfonate groups on C2-phenylethynyl substituents would provide high affinity at both mouse (m) and human (h) A3 adenosine receptors (ARs), while a N6-p-sulfo-phenylethyl substituent would determine higher hA3AR vs. mA3AR affinity. These modeling predictions, based on steric fitting of the binding cavity and crucial interactions with key residues, were confirmed by binding/efficacy studies of synthesized sulfonates. N6-3-Chlorobenzyl-2-(3-sulfophenylethynyl) derivative 7 (MRS5841) bound selectively to h/m A3ARs (Ki hA3AR 1.9 nM) as agonist, while corresponding p-sulfo isomer 6 (MRS5701) displayed mixed A1/A3AR agonism. Both nucleosides administered i.p. reduced mouse chronic neuropathic pain that was ascribed to either A3 or A1/A3ARs using A3AR genetic deletion. Thus, rational design methods based on A3AR homology models successfully predicted sites for sulfonate incorporation, for delineating adenosine’s CNS vs. peripheral actions. PMID:23789857

  16. Uniform Ni/SiO2@Au magnetic hollow microspheres: rational design and excellent catalytic performance in 4-nitrophenol reduction.

    PubMed

    Zhang, Shenghuan; Gai, Shili; He, Fei; Dai, Yunlu; Gao, Peng; Li, Lei; Chen, Yujin; Yang, Piaoping

    2014-06-21

    A unique and rational design was presented to fabricate Ni/SiO2@Au magnetic hollow microspheres (MHMs) with interesting structures and well-dispersed metal nanoparticles. Hierarchical nickel silicate hollow microspheres were synthesized using silica colloidal spheres as a chemical template. Then, Ni/SiO2 MHMs with well-dispersed Ni nanoparticles were prepared via an in situ reduction approach. Ni/SiO2@Au MHMs were finally obtained by immobilizing uniform Au nanoparticles onto Ni/SiO2 support through a low-temperature chemical reduction process. It was found that Ni/SiO2@Au MHMs inherit the shape and uniformity of the original silica scaffold, and Ni NPs and Au NPs, which were less than 5 nm in size, were well dispersed on the mesoporous silica shell with narrow size distribution. Both Ni/SiO2 and Ni/SiO2@Au MHMs showed excellent catalytic activity in the 4-nitrophenol reduction reaction. Importantly, introduction of a small amount of Au NPs onto Ni/SiO2 MHMs markedly improved the catalytic activity. In particular, Ni/SiO2@Au MHMs showed high conversion even after re-use for several cycles with magnetic separation. The unique structure, high catalytic performance, and ease of separation make Ni/SiO2@Au MHMs highly promising candidates for diverse applications.

  17. Rational design of heat-set and specific-ion-responsive supramolecular hydrogels based on the Hofmeister effect.

    PubMed

    Nebot, Vicent J; Ojeda-Flores, Juan J; Smets, Johan; Fernández-Prieto, Susana; Escuder, Beatriu; Miravet, Juan F

    2014-10-27

    Smart supramolecular hydrogels have been prepared from a bolaamphiphilic L-valine derivative in aqueous solutions of different salts. The hydrogels respond selectively to different ions and are either reinforced or weakened. In one case, in contrast to conventional systems, the hydrogels are formed upon heating of the system. The use of the hydrogels in the controlled release of an entrapped dye is described as a proof of the potential applications of these systems. The responsive hydrogels were rationally designed by taking into account the noticeable effect of different ions from the Hofmeister series in the solubility of the hydrogelator, which was assessed by using NMR experiments. On the one hand, kosmotropic anions such as sulfate produce a remarkable solubility decrease in the gelator, which is associated with gel reinforcement, as measured by rheological experiments. On the other hand, chaotropic species such as perchlorate weaken the gel. A dramatic effect was observed in the presence of guanidinium chloride, which boosted the solubility of the gelator, in accordance with its chaotropic behaviour reported in protein science. In this case, a direct interaction of the guanidinium species with the carbonyl groups of the hydrogelator is detected by (13) C NMR spectroscopy. The weakening of this interaction upon a temperature increase allows for the preparation of heat-set hydrogelating systems. PMID:25220485

  18. Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo.

    PubMed

    Yu, Dan; Dong, Zhiqiang; Gustafson, William Clay; Ruiz-González, Rubén; Signor, Luca; Marzocca, Fanny; Borel, Franck; Klassen, Matthew P; Makhijani, Kalpana; Royant, Antoine; Jan, Yuh-Nung; Weiss, William A; Guo, Su; Shu, Xiaokun

    2016-02-01

    Fluorescent proteins (FPs) are powerful tools for cell and molecular biology. Here based on structural analysis, a blue-shifted mutant of a recently engineered monomeric infrared fluorescent protein (mIFP) has been rationally designed. This variant, named iBlueberry, bears a single mutation that shifts both excitation and emission spectra by approximately 40 nm. Furthermore, iBlueberry is four times more photostable than mIFP, rendering it more advantageous for imaging protein dynamics. By tagging iBlueberry to centrin, it has been demonstrated that the fusion protein labels the centrosome in the developing zebrafish embryo. Together with GFP-labeled nucleus and tdTomato-labeled plasma membrane, time-lapse imaging to visualize the dynamics of centrosomes in radial glia neural progenitors in the intact zebrafish brain has been demonstrated. It is further shown that iBlueberry can be used together with mIFP in two-color protein labeling in living cells and in two-color tumor labeling in mice. PMID:26549191

  19. Rational design of carbonitrile-carboxaldehyde cation receptor models: probing the nature of the heteroatom-metal interaction.

    PubMed

    Rosli, Ahmad Nazmi; Abu Bakar, Maizathul Akmam; Lee, Vannajan Sanghiran; Zain, Sharifuddin Md; Ahmad, Mohd Rais; Abdul Manan, Ninie Suhana; Alias, Yatimah; Woi, Pei Meng

    2014-09-01

    In this work, hybrid functional and G4 methods were employed in the rational design of carbonitrile-carboxaldehyde receptor models for cation recognition. Electron-sharing and ionic interactions between the models and the cations were analyzed utilizing the concepts of overlap population, atomic valence, electrostatic potential, and CHELPG charge in order to elucidate the nature of the heteroatom-metal interaction, the N versus O disparity, and the effect of pH. Receptor fragment models from ionomycin were employed to rationalize the selection of receptor models for discriminating group I cations and enhancing the selectivity for Mg(II) rather than Ca(II), and to examine the effects of keto-enol forms and negatively charged sites. The changes in geometries, overlap population, metal valence, and CHELPG charge upon solvation in heptane medium as compared to the gas phase were negligible. The optimized geometries reveal that the interaction between group II cations and the keto, enol, and enolate forms of 2-cyanoethanal causes 12 % bending of the C-C-N angle from linearity. Overlap populations show that the electron-sharing interaction favors group II cations but that the same mechanism allows Li(I) to compete. The total spin of Li(I) is 17 % greater than that of Ca(II), but the G4 binding energies of the two are separated by more than 50 kcal/mol, favoring group II cations, which may eliminate interference from Li(I). 1,2-Dicyanoethylene, which has only one form, shows similar characteristics. CHELPG analysis shows that Mg(II) transfers 25 and 18 % of its positive charge to 2-cyanoethanal enolate and 1,2-dicyanoethylene, respectively. Hydrogen atoms receive most of the positive charge in both receptors, but the N-termini exhibit strikingly different characteristics. Electrostatic potential contour profiles were found to be in good agreement with the atomic charge distributions. The application of uncharged 1,3-dicarbonyl and 2-cyanocarbonyl receptors and a judicious

  20. Immunodiagnosis of snake bite.

    PubMed

    Greenwood, B M; Warrell, D A; Davidson, N M; Ormerod, L D; Reid, H A

    1974-12-28

    Management of a patient with snake bite is influenced by the nature of the offending snake. Species diagnosis based on the patient's history and physical signs is often unreliable and the possibility of making a species diagnosis by immunological means has therefore been investigated. Wound aspirates, blister fluids, sera, and urine samples from patients with snake bite were examined for the presence of species-specific venoms using immunodiffusion. A positive species diagnosis was made in 40 out of 101 patients. Immunodiagnosis was especially successful in patients bitten by the puff adder, Bitis arietans, and the African spitting cobra, Naja nigricollis. A higher success rate could probably be achieved using more specific antisera and more sensitive assay techniques. PMID:4216390

  1. Rational Emotive Education

    ERIC Educational Resources Information Center

    Knaus, William

    1977-01-01

    Rational Emotive Education--an outgrowth of theories developed by Albert Ellis--is a teaching design of mental health concepts and problem-solving activities designed to help students to approach and cope with their problems through experiential learning, via a structured, thematic sequence of emotive education lessons. (MJB)

  2. HYDROGEN INITIATIVE: AN INTEGRATED APPROACH TOWARD RATIONAL NANOCATALYST DESIGN FOR HYDROGEN PRODUCTION. Technical Report-Year 1

    SciTech Connect

    Vlachos, Dionisios G; Buttrey, Douglas J; Lauterbach, Jochen

    2007-03-29

    The overall objective of this grant is to develop a rational framework for the discovery of low cost, robust, and active nano-catalysts that will enable efficient hydrogen production. Our approach will be the first demonstration of integrated multiscale model, nano-catalyst synthesis, and nanoscale characterization assisted high throughput experimentation (HTE). We will initially demonstrate our approach with ammonia decomposition on noble metal catalysts. Our research focuses on many elements of the Hydrogen Initiative in the Focus Area of “Design of Catalysts at the Nanoscale’. It combines high-throughput screening methods with various nanostructure synthesis protocols, advanced measurements, novel in situ and ex situ characterization techniques, and multiscale theory, modeling and simulation. This project directly addresses several of the long-term goals of the DOE/BES program. In particular, new nanoscale catalytic materials will be synthesized, characterized and modeled for the production of hydrogen from ammonia and a computational framework will be developed for efficient extraction of information from experimental data and for rational design of catalysts whose impact goes well beyond the proposed hydrogen production project. In the first year of the grant, we have carried out HTE screening using a 16 parallel microreactor coupled with an FTIR analysis system. We screened nearly twenty single metals and several bimetallic catalysts as a function of temperature, catalyst loading, inlet composition, and temperature (order of 400 experiments). We have found that Ru is the best single metal catalyst and no better catalysts were found among the library of bimetallics we have created so far. Furthermore, we have investigated promoting effects (i.e., K, Cs, and Ba) of the Ru catalyst. We have found that K is the dominant promoter of increased Ru activity. Response surface experimental design has led to substantial improvements of the Ru catalyst with promotion

  3. Rational design of cyclic peptide modulators of the transcriptional coactivator CBP: a new class of p53 inhibitors.

    PubMed

    Gerona-Navarro, Guillermo; Yoel-Rodríguez; Mujtaba, Shiraz; Frasca, Antonio; Patel, Jigneshkumar; Zeng, Lei; Plotnikov, Alexander N; Osman, Roman; Zhou, Ming-Ming

    2011-02-23

    The CREB binding protein (CBP) is a human transcriptional coactivator consisting of several conserved functional modules, which interacts with distinct transcription factors including nuclear receptors, CREB, and STAT proteins. Despite the importance of CBP in transcriptional regulation, many questions regarding the role of its particular domains in CBP functions remain unanswered. Therefore, developing small molecules capable of selectively modulating a single domain of CBP is of invaluable aid at unraveling its prominent activities. Here we report the design, synthesis, and biological evaluation of conformationally restricted peptides as novel modulators for the acetyl-lysine binding bromodomain (BRD) of CBP. Utilizing a target structure-guided and computer-aided rational design approach, we developed a series of cyclic peptides with affinity for CBP BRD significantly greater than those of its biological ligands, including lysine-acetylated histones and tumor suppressor p53. The best cyclopeptide of the series exhibited a K(d) of 8.0 μM, representing a 24-fold improvement in affinity over that of the linear lysine 382-acetylated p53 peptide. This lead peptide is highly selective for CBP BRD over BRDs from other transcriptional proteins. Cell-based functional assays carried out in colorectal carcinoma HCT116 cells further demonstrated the efficacy of this compound to modulate p53 stability and function in response to DNA damage. Our results strongly argue that these CBP modulators can effectively inhibit p53 transcriptional activity by blocking p53K382ac binding to CBP BRD and promoting p53 instability by changes of its post-translational modification states, a different mechanism than that of the p53 inhibitors reported to date.

  4. Rational Molecular Design of Potent PLK1 PBD Domain-binding Phosphopeptides Using Preferential Amino Acid Building Blocks.

    PubMed

    Mao, Xin-Li; Wang, Kui-Feng; Zhu, Feng; Pan, Zhao-Hu; Wu, Guo-Min; Zhu, Hong-Yuan

    2016-08-01

    Polo-like kinase 1 (PLK1) is an important regulator in diverse aspects of the cell cycle and proliferation. The protein has a highly conserved polo-box domain (PBD) present in C-terminal noncatalytic region, which exhibits a relatively broad sequence specificity in recognizing and binding phosphorylated substrates to control substrate phosphorylation by the kinase. In order to elucidate the structural basis, thermodynamic property, and biological implication underlying PBD-substrate recognition and association, a systematic amino acid preference profile of phosphopeptide interaction with PLK1 PBD domain was established via virtual mutagenesis analysis and mutation energy calculation, from which the contribution of different amino acids at each residue position of two reference phosphopeptides to domain-peptide binding was characterized comprehensively and quantitatively. With the profile, we are able to determine the favorable, neutral, and unfavorable amino acid types for each position of PBD-binding phosphopeptides, and we also explored the molecular origin of the broad sequence specificity in PBD-substrate recognition. To practice computational findings, the profile was further employed to guide rational design of potent PBD binders; three 6-mer phosphopeptides (i.e., IQSpSPC, LQSpTPF, and LNSpTPT) were successfully developed, which can efficiently target PBD domain with high affinity (Kd = 5.7 ± 1.1, 0.75 ± 0.18, and 7.2 ± 2.6 μm, resp.) as measured by a fluorescence anisotropy assay. The complex structure of PLK1 PBD domain with a newly designed, potent phosphopeptide LQSpTPF as well as diverse noncovalent chemical forces, such as H-bonds and hydrophobic interactions at the complex interface, were examined in detail to reveal the molecular mechanism of high affinity and stability of the complex system.

  5. Identification of protective B-cell epitopes of Atroxlysin-I: A metalloproteinase from Bothrops atrox snake venom.

    PubMed

    Schneider, F S; de Almeida Lima, S; Reis de Ávila, G; Castro, K L; Guerra-Duarte, C; Sanchez, E F; Nguyen, C; Granier, C; Molina, F; Chávez-Olortegui, C

    2016-03-29

    Atroxlysin-I (Atr-I) is a hemorrhagic snake venom metalloproteinase (SVMP) from Bothrops atrox venom, the snake responsible for the majority of bites in the north region of South America. SVMPs like Atr-I produce toxic effects in victims including hemorrhage, inflammation, necrosis and blood coagulation deficiency. Mapping of B-cell epitopes in SVMPs might result in the identification of non-toxic molecules capable of inducing neutralizing antibodies and improving the anti-venom therapy. Here, using the SPOT-synthesis technique we identified two epitopes located in the N-ter region of Atr-I (AtrEp1-(22)YNGNSDKIRRRIHQM(36); and AtrEp2-(55)GVEIWSNKDLINVQ(68)). Based on the sequence of AtrEp1 and AtrEp2 a third peptide named Atr-I biepitope (AtrBiEp) was designed and synthesized ((23)NGNSDKIRRRIH(34)GG(55)GVEIWSNKDLINVQ(68)). AtrBiEp was used to immunize BALB/c mice. Anti-AtrBiEp serum cross-reacted against Atr-I in western blot and was able to fully neutralize the hemorrhagic activity of Atr-I. Our results provide a rational basis for the identification of neutralizing epitopes on Atr-I snake venom toxin and show that the use of synthetic peptides could improve the generation of immuno-therapeutics. PMID:26917009

  6. Identification of protective B-cell epitopes of Atroxlysin-I: A metalloproteinase from Bothrops atrox snake venom.

    PubMed

    Schneider, F S; de Almeida Lima, S; Reis de Ávila, G; Castro, K L; Guerra-Duarte, C; Sanchez, E F; Nguyen, C; Granier, C; Molina, F; Chávez-Olortegui, C

    2016-03-29

    Atroxlysin-I (Atr-I) is a hemorrhagic snake venom metalloproteinase (SVMP) from Bothrops atrox venom, the snake responsible for the majority of bites in the north region of South America. SVMPs like Atr-I produce toxic effects in victims including hemorrhage, inflammation, necrosis and blood coagulation deficiency. Mapping of B-cell epitopes in SVMPs might result in the identification of non-toxic molecules capable of inducing neutralizing antibodies and improving the anti-venom therapy. Here, using the SPOT-synthesis technique we identified two epitopes located in the N-ter region of Atr-I (AtrEp1-(22)YNGNSDKIRRRIHQM(36); and AtrEp2-(55)GVEIWSNKDLINVQ(68)). Based on the sequence of AtrEp1 and AtrEp2 a third peptide named Atr-I biepitope (AtrBiEp) was designed and synthesized ((23)NGNSDKIRRRIH(34)GG(55)GVEIWSNKDLINVQ(68)). AtrBiEp was used to immunize BALB/c mice. Anti-AtrBiEp serum cross-reacted against Atr-I in western blot and was able to fully neutralize the hemorrhagic activity of Atr-I. Our results provide a rational basis for the identification of neutralizing epitopes on Atr-I snake venom toxin and show that the use of synthetic peptides could improve the generation of immuno-therapeutics.

  7. Rational Teaching.

    ERIC Educational Resources Information Center

    Macmillan, C. J. B.

    1985-01-01

    The recognition of teaching as a special relationship among individuals is currently being overlooked in much contemporary educational research and policymaking. The author examines the philosophy of rationality in teaching and relates it to the educational vision presented in George Orwell's novel, "Nineteen Eighty-Four." (CB)

  8. Confucian Rationalism

    ERIC Educational Resources Information Center

    Lam, Chi-Ming

    2014-01-01

    Nowadays, there is still a widely held view that the Chinese and Western modes of thought are quite distinct from each other. In particular, the Chinese mode of thought derived from Confucianism is considered as comparatively less rational than the Western one. In this article, I first argue that although the analogical mode of argumentation,…

  9. Uniform Ni/SiO2@Au magnetic hollow microspheres: rational design and excellent catalytic performance in 4-nitrophenol reduction

    NASA Astrophysics Data System (ADS)

    Zhang, Shenghuan; Gai, Shili; He, Fei; Dai, Yunlu; Gao, Peng; Li, Lei; Chen, Yujin; Yang, Piaoping

    2014-05-01

    A unique and rational design was presented to fabricate Ni/SiO2@Au magnetic hollow microspheres (MHMs) with interesting structures and well-dispersed metal nanoparticles. Hierarchical nickel silicate hollow microspheres were synthesized using silica colloidal spheres as a chemical template. Then, Ni/SiO2 MHMs with well-dispersed Ni nanoparticles were prepared via an in situ reduction approach. Ni/SiO2@Au MHMs were finally obtained by immobilizing uniform Au nanoparticles onto Ni/SiO2 support through a low-temperature chemical reduction process. It was found that Ni/SiO2@Au MHMs inherit the shape and uniformity of the original silica scaffold, and Ni NPs and Au NPs, which were less than 5 nm in size, were well dispersed on the mesoporous silica shell with narrow size distribution. Both Ni/SiO2 and Ni/SiO2@Au MHMs showed excellent catalytic activity in the 4-nitrophenol reduction reaction. Importantly, introduction of a small amount of Au NPs onto Ni/SiO2 MHMs markedly improved the catalytic activity. In particular, Ni/SiO2@Au MHMs showed high conversion even after re-use for several cycles with magnetic separation. The unique structure, high catalytic performance, and ease of separation make Ni/SiO2@Au MHMs highly promising candidates for diverse applications.A unique and rational design was presented to fabricate Ni/SiO2@Au magnetic hollow microspheres (MHMs) with interesting structures and well-dispersed metal nanoparticles. Hierarchical nickel silicate hollow microspheres were synthesized using silica colloidal spheres as a chemical template. Then, Ni/SiO2 MHMs with well-dispersed Ni nanoparticles were prepared via an in situ reduction approach. Ni/SiO2@Au MHMs were finally obtained by immobilizing uniform Au nanoparticles onto Ni/SiO2 support through a low-temperature chemical reduction process. It was found that Ni/SiO2@Au MHMs inherit the shape and uniformity of the original silica scaffold, and Ni NPs and Au NPs, which were less than 5 nm in size, were well

  10. Broadening the cofactor specificity of a thermostable alcohol dehydrogenase using rational protein design introduces novel kinetic transient behavior.

    PubMed

    Campbell, Elliot; Wheeldon, Ian R; Banta, Scott

    2010-12-01

    Cofactor specificity in the aldo-keto reductase (AKR) superfamily has been well studied, and several groups have reported the rational alteration of cofactor specificity in these enzymes. Although most efforts have focused on mesostable AKRs, several putative AKRs have recently been identified from hyperthermophiles. The few that have been characterized exhibit a strong preference for NAD(H) as a cofactor, in contrast to the NADP(H) preference of the mesophilic AKRs. Using the design rules elucidated from mesostable AKRs, we introduced two site-directed mutations in the cofactor binding pocket to investigate cofactor specificity in a thermostable AKR, AdhD, which is an alcohol dehydrogenase from Pyrococcus furiosus. The resulting double mutant exhibited significantly improved activity and broadened cofactor specificity as compared to the wild-type. Results of previous pre-steady-state kinetic experiments suggest that the high affinity of the mesostable AKRs for NADP(H) stems from a conformational change upon cofactor binding which is mediated by interactions between a canonical arginine and the 2'-phosphate of the cofactor. Pre-steady-state kinetics with AdhD and the new mutants show a rich conformational behavior that is independent of the canonical arginine or the 2'-phosphate. Additionally, experiments with the highly active double mutant using NADPH as a cofactor demonstrate an unprecedented transient behavior where the binding mechanism appears to be dependent on cofactor concentration. These results suggest that the structural features involved in cofactor specificity in the AKRs are conserved within the superfamily, but the dynamic interactions of the enzyme with cofactors are unexpectedly complex.

  11. Rationally designed graphene-nanotube 3D architectures with a seamless nodal junction for efficient energy conversion and storage

    PubMed Central

    Xue, Yuhua; Ding, Yong; Niu, Jianbing; Xia, Zhenhai; Roy, Ajit; Chen, Hao; Qu, Jia; Wang, Zhong Lin; Dai, Liming

    2015-01-01

    One-dimensional (1D) carbon nanotubes (CNTs) and 2D single-atomic layer graphene have superior thermal, electrical, and mechanical properties. However, these nanomaterials exhibit poor out-of-plane properties due to the weak van der Waals interaction in the transverse direction between graphitic layers. Recent theoretical studies indicate that rationally designed 3D architectures could have desirable out-of-plane properties while maintaining in-plane properties by growing CNTs and graphene into 3D architectures with a seamless nodal junction. However, the experimental realization of seamlessly-bonded architectures remains a challenge. We developed a strategy of creating 3D graphene-CNT hollow fibers with radially aligned CNTs (RACNTs) seamlessly sheathed by a cylindrical graphene layer through a one-step chemical vapor deposition using an anodized aluminum wire template. By controlling the aluminum wire diameter and anodization time, the length of the RACNTs and diameter of the graphene hollow fiber can be tuned, enabling efficient energy conversion and storage. These fibers, with a controllable surface area, meso-/micropores, and superior electrical properties, are excellent electrode materials for all-solid-state wire-shaped supercapacitors with poly(vinyl alcohol)/H2SO4 as the electrolyte and binder, exhibiting a surface-specific capacitance of 89.4 mF/cm2 and length-specific capacitance up to 23.9 mF/cm, — one to four times the corresponding record-high capacities reported for other fiber-like supercapacitors. Dye-sensitized solar cells, fabricated using the fiber as a counter electrode, showed a power conversion efficiency of 6.8% and outperformed their counterparts with an expensive Pt wire counter electrode by a factor of 2.5. These novel fiber-shaped graphene-RACNT energy conversion and storage devices are so flexible they can be woven into fabrics as power sources. PMID:26601246

  12. Rational Design of Charge-Transfer Interactions in Halogen-Bonded Co-crystals toward Versatile Solid-State Optoelectronics.

    PubMed

    Zhu, Weigang; Zheng, Renhui; Zhen, Yonggang; Yu, Zhenyi; Dong, Huanli; Fu, Hongbing; Shi, Qiang; Hu, Wenping

    2015-09-01

    Charge-transfer (CT) interactions between donor (D) and acceptor (A) groups, as well as CT exciton dynamics, play important roles in optoelectronic devices, such as organic solar cells, photodetectors, and light-emitting sources, which are not yet well understood. In this contribution, the self-assembly behavior, molecular stacking structure, CT interactions, density functional theory (DFT) calculations, and corresponding physicochemical properties of two similar halogen-bonded co-crystals are comprehensively investigated and compared, to construct an "assembly-structure-CT-property" relationship. Bpe-IFB wire-like crystals (where Bpe = 1,2-bis(4-pyridyl)ethylene and IFB = 1,3,5-trifluoro-2,4,6-triiodobenzene), packed in a segregated stacking form with CT ground and excited states, are measured to be quasi-one-dimensional (1D) semiconductors and show strong violet-blue photoluminescence (PL) from the lowest CT1 excitons (ΦPL = 26.1%), which can be confined and propagate oppositely along the 1D axial direction. In comparison, Bpe-F4DIB block-like crystals (F4DIB = 1,4-diiodotetrafluorobenzene), packed in a mixed stacking form without CT interactions, are determined to be insulators and exhibit unique white light emission and two-dimensional optical waveguide property. Surprisingly, it seems that the intrinsic spectroscopic states of Bpe and F4DIB do not change after co-crystallization, which is also confirmed by theoretical calculations, thus offering a new design principle for white light emitting materials. More importantly, we show that the CT interactions in co-crystals are related to their molecular packing and can be triggered or suppressed by crystal engineering, which eventually leads to distinct optoelectronic properties. These results help us to rationally control the CT interactions in organic D-A systems by tuning the molecular stacking, toward the development of a fantastic "optoelectronic world".

  13. Rational design of an AKR1C3-resistant analog of PR-104 for enzyme-prodrug therapy.

    PubMed

    Mowday, Alexandra M; Ashoorzadeh, Amir; Williams, Elsie M; Copp, Janine N; Silva, Shevan; Bull, Matthew R; Abbattista, Maria R; Anderson, Robert F; Flanagan, Jack U; Guise, Christopher P; Ackerley, David F; Smaill, Jeff B; Patterson, Adam V

    2016-09-15

    The clinical stage anti-cancer agent PR-104 has potential utility as a cytotoxic prodrug for exogenous bacterial nitroreductases expressed from replicating vector platforms. However substrate selectivity is compromised due to metabolism by the human one- and two-electron oxidoreductases cytochrome P450 oxidoreductase (POR) and aldo-keto reductase 1C3 (AKR1C3). Using rational drug design we developed a novel mono-nitro analog of PR-104A that is essentially free of this off-target activity in vitro and in vivo. Unlike PR-104A, there was no biologically relevant cytotoxicity in cells engineered to express AKR1C3 or POR, under aerobic or anoxic conditions, respectively. We screened this inert prodrug analog, SN34507, against a type I bacterial nitroreductase library and identified E. coli NfsA as an efficient bioactivator using a DNA damage response assay and recombinant enzyme kinetics. Expression of E. coli NfsA in human colorectal cancer cells led to selective cytotoxicity to SN34507 that was associated with cell cycle arrest and generated a robust 'bystander effect' at tissue-like cell densities when only 3% of cells were NfsA positive. Anti-tumor activity of SN35539, the phosphate pre-prodrug of SN34507, was established in 'mixed' tumors harboring a minority of NfsA-positive cells and demonstrated marked tumor control following heterogeneous suicide gene expression. These experiments demonstrate that off-target metabolism of PR-104 can be avoided and identify the suicide gene/prodrug partnership of E. coli NfsA/SN35539 as a promising combination for development in armed vectors.

  14. Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design

    PubMed Central

    Zhang, Jinfeng; Shi, Hao; Xu, Linyu; Zhu, Xiaoyan; Li, Xiangqian

    2015-01-01

    To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg-1·min-1 of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg-1·min-1 of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes. PMID:26218520

  15. Rationally designed graphene-nanotube 3D architectures with a seamless nodal junction for efficient energy conversion and storage.

    PubMed

    Xue, Yuhua; Ding, Yong; Niu, Jianbing; Xia, Zhenhai; Roy, Ajit; Chen, Hao; Qu, Jia; Wang, Zhong Lin; Dai, Liming

    2015-09-01

    One-dimensional (1D) carbon nanotubes (CNTs) and 2D single-atomic layer graphene have superior thermal, electrical, and mechanical properties. However, these nanomaterials exhibit poor out-of-plane properties due to the weak van der Waals interaction in the transverse direction between graphitic layers. Recent theoretical studies indicate that rationally designed 3D architectures could have desirable out-of-plane properties while maintaining in-plane properties by growing CNTs and graphene into 3D architectures with a seamless nodal junction. However, the experimental realization of seamlessly-bonded architectures remains a challenge. We developed a strategy of creating 3D graphene-CNT hollow fibers with radially aligned CNTs (RACNTs) seamlessly sheathed by a cylindrical graphene layer through a one-step chemical vapor deposition using an anodized aluminum wire template. By controlling the aluminum wire diameter and anodization time, the length of the RACNTs and diameter of the graphene hollow fiber can be tuned, enabling efficient energy conversion and storage. These fibers, with a controllable surface area, meso-/micropores, and superior electrical properties, are excellent electrode materials for all-solid-state wire-shaped supercapacitors with poly(vinyl alcohol)/H2SO4 as the electrolyte and binder, exhibiting a surface-specific capacitance of 89.4 mF/cm(2) and length-specific capacitance up to 23.9 mF/cm, - one to four times the corresponding record-high capacities reported for other fiber-like supercapacitors. Dye-sensitized solar cells, fabricated using the fiber as a counter electrode, showed a power conversion efficiency of 6.8% and outperformed their counterparts with an expensive Pt wire counter electrode by a factor of 2.5. These novel fiber-shaped graphene-RACNT energy conversion and storage devices are so flexible they can be woven into fabrics as power sources. PMID:26601246

  16. Rational Design of Charge-Transfer Interactions in Halogen-Bonded Co-crystals toward Versatile Solid-State Optoelectronics.

    PubMed

    Zhu, Weigang; Zheng, Renhui; Zhen, Yonggang; Yu, Zhenyi; Dong, Huanli; Fu, Hongbing; Shi, Qiang; Hu, Wenping

    2015-09-01

    Charge-transfer (CT) interactions between donor (D) and acceptor (A) groups, as well as CT exciton dynamics, play important roles in optoelectronic devices, such as organic solar cells, photodetectors, and light-emitting sources, which are not yet well understood. In this contribution, the self-assembly behavior, molecular stacking structure, CT interactions, density functional theory (DFT) calculations, and corresponding physicochemical properties of two similar halogen-bonded co-crystals are comprehensively investigated and compared, to construct an "assembly-structure-CT-property" relationship. Bpe-IFB wire-like crystals (where Bpe = 1,2-bis(4-pyridyl)ethylene and IFB = 1,3,5-trifluoro-2,4,6-triiodobenzene), packed in a segregated stacking form with CT ground and excited states, are measured to be quasi-one-dimensional (1D) semiconductors and show strong violet-blue photoluminescence (PL) from the lowest CT1 excitons (ΦPL = 26.1%), which can be confined and propagate oppositely along the 1D axial direction. In comparison, Bpe-F4DIB block-like crystals (F4DIB = 1,4-diiodotetrafluorobenzene), packed in a mixed stacking form without CT interactions, are determined to be insulators and exhibit unique white light emission and two-dimensional optical waveguide property. Surprisingly, it seems that the intrinsic spectroscopic states of Bpe and F4DIB do not change after co-crystallization, which is also confirmed by theoretical calculations, thus offering a new design principle for white light emitting materials. More importantly, we show that the CT interactions in co-crystals are related to their molecular packing and can be triggered or suppressed by crystal engineering, which eventually leads to distinct optoelectronic properties. These results help us to rationally control the CT interactions in organic D-A systems by tuning the molecular stacking, toward the development of a fantastic "optoelectronic world". PMID:26226301

  17. Rationally designed graphene-nanotube 3D architectures with a seamless nodal junction for efficient energy conversion and storage.

    PubMed

    Xue, Yuhua; Ding, Yong; Niu, Jianbing; Xia, Zhenhai; Roy, Ajit; Chen, Hao; Qu, Jia; Wang, Zhong Lin; Dai, Liming

    2015-09-01

    One-dimensional (1D) carbon nanotubes (CNTs) and 2D single-atomic layer graphene have superior thermal, electrical, and mechanical properties. However, these nanomaterials exhibit poor out-of-plane properties due to the weak van der Waals interaction in the transverse direction between graphitic layers. Recent theoretical studies indicate that rationally designed 3D architectures could have desirable out-of-plane properties while maintaining in-plane properties by growing CNTs and graphene into 3D architectures with a seamless nodal junction. However, the experimental realization of seamlessly-bonded architectures remains a challenge. We developed a strategy of creating 3D graphene-CNT hollow fibers with radially aligned CNTs (RACNTs) seamlessly sheathed by a cylindrical graphene layer through a one-step chemical vapor deposition using an anodized aluminum wire template. By controlling the aluminum wire diameter and anodization time, the length of the RACNTs and diameter of the graphene hollow fiber can be tuned, enabling efficient energy conversion and storage. These fibers, with a controllable surface area, meso-/micropores, and superior electrical properties, are excellent electrode materials for all-solid-state wire-shaped supercapacitors with poly(vinyl alcohol)/H2SO4 as the electrolyte and binder, exhibiting a surface-specific capacitance of 89.4 mF/cm(2) and length-specific capacitance up to 23.9 mF/cm, - one to four times the corresponding record-high capacities reported for other fiber-like supercapacitors. Dye-sensitized solar cells, fabricated using the fiber as a counter electrode, showed a power conversion efficiency of 6.8% and outperformed their counterparts with an expensive Pt wire counter electrode by a factor of 2.5. These novel fiber-shaped graphene-RACNT energy conversion and storage devices are so flexible they can be woven into fabrics as power sources.

  18. Rational design of an AKR1C3-resistant analog of PR-104 for enzyme-prodrug therapy.

    PubMed

    Mowday, Alexandra M; Ashoorzadeh, Amir; Williams, Elsie M; Copp, Janine N; Silva, Shevan; Bull, Matthew R; Abbattista, Maria R; Anderson, Robert F; Flanagan, Jack U; Guise, Christopher P; Ackerley, David F; Smaill, Jeff B; Patterson, Adam V

    2016-09-15

    The clinical stage anti-cancer agent PR-104 has potential utility as a cytotoxic prodrug for exogenous bacterial nitroreductases expressed from replicating vector platforms. However substrate selectivity is compromised due to metabolism by the human one- and two-electron oxidoreductases cytochrome P450 oxidoreductase (POR) and aldo-keto reductase 1C3 (AKR1C3). Using rational drug design we developed a novel mono-nitro analog of PR-104A that is essentially free of this off-target activity in vitro and in vivo. Unlike PR-104A, there was no biologically relevant cytotoxicity in cells engineered to express AKR1C3 or POR, under aerobic or anoxic conditions, respectively. We screened this inert prodrug analog, SN34507, against a type I bacterial nitroreductase library and identified E. coli NfsA as an efficient bioactivator using a DNA damage response assay and recombinant enzyme kinetics. Expression of E. coli NfsA in human colorectal cancer cells led to selective cytotoxicity to SN34507 that was associated with cell cycle arrest and generated a robust 'bystander effect' at tissue-like cell densities when only 3% of cells were NfsA positive. Anti-tumor activity of SN35539, the phosphate pre-prodrug of SN34507, was established in 'mixed' tumors harboring a minority of NfsA-positive cells and demonstrated marked tumor control following heterogeneous suicide gene expression. These experiments demonstrate that off-target metabolism of PR-104 can be avoided and identify the suicide gene/prodrug partnership of E. coli NfsA/SN35539 as a promising combination for development in armed vectors. PMID:27453434

  19. Where Galactic Snakes Live

    NASA Technical Reports Server (NTRS)

    2006-01-01

    This infrared image from NASA's Spitzer Space Telescope shows what astronomers are referring to as a 'snake' (upper left) and its surrounding stormy environment. The sinuous object is actually the core of a thick, sooty cloud large enough to swallow dozens of solar systems. In fact, astronomers say the 'snake's belly' may be harboring beastly stars in the process of forming.

    The galactic creepy crawler to the right of the snake is another thick cloud core, in which additional burgeoning massive stars might be lurking. The colorful regions below the two cloud cores are less dense cloud material, in which dust has been heated by starlight and glows with infrared light. Yellow and orange dots throughout the image are monstrous developing stars; the red star on the 'belly' of the snake is 20 to 50 times as massive as our sun. The blue dots are foreground stars.

    The red ball at the bottom left is a 'supernova remnant,' the remains of massive star that died in a fiery blast. Astronomers speculate that radiation and winds from the star before it died, in addition to a shock wave created when it exploded, might have played a role in creating the snake.

    Spitzer was able to spot the two black cloud cores using its heat-seeking infrared vision. The objects are hiding in the dusty plane of our Milky Way galaxy, invisible to optical telescopes. Because their heat, or infrared light, can sneak through the dust, they first showed up in infrared images from past missions. The cloud cores are so thick with dust that if you were to somehow transport yourself into the middle of them, you would see nothing but black, not even a star in the sky. Now, that's spooky!

    Spitzer's new view of the region provides the best look yet at the massive embryonic stars hiding inside the snake. Astronomers say these observations will ultimately help them better understand how massive stars form. By studying the clustering and range of masses of the stellar embryos, they hope

  20. Fear the serpent: A psychometric study of snake phobia.

    PubMed

    Polák, Jakub; Sedláčková, Kristýna; Nácar, David; Landová, Eva; Frynta, Daniel

    2016-08-30

    Millions of people worldwide suffer from specific phobias. Almost any stimulus may trigger a phobic reaction, but snakes are among the most feared objects. Half of the population feel anxious about snakes and 2-3% meet the diagnostic criteria for snake phobia. Despite such a high ratio, only one instrument is commonly used, the Snake Questionnaire (SNAQ). The aim of this study was to develop a standardized Czech translation, describe its psychometric properties and analyze the distribution of snake fears. In a counter-balanced design 755 respondents were asked to complete the English and Czech SNAQ (first or last) with a 2-3 month delay; 300 of them completed both instruments. We found excellent test-retest reliability (0.94), although the total scores differed significantly when the English version was administered first. The mean score was 5.80 and Generalized Linear Models revealed significant effects of sex and field of study (women and people with no biology education scored higher than men and biologists). A cut-off point for snake phobia as derived from a previous study identified 2.6% of the subjects as phobic. Finally, the score distribution was similar to other countries supporting the view that fear of snakes is universal. PMID:27280527

  1. Rational Design and Characterization of the Novel, Broad and Potent Bispecific HIV-1 Neutralizing Antibody iMabm36

    PubMed Central

    Sun, Ming; Pace, Craig S.; Yao, Xin; Yu, Faye; Padte, Neal N.; Huang, Yaoxing; Seaman, Michael S.; Li, Qihan; Ho, David D.

    2014-01-01

    While broadly neutralizing monoclonal antibodies (bNAbs) have always been considered potential therapeutic options for the prophylactic and treatment of HIV infection, their lack of breadth against all HIV variants has been one of the limiting factors. To provide sufficient neutralization breadth and potency against diverse viruses, including neutralization escape variants, strategies to combine different bNAbs have been explored recently. We rationally designed and engineered a novel bispecific HIV-1 neutralizing antibody (bibNAb), iMabm36, for high potency and breadth against HIV. iMabm36 is composed of the anti-CD4 Ab ibalizumab (iMab) linked to two copies of the single-domain Ab m36 which targets a highly conserved CD4-induced epitope. iMabm36 neutralizes a majority of a large, multi-clade panel of pseudoviruses (96%, n=118) at an IC50 concentration of less than 10 μg/mL, with 83% neutralized at an IC50 concentration of less than 0.1μg/ml. In addition, iMabm36 neutralizes six replication-competent transmitted-founder viruses to 100% inhibition at a concentration of less than 0.1μg/ml in a PBMC-based neutralizing assay. Mechanistically, improved antiviral activity of iMabm36 is dependent on both CD4 binding activity of iMab component and CD4i binding activity of the m36 component. After characterizing viral resistance to iMabm36 neutralization was due to mutations residing in the bridging sheet of gp120, an optimized m36 variant was engineered that, when fused to iMab, improved antiviral activity significantly. Together inter-dependency of this dual mechanism of action enables iMabm36 to potently inhibit HIV-1 entry. These results demonstrate that mechanistic-based design of bibNAbs could generate potential preventive and therapeutic candidates for HIV/AIDS. PMID:24853313

  2. [Neurotoxins from snake venom].

    PubMed

    Larréché, S; Mion, G; Clapson, P; Debien, B; Wybrecht, D; Goyffon, M

    2008-04-01

    Many snakes are able to quickly immobilize prey, thanks to their venom neurotoxins. Most of these snakes belong to families Elapidae or Hydrophidae but neurotoxins were also isolated from families Viperidae and Colubridae. Ophidian neurotoxins can be classified into several categories: neurotoxins which inhibit synaptic transmission (postsynaptic and presynaptic neurotoxins) and neurotoxins which facilitate it excessively (dendrotoxin and fasciculin). Their toxicity is dose-dependent, and venom effects are extremely fast. The clinical feature is a potentially fatal neurological syndrome, the so called cobraic syndrome. Because death by respiratory arrest may occur quickly with cobraic syndrome, immunotherapy is a true emergency, because toxins irreversible fixing makes immunotherapy effect uncertain after a few hours passed.

  3. Reproductive strategies in snakes.

    PubMed Central

    Shine, Richard

    2003-01-01

    Snakes of both sexes display remarkable flexibility and diversity in their reproductive tactics. Many features of reproduction in female snakes (such as reproductive mode and frequency, seasonality and multiple mating) allow flexible maternal control. For example, females can manipulate not only the genotypes of their offspring (through mate choice or enhanced sperm competition) but also the phenotypes of their offspring (through allocation 'decisions', behavioural and physiological thermoregulation, and nest-site selection). Reliance on stored energy ('capital') to fuel breeding results in low frequencies of female reproduction and, in extreme cases, semelparity. A sophisticated vomeronasal system not only allows male snakes to locate reproductive females by following scent trails, but also facilitates pheromonally mediated mate choice by males. Male-male rivalry takes diverse forms, including female mimicry and mate guarding; combat bouts impose strong selection for large body size in males of some species. Intraspecific (geographical) variation and phenotypic plasticity in a wide array of reproductive traits (offspring size and number; reproductive frequency; incidence of multiple mating; male tactics such as mate guarding and combat; mate choice criteria) provide exceptional opportunities for future studies. PMID:12803888

  4. Rational design, synthesis, and biological evaluation of lactam-bridged gramicidin A analogues: discovery of a low-hemolytic antibacterial peptide.

    PubMed

    Mao, Ji; Kuranaga, Takefumi; Hamamoto, Hiroshi; Sekimizu, Kazuhisa; Inoue, Masayuki

    2015-03-01

    A linear peptide, gramicidin A (GA), folds into a β(6.3) -helix, functions as an ion channel in the cell membrane, and exerts antibacterial activity. Herein we describe the rational design, synthesis, and biological evaluation of lactam-bridged GA analogues. The GA analogue with a 27-membered macrolactam was found to adopt a stable β(6.3) -helical conformation and exhibits higher ion-exchange activity than GA. Furthermore, this GA analogue retains the potent antibiotic activity of GA, but its hemolytic activity and toxicity toward mammalian cells are significantly lower than those of GA. This study thus dissociates the antibacterial and hemolytic/cytotoxic activities of GA, and charts a rational path forward for the development of new ion-channel-based antibiotics.

  5. Snakes Have Feelings, Too: Elements of a Camp Snake Program.

    ERIC Educational Resources Information Center

    Allen, Robert Ross

    2001-01-01

    A camp snake program can help campers overcome their fear of snakes, and people cannot truly enjoy nature when they carry a phobia about any one part of it. It can also help overcome prejudice by teaching truth and respect, instilling compassion, and helping campers develop empathy. Advice on catching, handling, identifying, keeping, and feeding…

  6. Rationalization: A Bibliography.

    ERIC Educational Resources Information Center

    Pedrini, D. T.; Pedrini, Bonnie C.

    Rationalization was studied by Sigmund Freud and was specifically labeled by Ernest Jones. Rationalization ought to be differentiated from rational, rationality, logical analysis, etc. On the one hand, rationalization is considered a defense mechanism, on the other hand, rationality is not. Haan has done much work with self-report inventories and…

  7. Rational Design of Human Metapneumovirus Live Attenuated Vaccine Candidates by Inhibiting Viral mRNA Cap Methyltransferase

    PubMed Central

    Zhang, Yu; Wei, Yongwei; Zhang, Xiaodong; Cai, Hui; Niewiesk, Stefan

    2014-01-01

    ABSTRACT The paramyxoviruses human respiratory syncytial virus (hRSV), human metapneumovirus (hMPV), and human parainfluenza virus type 3 (hPIV3) are responsible for the majority of pediatric respiratory diseases and inflict significant economic loss, health care costs, and emotional burdens. Despite major efforts, there are no vaccines available for these viruses. The conserved region VI (CR VI) of the large (L) polymerase proteins of paramyxoviruses catalyzes methyltransferase (MTase) activities that typically methylate viral mRNAs at positions guanine N-7 (G-N-7) and ribose 2′-O. In this study, we generated a panel of recombinant hMPVs carrying mutations in the S-adenosylmethionine (SAM) binding site in CR VI of L protein. These recombinant viruses were specifically defective in ribose 2′-O methylation but not G-N-7 methylation and were genetically stable and highly attenuated in cell culture and viral replication in the upper and lower respiratory tracts of cotton rats. Importantly, vaccination of cotton rats with these recombinant hMPVs (rhMPVs) with defective MTases triggered a high level of neutralizing antibody, and the rats were completely protected from challenge with wild-type rhMPV. Collectively, our results indicate that (i) amino acid residues in the SAM binding site in the hMPV L protein are essential for 2′-O methylation and (ii) inhibition of mRNA cap MTase can serve as a novel target to rationally design live attenuated vaccines for hMPV and perhaps other paramyxoviruses, such as hRSV and hPIV3. IMPORTANCE Human paramyxoviruses, including hRSV, hMPV, and hPIV3, cause the majority of acute upper and lower respiratory tract infections in humans, particularly in infants, children, the elderly, and immunocompromised individuals. Currently, there is no licensed vaccine available. A formalin-inactivated vaccine is not suitable for these viruses because it causes enhanced lung damage upon reinfection with the same virus. A live attenuated vaccine

  8. Quantum snake walk on graphs

    SciTech Connect

    Rosmanis, Ansis

    2011-02-15

    I introduce a continuous-time quantum walk on graphs called the quantum snake walk, the basis states of which are fixed-length paths (snakes) in the underlying graph. First, I analyze the quantum snake walk on the line, and I show that, even though most states stay localized throughout the evolution, there are specific states that most likely move on the line as wave packets with momentum inversely proportional to the length of the snake. Next, I discuss how an algorithm based on the quantum snake walk might potentially be able to solve an extended version of the glued trees problem, which asks to find a path connecting both roots of the glued trees graph. To the best of my knowledge, no efficient quantum algorithm solving this problem is known yet.

  9. JESS: Java extensible snakes system

    NASA Astrophysics Data System (ADS)

    McInerney, Tim; Akhavan Sharif, M. Reza; Pashotanizadeh, Nasrin

    2005-04-01

    Snakes (Active Contour Models) are powerful model-based image segmentation tools. Although researchers have proven them especially useful in medical image analysis over the past decade, Snakes have remained primarily in the academic world and they have not become widely used in clinical practice or widely available in commercial packages. A number of confusing and specialized variants exist and there has been no standard open-source implementation available. To address this problem, we present a Java Extensible Snakes System (JESS) that is general, portable, and extensible. The system uses Java Swing classes to allow for the rapid development of custom graphical user interfaces (GUI's). It also incorporates the Java Advanced Imaging(JAI) class library, which provide custom image preprocessing, image display and general image I/O. The Snakes algorithm itself is written in a hierarchical fashion, consisting of a general Snake class and several subclasses that span the main variants of Snakes including a new, powerful, robust subdivision-curve Snake. These subclasses can be easily and quickly extended and customized for any specific segmentation and analysis task. We demonstrate the utility of these classes for segmenting various anatomical structures from 2D medical images. We also demonstrate the effectiveness of JESS by using it to rapidly build a prototype semi-automatic sperm analysis system. The JESS software will be made publicly available in early 2005.

  10. [Snake bite injuries].

    PubMed

    Turchányi, B; Szalontay, T; Zacher, G

    2000-05-14

    Authors treated five patients who suffered venomous snake-bite injury. Although these snakes are not native in Hungary, this kind of injury is estimated to be more frequent, because of the increasing number of the private collections and illegal import of these reptiles. The local and general symptoms, the therapeutic steps are summarised in this study considering the literature as well. Two patients did not show any systemic or local symptoms at the level of injury, they needed only short observation, and woundcare. The other three patients had serious transient systematic symptoms (vasolability, hypotension/shock, coagulopathy, confusion). Two of them were given specific antivenom. As the third patient did not agree with the serum therapy, plasmapheresis was the choice to treat him, and it seemed to be effective. Few hours later the patients needed surgery because of serious compartment syndrome of their affected upper extremity. Surgical decompression of all the compartments and different possibilities of the secondary skin closure technique are demonstrated. Two patient healed completely, but the right thumb of the third was lost. Authors summarise the effects of the poisons, the symptoms, and the basic therapeutic steps during the first aid and in the primary hospital phase, respectively. They point out the indications of the serum therapy and the correct surgical decompression of the injured extremity. PMID:10851889

  11. Theoretical Studies in Heterogenous Catalysis: Towards a Rational Design of Novel Catalysts for Hydrodesulfurization and Hydrogen Production

    SciTech Connect

    Rodriguez,J.A.; Liu, P.

    2008-10-01

    potential to become the next generation of industrial HDS catalysts. Then, systematic studies concerned with the hydrogen-evolution reaction (HER) on extended surfaces, organometallic complexes and enzymes are presented. Finally, the reasons for the high catalytic activity of Au-CeO{sub 2} and Cu-CeO{sub 2} in the production of hydrogen through the water-gas shift reaction (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) are analyzed. It is shown that theoretical methods are very valuable tools for helping in the rational design of heterogeneous catalysts.

  12. ENGINEERING OF THE AGS SNAKE COIL ASSEMBLY.

    SciTech Connect

    ANERELLA,M.GUPTA,R.KOVACH,P.MARONE,A.PLATE,S.POWER,K.SCHMALZLE,J.WILLEN,E.

    2003-05-12

    A 30% Snake superconducting magnet is proposed to maintain polarization in the AGS proton beam, the magnetic design of which is described elsewhere. The required helical coils for this magnet push the limits of the technology developed for the RHIC Snake coils. First, fields must be provided with differing pitch along the length of the magnet. To accomplish this, a new 3-D CAD system (''Pro/Engineer'' from PTC), which uses parametric techniques to enable fast iterations, has been employed. Revised magnetic field calculations are then based on the output of the mechanical model. Changes are made in turn to the model on the basis of those field calculations. To ensure that accuracy is maintained, the final solid model is imported directly into the CNC machine programming software, rather than by the use of graphics translating software. Next, due to the large coil size and magnetic field, there was concern whether the structure could contain the coil forces. A finite element analysis was performed, using the 3-D model, to ensure that the stresses and deflections were acceptable. Finally, a method was developed using ultrasonic energy to improve conductor placement during coil winding, in an effort to minimize electrical shorts due to conductor misplacement, a problem that occurred in the RHIC helical coil program. Each of these activities represents a significant improvement in technology over that which was used previously for the RHIC snake coils.

  13. Self-assembling magnetic "snakes"

    SciTech Connect

    2010-01-01

    Nickel particles float peacefully in a liquid medium until a giant snake seems to swim by and snatch several particles up, adding to its own mass. The self-assembled "snakes" act like biological systems, but they are not alive and are driven by a magnetic field. The research may someday offer some insight into the organization of life itself. Read more at Wired: http://www.wired.com/wiredscience/2009/03/snakes/ Research and video by Alex Snezhko and Igor Aronson, Argonne National Laboratory.

  14. Rational design of anatase TiO2 architecture with hierarchical nanotubes and hollow microspheres for high-performance dye-sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Gu, Jiuwang; Khan, Javid; Chai, Zhisheng; Yuan, Yufei; Yu, Xiang; Liu, Pengyi; Wu, Mingmei; Mai, Wenjie

    2016-01-01

    Large surface area, sufficient light-harvesting and superior electron transport property are the major factors for an ideal photoanode of dye-sensitized solar cells (DSSCs), which requires rational design of the nanoarchitectures and smart integration of state-of-the-art technologies. In this work, a 3D anatase TiO2 architecture consisting of vertically aligned 1D hierarchical TiO2 nanotubes (NTs) with ultra-dense branches (HTNTs, bottom layer) and 0D hollow TiO2 microspheres with rough surface (HTS, top layer) is first successfully constructed on transparent conductive fluorine-doped tin oxide glass through a series of facile processes. When used as photoanodes, the DSSCs achieve a very large short-current density of 19.46 mA cm-2 and a high overall power conversion efficiency of 8.38%. The remarkable photovoltaic performance is predominantly ascribed to the enhanced charge transport capacity of the NTs (function as the electron highway), the large surface area of the branches (act as the electron branch lines), the pronounced light harvesting efficiency of the HTS (serve as the light scattering centers), and the engineered intimate interfaces between all of them (minimize the recombination effect). Our work demonstrates a possibility of fabricating superior photoanodes for high-performance DSSCs by rational design of nanoarchitectures and smart integration of multi-functional components.

  15. Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation.

    PubMed

    Bunker, Alex; Magarkar, Aniket; Viitala, Tapani

    2016-10-01

    Combined experimental and computational studies of lipid membranes and liposomes, with the aim to attain mechanistic understanding, result in a synergy that makes possible the rational design of liposomal drug delivery system (LDS) based therapies. The LDS is the leading form of nanoscale drug delivery platform, an avenue in drug research, known as "nanomedicine", that holds the promise to transcend the current paradigm of drug development that has led to diminishing returns. Unfortunately this field of research has, so far, been far more successful in generating publications than new drug therapies. This partly results from the trial and error based methodologies used. We discuss experimental techniques capable of obtaining mechanistic insight into LDS structure and behavior. Insight obtained purely experimentally is, however, limited; computational modeling using molecular dynamics simulation can provide insight not otherwise available. We review computational research, that makes use of the multiscale modeling paradigm, simulating the phospholipid membrane with all atom resolution and the entire liposome with coarse grained models. We discuss in greater detail the computational modeling of liposome PEGylation. Overall, we wish to convey the power that lies in the combined use of experimental and computational methodologies; we hope to provide a roadmap for the rational design of LDS based therapies. Computational modeling is able to provide mechanistic insight that explains the context of experimental results and can also take the lead and inspire new directions for experimental research into LDS development. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  16. Enhanced Thermostability of Lipoxygenase from Anabaena sp. PCC 7120 by Site-Directed Mutagenesis Based on Computer-Aided Rational Design.

    PubMed

    Diao, Hanwen; Zhang, Chong; Wang, Shuicheng; Lu, Fengxia; Lu, Zhaoxin

    2016-04-01

    Lipoxygenase from Anabaena sp. PCC 7120 (Ana-LOX) was thermally unstable. So, improving the thermostability of the enzyme was quite essential. The target site of Ana-LOX selected for site-directed mutagenesis was based on computer-aided rational design. The thermostability and specific activity of Ana-LOX were improved with replacing valine with alanine at the target site 421 and the site 40. Compared to the wild-type enzyme which has a half-life (T 1/2) of inactivation of 3.8 min at 50 °C, the T 1/2 of mutant enzymes with V421A and V40A substitution increased to 4.4 and 7.0 min, respectively. The double mutant V421A/V40A showed a synergistic effect with a T 1/2 value of 8.3 min, resulting in a 1.18-fold improvement compared to the original Ana-LOX. V421A, V40A, and V421A/V40A also obtained 4.83, 41.58, and 80.07 % increase in specific activity, respectively. This study provides useful theoretical reference for enzyme molecular modification and computer-aided rational design.

  17. Material Specific Rational Design of A1B2C3O7 High-Tc Superconductors without Copper [A, B, C = Cations

    NASA Astrophysics Data System (ADS)

    Isikaku-Ironkwe, O'paul; Schaffer, Michael J.

    Soon after the discovery of YBa2Cu3O7 with Tc = 93K, a similar structured system with Ag replacing Cu was discovered with a Tc = 50K. Also, the discovery of Ba0 . 6 K0 . 4 BiO3 with Tc = 30K indicated that Cu was not indispensable for high temperature superconductivity (HTSC). Latter, the discoveries of the Pnictide and Chalcogenide high-Tc superconductors confirmed those earlier experimental indications. Using our recently developed Material Specific Characterization Dataset (MSCD) model for analysis and design of superconductors, we have computed many designs that satisfy the MSCD characteristics of YBa2Cu3O7 as a design model. Our design recognizes the valence state characteristics that make YBa2Cu3O6 a semiconductor, while YBa2Cu3O7is a superconductor. Here we present ten material specific rational design examples of potential A1B2C3O7 HTSCs without Cu, using the YBa2Cu3O7 design model. This MSCD design model opens the possibility for search and discovery of high-Tc oxide superconductor systems without copper.

  18. A Rationally Designed Nitrogen-Rich Metal-Organic Framework and Its Exceptionally High CO2 and H2 Uptake Capability

    PubMed Central

    Wang, Xiao-Jun; Li, Pei-Zhou; Chen, Yifei; Zhang, Quan; Zhang, Huacheng; Chan, Xiu Xiang; Ganguly, Rakesh; Li, Yongxin; Jiang, Jianwen; Zhao, Yanli

    2013-01-01

    On the way towards a sustainable low-carbon future, the design and construction of chemical or physical adsorbents for CO2 capture and clean energy storage are vital technology. The incorporation of accessible nitrogen-donor sites into the pore walls of porous adsorbents can dramatically affect the CO2 uptake capacity and selectivity on account of the dipole-quadrupole interactions between the polarizable CO2 molecule and the accessible nitrogen site. In the present work, a nitrogen-rich rth-type metal-organic framework (MOF) was constructed based on rational design and careful synthesis. The MOF presents exceptionally high uptake capacity not only for CO2 but also for H2, which is attributed to favorable interactions between the gas molecules and the nitrogen-rich triazole units of the MOF proved by both experimental measurements and theoretical molecular simulations. PMID:23359632

  19. A Rationally Designed Nitrogen-Rich Metal-Organic Framework and Its Exceptionally High CO2 and H2 Uptake Capability

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Jun; Li, Pei-Zhou; Chen, Yifei; Zhang, Quan; Zhang, Huacheng; Chan, Xiu Xiang; Ganguly, Rakesh; Li, Yongxin; Jiang, Jianwen; Zhao, Yanli

    2013-01-01

    On the way towards a sustainable low-carbon future, the design and construction of chemical or physical adsorbents for CO2 capture and clean energy storage are vital technology. The incorporation of accessible nitrogen-donor sites into the pore walls of porous adsorbents can dramatically affect the CO2 uptake capacity and selectivity on account of the dipole-quadrupole interactions between the polarizable CO2 molecule and the accessible nitrogen site. In the present work, a nitrogen-rich rth-type metal-organic framework (MOF) was constructed based on rational design and careful synthesis. The MOF presents exceptionally high uptake capacity not only for CO2 but also for H2, which is attributed to favorable interactions between the gas molecules and the nitrogen-rich triazole units of the MOF proved by both experimental measurements and theoretical molecular simulations.

  20. Development of Snake Fungal Disease after Experimental Challenge with Ophidiomyces ophiodiicola in Cottonmouths (Agkistrodon piscivorous)

    PubMed Central

    Allender, Matthew C.; Baker, Sarah; Wylie, Daniel; Loper, Daniel; Dreslik, Michael J.; Phillips, Christopher A.; Maddox, Carol; Driskell, Elizabeth A.

    2015-01-01

    Snake fungal disease (SFD) is a clinical syndrome associated with dermatitis, myositis, osteomyelitis, and pneumonia in several species of free-ranging snakes in the US. The causative agent has been suggested as Ophidiomyces ophiodiicola, but other agents may contribute to the syndrome and the pathogenesis is not understood. To understand the role of O. ophiodiicola in SFD, a cottonmouth snake model of SFD was designed. Five cottonmouths (Agkistrodon piscivorous) were experimentally challenged by nasolabial pit inoculation with a pure culture of O. ophiodiicola. Development of skin lesions or facial swelling at the site of inoculation was observed in all snakes. Twice weekly swabs of the inoculation site revealed variable presence of O. ophiodiicola DNA by qPCR in all five inoculated snakes for 3 to 58 days post-inoculation; nasolabial flushes were not a useful sampling method for detection. Inoculated snakes had a 40% mortality rate. All inoculated snakes had microscopic lesions unilaterally on the side of the swabbed nasolabial pit, including erosions to ulcerations and heterophilic dermatitis. All signs were consistent with SFD; however, the severity of lesions varied in individual snakes, and fungal hyphae were only observed in 3 of 5 inoculated snakes. These three snakes correlated with post-mortem tissue qPCR evidence of O. ophiodiicola. The findings of this study conclude that O. ophiodiicola inoculation in a cottonmouth snake model leads to disease similar to SFD, although lesion severity and the fungal load are quite variable within the model. Future studies may utilize this model to further understand the pathogenesis of this disease and develop management strategies that mitigate disease effects, but investigation of other models with less variability may be warranted. PMID:26469977