Well-understood Structure Research Articles

Structural motifs in the early metallation steps of Zn(II) and Cd(II) binding to apo-metallothionein 1a

Many proteins require a metal cofactor to function and these metals are often involved in the protein folding process. The protein metallothionein (MT) has a dynamic structure capable of binding to a variety of metals with different stoichiometries. The most well-understood structure is the seven-metal, two domain structure formed upon metallation using Zn(II) or Cd(II). However, the partially metallated states and the pathways to form these clusters are less well-understood, although it is known that the pathways are pH dependent. Using stopped flow methods, it is shown that the metallation rates of the less cooperative Zn(II) binding pathway is much more impacted by low pH conditions that that of the more cooperative Cd(II) binding pathway. Electrospray ionization mass spectrometry (ESI-MS) methods reveal specific mixtures of bridging and terminally bound MxSy structures form in the first few metallation steps. Using a combination of methods, the data show that the result of unfolding this intrinsically disordered apo-MT structure using guanidinium chloride is that the formation of preliminary bridging structures that form in the first few metallation steps is impeded. The data show that more terminally bound structures form. Our conclusion is that the compact conformation of the native apo-MT at physiological pH allows for rapid formation of complex metal-thiolate structures with high affinity that provides protection from oxidation, a function that is suppressed upon unfolding. Overall, these results highlight both the importance of the apo-MT structure in the metallation pathway, but also the differences in Zn(II) and Cd(II) binding under different conditions.

Surface vs Homogeneous Organo-Hafnium Catalyst Ion-Pairing and Ligand Effects on Ethylene Homo- and Copolymerizations

Heterogeneous catalysts have long dominated polyethylene and polypropylene production, but understanding their catalysis is challenged by uncertainties in active site structures and percentages. Surface-bound organometallic catalysts are an emerging strategy to combine successful homogeneous catalysts having well-understood structures, relatively high percentages of active sites, and exceptional control of selectivity, with the attractions of surface catalysts, to transition promising homogeneous systems to large-scale heterogeneous ones. Nevertheless, surface-bound olefin polymerization catalysts typically produce ultrahigh Mw’s but with low activity and comonomer selectivity. Here, we report the systematic synthesis and characterization of a series of pyridylamido–Hf complexes and their corresponding surface catalysts chemisorbed on sulfated alumina (AlS) and zirconia (ZrS). Comparative ethylene homo- and 1-octene copolymerizations reveal similar activity and 1-octene selectivity trends in the homogeneous and heterogeneous systems. For the surface pyridylamido–Hf catalyst series, large variations in activity (up to 10×) and 1-octene incorporation (up to 28×) are achieved by ligand and support manipulation. Interestingly, while the homogeneous catalysts exhibit positive comonomer effects in ethylene/1-octene copolymerization, the surface catalysts behave oppositely. Extended X-ray absorption fine structure (EXAFS) reveals significantly elongated Hf···O bond distances vs typical Hf–O covalent bonds (2.06 vs 1.97 Å). Density functional theory (DFT) analysis of the heterolytic ion pair separation enthalpies, olefin insertion energetics, and NBO/Bader charges also suggest electrostatic Hf cation–anionic support binding and catalytic patterns, which are modulated by the ion-pairing energetics and ligand architecture.

Discovering High Potent Hsp90 Inhibitors as Antinasopharyngeal Carcinoma Agents through Fragment Assembling Approach.

Hsp90 is a new promising target for cancer treatment. Many inhibitors have been discovered as therapeutic agents, and some have passed Phase I and II. However, no one is approved by FDA yet. Novel and druggable Hsp90 inhibitors are still demanding. Here, we report a new way to discover high potent Hsp90 inhibitors as antinasopharyngeal carcinoma agents through assembling fragments. With chemotyping analysis, we extract seven chemotypes from 3482 known Hsp90 inhibitors, screen 500 fragments that are compatible with the chemotypes, and confirm 15 anti-Hsp90 fragments. Click chemistry is employed to construct 172 molecules and synthesize 21 compounds among them. The best inhibitor 3d was further optimized and resulted in more potent 4f (IC50 = 0.16 μM). In vitro and in vivo experiments confirmed that 4f is a promising agent against nasopharyngeal carcinoma. This study may provide a strategy in discovering new ligands against targets without well-understood structures.

Editorial.

We are pleased to present this special issue of Artificial Life, which is dedicated to articles arising from a workshop held on September 6, 2012, as part of the Unconventional Computation and Natural Computation (UCNC) conference in Orléans, France. UCNC is now a well-established meeting in the portfolio of conferences dedicated to nonstandard computation, dating back to 1998. The 2012 conference was hosted by the Fundamental Computer Science Laboratory of the University of Orléans, and the Second Workshop on Biological and Chemical Information Technologies (BioChemIT) was organized by the COBRA project.COBRA was a three-year initiative (2010–2013), supported by the European Commission to encourage and nurture research and training in the field of biological and chemical information technology. Fundamentally, the field seeks to harness the capabilities of natural and chemical systems. Rather than simply deriving inspiration from living systems, biological and chemical IT researchers seek to directly use or construct these systems for the purposes of engineering and computation. Over the past few years, technological advances in chemistry, molecular biology, functional materials, and engineering have brought biological and chemical information processing within our control. The ability to build, design, and grow ICT systems that can exploit these processes will lead to revolutionary advances in the future [1].The five articles in this issue represent a broad swathe of work, mainly covering alternative computational substrates (such as droplet architectures, chemical media, and microbes) and novel theory (complexity measurement).The first two articles concern chemistry-based computing. The one by Jones et al. considers how an architecture composed of interacting autonomous droplets might (in future) be applied to applications in robotics. They give their design for a single droplet (capable of rudimentary sensing of its environment, processing, and actuation), which is based on the well-known Braitenberg vehicle, before presenting preliminary experimental results on the processing and actuation phases, using multiple droplets.Although the first two articles both use the Belousov-Zhabotinsky (BZ) reaction [4] as a basic underlying mechanism, the second one (by King et al.) takes a slightly different approach from the first, in that it considers the geometry of the vessel containing the reaction, and how this might be designed in order to obtain large networks of chemical oscillators. Coupled oscillators are fundamental to the study of complex systems, and their properties have been harnessed for the purposes of nonstandard computation in a variety of domains and substrates (e.g., [2]). This article presents detailed experimental investigations into the effect of channel geometry on BZ excitability, thus laying the ground for threshold-based chemical computing implemented by the combination of reactions and specific 3D reaction vessel structure.The third article, by Ozasa et al., concerns the use of single-celled organisms; specifically, microbes from the genus Euglena, which are capable of self-directed movement. Previously, single colonies have been used to implement simply neurocomputing algorithms [3], but a useful extension, demonstrated here, would be to connect multiple colonies, for the purposes of distributed processing. Euglena cells are naturally averse to blue light, and this property is used to externally direct the swimming behavior of colonies of cells. In this way, the isolated colonies may be optically coupled, which allows studies of both cooperative and competitive control of behavior and colony distribution.The fourth article, by Beneš et al., also concerns microbial computing, but in the context of synthetic biology. The engineering of genetic circuits within bacteria (and other simple organisms) is now well established, but there are inherent difficulties with the approach, due to the unpredictable nature of the biological substrate. The notion of evolving circuits in situ is therefore appealing, and here the authors present a scheme for using plasmids (short circular strands of DNA) to drive a population towards good solutions. Importantly, they present a dual selection mechanism, and simulation results suggest that this adds robustness to the process.The final article in this issue, by Lui et al., considers issues of complexity, and introduces a new definition based on Kolmogorov complexity and Shannon entropy. The article shows some applications of this new measure, one using the familiar cellular automata classification scheme of Wolfram, and the other using the self-organization of porphyrin molecules. The utility of the method is illustrated by convincing demonstrations that the results of measuring existing well-understood structures (using the new metric) are consistent with previous theory.We thank the European Commission for supporting COBRA (grant number 270371), the UCNC organizers for hosting our workshop, the Editor-in-Chief, Mark Bedau, for the opportunity to publish the special issue, and the anonymous reviewers for their timely, clear, and helpful assessments.

Defining and identifying cograph communities in complex networks

Community or module detection is a fundamental problem in complex networks. Most of the traditional algorithms available focus only on vertices in a subgraph that are densely connected among themselves while being loosely connected to the vertices outside the subgraph, ignoring the topological structure of the community. However, in most cases one needs to make further analysis on the interior topological structure of communities to obtain various meaningful subgroups. We thus propose a novel community referred to as a cograph community, which has a well-understood structure. The well-understood structure of cographs and their corresponding cotree representation allows for an immediate identification of structurally-equivalent subgroups. We develop an algorithm called the Edge P4 centrality-based divisive algorithm (EPCA) to detect these cograph communities; this algorithm is efficient, free of parameters and independent of additional measures mainly due to the novel local edge P4 centrality measure. Further, we compare the EPCA with algorithms from the existing literature on synthetic, social and biological networks to show it has superior or competitive performance in accuracy. In addition to the computational advantages over other community-detection algorithms, the EPCA provides a simple means of discovering both dense and sparse subgroups based on structural equivalence or homogeneous roles which may otherwise go undetected by other algorithms which rely on edge density measures for finding subgroups.

Biosimilars 2.0

In the European Union, biosimilar products have been approved since 2006 under an abbreviated pathway that leverages their similarity to an existing “reference” biological product. The products approved to date are based on recombinant versions of endogenous proteins with well-understood structures and pharmacology, but complicated safety and immunogenicity profiles. The period during the 2000s that included the first reviews, approvals, sale and use of biosimilars, is referred to herein as “Biosimilars 1.0.” Over the next several years, a new and advanced tranche of biosimilars will be developed for complex reference products, including medicines used in the treatment of cancer and autoimmune diseases. A global market for biosimilars is developing, and this may well foreshadow the beginning of the second era of product development. This Biosimilars 2.0 period will likely be characterized by the development of complex products, global harmonization of standards, and the increasing demand for long-term monitoring of pharmaceuticals. The products developed in this period should exhibit high levels of fidelity to the reference products and should be rigorously evaluated in analytical, non-clinical and clinical comparisons. Additionally, Biosimilars 2.0 manufacturers should strive for transparency in their labels and take proactive strides to be accountable to providers and patients for the quality of their products. An important opportunity now exists for the healthcare community, industry and regulators to work in partnership to outline the appropriate standards for these products to facilitate increased access while meeting patients’ needs.

Investigation on positron annihilation characteristics of CO 2-exposed zeolite

In this study, the lifetime spectra of positron annihilation for CO 2-exposed zeolite 4A at different conditions were measured. The effects of subjecting zeolite 4A to baking treatment and exposing it to CO 2 at different pressures on the positronium (Ps) annihilation characteristics was investigated using positron annihilation lifetime spectroscopy (PALS). Zeolite 4A was chosen as the medium because of its rigidity, stability, and well-understood structure. Its structure consists of cavities that can be classified into two types: α-cage and β-cage. Zeolite 4A at vacuum (or dehydrated) conditions gave the longest lifetime, whereas that at ambient (or hydrated) conditions, at which water molecules are sorbed in the cavities of zeolite 4A, gave the shortest lifetime. The water molecules in zeolite 4A cavities would inhibit the ortho-positronium (o-Ps) formation probability. At lower gas sorption, the CO 2 gas molecules exhibited the pore-filling effect, resulting in a decrease in the o-Ps lifetime. However, at higher CO 2 sorption, the shielding effect in the α-cage increased with CO 2 pressure and led to an increase in the o-Ps lifetime. When the α-cage cavity was filled with the CO 2 gas molecules at pressures greater than 5 atm, o-Ps tended to migrate from the α-cage to the β-cage.

Recombinant adenovirus vectors for gene therapy and clinical trials.

In the last decade adenovirus (AdV) vectors have emerged as promising technology in gene therapy. They have been used for genetic modification of a variety of somatic cells in vitro and in vivo. They have been widely used as gene delivery vectors in experiments both with curative and preventive purposes. AdV vectors have been used in the experimental and in some extent in the clinical gene therapy of a variety of cancers. The combination of recombinant AdV technology with chemotherapy (pro drug system) seems to be promising, too. AdV vectors offer several advantages over other vectors. Replication defective vectors can be produced in very high titers (10(11) pfu/ml) thus allowing a substantially greater efficiency of direct gene transfer; they have the capacity to infect both replicating and nonreplicating (quiescent) cells from a variety of tissues and species. Several important limitations of adenovirus mediated gene transfer are also known, such as the relatively short-term (transient) expression of foreign genes, induction of the host humoral and cellular immune response to viral proteins and viral infected cells, which may substantially inhibit the effect of repeated treatment with AdV vectors, the limited cloning capacity and the lack of target cell specificity. However, the well-understood structure, molecular biology and host cell interactions of AdV-s offer some potential solutions to these limitations.

Single and multiple scattering XAFS in BaZrO 3: A comparison between theory and experiment

A comparison between theory and experiments is made for the XAFS of the Zr and Ba K-edges in BaZrO 3. BaZrO 3 is chosen because of its simple and well-understood structure but combines metallic atoms with oxygens. It is found that adding phase corrections to the theoretical XAFS significantly improves the accuracy of the structural parameters. These corrections are changes in the core electron threshold energy E 0 for each single scattering path involving a different type of backscattering atom. This, together with the fact that no corrections were needed for pure metal Cu, suggests that the phase corrections needed are due to charge distribution effect which are neglected in the theory.