Insights into antibody catalysis: Structure of an oxygenation catalyst at 1.9-Å resolution

The x-ray crystal structures of the sulfide oxidase antibody 28B4 and of antibody 28B4 complexed with hapten have been solved at 2.2-Å and 1.9-Å resolution, respectively. To our knowledge, these structures are the highest resolution catalytic antibody structures to date and provide insight into the molecular mechanism of this antibody-catalyzed monooxygenation reaction. Specifically, the data suggest that entropic restriction plays a fundamental role in catalysis through the precise alignment of the thioether substrate and oxidant. The antibody active site also stabilizes developing charge on both sulfur and periodate in the transition state via cation-pi and electrostatic interactions, respectively. In addition to demonstrating that the active site of antibody 28B4 does indeed reflect the mechanistic information programmed in the aminophosphonic acid hapten, these high-resolution structures provide a basis for enhancing turnover rates through mutagenesis and improved hapten design

Memory system support for image processing

Journal ArticleProcessor speeds are increasing rapidly, but memory speeds are not keeping pace. Image processing is an important application domain that is particularly impacted by this growing performance gap. Image processing algorithms tend to have poor memory locality because they access their data in a non-sequential fashion and reuse that data infrequently. As a result, they often exhibit poor cache and TLB hit rates on conventional memory systems, which limits overall performance. Most current approaches to addressing the memory bottleneck focus on modifying cache organizations or introducing processor-based prefetching. The Impulse memory system takes a different approach: allowing application software to control how, when, and where data are loaded into a conventional processor cache. Impulse does this by letting software configure how the memory controller interprets the physical addresses exported by a processor. Introducing an extra level of address translation in the memory. Data that is sparse in memory can be accessed densely, which improves both cache and TLB utilization, and Impulse hides memory latency by prefectching data within the memory controller. We describe how Impulse improves the performance of three image processing algorithms: an Impulse memory system yields speedups of 40% to 226% over an otherwise identical machine with a conventional memory system

Use of Cerny epoxides for the accelerated synthesis of glycosaminoglycans

1,6:2,3-Dianhydrohexopyranoses (Cerny epoxides) are versatile intermediates for the synthesis of glycosaminoglycans. Complex heparan and chondroitin sulfate disaccharide synthons can be assembled from a single common precursor in a short sequence of steps

Processes in KaffeOS: lsolation, resource management, and sharing in Java

Journal ArticleSingle-language runtime systems, in the form of Java virtual machines, are widely deployed platforms for executing untrusted mobile code. These runtimes provide some of the features that operating systems provide: inter-application memory protection and basic system services. They do not. however, provide the ability to isolate applications from each other, or limit their resource consumption. This paper describes KaffeOS, a system that provides these features for a Java runtime. The KaffeOS architecture take many lessons from operating from operating system design, such as the use of a user/kernel boundary

The Chemical Neurobiology of Carbohydrates

The cell surface displays a complex array of oligosaccharides, glycoproteins, and glycolipids. This diverse mixture of glycans contains a wealth of information, modulating a wide range of processes such as cell migration, proliferation, transcriptional regulation, and differentiation. Glycosylation is one of the most ubiquitous forms of post-translational modification, with more than 50% of the human proteome estimated to be glycosylated. Glycosylation adds another dimension to the complexity of cellular signaling and expands the ability of a cell to modulate protein function. The structural complexity of glycan modifications ranges from the addition of a single monosaccharide unit to polysaccharides containing hundreds of sugars in branched or linear arrays. This chemical diversity enables glycans to impart a vast array of functions, from structural stability and proteolytic protection to protein recognition and modulation of cell signaling networks. Emerging evidence suggests a pivotal role for glycans in regulating nervous system development and function. For instance, glycosylation influences various neuronal processes, such as neurite outgrowth and morphology, and may contribute to the molecular events that underlie learning and memory. Glycosylation is an efficient modulator of cell signaling and has been implicated in memory consolidation pathways. Genetic ablation of glycosylation enzymes often leads to developmental defects and can influence various organismal behaviors such as stress and cognition. Thus, the complexity of glycan functions help to orchestrate proper neuronal development during embryogenesis, as well as influence behaviors in the adult organism. The importance of glycosylation is further highlighted by defects in glycan structures that often lead to human disease, as exhibited by congenital disorders of glycosylation (CDG).25–29 These are usually inherited disorders resulting from defects in glycan biosynthesis, which are accompanied by severe developmental abnormalities, mental retardation, and difficulties with motor coordination. Such disorders highlight the importance of glycan biosynthesis in human health and development. Because therapeutic treatments are currently limited, investigations into the structure–activity relationships of glycans, as well as disease-associated alterations to glycan structure, are crucial for developing strategies to combat these diseases. Understanding the structure–function relationships of glycans has been hampered by a lack of tools and methods to facilitate their analysis. In contrast to nucleic acids and proteins, oligosaccharides often have branched structures, and their biosynthesis is not template-encoded. As such, the composition and sequence of oligosaccharides cannot be easily predicted, and genetic manipulations are considerably less straightforward. Analytical techniques for investigating oligosaccharide composition, sequence, and tertiary structure are still undergoing development and are far from routine, unlike methods for DNA and protein analysis. Lastly, glycan structures are not under direct genetic control and, thus, are often heterogeneous. This heterogeneity complicates structure–function analyses by traditional biochemical approaches that rely on the isolation and purification of glycans from natural sources. The problems associated with oligosaccharide analysis have hindered efforts to understand the biology of oligosaccharides yet have given chemists a unique opportunity to develop new methods to overcome these challenges. The development of chemical tools for the analysis of glycan structure and function is essential to advance our understanding of the roles of glycoconjugates in regulating diverse biological processes. In this review, we will highlight the emerging area of glyconeurobiology with an emphasis on current chemical approaches for elucidating the biological functions of glycans in the nervous system

Glycan Engineering for Cell and Developmental Biology

Cell-surface glycans are a diverse class of macromolecules that participate in many key biological processes, including cell-cell communication, development, and disease progression. Thus, the ability to modulate the structures of glycans on cell surfaces provides a powerful means not only to understand fundamental processes but also to direct activity and elicit desired cellular responses. Here, we describe methods to sculpt glycans on cell surfaces and highlight recent successes in which artificially engineered glycans have been employed to control biological outcomes such as the immune response and stem cell fate

Synthetic probes of glycosaminoglycan function

Glycosaminoglycans (GAGs) participate in many critical biological processes by modulating the activities of a wide range of proteins, including growth factors, chemokines, and viral receptors. Recent studies using synthetic oligosaccharides and glycomimetic polymers have established the importance of specific structural determinants in controlling GAG function. These findings illustrate the power of synthetic molecules to elucidate glycan-mediated signaling events, as well as the prospect of further advancements to understand the roles of GAGs in vivo and explore their therapeutic potential

Dynamic glycosylation of the transcription factor CREB: A potential role in gene regulation

We report that CREB (cyclic AMP-responsive element-binding protein), a transcription factor essential for long-term memory, is O-GlcNAc glycosylated in the mammalian brain. Glycosylation occurs at two sites within the Q2 domain and disrupts the interaction between CREB and TAF_(II)130, thereby repressing the transcriptional activity of CREB in vitro. These findings have important implications for the role of O-GlcNAc glycosylation in gene regulation, and they provide a link between O-GlcNAc and information storage processes in the brain

Photoaffinity Probes for the Identification of Sequence-Specific Glycosaminoglycan-Binding Proteins

Glycosaminoglycan (GAG)–protein interactions mediate critical physiological and pathological processes, such as neuronal plasticity, development, and viral invasion. However, mapping GAG–protein interaction networks is challenging as these interactions often require specific GAG sulfation patterns and involve transmembrane receptors or extracellular matrix-associated proteins. Here, we report the first GAG polysaccharide-based photoaffinity probes for the system-wide identification of GAG-binding proteins in living cells. A general platform for the modular, efficient assembly of various chondroitin sulfate (CS)-based photoaffinity probes was developed. Systematic evaluations led to benzophenone-containing probes that efficiently and selectively captured known CS-E-binding proteins in vitro and in cells. Importantly, the probes also enabled the identification of >50 new proteins from living neurons that interact with the neuroplasticity-relevant CS-E sulfation motif. Several candidates were independently validated and included membrane receptors important for axon guidance, innate immunity, synapse development, and synaptic plasticity. Overall, our studies provide a powerful approach for mapping GAG–protein interaction networks, revealing new potential functions for these polysaccharides and linking them to diseases such as Alzheimer’s and autism