Current Opinion in Chemical Biology

Single molecule force spectroscopy presents a deceptively simple approach to probing interaction between molecules and molecular assemblies on the nanoscale by measuring forces that it takes to pull the molecules apart. Yet, a more detailed analysis reveals a wealth of different behaviors and interesting physics. This article aims to explore basic physical concepts behind these experiments from a strictly practical point of using these data to extract meaningful information about the interactions. It also focuses on different loading regimes in these experiments, different kinetics that they cause, and different data interpretation that is required for measurements in those regimes.

Metal ions are required to stabilize RNA tertiary structure and to begin the folding process. How different metal ions enable RNAs to fold depends on the electrostatic potential of the RNA and correlated fluctuations in the positions of the ions themselves. Theoretical models, fluorescence spectroscopy, small angle scattering and structural biology reveal that metal ions alter the RNA dynamics and folding transition states. Specifically coordinated divalent metal ions mediate conformational rearrangements within ribozyme active sites.

Widespread use of embryonic and adult stem cells for therapeutic applications will require reproducible production of large numbers of well-characterized cells under well-controlled conditions in bioreactors. During the past two years, substantial progress has been made towards this goal. Human mesenchymal stem cells expanded in perfused scaffolds retained multi-lineage potential. Mouse neural stem cells were expanded as aggregates in serum-free medium for 44 days in stirred bioreactors. Mouse embryonic stem cells expanded as aggregates and on microcarriers in stirred vessels retained expression of stem cell markers and could form embryoid bodies. Embryoid body formation from dissociated mouse embryonic stem cells, followed by embryoid body expansion and directed differentiation, was scaled up to gas-sparged, 2-l instrumented bioreactors with pH and oxygen control.

A suitable glycan structure is required for optimal protein-based therapeutics, such as antibody-dependent cell cytotoxicity in therapeutic antibodies, enzyme replacement therapy for lysosomal diseases, and controlled clearance of cytokines from the blood. Expressing proteins in unicellular organisms such as bacteria and yeast would be commercially advantageous compared with mammalian cells if these organisms could be engineered to produce human-type glycans. Although using bacteria and yeast to produce humanized glycoproteins and to conduct glycan remodeling of proteins remain a long-term goal for microbiologists and biochemists, recent studies in the field of microbial glycobiology in combination with synthetic chemical techniques suggest that this dream is close to being realized.

The concept of 'xenon biosensor' for magnetic resonance imaging (MRI) was first proposed by a Berkeley team in 2001, with evidence that hyperpolarized 129Xe bound to a biotin-labeled cryptophane can detect streptavidin at much lower concentrations (nM-microM) than is typical for contrast-enhanced MRI experiments. 129Xe biosensors have undergone many recent developments to address challenges in molecular imaging. For example, cryptophanes that exhibit 10-fold higher xenon affinity with distinct 129Xe magnetic resonance spectra have been synthesized. Also relevant are dendrimeric cryptophane assemblies and inorganic zeolites that localize many 129Xe atoms to rare targets. Finally, this article considers biosensors that produce measurable changes in 129Xe chemical shift based upon the activity of oligonucleotides, proteins, or enzymes, and includes the first cell studies.

Significant progress has been made in the past few years in the area of antibody drug conjugates (ADCs) for the selective delivery of cytotoxic drugs to tumors. Early work in this field incorporated clinically approved drugs and mouse monoclonal antibodies (mAbs), which had modest activities, and were generally immunogenic. The results of these studies prompted investigation that led to the identity of several key parameters that influenced activity and tolerability. These included the antigen target, the use of non-immunogenic mAb carriers, the incorporation of highly potent drugs and novel conditionally stable linker technologies, and the specific methods used to attach drugs to mAbs. As a result of these investigations, new agents with pronounced clinical activities have been developed. These include SGN-35, an ADC directed against the CD30-positive malignancies such as Hodgkin's disease and anaplastic large cell lymphoma, and trastuzumab-DM1 which has shown activity in metastatic breast carcinoma. This review details many of the technological advancements, and provides examples of promising ADCs that are currently in clinical trials.

The manufacture and use of protein microarrays with correctly folded and functional content presents significant challenges. Despite this, the feasibility and utility of such undertakings are now clear, and exciting progress has recently been demonstrated in the areas of content generation, printing strategies and protein immobilization. More importantly, we are now beginning to enjoy the fruits of these efforts as functional protein microarrays are being increasingly employed for biological discovery purposes. Recent examples of this include the characterization of autoantibody responses, antibody specificity profiling, protein-protein domain interaction profiling and a comprehensive characterization of coiled-coil interactions. The best, however, is yet to come.

Carbohydrate arrays, also referred to as glycan arrays, are composed of various oligosaccharides and/or polysaccharides immobilized on a solid support in a spatially defined arrangement. This technology provides a powerful, high-throughput approach to examining carbohydrate-macromolecule interactions, and glycan arrays have had a significant impact on the field of glycobiology. This review focuses on recent advances in glycan array technology, limitations, and opportunities for improvement. In particular, new methods for the production of natural glycan arrays and chemoenzymatic approaches are greatly expanding the diversity of structures on arrays. Since multivalent complex formation is generally required to achieve tight binding, methods to evaluate and modulate presentation are vital for enhancing the capabilities of this technology.

Antibodies have been the paradigm of binding proteins with desired specificities for more than one century and during the past decade their recombinant or humanized versions have entered clinical application with remarkable success. Meanwhile, a new generation of receptor proteins was born, which is derived from small and robust non-immunoglobulin "scaffolds" that can be equipped with prescribed binding functions using the methods of combinatorial protein design. Their ongoing development does not only provide valuable insights into the principles of molecular recognition and protein structure-function relationships but also yields novel reagents for medical use. This technology goes hand in hand with our expanding knowledge about the molecular pathologies of cancer, immunological, and infectious diseases. Currently, questions regarding the choice of suitable medically relevant targets with regard to a certain protein scaffold, the methodology for engineering high affinity, arming with effector functions, routes of administration, plasma half-life, and immunogenicity are in the focus. While many protein scaffolds have been proposed during the past years, the technology shows a trend toward consolidation with a smaller set of systems that are being applied against multiple targets and in different settings, with emphasis on the development of drug candidates for therapy or in vivo diagnostics: Adnectins, Affibodies, Anticalins, DARPins, and engineered Kunitz-type inhibitors, among others. Only few data from early clinical studies are available yet, but many more are likely to come in the near future, thus providing a growing basis for assessing the therapeutic potential--but possibly also some limitations--of this exciting new class of protein drugs.

Aromatic prenyltransferases catalyze the transfer of prenyl moieties to aromatic acceptor molecules and give rise to an astounding diversity of primary and secondary metabolites in plants, fungi and bacteria. Significant progress has been made in the biochemistry and genetics of this heterogeneous group of enzymes in the past years. After 30 years of extensive research on plant prenylflavonoid biosynthesis, finally the first aromatic prenyltransferases involved in the formation of these compounds have been cloned. In bacteria, investigations of the newly discovered family of ABBA prenyltransferases revealed a novel type of protein fold, the PT barrel. In fungi, a group of closely related indole prenyltransferase was found to carry out aromatic prenylations with different substrate specificity and regiospecificity, and to catalyze both regular and reverse prenylations.

Considerable progress has been made in manipulating oxidative biotransformations using oxygenases. Substrate acceptance, catalytic activity, regioselectivity and stereoselectivity have been improved significantly by substrate engineering, enzyme engineering or biocatalyst screening. Preparative biotransformations have been carried out to synthesize useful pharmaceutical intermediates or chiral synthons on the gram to several-hundred-gram scale, by use of whole cells of wild type or recombinant strains. The synthetic application of oxygenases in vitro has been shown to be possible by enzymatic or electrochemical regeneration of NADH or NADPH.

Changes in protein conformation play a vital role in biochemical processes, from biopolymer synthesis to membrane transport. Initial systematizations of protein flexibility, in a database framework, concentrated on the movement of domains and linkers. Movements were described in terms of simple sliding and hinging mechanisms of individual secondary structural elements. Recently, the accelerated pace and sophistication of methods for structural characterization of proteins has allowed high-resolution studies of increasingly complex assemblies and conformational changes. New data emphasize a breadth of possible structural mechanisms, particularly the ability to drastically alter protein architecture and the native flexibility of many structures.

The Hsp90 chaperone is a master regulator of the stability and activity of multiple oncoproteins such as Her2, Akt, Bcr-Abl, c-Kit, EGFR and mutant BRAF. The promise of inhibition of such a master regulator for cancer therapy is the potential to cause combinatorial inhibition of multiple oncogenic signaling pathways simultaneously. With the recent discovery of feedback loops that effectively negate the efficacy of selectively targeted anti-cancer agents, there is renewed interest in such a multi-pronged approach. There are now 14 drug candidates that target Hsp90 undergoing clinical trials in multiple indications as single agents or combination therapy. These compounds represent a diverse array of chemical matter stemming from natural product scaffolds to synthetic structure-based design. Although the compounds fall into distinct classes with unique properties, each inhibitor binds in the N-terminal ATP pocket and accumulates in tumor tissue while being rapidly cleared from circulation and normal tissue. The most advanced candidates are now in Phase 2 clinical trials and defining the therapeutic window, dosing schedule, and indication are the primary challenges for these potential first-in-class inhibitors.

Highlights ► DNA aptamer–nanomaterials combine unique optical or magnetic properties of nanomaterials with high selectivity of aptamers. ► Together they have enabled novel analytical techniques that advance our understanding of health and treatment of diseases. ► Recent work on using DNA aptamer–nanomaterials for analysis of intracellular components and metabolites are reviewed. ► Their recent applications in targeting and imaging of cancer cells and in cell-specific drug delivery are also highlighted.

Spectroscopic methods covering many energy regions together provide complementary insight into metalloenzyme active sites. These methods probe geometric and electronic structure and define these contributions to reactivity. Two recent advances--determination of the polarizations of electronic transitions in solution using magnetic circular dichroism, electron paramagnetic resonance and quantum chemistry, and experimental estimation of covalency using metal L-edges and ligand K-edges--are particularly important.

Are cytochrome P450 enzymes powerful industrial biocatalysts? Next to market demands, well-defined enzyme functionalities and process parameters allow generalizations on the basis of process windows. These can provide useful guidelines for the design of improved biocatalysts. Oxygenase-catalyzed reactions are of special interest for selective C-H bond oxidation. The versatile class of cytochrome P450 mono-oxygenases attracts particular attention, and impressive advances have been achieved with respect to mechanistic insight, enzyme activity, stability, and specificity. Recent major achievements include significant increases in productivities, yields, and rates of catalytic turnover as well as modification of substrate specificity and efficient multistep reactions in whole-cell biocatalysts. For some biocatalysts, these parameters are already of an industrially useful magnitude.

Among the many highlights of nickel metallobiochemistry in 1998 were the discoveries that Escherichia coli glyoxalase I is the first example of a nickel isomerase, and that the superoxide dismutase isolated from Streptomyces seoulensis is a new structural class of superoxide dismutase that features thiolate ligation.

The small-molecule macroarray represents a new tool to accelerate combinational library synthesis and screening. This array platform originates from the SPOT-synthesis technique, or the spatially addressed synthesis of peptides on cellulose supports. Recent advances in the field have expanded this technique beyond peptidic systems into the realm of complex small-molecule synthesis. Small-molecule macroarrays offer some significant advantages over traditional combinatorial synthesis platforms--these focused, 50-200 compound arrays are straightforward to synthesize, inexpensive, and amenable to numerous screening applications where the array compounds are either bound to or cleaved from the planar support. Critical advances in the small-molecule macroarray technique are highlighted herein, including the use of microwave-assisted organic reactions, multicomponent reactions, and automated spotting methods to further accelerate and broaden macroarray technology.

NMR spectroscopy and X-ray crystallography in conjunction with extended X-ray absorption fine structure spectroscopy, have contributed to the elucidation of the structural biology of protein-mediated mechanisms of heavy metal homeostasis. Among the most striking aspects of these investigations are the remarkable similarity of metal-ion-transport and sequestering systems across different species, and the need to continue the research to confirm hypotheses for the molecular mechanisms of transfers of metal ions between proteins.