The interplay of fold recognition and experimental structure determination in structural genomics

Achieving the goals of structural genomics initiatives depends on the outcomes of two groups of factors: the number and distribution of experimentally determined protein structures, and our ability to assign novel proteins to known structures (fold recognition) and use them to build models (modeling). The quality of the tools used for fold recognition defines the scope of experimental effort - the more distant the templates that can be recognized, the smaller the number of proteins that have to be solved. Recent improvements in fold recognition may have suggested that the goals of structural genomics initiatives are getting closer. However, problems that surfaced during the first few years of active work have put many of the early estimates in doubt and new ones are still slow in coming.     

Novel cytotoxic bufadienolides derived from bufalin by microbial hydroxylation and their structure-activity relationships

Microbial transformation was used to prepare novel cytotoxic bufadienolides. Twelve products (3-14) were obtained from bufalin (1) by the fungus Mucor spinosus. Their structures were elucidated by high-resolution mass spectroscopy (HR-MS) and extensive NMR techniques, including 1H NMR, 13C NMR, DEPT, 1H-1H correlation spectroscopy (COSY), two dimensional nuclear Overhauser effect correlation spectroscopy (NOESY), heteronuclear multiple quantum coherence (HMQC), and heteronuclear multiple bond coherence (HMBC). Compounds 3, 4, 9 and 11-14 are new mono- or dihydroxylated derivatives of bufalin with novel oxyfunctionalities at C-1beta, C-7beta, C-11beta, C-12beta and C-16alpha positions. The in vitro cytotoxic activities against human cancer cell lines of 3-14, together with 16 biotransformed products derived from cinobufagin (15-30) were determined by the MTT method, and their structure-activity relationships (SAR) were discussed.     

N-glycan branching requirement in neuronal and postnatal viability

The structural variations among extracellular N-glycans reflect the activity of glycosyltransferases and glycosidases that operate in the Golgi apparatus. More than other types of vertebrate glycans, N-glycans are highly branched oligosaccharides with multiple antennae linked to an underlying mannose core structure. The branching patterns of N-glycans consist of three types, termed high-mannose, hybrid, and complex. Though most extracellular mammalian N-glycans are of the complex type, some cells variably express hybrid and high-mannose forms. Nevertheless, a requirement for hybrid and complex N-glycan branching exists in embryonic development and postnatal function among mice and humans inheriting defective Mgat1 or Mgat2 alleles. The resulting defects in formation N-glycan branching patterns cause multiple abnormalities, including neurologic defects, and have inferred the presence of distinct functions for hybrid and complex N-glycan branches among different cell lineages. We have further explored N-glycan structure-function relationships in vivo by using Cre-loxP conditional mutagenesis to abolish hybrid and complex N-glycan branching specifically among neuronal cells. Our findings show that hybrid N-glycan branching is an essential posttranslational modification among neurons. Loss of Mgat1 resulted in a unique pattern of neuronal glycoprotein deficiency concurrent with caspase 3 activation and apoptosis. Such animals exhibited severe locomotor deficits, tremors, paralysis, and early postnatal death. Unexpectedly, neuronal Mgat2 deletion resulting in the loss of complex but not hybrid N-glycan branching was well tolerated without phenotypic markers of neuronal or locomotor dysfunction. Structural features associated with hybrid N-glycan branching comprise a requisite posttranslational modification to neuronal glycoproteins that permits normal cellular function and viability.     

Microbial glycosylation of four free anthraquinones by Absidia coerulea

Absidia coerulea transformed four anthraquinones from rhubarb, chrysophanol, physcion, emodin and aloe-emodin to their corresponding glycosylated metabolites. The structures of the products were characterized as chrysophanol 8-O-beta-D-glucoside, physcion 8-O-beta-D-glucoside, emodin 6-O-beta-D-glucoside, and aloe-emodin 1-O-beta-D-glucoside, respectively.     

Direct numerical simulations of micro-bubble expansion in gas embolotherapy

We are currently developing a novel gas embolotherapy technique that involves the selective, acoustic vaporization of liquid perfluorocarbon droplets in or near a tumor as a possible treatment for cancer The resulting bubbles can then stick within the tumor vasculature to occlude blood flow and "starve" the tumor The potential development of high stresses during droplet vaporization is a major concern for safe implementation of this technique. No prior study, either experimentally or theoretically, addresses this important issue. In this work, the acoustic vaporization procedure of the therapy is investigated by direct numerical simulations. The nonlinear, multiphase, computational model is comprised of an ideal gas bubble surrounded by liquid inside a long tube. Convective and unsteady inertia, viscosity, and surface tension affect the bubble dynamics and are included in this model, which is solved by a novel fixed-grid, sharp-interface, moving boundary method. We assess the potential for flow-induced wall stresses to rupture the vessel or damage the endothelium during vaporization under a range of operating conditions by varying dimensionless parameters--Reynolds, Weber, and Strouhal numbers, inertial energy and initial droplet size. It is found that the wall pressure is typically highest at the start of the bubble expansion, but the maximum wall shear stress occurs at a later time. Smaller initial bubble diameters, relative to the vessel diameter, result in lower wall stresses.     

A simple and sensitive method for glutamine:fructose-6-phosphate amidotransferase assay

For measuring glutamine:fructose-6-phosphate amidotransferase (GFAT) activity in cultured cells, an enzyme method -GDH method- was set up with high-efficiency, high-sensitivity and simple operation by determining the formed glutamate. During the process of making samples, reduced glutathione (GSH, 5 mM) and glucose-6-phosphate Na2 (5 mM) were added to the buffer for scraping the cells. The range of protein content in the samples was 80-150 microg. In the GFAT activity assay, the end product reduced acetylpyridine adenine dinucleotide (APADH) was determined at 370 nm directly. The suitable concentrations of the reactants fructose-6-phosphate (F-6-P), glutamine, acetylpyridine adenine dinucleotide (APAD) and glutamate dehydrogenase (GDH) were 0.8, 6 and 0.3 mM and 6 U, respectively. However, the excess of APAD may interfere with the APADH measurement. The reaction time course was 90 min. The GFAT activity in 3T3-L1, L6, HepG2 and HIRc cells were 1.84-8.51 nmol glutamate/mg protein.min.     

Pairwise protein structure alignment based on an orientation-independent backbone representation

Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI and LOCK.     

3-(7-Azaindolyl)-4-arylmaleimides as potent, selective inhibitors of glycogen synthase kinase-3

A novel series of acyclic 3-(7-azaindolyl)-4-(aryl/heteroaryl)maleimides was synthesized and evaluated for activity against GSK-3beta and selectivity versus PKC-betaII, as well as a broad panel of protein kinases. Compounds 14 and 17c potently inhibited GSK-3beta (IC(50)=7 and 26 nM, respectively) and exhibited excellent selectivity over PKC-betaII (325 and >385-fold, respectively). Compound 17c was also highly selective against 68 other protein kinases. In a cell-based functional assay, both 14 and 17c effectively increased glycogen synthase activity by inhibiting GSK-3beta.     

Specific inhibition effects of N-pentafluorobenzyl-1-deoxynojirimycin on human CD4+ T cells

We first synthesized N-pentafluorobenzyl-1-deoxynojirimycin (5F-DNM), one new derivative of 1-deoxynojirimycin (DNM). Effects on human peripheral blood mononuclear cells (PMBC) and secretion of cytokines from human PBMC by 5F-DNM were investigated. It was first found that 5F-DNM remarkably inhibited the secretion of interleukin-4 (IL-4) and had a specific inhibition on the expression of CD4 molecules. 5F-DNM, much less toxic than cyclosporin A, might be used as a new candidate of immunosuppressant for specifically treating Th2-mediated immune diseases.