The Structures and Physicochemical Properties of Organic Cofactors in Biocatalysis

Many crucial biochemical reactions in the cell require not only enzymes for catalysis but also organic cofactors or metal ions. Here, we analyse the physicochemical properties, chemical structures and functions of organic cofactors. Based on a thorough analysis of the literature complemented by our quantitative characterisation and classification, we found that most of these molecules are constructed from nucleotide and amino-acid-type building blocks, as well as some recurring cofactor-specific chemical scaffolds. We show that, as expected, organic cofactors are on average significantly more polar and slightly larger than other metabolites in the cell, yet they cover the full spectrum of physicochemical properties found in the metabolome. Furthermore, we have identified intrinsic groupings among the cofactors, based on their molecular properties, structures and functions, that represent a new way of considering cofactors. Although some classes of cofactors, as defined by their physicochemical properties, exhibit clear structural communalities, cofactors with similar structures can have diverse functional and physicochemical profiles. Finally, we show that the molecular functions of the cofactors not only may duplicate reactions performed by inorganic metal cofactors and amino acids, the cell's other catalytic tools, but also provide novel chemistries for catalysis.     

Site-specific interplay between O-GlcNAcylation and phosphorylation in cellular regulation

Ser(Thr)-O-linked β-N-acetylglucosamine (O-GlcNAc) is a ubiquitous modification of nucleocytoplasmic proteins. Extensive crosstalk exists between O-GlcNAcylation and phosphorylation, which regulates signaling in response to nutrients/stress. The development of novel O-GlcNAc detection and enrichment methods has improved our understanding of O-GlcNAc functions. Mass spectrometry has revealed O-GlcNAc’s many interactions with phosphorylation-mediated signaling. However, mechanisms regulating O-GlcNAcylation and phosphorylation are quite different. Phosphorylation is catalyzed by hundreds of distinct kinases. In contrast, in mammals, uridine diphospho-N-acetylglucosamine:polypeptide β-N-acetylglucosaminyl transferase (OGT) and β-D-N-acetylglucosaminidase (OGA) are encoded by single highly conserved genes. Both OGT’s and OGA’s specificities are determined by their transient associations with many other proteins to create a multitude of specific holoenzymes. The extensive crosstalk between O-GlcNAcylation and phosphorylation represents a new paradigm for cellular signaling.     

The antiviral protein viperin is a radical SAM enzyme

Viperin, an interferon-inducible antiviral protein, is shown to bind an iron-sulfur cluster, based on iron analysis as well as UV-Vis and electron paramagnetic resonance spectroscopic data. The reduced protein contains a [4Fe-4S]¹⁺ cluster whose g-values are altered upon addition of S-adenosylmethionine (SAM), consistent with SAM coordination to the cluster. Incubation of reduced viperin with SAM results in reductive cleavage of SAM to produce 5′-deoxyadenosine (5′-dAdo), a reaction characteristic of the radical SAM superfamily. The 5′-dAdo cleavage product was identified by a combination of HPLC and mass spectrometry analysis.     

Enzymatic stereospecific preparation of fluorescent S-adenosyl-l-methionine analogs

S-Adenosyl-l-methionine (SAM) is the preferred cofactor for biological methyl group transfers to various substrates such as nucleic acids, proteins, and lipids. Here we present stereospecific (>95% of the desired enantiomer) and high-yield preparation of four fluorescent and biologically active SAM analogs and demonstrate their usefulness in binding studies. Using a fluorescence titration experiment, we obtained a K_d of 0.38 μM for the S-2,6-diaminopurinylmethionine-SAM-III riboswitch complex.     

Selection of genetically modified hematopoietic cells in vitro and in vivo using alkylating agent lysomustine

Efficient gene transfer into hematopoietic stem cells is vital for the success of gene therapy of hematopoietic and immune system disorders. An in vivo selection system based on a mutant form of the O⁶-methylguanine-DNA-methyltransferase gene (MGMTm) is considered one of the more promising strategies for expansion of hematopoietic cells transduced with viral vectors. Here we demonstrate that MGMTm-expressing cells can be efficiently selected using lysomustine, a nitrosourea derivative of lysine. K562 and murine bone marrow cells expressing MGMTm are protected from the cytotoxic action of lysomustine in vitro. We also show in a murine model that MGMTm-transduced hematopoietic cells can be expanded in vivo on transplantation into sublethally irradiated recipients followed by lysomustine treatment. These results indicate that lysomustine can be used as a potent novel chemoselection drug applicable for gene therapy of hematopoietic and immune system disorders.     

Phlorotannins as Radical Scavengers from the Extract of Sargassum ringgoldianum

To screen algal phlorotannins with antioxidative activities, 50% ethanol extracts of 25 Japanese marine algae were evaluated. Scavenging activity against superoxide anion radicals was frequently found with a high content of total phenolic compounds. Among these, the extract from the brown seaweed, Sargassum ringgoldianum, showed the strongest scavenging activity. The active fraction contained a mixture of high molecular weight polyphenols, phlorotannins that were found to be polymerized bifuhalol, as analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The scavenging activity of the fraction against superoxide anion radicals was estimated to be 1.0 μg/ml (IC₅₀), which were approximately five times stronger than that of catechin.     

Towards an integrated computational tool for spatial analysis in macroecology and biogeography

Because most macroecological and biodiversity data are spatially autocorrelated, special tools for describing spatial structures and dealing with hypothesis testing are usually required. Unfortunately, most of these methods have not been available in a single statistical package. Consequently, using these tools is still a challenge for most ecologists and biogeographers. In this paper, we present sam (Spatial Analysis in Macroecology), a new, easy-to-use, freeware package for spatial analysis in macroecology and biogeography. Through an intuitive, fully graphical interface, this package allows the user to describe spatial patterns in variables and provides an explicit spatial framework for standard techniques of regression and correlation. Moran's I autocorrelation coefficient can be calculated based on a range of matrices describing spatial relationships, for original variables as well as for residuals of regression models, which can also include filtering components (obtained by standard trend surface analysis or by principal coordinates of neighbour matrices). sam also offers tools for correcting the number of degrees of freedom when calculating the significance of correlation coefficients. Explicit spatial modelling using several forms of autoregression and generalized least-squares models are also available. We believe this new tool will provide researchers with the basic statistical tools to resolve autocorrelation problems and, simultaneously, to explore spatial components in macroecological and biogeographical data. Although the program was designed primarily for the applications in macroecology and biogeography, most of sam 's statistical tools will be useful for all kinds of surface pattern spatial analysis. The program is freely available at http://www.ecoevol.ufg.br/sam (permanent URL at http://purl.oclc.org/sam/ ).     

Solution structure of the Vts1 SAM domain in the presence of RNA

The yeast Vts1 SAM (sterile alpha motif) domain is a member of a new class of SAM domains that specifically bind RNA. To elucidate the structural basis for RNA binding, the solution structure of the Vts1 SAM domain, in the presence of a specific target RNA, has been solved by multidimensional heteronuclear NMR spectroscopy. The Vts1 SAM domain retains the "core" five-helix-bundle architecture of traditional SAM domains, but has additional short helices at N and C termini, comprising a small substructure that caps the core helices. The RNA-binding surface of Vts1, determined by chemical shift perturbation, maps near the ends of three of the core helices, in agreement with mutational data and the electrostatic properties of the molecule. These results provide a structural basis for the versatility of the SAM domain in protein and RNA-recognition.