New approaches to enzymatic glycoside synthesis through directed evolution

The expanding field of glycobiology requires tools for the synthesis of structurally defined oligosaccharides and glycoconjugates, while any potential therapeutic applications of sugar-based derivates would require access to substantial quantities of such compounds. Classical chemical approaches are not well suited for such large-scale syntheses, thus enzymatic approaches are sought. Traditional routes to the enzymatic assembly of oligosaccharides have involved the use of either Nature’s own biosynthetic enzymes, the glycosyl transferases, or glycosidases run in transglycosylation mode. However, each approach has drawbacks that have limited its application. Glycosynthases are mutant glycosidases in which the catalytic nucleophile has been replaced by mutation, inactivating them as hydrolases. When used in conjunction with glycosyl fluorides of the opposite anomeric configuration to that of the substrate, these enzymes function as highly efficient transferases, frequently giving stoichiometric yields of products. Further improvements can be obtained through directed evolution of the gene encoding the enzyme in question, but this requires the ability to screen very large libraries of catalysts. In this review we survey new screening methods for the formation of glycosidic linkages using high-throughput techniques, such as FACS, chemical complementation, and robot-assisted ELISA assays. Enzymes were evolved to have higher catalytic activity with their natural substrates, to show altered substrate specificities or to be promiscuous for efficient application in oligosaccharide, glycolipid, and glycoprotein synthesis.     

Mechanistic approaches to chemoprevention of mutation and cancer

This is the eighth special issue of 'Mutation Research' to focus on antimutagenesis and anticarcinogenesis. It covers a wide range of mechanisms from prevention of cancer initiation by antimutagens through to inhibition of tumour angiogenesis and selective estrogen receptor modulators. New screening methods and new biomarkers are also elucidated. There is increasing reason to believe that the long-term use of a combination of anticarcinogens, over an extended time span, may provide a realistic prospect of reducing the current burden of human cancers.     

Molecular approaches to the study of evolution and phylogeny of the Nemertina

Molecular biological tools currently available to us are revolutionizing the way in which we can address questions in evolutionary biology. The purpose of this article is to provide an overview of molecular techniques and applications available to biologists who are interested in evolutionary studies but who have little acquaintance with molecular biology. In evolutionary biology, techniques designed to determine degree of nucleic acid similarity are in common use and will be dealt with first. Another approach, namely gene expression studies, has strong implications for evolutionary biology but generally requires substantial familiarity with molecular biological tools. Expression studies provide powerful tools for discerning processes of speciation, as in the selection of genetic variants, as well as discerning lineages, e.g., expression of specific homeobox genes during segment formation. For investigations where either nucleic acid identity or gene expression are the ultimate goal, detailed information, protocols and appropriate controls are beyond the scope of this work but, where possible, recent review articles are cited.     

Mechanistic investigation of platinum-catalysed hydroformylation of propene: A density functional study

The mechanism of hydroformylation of propene in the presence of both cis-PtH(SnCl₃)(PH₃)₂ and trans-PtH(SnCl₃)(PH₃)₂ catalysts has been investigated. A density functional study has been carried out for all of the elementary steps of the catalytic cycle, i.e. for the alkene coordination, for its insertion into the Pt-H bond, carbon monoxide activation and its subsequent insertion into the Pt-alkyl bond. Finally, the product forming step, the dihydrogen activation and aldehyde elimination have been investigated.It has been found that the regioselectivity of hydroformylation is determined in the olefin insertion step. The computed ratio of the linear regioisomer, n-butanal is predicted to be 83% when solvation corrections were employed, being in very good agreement with the experimental result. Among the elementary steps the hydrogenolysis has been found to be the slowest followed by the migratory carbon monoxide insertion step. Due to the crucial role of the trichlorostannato ligand the electronic effects of SnCl₃ has been analysed employing the charge decomposition analysis (CDA), the natural bond orbital (NBO) and the atoms in molecules (AIM) methods.     

Potential functional differentiation of genome in the course of evolution and approaches to its study. I. Neontological annals of evolution and its analysis]

It is shown that the division of phylogenetical branches descends anisotomically. One new branch becomes evolutionary not active. Another one continues actively to develop. It allows to consider a system of present-day organisms as neonatological annals of evolution. A question arises on distinctions in the constitution of genomes of organisms belonging to active and inactive phylogenetic branches.     

Asthma phenotypes: the evolution from clinical to molecular approaches

Although asthma has been considered as a single disease for years, recent studies have increasingly focused on its heterogeneity. The characterization of this heterogeneity has promoted the concept that asthma consists of multiple phenotypes or consistent groupings of characteristics. Asthma phenotypes were initially focused on combinations of clinical characteristics, but they are now evolving to link biology to phenotype, often through a statistically based process. Ongoing studies of large-scale, molecularly and genetically focused and extensively clinically characterized cohorts of asthma should enhance our ability to molecularly understand these phenotypes and lead to more targeted and personalized approaches to asthma therapy.     

Game-theoretical approaches to studying the evolution of biochemical systems

Evolutionary optimization has been successfully used to increase our understanding of key properties of biochemical systems. Traditional optimization is, however, often insufficient for gaining deeper insights into the evolution of such systems because usually there is a mutual relationship between the properties optimized by evolution and the properties of the environment. Thus, by evolving towards optimal properties, organisms change their environment, which in turn alters the optimum. Evolutionary game theory provides an appropriate framework for analyzing evolution in such 'dynamic fitness landscapes'. We therefore argue that it is a promising approach to studying the evolution of biochemical systems. Indeed, recent studies have applied evolutionary game theory to key issues in the evolution of energy metabolism.     

Distinguishing four fundamental approaches to the evolution of helping

The evolution and stability of helping behaviour has attracted great research efforts across disciplines. However, the field is also characterized by a great confusion over terminology and a number of disagreements, often between disciplines but also along taxonomic boundaries. In an attempt to clarify several issues, we identify four distinct research fields concerning the evolution of helping: (1) basic social evolution theory that studies helping within the framework of Hamilton's inclusive fitness concept, i.e. direct and indirect benefits, (2) an ecological approach that identifies settings that promote life histories or interaction patterns that favour unconditional cooperative and altruistic behaviour, e.g. conditions that lead to interdependency or interactions among kin, (3) the game theoretic approach that identifies strategies that provide feedback and control mechanisms (protecting from cheaters) favouring cooperative behaviour (e.g. pseudo-reciprocity, reciprocity), and (4) the social scientists' approach that particularly emphasizes the special cognitive requirements necessary for human cooperative strategies. The four fields differ with respect to the 'mechanisms' and the 'conditions' favouring helping they investigate. Other major differences concern a focus on either the life-time fitness consequences or the immediate payoff consequences of behaviour, and whether the behaviour of an individual or a whole interaction is considered. We suggest that distinguishing between these four separate fields and their complementary approaches will reduce misunderstandings, facilitating further integration of concepts within and across disciplines.     

Potential functional differentiation of genome in the course of evolution and approaches to its study. II. Elucidation of diversity of phylogenetic lines]

It has been shown elsewhere (Chupov, 2001) that the branching of phylogenetical trunks goes by anisotomical way. Thus, in one of newly formed branches a possibility remains of a further evolutionary transformation, while taxa belonging to another branch sink into a prolonged evolutionary stasis. In the author's opinion, such a phenomenon is to be accompanied by distinctions in constitution of genetical cell devices of the taxa belonging to the branches with evolutionary contrasting potencies. In the article, an attempt is done to consider some other approaches relevant to this problem.     

Two approaches to the synthesis of 3-beta-D-glucopyranosyl-D-glucitol

Glycosidation of 1,2:5,6-di-O-isopropylidene-D-glucose with tetra-O-acetyl-glucosyl bromide in 1:1 benzene-MeNO2 afforded approximately equal amounts of the 3-O-beta-D-glycoside and the rearranged 6-O-beta-D-glycoside, while in MeCN only the latter was formed. When tetra-O-acetyl-beta-thiophenylglucoside was used as donor in CH2Cl2 in the presence of NIS/TfOH as activator, the 6-O-beta-D-glycoside and a 3-O-orthoester were formed in a 1:2 ratio at -20 degrees C, while at 20 degrees C only the former could be isolated. Glycosidation of 1-O-benzoyl-2,4-O-benzylidene-5,6-O-isopropylidene-d-glucitol with tetra-O-acetyl-glucosyl bromide in MeCN in the presence of Hg(CN)2 afforded the corresponding 3-O-alpha- and 3-O-beta-glycopyranoside in a 1:4 ratio in MeCN and 1:5 in 1:1 benzene-MeNO2, respectively. When Hg(CN)2/HgBr2 was used as promoter, the corresponding orthoester was also formed. When tetra-O-acetyl-beta-thiophenylglucoside was used as donor, the 3-O-beta-anomer and the orthoester were obtained predominantly in a 3:2 ratio together with traces of the 3-O-alpha-glycoside. Both beta-glycosides could be smoothly converted into 3-beta-D-glucopyranosyl-D-glucitol.     

Terminating substrates of DNA polymerases: synthesis and functional study

In order to study the mechanisms of DNA biosynthesis a number of modified nucleoside - substrates of DNA polymerases was synthesized. The absence of hydroxyl at 3'-position of ribose results in terminating properties of DNA biosynthesis of these analogues. A single step synthesis of triphosphates and alpha-thiotriphosphates of natural and 3'-modified 2'-deoxynucleosides is described.     

New approaches to the synthesis of antiviral nucleosides.

There is a pressing, worldwide need for new antiviral agents. The chemical synthesis of novel nucleosides for chemotherapeutic screening usually involves multistage processes which can be time consuming. The application of enzymatic methods for the synthesis and modification of antiviral nucleosides shows great promise because of the simplicity and high specificity of enzymatic reactions.     

Chemical synthesis approaches to the engineering of ion channels

Chemoselective ligation strategies have previously provided synthetic access to water-soluble proteins with novel properties, and more recently these strategies have been used to prepare ion channels. Examples of ion channels prepared by total chemical synthesis include bacterial mechanosensitive channels, and viral ion channels. Chemical protein synthesis allows for the generation of ion channel proteins with both native, and engineered structural or conductance properties.     

New approaches to synthesis of stereospecific sphingomyelin

Enormous progress in the asymmetric synthesis of stereochemically and chemically pure D-erythro-sphingosine and ceramides led to the development of a practical, efficient, easily scaleable process to provide industrial quantities of chiral sphingosine and ceramides. This established a new platform of chiral starting materials which facilitate the synthesis of complex sphingolipids. Utilizing stereochemically homogeneous, fully synthetic ceramides, two efficient synthetic methods were developed for the preparation of ultra pure stereochemically homogeneous sphingomyelins. The first method adapted highly efficient phosphoramidite technology from oligonucleotide chemistry. This method allows selective insertion of a phosphocholine moiety into 3-O-protected ceramide through phosphitylation, followed by choline attachment, phosphite oxidation and deprotection. This route provides stereochemically homogeneous sphingomyelin in 35-79% yield. The second route is based on the reaction of selectively protected ceramides with cyclic chlorophosphate followed by treatment with trimethylamine to give the desired sphingomyelins in 50% yield. Multigram quantities of 14C-labeled N-palmitoyl-D-erythro-sphingomyelin were produced with specific activity > 1000 dpm/nmol.     

Insights into Maize LEA proteins: from proteomics to functional approaches

LEA (late embryogenesis abundant) proteins participate in plant stress tolerance responses, but the mechanisms by which protection occurs are not fully understood. In the present work the unfolded proteins from maize dry embryos were analyzed by mass spectrometry. Twenty embryo proteins were identified, and among them 13 corresponded to LEA-type proteins. We selected three major LEA proteins, Emb564, Rab17 and Mlg3, belonging to groups 1, 2 and 3, respectively, and we undertook a comparative study in order to highlight differences among them. The post-translational modifications of native proteins were analyzed and the anti-aggregation properties of recombinant Emb564, Rab17 and Mgl3 proteins were evaluated in vitro. In addition, the protective effects of the LEA proteins were assessed in living cells under stress in Escherichia coli cells and in Nicotiana bentamiana leaves agroinfiltrated with fluorescent LEA-green fluorescent protein (GFP) fusions. Protein visualization by confocal microscopy indicated that cells expressing Mg3-GFP showed reduced cell shrinkage effects during dehydration and that Rab17-GFP co-localized to leaf oil bodies after heat shock. Overall, the results highlight differences and suggest functional diversity among maize LEA groups.     

Standardized phylogenetic tree: a reference to discover functional evolution

Functional evolution is often driven by positive natural selection. Although it is thought to be rare in evolution at the molecular level, its effects may be observed as the accelerated evolutionary rates. Therefore one of the effective ways to identify functional evolution is to identify accelerated evolution. Many methods have been developed to test the statistical significance of the accelerated evolutionary rate by comparison with the appropriate reference rate. The rates of synonymous substitution are one of the most useful and popular references, especially for large-scale analyses. On the other hand, these rates are applicable only to a limited evolutionary time period because they saturate quickly--i.e., multiple substitutions happen frequently because of the lower functional constraint. The relative rate test is an alternative method. This technique has an advantage in terms of the saturation effect but is not sufficiently powerful when the evolutionary rate differs considerably among phylogenetic lineages. For the aim to provide a universal reference tree, we propose a method to construct a standardized tree which serves as the reference for accelerated evolutionary rate. The method is based upon multiple molecular phylogenies of single genes with the aim of providing higher reliability. The tree has averaged and normalized branch lengths with standard deviations for statistical neutrality limits. The standard deviation also suggests the reliability level of the branch order. The resulting tree serves as a reference tree for the reliability level of the branch order and the test of evolutionary rate acceleration even when some of the species lineages show an accelerated evolutionary rate for most of their genes due to bottlenecking and other effects.     

Biochemical approaches to C4 photosynthesis evolution studies: the case of malic enzymes decarboxylases

C₄ photosynthesis enables the capture of atmospheric CO₂ and its concentration at the site of RuBisCO, thus counteracting the negative effects of low atmospheric levels of CO₂ and high atmospheric levels of O₂ (21 %) on photosynthesis. The evolution of this complex syndrome was a multistep process. It did not occur by simply recruiting pre-exiting components of the pathway from C₃ ancestors which were already optimized for C₄ function. Rather it involved modifications in the kinetics and regulatory properties of pre-existing isoforms of non-photosynthetic enzymes in C₃ plants. Thus, biochemical studies aimed at elucidating the functional adaptations of these enzymes are central to the development of an integrative view of the C₄ mechanism. In the present review, the most important biochemical approaches that we currently use to understand the evolution of the C₄ isoforms of malic enzyme are summarized. It is expected that this information will help in the rational design of the best decarboxylation processes to provide CO₂ for RuBisCO in engineering C₃ species to perform C₄ photosynthesis.     

New approaches to the chemical synthesis of bioactive oligosaccharides.

The past year has seen some major advances in the area of carbohydrate synthesis using chemical methods. Progress in all areas of synthetic methodology, including new protecting groups and coupling methods, has been reported. A number of complex carbohydrate structures have been prepared using known, as well as new, methods. The goal to allow nonspecialists access to defined carbohydrate structures for biochemical, biophysical and biological studies has drawn closer by the introduction of two approaches towards synthesis automation. A one-pot glycosylation strategy utilized computer-assisted synthesis planning and the first solid-phase automated synthesizer was introduced very recently.