Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design

Many research groups successfully rely on whole-gene random mutagenesis and recombination approaches for the directed evolution of enzymes. Recent advances in enzyme engineering have used a combination of these random methods of directed evolution with elements of rational enzyme modification to successfully by-pass certain limitations of both directed evolution and rational design. Semi-rational approaches that target multiple, specific residues to mutate on the basis of prior structural or functional knowledge create 'smart' libraries that are more likely to yield positive results. Efficient sampling of mutations likely to affect enzyme function has been conducted both experimentally and, on a much greater scale, computationally, with remarkable improvements in substrate selectivity and specificity and in the de novo design of enzyme activities within scaffolds of known structure.

Pathway engineering by designed divergent evolution

Designed divergent evolution is a proposed protein engineering methodology to redesign enzyme function. The methodology was developed on the basis of the theories of divergent molecular evolution: (i) enzymes with more active and specialized functions have evolved from ones with promiscuous functions; (ii) this process is driven by small numbers of amino acid substitutions (plasticity); and (iii) the effects of double or multiple mutations are often additive (quasi-additive assumption). Thus, in many cases the impact of multiple mutations can be calculated by first determining the effects of a mutation at a single position and subsequently summing these effects using the quasi-additive assumption. In this way, the shape of the fitness landscape of a particular enzyme function can be estimated. The combinations of mutations predicted to yield global optima for desired functions can then be selected and introduced into the enzymes. The methodology has been demonstrated to be very powerful to redesign enzyme function. The use of multiple redesigned enzymes in novel or reconstructed metabolic pathways will enable the production of natural and unnatural products that will find use as pharmaceuticals, agrochemicals and many other applications.

Intramyocellular triacylglycerol as a substrate source during exercise

The role of intramyocellular triacylglycerol (IMTG) as a substrate source during exercise has recently regained much attention as a result of the proposed functional relationship between IMTG accumulation and the development of insulin resistance. It has been speculated that elevated NEFA delivery and/or impaired fatty acid (FA) oxidation result in intramyocellular accumulation of triacylglycerol and FA metabolites, which are likely to induce defects in the insulin signalling cascade, causing insulin resistance. The progressive accumulation of IMTG in sedentary patients and patients who are obese and/or have type 2 diabetes should therefore form a major therapeutic target, and efforts should be made to develop interventions that prevent excess IMTG accretion by stimulating their rate of oxidation. Although regular exercise is likely to represent such an effective means, there is much controversy about the actual contribution of the IMTG pool as a substrate source during exercise. The apparent discrepancy in the published literature might be explained by differences in the applied research protocol and the selected subject population, but most of all by the techniques that have been employed to estimate IMTG use during exercise. Data obtained in trained-endurance athletes indicate that athletes can substantially reduce their IMTG pool following a single exercise session. With the growing awareness that skeletal muscle has a tremendous potential to oxidise IMTG during prolonged moderate-intensity exercise, more research is warranted to develop combined exercise, nutritional and/or pharmacological interventions that can stimulate IMTG oxidation in sedentary patients and patients who are obese and/or have type 2 diabetes.

Modeling chemical reactions for drug design

Chemical reactions are involved at many stages of the drug design process. This starts with the analysis of biochemical pathways that are controlled by enzymes that might be downregulated in certain diseases. In the lead discovery and lead optimization process compounds have to be synthesized in order to test them for their biological activity. And finally, the metabolism of a drug has to be established. A better understanding of chemical reactions could strongly help in making the drug design process more efficient. We have developed methods for quantifying the concepts an organic chemist is using in rationalizing reaction mechanisms. These methods allow a comprehensive modeling of chemical reactivity and thus are applicable to a wide variety of chemical reactions, from gas phase reactions to biochemical pathways. They are empirical in nature and therefore allow the rapid processing of large sets of structures and reactions. We will show here how methods have been developed for the prediction of acidity values and of the regioselectivity in organic reactions, for designing the synthesis of organic molecules and of combinatorial libraries, and for furthering our understanding of enzyme-catalyzed reactions and of the metabolism of drugs.

Evolvable self-reproducing cells in a two-dimensional artificial chemistry

We present a novel unit of evolution: a self-reproducing cell in a two-dimensional artificial chemistry. The cells have a strip of genetic material that is used to produce enzymes, each catalyzing a specific reaction that may affect the survival of the cell. The enzymes are kept inside the cell by a loop of membrane, thus ensuring that only the cell that produced them gets their benefit. A set of reaction rules, each simple and local, allows the cells to copy their genetic information and physically divide. The evolutionary possibilities of the cells are explored, and it is suggested that the system provides a useful framework for testing hypotheses about self-driven evolution.

Engineering enzymes for biocatalysis

Protein engineering techniques have been available for over two decades beginning with the development of methods for genetic engineering. Since that time, the engineering of enzymes has advanced rapidly along with a revolution in the range and efficiency of new techniques and strategies for designing and evolving proteins in the laboratory. While recent advances in high-throughput screening techniques are permitting larger libraries of enzymes to be screened more rapidly, a combination of new genetic tools and computational methods are enabling the efficient application of random mutagenesis targeted to areas of enzyme structures that are more likely to elicit the desired enhancement of their biocatalytic properties. Meanwhile the rational design of enzyme properties, in particular, by computational design is showing great potential. This review article summarises recent and important patents relating to the engineering of enzymes for biocatalysis.

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system (http://www.brenda.uni-koeln.de) is the largest publicly available enzyme information system worldwide. The major parts of its contents are manually extracted from primary literature. It is not restricted to specific groups of enzymes, but includes information on all identified enzymes irrespective of the enzyme's source. The range of data encompasses functional, structural, sequence, localisation, disease-related, isolation, stability information on enzyme and ligand-related data. Each single entry is linked to the enzyme source and to a literature reference. Recently the data repository was complemented by text-mining data in AMENDA (Automatic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta). A genome browser, membrane protein prediction and full-text search capacities were added. The newly implemented web service provides instant access to the data for programmers via a SOAP (Simple Object Access Protocol) interface. The BRENDA data can be downloaded in the form of a text file from the beginning of 2007.

Critical enzymes involved in endocannabinoid metabolism

Investigations of the pathways involved in the metabolism of endocannabinoids have grown exponentially in recent years following the discovery of cannabinoid receptors (CB) and their endogenous ligands, such as anandamide (AEA) and 2-arachidonoylglycerol (2-AG). The in vivo biosynthesis of AEA has been shown to occur through several pathways mediated by N-acylphosphatidylethanolamide-phospholipase D (NAPE-PLD), a secretory PLA(2) and PLC. 2-AG, a second endocannabinoid is generated through the action of selective enzymes such as phosphatidic acid phsophohydrolase, diacylglycerol lipase (DAGL), phosphoinositide-specific PLC (PI-PLC) and lyso-PLC. A putative membrane transporter or facilitated diffusion is involved in the cellular uptake or release of endocannabinoids. AEA is metabolized by fatty acid amidohydrolase (FAAH) and 2-AG is metabolized by both FAAH and monoacylglycerol lipase (MAGL). The author presents an integrative overview of current research on the enzymes involved in the metabolism of endocannabinoids and discusses possible therapeutic interventions for various diseases, including addiction.

Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuitry

A large body of experimental evidence indicates that the specific molecular interactions and/or chemical conversions depicted as links in the conventional diagrams of cellular signal transduction and metabolic pathways are inherently probabilistic, ambiguous and context-dependent. Being the inevitable consequence of the dynamic nature of protein structure in solution, the ambiguity of protein-mediated interactions and conversions challenges the conceptual adequacy and practical usefulness of the mechanistic assumptions and inferences embodied in the design charts of cellular circuitry. It is argued that the reconceptualization of molecular recognition and cellular organization within the emerging interpretational framework of self-organization, which is expanded here to include such concepts as bounded stochasticity, evolutionary memory, and adaptive plasticity offers a significantly more adequate representation of experimental reality than conventional mechanistic conceptions do. Importantly, the expanded framework of self-organization appears to be universal and scale-invariant, providing conceptual continuity across multiple scales of biological organization, from molecules to societies. This new conceptualization of biological phenomena suggests that such attributes of intelligence as adaptive plasticity, decision-making, and memory are enforced by evolution at different scales of biological organization and may represent inherent properties of living matter.

A Markovian engine for a biological energy transducer: the catalytic wheel

The molecular machines in biological cells are made of proteins, DNAs and other classes of molecules. The structures of these molecules are characteristically "soft", highly flexible, and yet their interactions with other molecules or ions are specific and selective. This chapter discusses a prevalent form, the catalytic wheel, or the energy transducer of cells, examines its mechanism of action, and extracts from it a set of simple but general rules for understanding the energetics of the biomolecular devices. These rules should also benefit design of manmade nanometer scale machines such as rotary motors or track-guided linear transporters. We will focus on an electric work that, by matching system dynamics and then enhancing the conformational fluctuation of one or several driver proteins, converts stochastic input of energy into rotation or locomotion of a receptor protein. The spatial (or barrier) and temporal symmetry breakings required for selected driver/receptor combinations are examined. This electric ratchet consists of a core engine that follows the Markovian dynamic, alleviates difficulties encountered in rigid mechanical model, and tailors to the soft-matter characteristics of the biomolecules.

Impact of transient stress and stress enzymes on development

Stress enzymes triggered by transient stress mediate reprioritization of developmental and homeostatic events to flexibly accomplish the next essential developmental event. This review analyzes recent studies on stress and stress enzyme function during early mammalian development and describes the diverse consequences that result from measurement, analysis of function, and management of stress and stress enzymes during development.

Organization of the biosynthetic gene cluster in Streptomyces sp. DSM 4137 for the novel neuroprotectant polyketide meridamycin

Meridamycin is a non-immunosuppressant, FKBP-binding macrocyclic polyketide, which has major potential as a neuroprotectant in a range of neurodegenerative disorders including dementia, Parkinson's disease and ischaemic stroke. A biosynthetic cluster predicted to encode biosynthesis of meridamycin was cloned from the prolific secondary-metabolite-producing strain Streptomyces sp. DSM 4137, not previously known to produce this compound, and specific gene deletion was used to confirm the role of this cluster in the biosynthesis of meridamycin. The meridamycin modular polyketide synthase consists of 14 extension modules distributed between three giant multienzyme proteins. The terminal module is flanked by a highly unusual cytochrome P450-like domain. The characterization of the meridamycin biosynthetic locus in this readily manipulated streptomycete species opens the way to the engineering of new, altered meridamycins of potential therapeutic importance.

Vitamins: not just for enzymes

Vitamins have traditionally played the role of coenzymes, organic molecules that facilitate the chemical reactions catalyzed by enzymes. However, several vitamins assume additional endocrine-like actions; this review will discuss four such vitamins. Vitamin K2 is involved in the gamma-carboxylation of coagulation factors and bone proteins, but it can also bind and activate the steroid and xenobiotic receptor in order to mediate transcription in bone tissue, and has been used to treat osteoporosis. Biotin is critical for some carboxylation reactions, but it also induces epidermal differentiation and has been used to treat lameness in animals and brittle nails in humans. Pyridoxal phosphate (the active form of vitamin B6) is involved in a multitude of reactions, including decarboxylation and transamination; it can also inhibit DNA polymerases and several steroid receptors and may prove useful as an adjunct in cancer chemotherapy. Finally, nicotinic acid is converted to NAD+ and NADP+, which are used as hydrogen/electron carriers in redox reactions. However, it also possesses vasodilatory and antilipolytic activities.

Evolution of enzyme superfamilies

Enzyme evolution is often constrained by aspects of catalysis. Sets of homologous proteins that catalyze different overall reactions but share an aspect of catalysis, such as a common partial reaction, are called mechanistically diverse superfamilies. The common mechanistic steps and structural characteristics of several of these superfamilies, including the enolase, Nudix, amidohydrolase, and haloacid dehalogenase superfamilies have been characterized. In addition, studies of mechanistically diverse superfamilies are helping to elucidate mechanisms of functional diversification, such as catalytic promiscuity. Understanding how enzyme superfamilies evolve is vital for accurate genome annotation, predicting protein functions, and protein engineering.

Enzyme promiscuity: evolutionary and mechanistic aspects

The past few years have seen significant advances in research related to the 'latent skills' of enzymes - namely, their capacity to promiscuously catalyze reactions other than the ones they evolved for. These advances regard (i) the mechanism of catalytic promiscuity - how enzymes, that generally exert exquisite specificity, promiscuously catalyze other, and sometimes barely related, reactions; (ii) the evolvability of promiscuous functions - namely, how latent activities evolve further, and in particular, how promiscuous activities can firstly evolve without severely compromising the original activity. These findings have interesting implications on our understanding of how new enzymes evolve. They support the key role of catalytic promiscuity in the natural history of enzymes, and suggest that today's enzymes diverged from ancestral proteins catalyzing a whole range of activities at low levels, to create families and superfamilies of potent and highly specialized enzymes.

Anticoagulant proteins from snake venoms: structure, function and mechanism

Over the last several decades, research on snake venom toxins has provided not only new tools to decipher molecular details of various physiological processes, but also inspiration to design and develop a number of therapeutic agents. Blood circulation, particularly thrombosis and haemostasis, is one of the major targets of several snake venom proteins. Among them, anticoagulant proteins have contributed to our understanding of molecular mechanisms of blood coagulation and have provided potential new leads for the development of drugs to treat or to prevent unwanted clot formation. Some of these anticoagulants exhibit various enzymatic activities whereas others do not. They interfere in normal blood coagulation by different mechanisms. Although significant progress has been made in understanding the structure-function relationships and the mechanisms of some of these anticoagulants, there are still a number of questions to be answered as more new anticoagulants are being discovered. Such studies contribute to our fight against unwanted clot formation, which leads to death and debilitation in cardiac arrest and stroke in patients with cardiovascular and cerebrovascular diseases, arteriosclerosis and hypertension. This review describes the details of the structure, mechanism and structure-function relationships of anticoagulant proteins from snake venoms.

PlyC: a multimeric bacteriophage lysin

Lysins are murein hydrolases produced by bacteriophage that act on the bacterial host cell wall to release progeny phage. When added extrinsically in their purified form, these enzymes produce total lysis of susceptible Gram-positive bacteria within seconds, suggesting a unique antimicrobial strategy. All known Gram-positive lysins are produced as a single polypeptide containing a catalytic activity domain, which cleaves one of the four major peptidoglycan bonds, and a cell-wall-binding domain, which may bind a species-specific carbohydrate epitope in the cell wall. Here, we have cloned and expressed a unique lysin from the streptococcal bacteriophage C(1), termed PlyC. Molecular characterization of the plyC operon reveals that PlyC is, surprisingly, composed of two separate gene products, PlyCA and PlyCB. Based on biochemical and biophysical studies, the catalytically active PlyC holoenzyme is composed of eight PlyCB subunits for each PlyCA. Inhibitor studies predicted the presence of an active-site cysteine, and bioinformatic analysis revealed a cysteine, histidine-dependent amidohydrolase/peptidase domain within PlyCA. Point mutagenesis confirmed that PlyCA is responsible for the observed catalytic activity, and Cys-333 and His-420 are the active-site residues. PlyCB was found to self-assemble into an octamer, and this complex alone was able to direct streptococcal cell-wall-specific binding. Similar to no other proteins in sequence databases, PlyC defines a previously uncharacterized structural family of cell-wall hydrolases.

Cloning and expression pattern of peroxisomal enzymes in the mussel Mytilus galloprovincialis and in the thicklip grey mullet Chelon labrosus: generation of new tools to study peroxisome proliferation

Aquatic organisms living in coastal/estuarine areas show peroxisome proliferation after exposure to different environmentally relevant pollutants. In order to generate new tools to assess peroxisome proliferation in aquatic animals, peroxisomal enzymes were cloned using degenerate primers in the mussel Mytilus galloprovincialis and in the thicklip grey mullet Chelon labrosus. Fragments of catalase (CAT), thiolase (THIO), polyamine oxidase (POX) and xanthine oxidoreductase (XOR) were cloned and their expression pattern studied in different tissues by semi-quantitative RT-PCR. In mussels, CAT, THIO, POX and XOR were expressed in digestive gland, mantle and gills while in mullets CAT, THIO and POX were expressed in liver, spleen, brain, heart, muscle and gills. XOR was mainly expressed in liver and heart. Mature mullets showed the highest expression of peroxisomal enzymes in liver, spleen and brain, while in juveniles expression was mainly found in muscle tissues, liver and gills. Laboratory experiments of exposure to organic pollutants are being performed to study the usefulness of these tools to study peroxisome proliferation in pollution biomonitoring programmes.

Synthesis and enzymatic susceptibility of a series of novel GM2 analogs

A series of GM2 analogs in which GM2 epitope was coupled to a variety of glycosyl lipids were designed and synthesized to investigate the mechanism of enzymatic hydrolysis of GM2 ganglioside. The coupling of N-Troc-protected sialic acid and p-methoxyphenyl galactoside acceptor gave the crystalline disaccharide, which was further coupled with galactosamine donor to give the desired GM2 epitope trisaccharide. After conversion into the corresponding glycosyl donor, the trisaccharide was coupled with galactose, glucose and artificial ceramide (B30) to give the final compounds. The result on hydrolysis of GM2 analogs indicates that GM2 activator protein requires one spacer sugar between GM2 epitope and the lipid moiety to assist the hydrolysis of the terminal GalNAc residue.

Raising enzymes from the dead and the secrets they can tell

The complexity of partners and reaction sequence has made the deciphering eukaryotic signaling pathways particularly difficult. Various approaches have yielded important results. A recent paper reports on an advance that uses chemical rescue of inactive mutant of Src. The rescue was done in cells, and the results obtained showing new aspects of Src function point the way toward a general use of this chemical tool in the sorting out of complex biological processes.

Dual function of rice OsDR8 gene in disease resistance and thiamine accumulation

The function of OsDR8, a rice disease resistance-responsive gene, was studied. Silencing of OsDR8 using an RNA interference approach resulted in phenotypic alteration of the plants. The transgenic plants with repressed expression of OsDR8 showed reduced resistance or susceptibility to Xanthomonas oryzae pv. oryzae and Magnaporthe grisea causing bacterial blight and blast, which are two of the most devastating diseases in rice worldwide, respectively. The putative product of OsDR8 was highly homologous to an enzyme involved in the biosynthesis of the thiazole precursor of thiamine. Transgenic plants showing repressed expression of OsDR8 and reduced resistance had significantly lower levels of thiamine than the control plants. Exogenous application of thiamine could complement the compromised defense of the OsDR8-silenced plants. The expression level of several defense-responsive genes including the earlier functional genes of defense transduction pathway, OsPOX and OsPAL, and the downstream genes of the pathway, OsPR1a, OsPR1b, OsPR4, OsPR5 and OsPR10, was also decreased in the OsDR8-silenced plants. These results suggest that the impact of OsDR8 on disease resistance in rice may be through the regulation of expression of other defense-responsive genes and the site of OsDR8 function is on the upstream of the signal transduction pathway. In addition, the accumulation of thiamine may be essential for bacterial blight resistance and blast resistance.

Transcreener™: screening enzymes involved in covalent regulation

Enzymes that catalyse group transfer reactions comprise a significant fraction of the human proteome and are a rich source of drug targets because of their role in covalent regulatory cycles. Phosphorylation, glycosylation, sulfonation, methylation and acetylation represent some of the key types of group transfer reactions that modulate the function of diverse biomolecules through covalent modification. Development of high-throughput screening methods for these enzymes has been problematic because of the diversity of acceptor substrates. Recently, the authors developed a novel assay platform called Transcreener that relies upon fluorescence detection of the invariant reaction product of a group transfer reaction, usually a nucleotide. This platform enables screening of any isoform in a family of group transfer enzymes, with any acceptor substrate, using the same assay reagents.