Effect of xylitol on salivary ß-glucosidase in humans.

Dental biofilm - in which a diverse set of microorganisms are embedded in a complex polysaccharide matrix that adheres to oral components - is one of the most complex microbial communities in the human body. As biofilm formation is related to oral infections, such as caries and periodontal diseases, strategies for biofilm control are crucial for maintaining oral health. Xylitol, a synthetic sugar used as a sucrose substitute, has been shown to reduce biofilm formation. However, its precise mechanism of action on biofilm reduction has so far not been elucidated. Previous studies demonstrate that bacterial ß-glucosidase action is crucial for biofilm formation. Here, we investigated the correlation between salivary ß-glucosidase activity and dental plaque occurrence. We found a positive correlation between enzymatic activity and the presence of dental biofilm. We observed that xylitol inhibits ß-glucosidase in human saliva. Kinetic studies also confirmed that xylitol acts as a mixed type inhibitor of salivary ß-glucosidase. Based on our data, we suggest that xylitol impairs oral biofilm formation by the inhibition of bacterial ß-glucosidase, which is essential for biofilm formation in the oral cavity.

Beta glucosidase from Bacillus polymyxa is activated by glucose-6-phosphate.

Optimization of cellulose enzymatic hydrolysis is crucial for cost effective bioethanol production from lignocellulosic biomass. Enzymes involved in cellulose hydrolysis are often inhibited by their end-products, cellobiose and glucose. Efforts have been made to produce more efficient enzyme variants that are highly tolerant to product accumulation; however, further improvements are still necessary. Based on an alternative approach we initially investigated whether recently formed glucose could be phosphorylated into glucose-6-phosphate to circumvent glucose accumulation and avoid inhibition of beta-glucosidase from Bacillus polymyxa (BGLA). The kinetic properties and structural analysis of BGLA in the presence of glucose-6-phosphate (G6P) were investigated. Kinetic studies demonstrated that enzyme was not inhibited by G6P. In contrast, the presence of G6P activated the enzyme, prevented beta glucosidase feedback inhibition by glucose accumulation and improved protein stability. G6P binding was investigated by fluorescence quenching experiments and the respective association constant indicated high affinity binding of G6P to BGLA. Data reported here are of great impact for future design strategies for second-generation bioethanol production.

A general RNA motif for cellular transfection.

We have developed a selection scheme to generate nucleic acid sequences that recognize and directly internalize into mammalian cells without the aid of conventional delivery methods. To demonstrate the generality of the technology, two independent selections with different starting pools were performed against distinct target cells. Each selection yielded a single highly functional sequence, both of which folded into a common core structure. This internalization signal can be adapted for use as a general purpose reagent for transfection into a wide variety of cell types including primary cells.

Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding.

We have performed a detailed analysis of streptavidin variants with altered specificity towards desthiobiotin. In addition to changes in key residues which widen the ligand binding pocket and accommodate the more structurally flexible desthiobiotin, the data revealed the role of a key, non-active site mutation at the base of the flexible loop (S52G) which slows dissociation of this ligand by approximately sevenfold. Our data suggest that this mutation results in the loss of a stabilizing contact which keeps this loop open and accessible in the absence of ligand. When this mutation was introduced into the wild-type protein, destabilization of the opened loop conferred a ∼10-fold decrease in both the on-rate and off-rate for the ligand biotin-4-fluoroscein. A similar effect was observed when this mutation was added to a monomeric form of this protein. Our results provide key insight into the role of the streptavidin flexible loop in ligand binding and maintaining high affinity interactions.

Kinetic and mechanistic analysis of the Escherichia coli ribD-encoded bifunctional deaminase-reductase involved in riboflavin biosynthesis.

Riboflavin is biosynthesized by most microorganisms and plants, while mammals depend entirely on the absorption of this vitamin from the diet to meet their metabolic needs. Therefore, riboflavin biosynthesis appears to be an attractive target for drug design, since appropriate inhibitors of the pathway would selectively target the microorganism. We have cloned and solubly expressed the bifunctional ribD gene from Escherichia coli, whose three-dimensional structure was recently determined. We have demonstrated that the rate of deamination (370 min (-1)) exceeds the rate of reduction (19 min (-1)), suggesting no channeling between the two active sites. The reductive ring opening reaction occurs via a hydride transfer from the C 4- pro-R hydrogen of NADPH to C'-1 of ribose and is the rate-limiting step in the overall reaction, exhibiting a primary kinetic isotope effect ( (D) V) of 2.2. We also show that the INH-NADP adduct, one of the active forms of the anti-TB drug isoniazid, inhibits the E. coli RibD. On the basis of the observed patterns of inhibition versus the two substrates, we propose that the RibD-catalyzed reduction step follows a kinetic scheme similar to that of its structural homologue, DHFR.

Kinetic and structural analysis of bisubstrate inhibition of the Salmonella enterica aminoglycoside 6'-N-acetyltransferase.

Aminoglycosides are antibacterial compounds that act by binding to the A site of the small 30S bacterial ribosomal subunit and inhibiting protein translation. Clinical resistance to aminoglycosides is generally the result of the expression of enzymes that covalently modify the antibiotic, including phosphorylation, adenylylation, and acetylation. Bisubstrate analogs for the aminoglycoside N-acetyltransferases are nanomolar inhibitors of Enterococcus faecium AAC(6')-Ii. However, in the case of the Salmonella enterica aac(6')-Iy-encoded aminoglycoside N-acetyltransferase, we demonstrate that a series of bisubstrate analogs are only micromolar inhibitors. In contrast to studies with AAC(6')-Ii, the inhibition constants toward AAC(6')-Iy are essentially independent of both the identity of the aminoglycoside component of the bisubstrate and the number of carbon atoms that are used to link the CoA and aminoglycoside components. The patterns of inhibition suggest that the CoA portion of the bisubstrate analog can bind to the enzyme-aminoglycoside substrate complex and that the aminoglycoside portion can bind to the enzyme-CoA product complex. However, at the high concentrations of bisubstrate analog used in crystallization experiments, we could crystallize and solve the three-dimensional structure of the enzyme-bisubstrate complex. The structure reveals that both the CoA and aminoglycoside portions bind in essentially the same positions as those previously observed for the enzyme-CoA-ribostamycin complex, with only a modest adjustment to accommodate the "linker". These results are compared to previous studies of the interaction of similar bisubstrate analogs with other aminoglycoside N-acetyltransferases.

Bisubstrate inhibition: Theory and application to N-acetyltransferases.

Bisubstrate inhibitors represent a potentially powerful group of compounds that have found significant therapeutic utility. Although these compounds have been synthesized and tested against a number of enzymes that catalyze sequential bireactant reactions, the detailed theory for predicting the expected patterns of inhibition against the two substrates for various bireactant kinetic mechanisms has, heretofore, not been presented. We have derived the rate equations for all likely sequential bireactant mechanisms and provide two examples in which bisubstrate inhibitors allow the kinetic mechanism to be determined. Bisubstrate inhibitor kinetics is a powerful diagnostic for the determination of kinetic mechanisms.

Functional shikimate dehydrogenase from Mycobacterium tuberculosis H37Rv: purification and characterization.

Tuberculosis (TB) poses a major worldwide public health problem. The increasing prevalence of TB, the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, the causative agent of TB, and the devastating effect of co-infection with HIV have highlighted the urgent need for the development of new antimycobacterial agents. Analysis of the complete genome sequence of M. tuberculosis shows the presence of genes involved in the aromatic amino acid biosynthetic pathway. Experimental evidence that this pathway is essential for M. tuberculosis has been reported. The genes and pathways that are essential for the growth of the microorganisms make them attractive drug targets since inhibiting their function may kill the bacilli. We have previously cloned and expressed in the soluble form the fourth shikimate pathway enzyme of the M. tuberculosis, the aroE-encoded shikimate dehydrogenase (mtSD). Here, we present the purification of active recombinant aroE-encoded M. tuberculosis shikimate dehydrogenase (mtSD) to homogeneity, N-terminal sequencing, mass spectrometry, assessment of the oligomeric state by gel filtration chromatography, determination of apparent steady-state kinetic parameters for both the forward and reverse directions, apparent equilibrium constant, thermal stability, and energy of activation for the enzyme-catalyzed chemical reaction. These results pave the way for structural and kinetic studies, which should aid in the rational design of mtSD inhibitors to be tested as antimycobacterial agents.

The kinetic mechanism of AAC3-IV aminoglycoside acetyltransferase from Escherichia coli.

The aminoglycoside 3-N-acetyltransferase AAC(3)-IV from Escherichia coli exhibits a very broad aminoglycoside specificity, causing resistance to a large number of aminoglycosides, including the atypical veterinary antibiotic, apramycin. We report here on the characterization of the substrate specificity and kinetic mechanism of the acetyl transfer reaction catalyzed by AAC(3)-IV. The steady-state kinetic parameters revealed a narrow specificity for the acyl-donor and broad range of activity for aminoglycosides. AAC(3)-IV has the broadest substrate specificity of all AAC(3)'s studied to date. Dead-end inhibition and ITC experiments revealed that AAC(3)-IV follows a sequential, random bi-bi kinetic mechanism. The analysis of the pH dependence of the kinetic parameters revealed acid- and base-assisted catalysis and the existence of three additional ionizable groups involved in substrate binding. The magnitude of the solvent kinetic isotope effects suggests that a chemical step is at least partially rate limiting in the overall reaction.

Cloning and expression of functional shikimate dehydrogenase (EC 1.1.1.25) from Mycobacterium tuberculosis H37Rv.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, continues to be one of the deadliest diseases in the world. TB resurged in the late 1980s and now kills more than 2 million people a year. Possible factors underlying the reemergence of TB are the high susceptibility of human immunodeficiency virus-infected persons to the disease, the proliferation of multi-drug-resistant (MDR) strains, patient noncompliance in completing the standard "short-course" therapy, and decline of health care systems. Thus, there is a need for the development of new antimycobacterial agents to treat MDR strains of M. tuberculosis, to provide for more effective treatment of latent tuberculosis infection, and to shorten the treatment course to improve patient compliance. The shikimate pathway is an attractive target for antimicrobial agents development because it is essential in algae, higher plants, bacteria, and fungi, but absent in mammals. Homologs to enzymes in the shikimate pathway have been identified in the genome sequence of M. tuberculosis. The M. tuberculosis aroE-encoded shikimate dehydrogenase was PCR amplified, cloned, sequenced, and expressed in Escherichia coli BL21(DE3). Recombinant protein expression was achieved by a low-cost and simple protocol. Although cell lysis resulted in the formation of insoluble aggregates of the recombinant protein, soluble and functional M. tuberculosis shikimate dehydrogenase could be obtained by repeated cycles of freezing and thawing. Enzyme activity measurements demonstrated that there was approximately a 5-fold increase in specific activity for M. tuberculosis shikimate dehydrogenase. Moreover, the enzyme activity was linearly dependent upon the amount of recombinant protein added to the assay mixture, thus, confirming cloning and expression of functional mycobacterial shikimate.