Understanding the mode of action of ThDP in benzoylformate decarboxylase

The mechanism of all elementary steps involved in the catalytic cycle of benzoylformate decarboxylase (BFD, E.C. 4.1.1.7) to generate the acyloin linkage is investigated by extensive molecular dynamics simulations. Models involving different charge states of amino acids and/or mutants of critical residues were constructed to understand the involvement of the catalytically active residues and the reactivity differences between different substrates in this reaction. Our calculations confirm that H70, S26, and H281 are catalytically active amino acids. H281 functions as a base to accept H_donor in the first nucleophilic attack and as an acid in the second, to donate the proton back to O_acceptor. S26 assists H281 in deprotonation of the donor aldehyde and protonation of the acceptor aldehyde. In both the first and second nucleophilic attacks, H70 interacts with O_aldehyde and aligns it toward the nucleophilic center. H70 has been found to have an electrostatic effect on the approaching aldehyde whose absence would block the initiation of the reaction. The reactivity difference between benzaldehyde (BA) and acetaldehyde (AA) is mainly explained by the steric interactions of the acceptor aldehyde with the surrounding amino acids in the active center of the enzyme. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 32–46, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Enzymatic asymmetric synthesis by decarboxylases

Decarboxylation reactions using microbial cells or enzymes are increasingly being used for the synthesis of enantiomerically pure compounds because of their high degree of regio- and stereo-specificity. Pyruvate decarboxylase, benzoylformate decarboxylase and phenylpyruvate decarboxylase enzymes are capable of acyloin-type condensation reactions leading to formation of chiral alpha-hydroxy ketones, which are versatile building blocks in the pharmaceutical and chemical industries. Availability of three-dimensional structures of some decarboxylases in recent years has facilitated understanding of reaction mechanisms and the creation of mutants with enhanced activity and stability.     

Equilibrium Yields of Mono- and Di-lauroyl Mannoses Through Lipase-catalyzed Condensation in Acetone in the Presence of Molecular Sieves

Modification was made to our previously reported method to predict the equilibrium yields for the synthesis of mono- and di-lauroyl mannoses through the lipase-catalyzed condensation of lauric acid and mannose in acetone in the presence of molecular sieves. HPLC and mass spectra (MS) analyses indicated that two types of dilauroyl mannoses, which would be positional isomers of each other and are designated dilauroyl mannose I and II, were produced as well as monolauroyl mannose. The predicted yields of total mannose esters and dilauroyl mannose I agreed well with the experimental ones on the whole. The equilibrium yields of dilauroyl mannose II were higher than the predicted values, while the experimental values of monolauroyl mannose were lower than the predicted values. Revisions requested 26 October 2005; Revisions received 14 December 2005     

Factors influencing reproductive success in the clonal moss, Hylocomium splendens

Female reproductive success in the unisexual perennial clonal moss Hylocomium splendens was examined by recording, if the segment was reproductive [produced sporophyte(s)] or not, together with several distance-to-male and male density variables, and segment size. This was done for every female segment in a population over a 5 year study period. A high fraction of the population could be sexed because we monitored the population in situ for 5 years, and thereafter harvested the population for electrophoretic analysis from which the clonal identity and expressed sex could be deduced. Fertilization distances in H. splendens were short, indicated by the fact that as many as 85% of the female segments with sporophytes were situated within a distance of 5.0 cm from the nearest male. The longest distance measured between a sporophytic female and the closest male was 11.6 cm. However, analysed within a generalized linear modelling (GLM) framework, the year was the best single predictor for the presence of H. splendens sporophyte although female-segment size and distance to the closest situated male were also strongly significant. The two latter factors explained larger fractions of variation in sporophyte presence in a GLM model with three predictors than in single-predictor models. This is because (i) the large variation in sporophyte production among years partly obscures the strong general increase in sporophyte production with increasing female-segment size and vitality, and (ii) the between-year variation and the size obscure the effect of the distance to the most proximate male. To our knowledge, this study is the first to incorporate into one model the relative importance of several factors for bryophyte reproductive success. Our results demonstrate the value of multiple-predictor approaches in studies of reproductive success.     

Counterion charge density determines the position and plasticity of RNA folding transition states

The self-assembly of RNA structure depends on the interactions of counterions with the RNA and with each other. Comparison of various polyamines showed that the tertiary structure of the Tetrahymena ribozyme is more stable when the counterions are small and highly charged. By monitoring the folding kinetics of the ribozyme as a function of polyamine concentration, we now find that the charge density of the counterions determines the positions of the folding transition states. The transition state ensemble (TSE) between U and N moves away from the native state as the counterion valence and charge density increase, as predicted by the Hammond postulate. The TSE is broader and less structured when the RNA is refolded in polyamines rather than Mg2+. That the charge density of the counterions determines the plasticity of the TSE demonstrates the importance of interactions among condensed counterions for the self-assembly of RNA structures. We propose that the major barrier to RNA folding is dominated by entropy changes when counterion charge density is low and enthalpy differences when it is high.     

Molecular flexibility of extended and compacted polynucleosomes

We have studied the effects of Na⁺ (5–120 mM) and Mg²⁺ (0–6 mM) on the internal and overall flexibility of polynucleosome fragments from nucleasesolubilized chromatin from Ehrlich ascites cells. The mobility was monitored by the steady-state fluorescence polarization of the intercalated ethidium cation. The internal polynucleosome flexibility decreases continuously as the extended chromatin fragments are being compacted at increasing salt concentrations, and it can be further suppressed at ionic strengths above those where the 30 nm fiber is formed. The effect may be visualized as an initial formation of a loose 30 nm fiber that is further compacted at increasing ionic strengths. We observe several differences in the effects of Na⁺ and Mg²⁺ upon chromatin compaction. First, chromatin compacted by Mg²⁺ is less flexible than that compacted by Na⁺, suggesting a tighter chromatin structure with Mg²⁺. Second, Mg²⁺ affects the internal mobility in polynucleosome fragments shorter than 6–7 nucleosomes, which are too short to be compacted with Na⁺. Third, Mg²⁺ causes extensive macroscopic aggregation at concentrations above 0.2–0.3 mM, but the aggregation is uncorrelated with the intramolecular compaction. A quantitative evaluation of the overall polynucleosome tumbling mobility indicates that the compacted fragments possess more internal flexibility than do corresponding high molecular weight chromatin fibers. Finally, we note a correlation between the ethidium binding constant and the internal chromatin flexibility, possibly arising from lower torsional and unwinding flexibility of the linker DNA segments of compacted chromatin fibers.Abbreviations FPA fluorescence polarization anisotropy - CT calf thymus - HMW high molecular weight - ARF amplitude reduction factor - kbp kilobasepairs This project is supported by the Swedish Natural Research Council. P.E.N. is the recipient of a Hallas-Mølle Fellowship through the NOVO Foundataion     

Caffeine-induced uncoupling of mitosis from DNA replication in tobacco BY-2 cells

Caffeine induced a mitosis-like state in cultured tobacco (Nicotiana tabacum L.) BY-2 cells after DNA synthesis had been arrested by aphidicolin. Cells were synchronized upon removal of aphidicolin. When aphidicolin was readded, the cell cycle was again interrupted and caffeine, when added with aphidicolin, induced the mitosis-like state in 5–10% of cells.     

Salt-induced inhibition of phosphorus transport in lettuce plants

Copper interferes with numerous physiological processes and can be toxic at low concentrations. We examined the effect of a 2-week exposure to various concentrations of copper on the structure of the nucleus in maize root meristem cells by transmission electron microscopy. Copper uptake and distribution in the plants, as well as DNA synthesis were also investigated. Treatment with Cu induced alterations in the structure of the nucleus, resulting mainly in a greater density of chromatin. Morphometric analysis showed that the part of the condensed chromatin in the nucleus might be increased by Cu, an observation that was correlated with decreased DNA synthesis as measured by incorporation of ³H-thymidine. Copper may therefore play a role in chromatin structure and one of the manifestations of Cu toxicity is an alteration in the structure of the nucleus, leading to decreased DNA synthesis.