A quantum chemical study of the catalysis for cytidine deaminase: contribution of the extra water molecule

Cytidine deaminase is known as an important enzyme responsible for the hydrolytic deamination of cytidine, which is applied as a key step to the conversion of the precursor of the cancer drug to an active form in the living body. Cytidine with water is efficiently converted to uridine with ammonia in the cleft of cytidine deaminase. In this work, the catalysis of cytidine deaminase for the hydrolytic deamination was examined using cytosine as a model of cytidine and the model molecules for the active site of cytidine deaminase by means of the quantum chemical method. We especially investigated the contribution of the water molecule from the solvent to the catalysis, because the X-ray diffraction analysis of a crystal structure has revealed the existence of the water molecule in the vicinity of the substrate bound to the active site inside the cleft. Our computations showed that the extra water molecule from the solvent has a possibility to support the catalysis of cytidine deaminase.     

Adsorption of biopolyester depolymerase on silicon wafer and poly[(R)-3-hydroxybutyric acid] single crystal revealed by real-time AFM

The adsorption behavior of PHB depolymerase from R. pickettii T1 on a silicon wafer and on P(3HB) single crystals has been studied by real-time and AFM in air and a buffer solution. First, the morphology of PHB depolymerase adsorbed on a silicon wafer was characterized to show that one molecule of PHB depolymerase has dimensions of 2.2 +/- 0.7 nm height and 16 +/- 5 nm width. The observation of PHB depolymerase adsorbed on a P(3HB) single crystal indicated that the dimensions of enzyme on the crystalline surface in air were 1.2 +/- 0.5 nm high and 28 +/- 7 nm wide, while enzyme molecules with dimensions of 2.1 +/- 0.6 nm height and 16 +/- 7 nm width were detected in a buffer solution. Comparison of the dimensions of PHB depolymerase in air with those in a buffer solution showed that the enzyme was squashed in air, but not in a buffer solution. In addition, the influence of enzymatic adsorption on the molecular state of the P(3HB) crystalline surface was investigated. The AFM images of P(3HB) single crystals after enzymatic adsorption and washing with ethanol indicated that the adhesion of PHB depolymerase changed the molecular state and generated holes on the crystalline surface.     

Dimerization and double proton transfer-induced tautomerism of 4(3H)-pyrimidinone in solution studied by IR spectroscopy and quantum chemical calculations

The tautomerism and dimerization of 4(3H)-pyrimidinone (4(3H)Pyr) in carbon tetrachloride (CCl4) and chloroform (CHCl3) solutions were investigated using IR spectroscopy and quantum chemical calculations. The observed IR spectra in the NH and OH stretching regions clearly revealed the predominance of the keto tautomer in both solvent systems. The enol form only exists in a very small proportion in the CCl4 solution. The tautomeric constant for the two monomers KT[OH/NH] = 0.012 and DeltaE = 2.62 kcal/mol were estimated at 25 degrees C. This result was supported by the self-consistent reaction field/polarizable continuum (SCRF/PCM) calculation at the MP4(full, SDQ)/aug-cc-pVDZ level, which predicted DeltaE = 3.06 kcal/mol in CCl4. In the C=O stretching region, two bands were observed, suggesting the coexistence of two keto structures at equilibrium. The calculated IR spectra indicated that the bands at 1711 and 1675 cm(-1) arise from the keto monomer and keto-keto (KK) ring dimer, respectively. At elevated temperature, the populations of both the keto and enol monomers increased for the CCl4 solution. The present study revealed that the keto <--> enol tautomerization does not occur in the isolated monomer molecule. The double proton transfer (DPT) reaction in the KK ring dimer presumably plays a substantial role in the population increase of the enol monomer. To our knowledge, this may be the first observation of the tautomerization in a model base pair via the temperature-induced ground-state DPT reaction under a nonpolar liquid environment reported so far. This tautomerism can serve as a mimic circumstance for the spontaneous mutations induced by proton transfer in the DNA base pairs.     

Variations in steady-state and time-resolved background luminescence from surface-enhanced resonance Raman scattering-active single Ag nanoaggregates

We observed a background luminescence emission that was associated with surface-enhanced resonance Raman scattering (SERRS) of rhodamine 6G (R6G) molecules adsorbed on single Ag nanoaggregates and investigated the origin of the background luminescence. Thanks to the observation of single nanoaggregates, we clearly identified nanoaggregate-by-nanoaggregate variations in the steady-state and time-resolved background luminescence spectra of each nanoaggregate. From the variations in the steady-state spectra, two kinds of key properties were revealed. First, the background luminescence spectra were divided into four components: one fluorescence band corresponding to the monomers of R6G and three Lorentzian bands whose maxima were red-shifted from the fluorescence maximum of the monomer by several tens of nanometers. On the basis of the red-shifted luminescence maxima, and experimental and theoretical studies of background luminescence, we attributed the three background luminescences to fluorescence from aggregates (dimer and two kinds of higher-order aggregates) of R6G molecules on an Ag surface. Second, a positive correlation was observed between wavelengths of background luminescence maxima and wavelengths of plasmon resonance maxima. This positive correlation invoked the idea that the dipoles of both the background luminescence and the plasmon radiation are coupled with each other. From the key observations in the steady-state background luminescence spectra, we propose that two factors contribute to the variations in the steady-state background luminescence spectra; one is the aggregation (monomer, dimer, and two kinds of higher-order aggregates) of R6G molecules on an Ag surface, and the other is plasmon resonance maxima of single Ag nanoaggregates. Considering these two factors, we propose that the variations in the time-resolved background luminescence spectra are associated with deaggregation of R6G molecules (higher- to lower-order aggregates) and temporal shifts in the plasmon resonance maxima of single Ag nanoaggregates.     

Mutation effects of a conserved alanine (Ala510) in type I polyhydroxyalkanoate synthase from Ralstonia eutropha on polyester biosynthesis

Type I polyhydroxyalkanoate (PHA) synthases, as represented by Ralstonia eutropha enzyme (PhaC(Re)), have narrow substrate specificity toward (R)-3-hydroxyacyl-coenzyme A with acyl chain length of C3-C5 to yield PHA polyesters. In this study, saturation point mutagenesis of a highly conserved alanine at position 510 (A510) in PhaC(Re) was carried out to investigate the effects on the polymerization activity and the substrate specificity for in vivo PHA biosynthesis in bacterial cells. A series of saturation mutants were first applied for poly[(R)-3-hydroxybutyrate] homopolymer synthesis in Escherichia coli and R. eutropha PHB(-)4 (PHA negative mutant) cells to assess the polymerization activity. All mutants showed quantitatively similar polymerization activities when R. eutropha PHB(-)4 was used for assay, whereas several mutants such as A510P showed low activities in E. coli. Further analysis has revealed that majority of mutants synthesize polyesters with higher molecular weights than the wild-type. In particular, substitution by acidic amino acids, A510D(E), led to remarkable increases in molecular weights. Subsequently, PHA copolymer synthesis from dodecanoate (C12 fatty acid) was examined. The copolymer compositions were varied depending on the mutants used. Significant increased fractions of long monomer units (C6 and C8) in PHA copolymers were observed for three mutants [A510M(Q,C)]. From these results, the mutations at this potion are beneficial to change the molecular weight of polyesters and the substrate specificity of PhaC(Re). Molecular weight distributions of PHA polymers synthesized by the wild-type enzyme (PhaC(Re)) and its mutants.     

Characteristics of the Watson-Crick type hydrogen-bonded DNA base pairs: An ab initio molecular orbital study

Characteristics of the Watson-Crick-type hydrogen-bonded base pairs, thymine-adenine and cytosineguanine, are presented. These were established using an ab initio molecular orbital method. Base–base interactions are revealed to have dominant roles in the structures of nucleic acids and also in their functions. The most stable conformations in Watson-Crick-type base pairs are almost in accord with the structure observed in fiber X-ray diffraction study. Explanations are given of the origin of the sequencedependent local structures which differ from one base pair to the next, as observed in single-crystal X-ray analyses. In the case of the thymine-adenine base pair, it is shown that various geometrical parameters having almost the same stability are available. According to the propeller twist, the instability is not large enough for a base pair to be twisted readily.     

Biosynthesis of polyhydroxyalkanoate (PHA) copolymer from fructose using wild-type and laboratory-evolved PHA synthases

Eleven laboratory-evolved polyhydroxyalkanoate (PHA) synthases which originated from Pseudomonas sp. 61-3 enzyme (PhaC1(Ps)), together with the wild-type enzyme, were applied for PHA synthesis from fructose using Ralstonia eutropha PHB(-)4 as a host strain. The evolved PhaC1(Ps) mutants had amino acid substitution(s) at position 325 and/or position 481. In these mutants, serine-325 (S325) was replaced by cysteine (C) or threonine (T), while glutamine-481 (Q481) was replaced by lysine (K), methionine (M) or arginine (R). All recombinant strains harboring the genes of the evolved PhaC1(Ps) mutants produced a significantly increased amount of PHA (55-68 wt.-%) compared with the one harboring the wild-type gene (49 wt.-%). Particularly, those evolved PhaC1(Ps) mutants having multiple amino acid substitutions showed higher activities for PHA synthesis. Characterization of the PHA by NMR spectroscopy revealed that they were copolymers consisting of (R)-3-hydroxybutyrate (98-99 mol-%) and medium-chain-length comonomers (1-2 mol-%). This study also confirmed that amino acid substitution at position 481 in PhaC1(Ps) led to an increasing molecular weight of PHA. The number-average molecular weight (Mn) of PHA (Mn = 240,000) synthesized by the evolved PhaC1(Ps) (Q481K) mutant was 4.6-fold greater than that (Mn = 52,000) synthesized by the wild-type enzyme.     

Synthetic studies on β-lactam antibiotics. 19. Synthesis of 3′-nor-type 1-oxacephems

Synthesis of optically active 3′-nor-type 1-oxacephems from 6-APA was described. $\text{p}$-Nitrobenzyl 7β-amino-3-chloro-7α-methoxy-1-oxa-3-cephem-4-carboxylate $\text{39}$ was also prepared.     

Formation and properties of n-alkylammonium complexes with layered tri- and tetra-titanates

The formation of n-alkylammonium complexes was studied using Na₂Ti₃O₇ and K₂Ti₄O₉ and the results for both compounds were compared. Alkylammonium complexes could be obtained from H₂Ti₃O₇ and H₂Ti₄O₉·H₂O, which were prepared by HCl treatment of Na₂Ti₃O₇ and K₂Ti₄O₉ respectivel The complexes were formed by exchange of H⁺ with alkylammonium ions. Molecular intercalation of alkylamine was also possible with H₂Ti₄O₉·H₂O. However, alkylammonium complexes were not formed directly from Na₂Ti₃O₇ and from K₂Ti₄O₉. Orientations of alkylammonium ions in the interlayer are also discussed in relation to the structure of the titanate layers.