Angelman syndrome and severe infections in a patient with de novo 15q11.2–q13.1 deletion and maternally inherited 2q21.3 microdeletion

Angelman syndrome is a neurodevelopmental disorder characterized by mental retardation, severe speech disorder, facial dysmorphism, secondary microcephaly, ataxia, seizures, and abnormal behaviors such as easily provoked laughter. It is most frequently caused by a de novo maternal deletion of chromosome 15q11–q13 (about 70–90%), but can also be caused by paternal uniparental disomy of chromosome 15q11–q13 (3–7%), an imprinting defect (2–4%) or in mutations in the ubiquitin protein ligase E3A gene UBE3A mostly leading to frame shift mutation. In addition, for patients with overlapping clinical features (Angelman-like syndrome), mutations in methyl-CpG binding protein 2 gene MECP2 and cyclin-dependent kinase-like 5 gene CDKL5 as well as a microdeletion of 2q23.1 including the methyl-CpG binding domain protein 5 gene MBD5 have been described. Here, we describe a patient who carries a de novo 5 Mb-deletion of chromosome 15q11.2–q13.1 known to be associated with Angelman syndrome and a further, maternally inherited deletion 2q21.3 (~ 364 kb) of unknown significance. In addition to classic features of Angelman syndrome, she presented with severe infections in the first year of life, a symptom that has not been described in patients with Angelman syndrome. The 15q11.2–q13.1 deletion contains genes critical for Prader–Willi syndrome, the Angelman syndrome causing genes UBE3A and ATP10A/C, and several non-imprinted genes: GABRB3 and GABRA5 (both encoding subunits of GABA A receptor), GOLGA6L2, HERC2 and OCA2 (associated with oculocutaneous albinism II). The deletion 2q21.3 includes exons of the genes RAB3GAP1 (associated with Warburg Micro syndrome) and ZRANB3 (not disease-associated). Despite the normal phenotype of the mother, the relevance of the 2q21.3 microdeletion for the phenotype of the patient cannot be excluded, and further case reports will need to address this point.     

Substrate‐shielding and hydrolytic reaction in hydrolases

In general, transferases undergo large structural changes and sequester substrate molecules, to shield them from water. By contrast, hydrolases exhibit only small structural changes, and expose substrate molecules to water. However, some hydrolases deeply bury their substrates within the proteins. To clarify the relationship between substrate‐shielding and enzymatic functions, we investigated 70 representative hydrolase structures, and examined the relative accessible surface areas of their substrates. As compared to the hydrolases employing the single displacement reaction, the hydrolases employing the double displacement reaction bury the substrate within the proteins. The exo hydrolases display significantly more substrate‐shielding from water than the endo hydrolases. It suggests that the substrate‐shielding is related to the chemical reaction mechanism of the hydrolases and the substrate specificity. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Molecular Mechanics Studies of Molybdenum Disulphide Catalysts Parameterisation of Molybdenum and Sulphur

Abstract

A method for the parameterisation of molybdenum disulphide is presented which reproduces the crystal structure accurately. The method involves calculating parameters such that there is no net force contribution from any individual term of the potential on any atom. Ideal bond lengths and bond angles are taken from the X-ray crystal structure; stretching and bending force constants are calculated from a combination of spectroscopic data and quantum mechanics calculations, whereby the energy function with bond length or bond angle is calculated and fitted with an harmonic potential. For the non-bonded Lennard-Jones parameters, the dispersion coefficient C was calculated by an interpolation of existing published parameters using a multiple regression and then the crystal energy was minimised with respect to the van der Waals radius r₀ using a fixed crystal fragment.

These parameters were tested for various models of the hexagonal and rhombohedral forms of MoS₂. RMS fits between structures minimised with molecular mechanics and experimental models ranged from 0.006 Å to 0.012 Å.     

Enantioselective Synthesis and Antimicrobial Activities of Tetrahydro‐Β‐Carboline Diketopiperazines

A series of single isomers tetrahydro‐β‐carboline diketopiperazines were stereoselectively synthesized starting from l ‐tryptophan methyl ester hydrochloride and six aldehydes through a four‐step reaction including Pictet‐Spengler reaction, crystallization‐induced asymmetric transformations (CIAT), Schotten‐Baumann reaction, and intramolecular ester amidation. The chemical structures were characterized by nuclear magnetic resonance (NMR) and elemental analysis, among which two compounds were determined by x‐ray single crystal diffraction. Moreover, antimicrobial activities of all the compounds were also tested. Chirality 25:656–662, 2013. © 2013 Wiley Periodicals, Inc.     

Asymmetric Zinc‐Catalyzed Hydrosilylation of Ketones and the Effect of Carboxylate on the Enantioselectivity

Several chiral ligands containing (R,R)‐diaminocyclohexane moieties and pyrrole, furan, or benzene have been synthesized. These ligands were tested in enantioselective zinc‐catalyzed hydrosilylation reactions; excellent enantioselectivities were obtained when the ligands containing (R,R)‐diaminocyclohexane moieties and furan rings were used. For comparison, zinc chloride combined with different potassium carboxylate salts and ligands were also tested for catalytic hydrosilylation reactions. Chirality 25:275–280, 2013. © 2013 Wiley Periodicals, Inc.     

Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II

The DNA religation reaction of yeast type II topoisomerase (topo II) was investigated to elucidate its metal-dependent general acid/base catalysis. Quantum mechanical/molecular mechanical calculations were performed for the topo II religation reaction, and the proton transfer pathway was examined. We found a substrate-mediated proton transfer of the topo II religation reaction, which involves the 3′ OH nucleophile, the reactive phosphate, water, Arg781, and Tyr782. Metal A stabilizes the transition states, which is consistent with a two-metal mechanism in topo II. This pathway may be required for the cleavage/religation reaction of topo IA and II and will provide a general explanation for the catalytic mechanism in the topo IA and II.     

Hydrolases: The Correlation Between Informational Structure and the Catalytic Sites Organization

Abstract

The novel method allowing identification of protein structure elements responsible for catalytic activity manifestation is proposed. Structural organization of various hydrolases was studied using the ANIS (ANalysis of Informational Structure) method. ANIS allows to reveal a hierarchy of the ELements of Information Structure (ELIS) using protein amino acid sequence. The ELIS corresponds to the variable length sites with an increased density of structural information. The amino acid residues forming the enzyme catalytic site were shown to belong to the different top-ranking ELIS located in the contact area of the corresponding spatial structure clusters. In the protein spatial structure catalytic sites are located in the area of contact between fragments of polypeptide chain (structural blocs) allocation to the different top-ranking ELIS. According to our results we concluded that structural blocks corresponding to top-ranking ELIS are crucial for protein functioning. Such regions are structurally independent, and their determinate mobility relative to each other is vital for an efficient enzymatic reaction to occur.     

Characterization of the biochemical properties of Campylobacter jejuni RNase III

Campylobacter jejuni is a foodborne bacterial pathogen, which is now considered as a leading cause of human bacterial gastroenteritis. The information regarding ribonucleases in C. jejuni is very scarce but there are hints that they can be instrumental in virulence mechanisms. Namely, PNPase (polynucleotide phosphorylase) was shown to allow survival of C. jejuni in refrigerated conditions, to facilitate bacterial swimming, cell adhesion, colonization and invasion. In several microorganisms PNPase synthesis is auto-controlled in an RNase III (ribonuclease III)-dependent mechanism. Thereby, we have cloned, overexpressed, purified and characterized Cj-RNase III (C. jejuni RNase III). We have demonstrated that Cj-RNase III is able to complement an Escherichia coli rnc-deficient strain in 30S rRNA processing and PNPase regulation. Cj-RNase III was shown to be active in an unexpectedly large range of conditions, and Mn²⁺ seems to be its preferred co-factor, contrarily to what was described for other RNase III orthologues. The results lead us to speculate that Cj-RNase III may have an important role under a Mn²⁺-rich environment. Mutational analysis strengthened the function of some residues in the catalytic mechanism of action of RNase III, which was shown to be conserved.     

Local genetic structure in the critically endangered,cave‐associated perennial herb Primulina tabacum (Gesneriaceae)

The local spatial genetic structures of cave‐associated plants are seldom studied. Given that these plants are mainly confined to small areas in and around the entrances of caves, we hypothesized that they might lack genetic structures at local scales. To test this hypothesis, we sampled two large populations (named D and T) of a critically endangered perennial herb, Primulina tabacum, which is endemic to karst caves in southern China. We analysed nine microsatellite loci and sequenced four chloroplast DNA (cpDNA) intergenic spacer regions to study the genetic diversity and structure within and between both populations. Both populations have distinct genetic characteristics. Samples from two subpopulations in population D showed considerable genetic divergence. This is not consistent with the hypothesis that P. tabacum has a weak genetic structure at a local scale. However, 94% of the individuals in population T shared the same multilocus genotype, which indicates little genetic structure within this population. The contributions of seed flow, pollen flow and (sub)population history to the genetic diversity and structure in each and both populations are discussed. Our study is the first to investigate local genetic diversity and structure in a cave‐associated plant, and provides valuable information for the sustainable conservation of such species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 747–756.     

Comparative characterization of novel ene‐reductases from cyanobacteria

The growing importance of biocatalysis in the syntheses of enantiopure molecules results from the benefits of enzymes regarding selectivity and specificity of the reaction and ecological issues of the process. Ene‐reductases (ERs) from the old yellow enzyme family have received much attention in the last years. These flavo‐enzymes catalyze the trans‐specific reduction of activated C?C bonds, which is an important reaction in asymmetric synthesis, because up to two stereogenic centers can be created in one reaction. However, limitations of ERs described in the literature such as their moderate catalytic activity and their strong preference for NADPH promote the search for novel ERs with improved properties. In this study, we characterized nine novel ERs from cyanobacterial strains belonging to different taxonomic orders and habitats. ERs were identified with activities towards a broad spectrum of alkenes. The reduction of maleimide was catalyzed with activities of up to 35.5 U mg^?1 using NADPH. Ketoisophorone and (R)‐carvone, which were converted to the highly valuable compounds (R)‐levodione and (2R,5R)‐dihydrocarvone, were reduced with reaction rates of up to 2.2 U mg^?1 with NADPH. In contrast to other homologous ERs from the literature, NADH was accepted at moderate to high rates as well: Enzyme activities of up to 16.7 U mg^?1 were obtained for maleimide and up to 1.3 U mg^?1 for ketoisophorone and (R)‐carvone. Additionally, excellent stereoselectivities were achieved in the reduction of (R)‐carvone (97–99% de). In particular, AnabaenaER3 from Anabaena variabilis ATCC 29413 and AcaryoER1 from Acaryochloris marina MBIC 11017 were identified as useful biocatalysts. Therefore, novel ERs from cyanobacteria with high catalytic efficiency were added to the toolbox for the asymmetric reduction of alkenes. Biotechnol. Bioeng. 2013; 110: 1293–1301. © 2012 Wiley Periodicals, Inc.