Characterization of production and enzyme properties of an endo-β-1,4-glucanase fromBacillus subtilis CK-2 isolated from compost soil

Bacillus subtilis CK-2, isolated from garden organic waste compost, was found to have high hydrolytic activity against carboxymethylcellulose (CMC) due to the secretion of an endo--1,4-glucanase. Enzyme production was related to the sporulation process, and was regulated by the concentration of readily metabolizable carbohydrate in growth medium. Enzyme production did not require CMC or other cellulose containing materials. The endo--1,4-glucanase activity was optimal at pH 5.6–5.8 and at 65 MoC, and achieved thermal stability up to 55 MoC. The activity was inhibited by Hg²⁺. The purified enzyme gave a single band corresponding to a MW of 35.5 kDa on SDS-PAGE, while the Sephadex G-75 chromatography revealed a molecular weight of the active enzyme around 70 kDa, indicating a dimeric form of the active enzyme. The enzyme activity was irreversibly inhibited by SDS. Native PAGE and IEF revealed three different isoelectric forms of the enzyme, all with an identical N-terminal amino-acid sequence.Abbreviations CMC carboxymethylcellulose - DNS dinitrosalicylic - SDS sodium dodecyl sulfate     

Chromatographic characteristics and subcellular localization of synthase phosphatase,phosphorylase phosphatase and histone phosphatase in human polymorphonuclear leukocytes

Summary Synthase phosphatase, phosphorylase phosphatase and histone phosphatase activity in a leukocyte homogenate were found to have different sedimentation charcteristics: both synthase phosphatase and phosphorylase phosphatase activity are associated with the microsomal fraction, while the majority of histone phosphatase activity (75–85%) was found in the cytosol. Synthase phosphatase, phosphorylase phosphatase and histone phosphatase activities accompanying the microsomal fraction are readily solubilized by 0.3% Triton X-100.When the solubilized microsomal enzymes were chromatographed on Sephadex G-200, the majority of synthase phosphatase, phosphorylase phosphatase and histone phosphatase activity migrated in single peaks corresponding to apparent molecular weights of 380 000, 250 000 and 68 000, respectively. A minor peak of 30 000, which had phosphatase activity against all three substrates was also obtained.Ethanol treatment resulted in solubilization and dissociation of the three phosphatase activities. It was found that although ethanol treatment resulted in a 4-fold increase of phosphorylase phosphatase activity, histone phosphatase activity was decreased (by 60%), while synthase phosphatase activity remained stable. Similar results were obtained when ethanol treatment was performed on the 17 000 × g supernatant.Chromatography of the ethanol-treated microsomes (or homogenate) on Sephadex G-200 showed that the phosphatase activity towards synthase D, phosphorylase a and phosphohistone coincided a M_r 30 000 species. Heat treatment of the M_r 30 000 peak resulted in dissociation of synthase phosphatase and phosphorylase phosphatase activity.Synthase phosphatase was inhibited by phosphorylase a in a kinetically non-competitive manner while histone phosphatase activity was notinhibited by synthase D (8.5 unit/ ml) orby phosphorylase a(12 unit/ ml).     

Purification and steady state kinetic mechanism of glycogen synthase-D from human polymorpho-nuclear leukocytes

Summary The authors' work on the purification and steady state kinetic investigation of the enzyme glycogen synthase D (UDP-glucose: glycogen 4--glucosyl-transferase, EC 2.4.1.11) from human polymorphonuclear leukocytes is reviewed. The main features of the kinetic mechanism for catalysis of the reaction UDPG + glycogen_n UDP + glycogen_(n+1) are: (i) Lineweaver-Burk plots in both substrates are linear, exhibiting intersecting patterns; (ii) UDP is a competitive, respectively noncompetitive, inhibitor towards the substrates UDPG and glycogen; (iii) the essential activator glucose-6-phosphate (G-6-P) showed an intersecting pattern towards glycogen and an equilibrium ordered pattern towards UDPG. These features identify in this case the mechanism as a rapid equilibrium random bi-bi mechanism, with G-6-P adding to the enzyme prior to the substrate UDPG. New results on the influence of the modifiers NaCl, Ca⁺⁺, Mn⁺⁺, Mg⁺⁺, HPO₄ ^–-, SO₄ ^–-, and ATP on the enzyme are reported. Interpreting the observations in terms of the established mechanism, the following results are obtained: The effect of salt (NaCl) is nonspecific and fairly small, probably reflecting a general action of the electrolyte medium on the conformation of the enzyme. Divalent cations affect only the rate limiting step, i.e. the interconversion of the quaternary enzyme-substrate-activator complexes. The anions interact exclusively with the G-6-P binding site of the enzyme. The dissociation constants for the enzyme-modifier complexes are determined, and a kinetic mechanism for the action of the anions is proposed, leading to activation or inhibition, depending on the concentration of G-6-P.An invited article     

Determination of phosphorylase kinase activity in crude homogenates by affinity chromatography on 5′-AMP Sepharose

A sensitive method for measuring phosphorylase kinase activity by the incorporation of ³²P from [γ-³²]ATP into phosphorylase in the presence of other phosphorylation reactions is described. The kinase reaction is carried out in a crude homogenate. After stopping the reaction, a portion of the reaction mixture is withdrawn for assay of phosphorylase conversion and the rest is applied on a 5′-AMP Sepharose column. Phosphorylase in both forms is retained on the column while other phosphorylated proteins and [γ-³²P]ATP are washed out. The phosphorylase is then eluted by 10 mm AMP and the radioactivity incorporated is counted.     

REINFORCING SELECTION IS EFFECTIVE UNDER A RELATIVELY BROAD SET OF CONDITIONS IN A MOSAIC HYBRID ZONE

Many hybrid zones have a mosaic structure, yet we know of no theoretical work that examines the impact of mosaicism on the outcome of evolution. We developed a computer simulation model designed to test whether the outcome of reinforcing selection differs in a mosaic and a clinal hybrid zone. Our model was a one-dimensional stepping-stone model. The mosaic and clinal hybrid zones that we modeled were, respectively, a mosaic maintained by differential fitness of the interacting taxa in patchy habitats and a tension zone. We modeled changes in gene frequency at two biallelic loci, A and B. Hybrids at the A locus were selected against. An allele at the B locus caused assortative mating at the A locus, which promoted reinforcement; there was a selective cost to this allele. In a mosaic hybrid zone, spatial variation in the fitness of A-locus homozygotes in different patches caused gene and genotype frequencies at the A and B loci to differ greatly from those in a tension zone. Compared to a tension zone, a mosaic hybrid zone had a broader region in which hybrids could be formed and, thus, a broader region in which the assortative-mating allele provided a net selective advantage (via decreased production of the less fit A-locus hybrids). This caused the assortative-mating allele to be favored under a broader set of conditions in a mosaic hybrid zone than in a tension zone. In mosaic and tension hybrid zones, both low and high levels of migration could prevent the establishment of the allele that promoted reinforcement, but the allele could establish under a wider range of migration rates in a mosaic than in a tension zone. In a tension zone, both low and high levels of selection against A-locus hybrids could prevent the establishment of the assortative-mating allele. In a mosaic hybrid zone, the assortative-mating allele established under lower levels of selection against hybrids than in a tension zone, and high levels of selection did not impede the establishment of this allele. Overall, our work illustrates how the structure of a hybrid zone can alter the outcome of an important evolutionary process, in this case, reinforcement.     

A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices

Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions. These evolutionary pressures are sufficiently consistent over time and across protein families to produce substitution patterns, summarized in global amino acid substitution matrices such as BLOSUM, JTT, WAG, and LG, which can be used to successfully detect homologs, infer phylogenies, and reconstruct ancestral sequences. Although the factors that govern the variation of amino acid substitution rates have received much attention, the influence of thermodynamic stability constraints remains unresolved. Here we develop a simple model to calculate amino acid substitution matrices from evolutionary dynamics controlled by a fitness function that reports on the thermodynamic effects of amino acid mutations in protein structures. This hybrid biophysical and evolutionary model accounts for nucleotide transition/transversion rate bias, multi‐nucleotide codon changes, the number of codons per amino acid, and thermodynamic protein stability. We find that our theoretical model accurately recapitulates the complex yet universal pattern observed in common global amino acid substitution matrices used in phylogenetics. These results suggest that selection for thermodynamically stable proteins, coupled with nucleotide mutation bias filtered by the structure of the genetic code, is the primary driver behind the global amino acid substitution patterns observed in proteins throughout the tree of life.     

High‐accuracy modeling of antibody structures by a search for minimum‐energy recombination of backbone fragments

Current methods for antibody structure prediction rely on sequence homology to known structures. Although this strategy often yields accurate predictions, models can be stereo‐chemically strained. Here, we present a fully automated algorithm, called AbPredict, that disregards sequence homology, and instead uses a Monte Carlo search for low‐energy conformations built from backbone segments and rigid‐body orientations that appear in antibody molecular structures. We find cases where AbPredict selects accurate loop templates with sequence identity as low as 10%, whereas the template of highest sequence identity diverges substantially from the query's conformation. Accordingly, in several cases reported in the recent Antibody Modeling Assessment benchmark, AbPredict models were more accurate than those from any participant, and the models' stereo‐chemical quality was consistently high. Furthermore, in two blind cases provided to us by crystallographers prior to structure determination, the method achieved <1.5 Ångstrom overall backbone accuracy. Accurate modeling of unstrained antibody structures will enable design and engineering of improved binders for biomedical research directly from sequence. Proteins 2016; 85:30–38. © 2016 Wiley Periodicals, Inc.     

Estrogenic and progestogenic effects of hormonal contraceptives in relation to sexual behavior: insights into extended sexuality

Women's mating adaptations may vary between fertile and luteal phases, given different costs and benefits of sexual activity during each phase. Women's non-conceptive (“extended”) sexuality might function in the context of pair-bonding. The current studies examined associations between women's loyalty and faithfulness to their relationships and frequency of sexual intercourse in women using hormonal contraception. As predicted, in study 1 estimated levels (adjusted for potency) of both synthetic estrogen and progestin delivered to women moderated the association between women's loyalty/faithfulness to their partner and frequency of intercourse: as estradiol levels diminished, and progestin levels increased, women's loyalty/faithfulness became more positively associated with frequency of intercourse. Study 2 replicated these findings in a sample of women studied over a 12 week period. Results further support claims for a possible function of extended sexuality, and speak to hormonal mechanisms affecting it. They also have important methodological and applied implications.