Free energy analysis of ω-transaminase reactions to dissect how the enzyme controls the substrate selectivity

ω-Transaminase (ω-TA) is the only naturally occurring enzyme allowing asymmetric amination of ketones for production of chiral amines. The active site of the enzyme was proposed to consist of two differently sized substrate binding pockets and the stringent steric constraint in the small pocket has presented a significant challenge to production of structurally diverse chiral amines. To provide a mechanistic understanding of how the (S)-specific ω-TA from Paracoccus denitrificans achieves the steric constraint in the small pocket, we developed a free energy analysis enabling quantification of individual contributions of binding and catalytic steps to changes in the total activation energy caused by structural differences in the substrate moiety that is to be accommodated by the small pocket. The analysis exploited kinetic and thermodynamic investigations using structurally similar substrates and the structural differences among substrates were regarded as probes to assess how much relative destabilizations of the reaction intermediates, i.e. the Michaelis complex and the transition state, were induced by the slight change of the substrate moiety inside the small pocket. We found that ≈80% of changes in the total activation energy resulted from changes in the enzyme-substrate binding energy, indicating that substrate selectivity in the small pocket is controlled predominantly by the binding step (K_M) rather than the catalytic step (k_cat). In addition, we examined the pH dependence of the kinetic parameters and the pH profiles of the K_M and k_cat values suggested that key active site residues involved in the binding and catalytic steps are decoupled. Taken together, these findings suggest that the active site residues forming the small pocket are mainly engaged in the binding step but not significantly involved in the catalytic step, which may provide insights into how to design a rational strategy for engineering of the small pocket to relieve the steric constraint toward bulky substituents.     

Can one measure the free energy of binding of the histone octamer to different DNA sequences by salt-dependent reconstitution?

I explain why many recently reported measurements for the "free energy" of positioning of the histone octamer on different DNA sequences are likely to be in error: i.e. because histone octamers do not equilibrate between different DNA molecules at low salt, but only at high salt. Thus, the reported "free energies" refer to an equilibrium at high salt, under nearly dissociating conditions between protein and DNA, and they are likely to be much too small on an absolute scale. There are many other lines of evidence to suggest that the preferences of the histone octamer for different DNA sequences are rather strong and of importance in biological systems.     

Time and energy constraints and the evolution of sexual size dimorphism — to eat or to mate?

Summary We present an empirical test of the Ghiselin—Reiss small-male hypothesis for the evolution of sexual size dimorphism (SSD). In mating systems dominated by scramble competition, where male reproductive success is a function of encounter rate with females, small males may be favoured when food is limiting because they require lower absolute amounts of food. Given a trade-off between time and energy devoted to foraging and to mate acquisition, small males should be able to devote more time to the latter. If at the same time larger females are favoured, this mechanism will contribute to the evolution of SSD and may be the major determinant of the female-biased SSDs that characterize most animal taxa. We tested this hypothesis using the water strider,Aquarius remigis (Heteroptera: Gerridae), a scramble competitor which mates many times over a prolonged mating season and which shows female-biased SSD. Laboratory experiments demonstrated that foraging success and giving up times (GUTs) are lower for males than for females during the reproductive season and that male water striders flexibly alter their time budgets under conditions of energy limitation. Controlled feeding experiments showed that male and female longevity, female fecundity and male mating success are positively related to food availability. As predicted, male body size is negatively correlated with several indices of male fitness (longevity, number of mating attempts and mating success), while female body size is positively correlated with longevity. These results are consistent with the hypothesis that scramble competition for mates favours small males in this species and provides empirical support for the Ghiselin—Reiss small-male hypothesis.     

Elastic energy of the discocyte–stomatocyte transformation

The aim of this study is to calculate the membrane elastic energy for the different shapes observed in the discocyte–stomatocyte sequence. This analysis can provide a better quantitative understanding of the hypothesis put forward over the last decades to explain how red blood cells produce and maintain their typical shape. For this purpose, we use geometrical models based on parametric equations. The energy model considered for the elastic properties of RBC membrane includes the local and nonlocal resistance effects of the bilayer to bending. In particular, the results confirm the discocyte as the lowest energy value configuration among the sets of different red blood cell deformations considered in the sequence.     

Performance evaluation of the SITE® model to estimate energy flux in a tropical semi-deciduous forest of the southern Amazon Basin

The SITE® model was originally developed to study the response of tropical ecosystems to varying environmental conditions. The present study evaluated the applicability of the SITE model to simulation of energy fluxes in a tropical semi-deciduous forest of the southern Amazon Basin. The model was simulated with data representing the wet and dry season, and was calibrated according to each season. The output data of the calibrated model [net radiation (Rn), latent heat flux (LE) and sensible heat flux (H)] were compared with data observed in the field for validation. Considering changes in parameter calibration for a time step simulation of 30 min, the magnitude of variation in temporal flux was satisfactory when compared to observation field data. There was a tendency to underestimate and overestimate LE and H, respectively. Of all the calibration parameters, the soil moisture parameter presented the highest variation over the seasons, thus influencing SITE model performance.     

Is dihydrolipoic acid among the reductive activators of parasite CysHis proteases?

Activities of mature CysHis proteases depend upon relative rates of oxidations vs. reductions of catalytic sulfur by multiple enzymatic and non-enzymatic reactions. CysHis peptidolysis is inhibited by Fe3+ but not Fe2+. Others report the paradox that malarial parasites require exogenous free lipoic acid (LA) from human host, although the apicoplast organelle produces it. Extra-cellular LA disulfide can be taken up and reduced to dihydrolipoic acid (DHLA) by reductases of any cell type. Here, the opposing effects of DHLA vs. Fe3+ on the falcipain-2 hemoglobinase were investigated employing Z-Phe-Arg-AMC substrate. Despite limited solubility, non-regenerated DHLA (10 microM, threshold 2 microM) was found to be the most potent activator of the air-inactivated (sulfoxygenated) protease discovered thus far. Activation was preemptively opposed by Fe3+, but not Fe2+. However, cruzain from T. cruzi, and cathepsin B from mammal were indistinguishable in their responsiveness to DHLA and Fe redox. Thus, DHLA activation vs. Fe3+ inhibition is not unique to falcipain-2 or apicomplexans but is rather a primordial feature of CysHis peptidolysis. Free LA and/or unassociated lipoylated enzyme subunits could be among multiple pathways shuttling reducing equivalents to reduction of proteins, including CysHis proteases. It is discussed that opposing DHLA-Fe3+ modification of plasmodial proteolysis might be a specialized adaptation to intra-erythrocytic growth.     

How does the ratio of ATP yield from the complete oxidation of palmitic acid to that of glucose compare with the relative energy contents of fat and carbohydrate?

The authors of many recent popular textbooks of biochemistry quote values for the ‘energy content’ of triacylglcyerol and dry carbohydrate on a weight basis as well as presenting calculations for the yield of ATP obtained when a molecule of glucose, or palmitic acid, is completely oxidised to CO₂ and H₂O. By extending these calculations and computing the yield of ATP in terms of the weight of glucose or palmitic acid oxidised to CO₂ and H₂O, it can be shown that the value for the ratio of the energy content of fat to that of carbohydrate is almost identical to the ratio of the yield of ATP per gram of palmitic acid oxidised, compared with that of glucose. Therefore, the efficiency (on a per gram basis) by which energy is made available as ATP is comparable for both the oxidation of fat and carbohydrate, thus underscoring the fact that the catabolic pathways for both fat and carbohydrate ultimately use the same means of generating ATP, namely, oxidative phosphorylation.     

Conjugation of oligosaccharides by reductive amination to amine modified chondroitin oligomer and γ-cyclodextrin

Carbohydrates present on cell surfaces participate in numerous biological recognition phenomena including cell–cell interactions, cancer metastasis and pathogen invasion. Therefore, synthetic carbohydrates have a potential to act as pharmaceutical substances for treatment of various pathological phenomena by inhibiting specifically the interaction between cell surface carbohydrates and their protein receptors (lectins). However, the inherently low affinity of carbohydrate-protein interactions has often been an obstacle for successful generation of carbohydrate based pharmaceuticals. Multivalent glycoconjugates, i.e. structures carrying several copies of the active carbohydrate sequence in a carrier molecule, have been constructed to overcome this problem. Here we present two novel types of multivalent carbohydrate conjugates based on chondroitin oligomer and cyclodextrin carriers. These carriers were modified to express primary amino groups, and oligosaccharides were then bound to carrier molecules by reductive amination. Multivalent conjugates were produced using the human milk type oligosaccharides LNDFH I (Lewis-b hexasaccharide), LNnT, and GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4Glc.     

Does the energy equivalence rule apply to intertidal macrobenthic communities?

Energy equivalence assumes equal contribution of large and small species to production and energy flow in communities. As in a double logarithmic plot, physiological rates decline with body weight by –0.25, log biomass should increase by 0.25 and log abundance decline by –0.75 with log species weight, when this concept is valid. This was tested with annual data sets of the macrobenthos of 4 intertidal sites in the German Wadden Sea (Königshafen) and 3 sites in a south Portuguese lagoon (Ria Formosa). Only abundance data from two of these sites displayed significantly negative slopes with mean body size of the species. Biomass and secondary production data were significantly positively correlated with mean body size for all Ria Formosa sites and also for the biomass of a mussel bed in Königshafen. However, high variation in body size of the individuals of a species limits interpretation of these plots.It is preferable to test this concept by body weight classes regardless of its species composition. At Königshafen, biomass and production displayed two distinct peaks. One peak at small body size was caused by browsing species. The other peak at larger body size was caused by animals which potentially extract their food from the water column. This bimodality was only vaguely reflected at one station in the Ria Formosa, possibly because of a dominance of detritus feeding species. In a normalized form (log biomass or production / width of size classvs. log size class), these spectra imply a dominance of small individuals in biomass and production at all sites (except for a mussel bank at Königshafen). This is interpreted as a consequence of permanent disturbances.     

Superimposing the 27 crystal protein/inhibitor complexes of β-secretase to calculate the binding affinities by the linear interaction energy method

BACE-1 is an important target for designing therapeutic agents for the treatment of Alzheimer's disease. An improved linear interaction energy (LIE) model has been developed to calculate the binding free energies of β-secretase (BACE-1) by superimposing the 27 crystal BACE-1/inhibitor complexes to put a diverse set of 27 co-crystallized ligands into the binding pocket. These co-crystallized conformations of ligands were set as the initial binding conformations for LIE simulation. The effects of two protein conformations (i.e., 1W51 and 1FKN), two sampling methods (i.e., energy minimization and hybrid Monte Carlo [HMC]), and energy terms were studied. Using 1W51 crystal structure and HMC sampling technique, the best binding affinity model for the full set of ligands was found to have a root-mean-square error of 0.996 kcal/mol.     

Structural analysis of the oligosaccharide-alditols released by reductive β-elimination from oviducal mucins of Rana temporaria

The carbohydrate chains of the mucins which constitute the jelly coat surrounding the eggs of Rana temporaria were released by alkaline borohydride treatment. Neutral and acidic oligosaccharide-alditols were purified by ion-exchange chromatography and HPLC. From the structural analysis, based upon 1H and 13C-NMR spectroscopy in combination with MALDI-TOF, the following glycan units are proposed. Abbreviations: MALDI-TOF, matrix assisted laser desorption ionization - time of flight; HPLC, high performance liquid chromatography; COSY, correlation spectroscopy; HSQC, heteronuclear single-quantum coherence spectroscopy; HMQC, heteronuclear multiple-quantum coherence spectroscopy; ROESY, rotating-frame overhauser enhancement spectroscopy; Fuc, fucose; Gal, galactose; GlcNAc, N-acetylglucosamine; GalNAc, N-acetylgalactosamine; GalNAc-ol, N-acetylgalactosaminitol; GlcA, glucuronic acid     

Hormonal and neuroendocrine regulation of energy balance‐the role of leptin

A new dimension to the regulation of energy balance has come from the identification of the ob (obese) gene and its protein product, leptin. Leptin is produced primarily in white adipose tissue, but synthesis also occurs in brown fat and the placenta. Several physiological functions have been described for leptin‐the inhibition of food intake, the stimulation/maintenance of energy expenditure, as a signal of energy reserves to the reproductive system, and as a factor in haematopoiesis. The production of leptin by white fat is influenced by a number of factors, including insulin and glucocorticoids (which are stimulatory), and fasting, cold exposure and ß‐adrenoceptor agonists (which are inhibitory). A key role in the regulation of leptin production is envisaged for the sympathetic nervous system, operating through ß3‐adreno‐ceptors. The leptin receptor gene is expressed in a wide range of tissues, and several splice variants are evident. A long form variant (Ob‐Rb) with an intracellular signalling domain is found particularly in the hypothalamus. Leptin exerts its central effects through neuropeptide Y, and through the glucagon‐like peptide‐1 and melanocortin systems, but it may also interact with other neuroendocrine pathways. The role and function of the leptin system in agricultural animals has not been established, but it offers a potential new target for the manipulation of body fat.     

Anaerobic energy metabolism of the sulfur-reducing bacterium “Spirillum” 5175 during dissimilatory nitrate reduction to ammonia

In a batch culture experiment the microaerophilic Campylobacter-like bacterium “Spirillum” 5175 derived its energy for growth from the reduction of nitrate to nitrite and nitrite to ammonia. Hereby, formate served as electron donor, acetate as carbon source, and l-cysteine as sulfur source. Nitrite was quantitatively accumulated in the medium during the reduction of nitrate; reduction of nitrite began only after nitrate was exhausted from the medium. The molar growth yield per mol formate consumed, Y_m, was 2.4g/mol for the reduction of nitrate to nitrite and 2.0 g/mol for the conversion of nitrite to ammonia. The gain of ATP per mol of oxidized formate was 20% higher for the reduction of nitrate to nitrite, compared to the reduction of nitrite to ammonia. With succinate as carbon source and nitrite as electron acceptor, Y_m was 3.2g/mol formate, i.e. 60% higher than with acetate as carbon source. No significant amount of nitrous oxide or dinitrogen was produced during growth with nitrate or nitrite both in the presence or absence of acetylene. No growth on nitrous oxide was found. The hexaheme c nitrite reductase of “Spirillum” 5175 was an inducible enzyme. It was present in cells cultivated with nitrate or nitrite as electron acceptor. It was absent in cells grown with fumarate, but appeared in high concentration in “Spirillum” 5175 grown on elemental sulfur. Furthermore, the dissimilatory enzymes nitrate reductase and hexaheme c nitrite reductase were localized in the periplasmic part of the cytoplasmic membrane.     

A kinetic study on the reductive opening of the diphenylmethylene acetal in methyl 2,3-O-diphenylmethylene-α-L-rhamnopyranoside

Reductive opening of the diphenylmethyl acetal in methyl 2,3-O-diphenylmethylene-α-l-rhamnopyranoside has been investigated by kinetic studies, and the results have been compared to those recently obtained by quantum chemical calculations. In contrast to the previous theoretical calculations which related only to the presumably rate limiting step of the reductive opening, the reaction system LiAlH(4), AlCl(3), and the title compound consists of at least four simultaneous reactions. Nevertheless, reasonable agreement can be found between the activation Gibbs free energy obtained from kinetic measurements and the theoretically calculated ones in spite of the experimental errors and the approximate nature of theoretical calculations.     

Is inosine the physiological energy source of pig erythrocytes?

Pig erythrocytes are unable to metabolize glucose and their physiological energy source is unknown. These cells have a high-capacity nucleoside transport system with similar properties to that responsible for nucleoside transport in other species. Nucleoside transport is sufficiently rapid to allow the possibility that inosine and/or adenosine may represent major energy substrates for pig erythrocytes in vivo. Normal and adenosine deaminase-deficient pig erythrocytes have similar ATP levels, suggesting that adenosine is not important in this respect. However, it was calculated that an extracellular inosine concentration of only 40 nM could support the cells' entire energy requirement, a value 40-fold lower than plasma levels of this nucleoside.     

What is the real value of chitosan's surface energy?

Because of conflicting reports and unrealistic literature values, a systematic study of the surface energy of chitin, chitosan, and their respective monomeric counterparts was carried out using contact angle measurements on films and pellets, before and after different purification procedures. All the commercial samples of these polymers were shown to contain nonpolar impurities that gave rise to enormous errors in the determination of the polar component of their surface energy. After their thorough removal, the value of the total surface energy (gamma(s)), and particularly of its polar component, increased considerably and reached the classical polysaccharide figures of gamma(s)d approximately 30 and gamma(s)p approximately 30 mJ/m2. The characterization of the impurities by gas chromatography/mass spectrometry analysis indicated the presence of significant amounts of higher alkanes, fatty acids, and alcohols and sterols.     

Effects of energy content and energy density of pre-portioned entrées on energy intake

Pre-portioned entrées are commonly consumed to help control portion size and limit energy intake. The influence of entrée characteristics on energy intake, however, has not been well studied. We determined how the effects of energy content and energy density (ED, kcal/g) of pre-portioned entrées combine to influence daily energy intake. In a crossover design, 68 non-dieting adults (28 men and 40 women) were provided with breakfast, lunch, and dinner on 1 day a week for 4 weeks. Each meal included a compulsory, manipulated pre-portioned entrée followed by a variety of unmanipulated discretionary foods that were consumed ad libitum. Across conditions, the entrées were varied in both energy content and ED between a standard level (100%) and a reduced level (64%). Results showed that in men, decreases in the energy content and ED of pre-portioned entrées acted independently and added together to reduce daily energy intake (both P < 0.01). Simultaneously decreasing the energy content and ED reduced total energy intake in men by 16% (445 ± 47 kcal/day; P < 0.0001). In women, the entrée factors also had independent effects on energy intake at breakfast and lunch, but at dinner and for the entire day the effects depended on the interaction of the two factors (P < 0.01). Simultaneously decreasing the energy content and ED reduced daily energy intake in women by 14% (289 ± 35 kcal/day; P < 0.0001). Both the energy content and ED of pre-portioned entrées affect daily energy intake and could influence the effectiveness of such foods for weight management.     

Dual energy landscape: the functional state of the β-barrel outer membrane protein G molds its unfolding energy landscape

We applied dynamic single-molecule force spectroscopy to quantify the parameters (free energy of activation and distance of the transition state from the folded state) characterizing the energy barriers in the unfolding energy landscape of the outer membrane protein G (OmpG) from Escherichia coli. The pH-dependent functional switching of OmpG directs the protein along different regions on the unfolding energy landscape. The two functional states of OmpG take the same unfolding pathway during the sequential unfolding of β-hairpins I-IV. After the initial unfolding events, the unfolding pathways diverge. In the open state, the unfolding of β-hairpin V in one step precedes the unfolding of β-hairpin VI. In the closed state, β-hairpin V and β-strand S11 with a part of extracellular loop L6 unfold cooperatively, and subsequently β-strand S12 unfolds with the remaining loop L6. These two unfolding pathways in the open and closed states join again in the last unfolding step of β-hairpin VII. Also, the conformational change from the open to the closed state witnesses a rigidified extracellular gating loop L6. Thus, a change in the conformational state of OmpG not only bifurcates its unfolding pathways but also tunes its mechanical properties for optimum function.     

Does the response of the intestinal epithelium to keratinocyte growth factor vary according to the method of administration?

BACKGROUND: Keratinocyte growth factor (KGF) is a potent mitogen and may be of value for the treatment of conditions such as short bowel syndrome and chemotherapy-induced mucositis. However the most efficacious route and method of administration is unclear. METHODS: Rats maintained by total parenteral nutrition (TPN) were given KGF (1 mg/kg/rat/day, i.v.) infused continuously or as a once-daily injection. The same dose was also given s.c. to chow-fed rats. Changes in gut growth were assessed by measurement of wet weight, proliferation (vincristine induced metaphase arrest) and crypt branching index. Changes in gut hormone profile were also determined to examine if any trophic effects were mediated via this mechanism. RESULTS: KGF caused a 70-100% increase in wet weight of the stomach, small and large intestine of TPN-fed rats (P < 0.01) with no significant differences seen between the two methods of administration. The increase in metaphase counts was greatest in the stomach (about seven-fold P < 0.01), but was less pronounced in the distal small intestine and colon (about 50% increase). The trophic effect of KGF was much less prominent in orally-fed rats. Crypt branching index was significantly reduced by KGF in the proximal small intestine of TPN, but not orally-fed rats. Plasma gastrin, PYY, total glucagon, enteroglucagon and GLP-1 all increased by two-three-fold (all P < 0.01) in response to KGF whereas insulin levels fell by about 25% in the TPN group. CONCLUSIONS: The mitogenic action of KGF occurred predominantly in the stomach and proximal small intestine. Its efficacy was less pronounced in orally-fed animals, suggesting KGF may be of greatest benefit in conditions associated with lowered intestinal proliferation. Clinical trials of KGF can probably use single daily i.v. injections without reduction in efficacy.     

The polymorphism of the genes/enzymes involved in the last two reductive steps of monolignol synthesis: what is the functional significance?

The polymorphism of genes and enzymes involved in the last two steps of monolignol synthesis is examined in the light of recent data coming from genomic studies and mutant/transformant analyses. The two catalytic activities considered--cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD)--are encoded by small multigene families. While some degree of diversification can be noted at the sequence level, it is often difficult to use this information to assign substrate specificities to each member of a gene family. Expression profiles, however, suggest for both CAD and CCR the existence of two sub-families: one devoted to developmental lignification, and the other involved in the synthesis of defence-related compounds.