Rational approaches for engineering novel functionalities in carbon-carbon bond forming enzymes

Enzymes that catalyze carbon-carbon bond formation can be exploited as biocatalyst for synthetic organic chemistry. However, natural enzymes frequently do not possess the required properties or specificities to catalyze industrially useful transformations. This mini-review describes recent work using knowledge-guided site-specific mutagenesis of key active site residues to alter substrate specificity, stereospecificity and reaction specificity of these enzymes. In addition, examples of de novo designed enzymes that catalyze C-C bond reactions not found in nature will be discussed.

Substrate specificity, substrate channeling, and allostery in BphJ: an acylating aldehyde dehydrogenase associated with the pyruvate aldolase BphI

BphJ, a nonphosphorylating acylating aldehyde dehydrogenase, catalyzes the conversion of aldehydes to form acyl-coenzyme A in the presence of NAD(+) and coenzyme A (CoA). The enzyme is structurally related to the nonacylating aldehyde dehydrogenases, aspartate-β-semialdehyde dehydrogenase and phosphorylating glyceraldehyde-3-phosphate dehydrogenase. Cys-131 was identified as the catalytic thiol in BphJ, and pH profiles together with site-specific mutagenesis data demonstrated that the catalytic thiol is not activated by an aspartate residue, as previously proposed. In contrast to the wild-type enzyme that had similar specificities for two- or three-carbon aldehydes, an I195A variant was observed to have a 20-fold higher catalytic efficiency for butyraldehyde and pentaldehyde compared to the catalytic efficiency of the wild type toward its natural substrate, acetaldehyde. BphJ forms a heterotetrameric complex with the class II aldolase BphI that channels aldehydes produced in the aldol cleavage reaction to the dehydrogenase via a molecular tunnel. Replacement of Ile-171 and Ile-195 with bulkier amino acid residues resulted in no more than a 35% reduction in acetaldehyde channeling efficiency, showing that these residues are not critical in gating the exit of the channel. Likewise, the replacement of Asn-170 in BphJ with alanine and aspartate did not substantially alter aldehyde channeling efficiencies. Levels of activation of BphI by BphJ N170A, N170D, and I171A were reduced by ≥3-fold in the presence of NADH and ≥4.5-fold when BphJ was undergoing turnover, indicating that allosteric activation of the aldolase has been compromised in these variants. The results demonstrate that the dehydrogenase coordinates the catalytic activity of BphI through allostery rather than through aldehyde channeling.

A national analysis of complications following hemiarthroplasty for hip fracture in older patients

BACKGROUND

There is emerging evidence that patients with fractured neck of femur (FNOF) aged >85 years have different demands on a health-care system when compared to younger patients.

AIM

We sought to better quantify this in terms of comorbidity and complication rates.

DESIGN

Retrospective review of national database.

METHODS

Data on all patients who underwent hip hemiarthroplasty for FNOF between January 2005 and December 2008 were extracted from the English hospital episode statistics database.

RESULTS

There were 41 770 patients aged 65-84 years and 35 321 patients aged ≥85 years. The older cohort was less likely to have diabetes, chronic obstructive pulmonary disease and rheumatoid arthritis. However, they exhibited a significantly higher risk of lower respiratory tract infection [odds ratio (OR) = 1.58, 95% confidence interval (CI) 1.50-1.67)], myocardial infarction (OR = 1.67, 1.52-1.83) and acute renal failure (OR = 1.54, 1.40-1.70) within 30 days of surgery with an inpatient mortality risk at 90 days, double that of the younger age group. Length of stay (LoS) was significantly longer in patients >85 years compared to younger patients (median 18 days vs. 15, P < 0.001).

CONCLUSION

Patients aged ≥85 years admitted for FNOF were found to have a lower incidence of major chronic disease but exhibited a greater incidence of acute events following hemiarthroplasty and their LoS was increased. Targeted medical interventions that focus upon this susceptible patient group may help reduce morbidity and improve survival.

Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes

Bacterial aldolase-dehydrogenase complexes catalyze the last steps in the meta cleavage pathway of aromatic hydrocarbon degradation. The aldolase (TTHB246) and dehydrogenase (TTHB247) from Thermus thermophilus were separately expressed and purified from recombinant Escherichia coli. The aldolase forms a dimer, while the dehydrogenase is a monomer; these enzymes can form a stable tetrameric complex in vitro, consisting of two aldolase and two dehydrogenase subunits. Upon complex formation, the K(m) value of 4-hydroxy-2-oxopentanoate, the substrate of TTHB246, is decreased 4-fold while the K(m) of acetaldehyde, the substrate of TTHB247, is increased 3-fold. The k(cat) values of each enzyme were reduced by ~2-fold when they were in a complex. The half-life of TTHB247 at 50 °C increased by ~4-fold when it was in a complex with TTHB246. The acetaldehyde product from TTHB246 could be efficiently channelled directly to TTHB247, but the channeling efficiency for the larger propionaldehyde was ~40% lower. A single A324G substitution in TTHB246 increased the channeling efficiency of propionaldehyde to a value comparable to that of acetaldehyde. Stable and catalytically competent chimeric complexes could be formed between the T. thermophilus enzymes and the orthologous aldolase (BphI) and dehydrogenase (BphJ) from the biphenyl degradation pathway of Burkholderia xenovorans LB400. However, channeling efficiencies for acetaldehyde in these chimeric complexes were ~10%. Structural and sequence analysis suggests that interacting residues in the interface of the aldolase-dehydrogenase complex are highly conserved among homologues, but coevolution of partner enzymes is required to fine-tune this interaction to allow for efficient substrate channeling.

Directional limits on persistent gravitational waves using LIGO S5 science data

The gravitational-wave (GW) sky may include nearby pointlike sources as well as stochastic backgrounds. We perform two directional searches for persistent GWs using data from the LIGO S5 science run: one optimized for pointlike sources and one for arbitrary extended sources. Finding no evidence to support the detection of GWs, we present 90% confidence level (C.L.) upper-limit maps of GW strain power with typical values between 2-20×10(-50)  strain(2) Hz(-1) and 5-35×10(-49)  strain(2) Hz(-1) sr(-1) for pointlike and extended sources, respectively. The latter result is the first of its kind. We also set 90% C.L. limits on the narrow-band root-mean-square GW strain from interesting targets including Sco X-1, SN 1987A and the Galactic center as low as ≈7×10(-25) in the most sensitive frequency range near 160 Hz.

Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling

HpaI and BphI are two pyruvate class II aldolases found in aromatic meta-cleavage degradation pathways that catalyze similar reactions but are not related in sequence. Steady-state kinetic analysis of the aldol addition reactions and product inhibition assays showed that HpaI exhibits a rapid equilibrium random order mechanism while BphI exhibits a compulsory order mechanism, with pyruvate binding first. Both aldolases are able to utilize aldehyde acceptors two to five carbons in length; however, HpaI showed broader specificity and had a preference for aldehydes containing longer linear alkyl chains or C2-OH substitutions. Both enzymes were able to bind 2-keto acids larger than pyruvate, but only HpaI was able to utilize both pyruvate and 2-ketobutanoate as carbonyl donors in the aldol addition reaction. HpaI lacks stereospecific control producing racemic mixtures of 4-hydroxy-2-oxopentanoate (HOPA) from pyruvate and acetaldehyde while BphI synthesizes only (4S)-HOPA. BphI is also able to utilize acetaldehyde produced by the reduction of acetyl-CoA catalyzed by the associated aldehyde dehydrogenase, BphJ. This aldehyde was directly channeled from the dehydrogenase to the aldolase active sites, with an efficiency of 84%. Furthermore, the BphJ reductive deacylation reaction increased 4-fold when BphI was catalyzing the aldol addition reaction. Therefore, the BphI-BphJ enzyme complex exhibits unique bidirectionality in substrate channeling and allosteric activation.

Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway

An aldolase and dehydrogenase complex from the polychlorinated biphenyl degradation pathway of the bacterium Burkholderia xenovorans LB400 was purified. The aldolase, BphI, had the highest activity with Mn(2+) as the cofactor and was able to transform 4-hydroxy-2-oxopentanoate and 4-hydroxy-2-oxohexanoate to pyruvate and acetaldehyde or propionaldehyde with similar specificity constants. Aldolase activity was competitively inhibited by the pyruvate enolate analogue, oxalate, with a K(ic) of 0.93 microM. The pH-rate profiles suggested the involvement of a pK(a) 7.7 catalytic base in the reaction mechanism. BphI activity was activated 15-fold when substrate turnover was occurring in the dehydrogenase, BphJ, which can be attributed partially to nicotinamide coenzyme binding to BphJ. BphJ had similar specificity constants for acetaldehyde or propionaldehyde and was able to utilize aliphatic aldehydes from two to five carbons in length as substrates, although K(m) values for these aldehyes were >20 mM. When 4-hydroxy-2-oxopentanoate was provided as a substrate to the BphI-BphJ complex in a coupled enzyme assay, no lag in the progress curve of BphJ was observed. When 1 mM propionaldehyde was added exogenously to a reaction mixture containing 0.1 mM 4-hydroxy-2-oxopentanoate, 95% of the CoA esters produced was acetyl CoA. Conversely, 99% of the CoA esters produced was propionyl CoA when a 10-fold molar excess of exogenous acetaldehyde was added in a reaction mixture containing 4-hydroxy-2-oxohexanoate. These results demonstrate that acetaldehyde and propionaldehyde, products of the BphI reaction, are not released in the bulk solvent but are channeled directly to the dehydrogenase.

Use of proteomic patterns as a novel screening tool in pre-eclampsia

This pilot study aimed to use Ciphergen ProteinChip technology to determine differences in protein profiles in plasma, taken at 26 weeks, from women at risk of developing pre-eclampsia. Five proteins were found to be significantly up-regulated in samples from women who subsequently developed pre-eclampsia compared with women who remained normotensive.

Responses of isolated pressurised rat uterine arteries to changes in pressure: effects of pre-constriction, endothelium and pregnancy

Pregnancy-induced changes in uterine artery function play a critical role in ensuring adequate placental perfusion. Responses of these vessels to pressure (myogenic responsiveness) may contribute to this. The overall myogenic properties of uterine arteries may depend upon the integration of a number of different factors, including effects of pre-constrictor stimuli, and should be considered in terms of both initial and stable diameters both of which may be modulated by pregnancy. This study thus investigated the effects of pre-constriction, the endothelium and pregnancy on responses of isolated rat uterine arteries to changes in intravascular pressure (IvP). The effects on both the immediate transient diameter changes and stable diameters (myogenic tone) were studied. Isolated 3rd order uterine arteries from non-pregnant and days 19-21 pregnant Sprague-Dawley rats were mounted on a pressure myograph and responses to changes in IvP (20-120 mm Hg) examined. Arteries did not exhibit active responses to pressure in the absence of stimulation, however, all showed active myogenic constriction when pre-constricted by depolarization (30 or 60mM KCl) or arginine vasopressin (AVP). Pregnancy enhanced stable levels of myogenic tone with AVP, but not depolarization. This difference was not dependent upon the endothelium. Initial peak diameters were enhanced in arteries from pregnant rats due to endothelium-dependent mechanisms. Thus, both the peak and stable response of isolated rat uterine arteries to pressure can be differentially regulated and thus must both be considered when considering the influence of pressure on uterine artery reactivity during pregnancy.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.