Understanding promiscuity in class II pyruvate aldolases

Aldolases are grouped based on their strict donor specificity. To expand the use of these versatile enzymes it is essential to identify aldolases that utilize different donors. Recently a number of pyruvate aldolases that accepted hydroxypyruvate was identified [1]. The class II hydroxy ketoacid aldolase A5VH82 from Sphingomonas wittichii RW1 (SwHKA) accepts hydroxypyruvate and was expressed for detailed studies. A thorough investigation including X-ray crystallography allowed new insights into the mechanistic details. This revealed a phosphate dependence of the enzyme and a preference for Mn (II) [2]. More importantly the substrate scope was studied. SwHKA is promiscuous for the donor, it accepted pyruvate, hydroxypyruvate and the halopyruvates as donor molecules. This expands the range of products that can be synthesized with aldolases. In particular since the halogen containing products can easily be further modified by SN2 reactions. Additionally, the substituted pyruvates yield products with not just one but two new stereocentres. Based on mutational studies, supported by structural elucidation by X-ray crystallography the stereochemical results will be discussed. Moreover, the acceptor molecules range far beyond the common sugar-type acceptors found in much pyruvate dependent aldolase chemistry. Overall SwHKA enables with its promiscuous properties a significant extension of the aldolase toolbox (Figure 1). Please click Additional Files below to see the full abstract

Expression and characterization of the nitrile reductase queF from E. coli

AbstractThe expression and characterization of a nitrile reductase from Escherichia coli K-12 (EcoNR), a newly discovered enzyme class, is described. This enzyme has a potential application for an alternative nitrile reduction pathway. The enzyme activity towards its natural substrate, preQ0, was demonstrated and optimal working conditions were found to be at 37°C and at pH 7 with Tris buffer

Evolution of the ThDP dependent pyruvate dehydrogenase E1 subunit for the conversion of long chain aliphatic ketoacids

Thiamine diphosphate (ThDP) dependent enzymes can catalyse the synthesis of chiral acyloins from both aldehydes and ketoacids as donor substrates, but the latter are generally preferred as they render the reaction under kinetic control.[1] While a large variety of aromatic aldehydes and polar donor substrates such as hydroxypyruvate and oxoglutarate are accepted by wild-type enzymes, the conversion of linear and branched chain aliphatic ketoacids remains a formidable challenge even after several rounds of directed evolution.[2] Due to its naturally large active site volume, the pyruvate dehydrogenase E1 subunit from E.coli (EcPDH E1) is a promising enzyme scaffold for directed evolution towards the conversion of sterically demanding, aliphatic ketoacids. Here we present initial results on the enzyme’s kinetic properties and its substrate scope. Please click Additional Files below to see the full abstract

Hydrogen bond networks facilitate the conversion of aliphatic aldehydes in the charged active site of S. cerevisiae transketolase

Naturally, transketolase (TK, E.C. 2.2.1.1) catalyzes asymmetric C-C bond formation in glycolysis derived metabolites to afford carbohydrates for nucleotide synthesis and the production of essential aromatic amino acids.[1] While results obtained earlier in our group showed that a decrease in active site polarity in S. cerevisiae transketolase was beneficial for the conversion of non-phosphorylated substrates,[2] the charged mutation D469E was counterintuitively found to promote the conversion of aliphatic aldehydes in E. coli transketolase.[3] Here we present a comparative study of the most beneficial single and double point mutants obtained from both reports for the conversion of aliphatic aldehydes using S. cerevisiae transketolase.[4] It was confirmed that a complete change of active site polarity is not required for the successful conversion of aliphatic aldehydes and surprisingly was found more beneficial than charge neutral mutations. These results were rationalized in docking studies, where a molecule of water was identified at the center of a hydrogen bond network, essential for substrate binding and correct orientation towards the cofactor, thus allowing the conversion of aliphatic aldehydes in the charged active site of transketolase. Please click Additional Files below to see the full abstract

Cofactor switch: Development of A Nad+-dependent cascade for the production of ursodeoxycholic acid (UDCA)

The employment of alcohol dehydrogenases in cascade reactions is often limited by the different cofactor specificity of the enzymes involved: the employment of additional cofactor regeneration systems and the excess amount of sacrificial substrates frequently increase the environmental impact and the costs of biocatalytic processes. Additionally, a NADP+-dependent process is generally less desirable, inasmuch this cofactor is more expensive, unstable and less naturally available than NAD+, leading to an increase of the process costs. Nowadays, protein engineering offers the possibility to switch the cofactor dependency of enzymes introducing few targeted mutation1. Please click Additional Files below to see the full abstract

Failure of catecholamines to shift T-cell cytokine responses toward a Th2 profile in patients with rheumatoid arthritis

To further understand the role of neuro-immunological interactions in the pathogenesis of rheumatoid arthritis (RA), we studied the influence of sympathetic neurotransmitters on cytokine production of T cells in patients with RA. T cells were isolated from peripheral blood of RA patients or healthy donors (HDs), and stimulated via CD3 and CD28. Co-incubation was carried out with epinephrine or norepinephrine in concentrations ranging from 10(-5 )M to 10(-11 )M. Interferon (IFN)-γ, tumour necrosis factor (TNF)-α, interleukin (IL)-4, and IL-10 were determined in the culture supernatant with enzyme-linked immunosorbent assay. In addition, IFN-γ and IL-10 were evaluated with intracellular cytokine staining. Furthermore, basal and agonist-induced cAMP levels and catecholamine-induced apoptosis of T cells were measured. Catecholamines inhibited the synthesis of IFN-γ, TNF-α, and IL-10 at a concentration of 10(-5 )M. In addition, IFN-γ release was suppressed by 10(-7 )M epinephrine. Lower catecholamine concentrations exerted no significant effect. A reduced IL-4 production upon co-incubation with 10(-5 )M epinephrine was observed in RA patients only. The inhibitory effect of catecholamines on IFN-γ production was lower in RA patients as compared with HDs. In RA patients, a catecholamine-induced shift toward a Th2 (type 2) polarised cytokine profile was abrogated. Evaluation of intracellular cytokines revealed that CD8-positive T cells were accountable for the impaired catecholaminergic control of IFN-γ production. The highly significant negative correlation between age and catecholamine effects in HDs was not found in RA patients. Basal and stimulated cAMP levels in T-cell subsets and catecholamine-induced apoptosis did not differ between RA patients and HDs. RA patients demonstrate an impaired inhibitory effect of catecholamines on IFN-γ production together with a failure to induce a shift of T-cell cytokine responses toward a Th2-like profile. Such an unfavorable situation is a perpetuating factor for inflammation

Knowledge-based design of bimodular and trimodular polyketide synthases based on domain and module swaps: a route to simple statin analogues

AbstractBackground: Polyketides are structurally diverse natural products that have a range of medically useful activities. Nonaromatic bacterial polyketides are synthesised on modular polyketide synthase (PKS) multienzymes, in which each cycle of chain extension requires a different ‘module’ of enzymatic activities. Attempts to design and construct modular PKSs that synthesise specified novel polyketides provide a particularly stringent test of our understanding of PKS structure and function.Results: We have constructed bimodular and trimodular PKSs based on DEBS1-TE, a derivative of the erythromycin PKS that contains only modules 1 and 2 and a thioesterase (TE), by substituting multiple domains with appropriate counterparts derived from the rapamycin PKS. Hybrid PKSs were obtained that synthesised the predicted target triketide lactones, which are simple analogues of cholesterol-lowering statins. In constructing intermodular fusions, whether between modules in the same or in different proteins, it was found advantageous to preserve intact the acyl carrier protein-ketosynthase (ACP-KS) didomain that spans the junction between successive modules.Conclusions: Relatively simple considerations govern the construction of functional hybrid PKSs. Fusion sites should be chosen either in the surface-accessible linker regions between enzymatic domains, as previously revealed, or just inside the conserved margins of domains. The interaction of an ACP domain with the adjacent KS domain, whether on the same polyketide or not, is of particular importance, both through conservation of appropriate protein-protein interactions, and through optimising molecular recognition of the altered polyketide chain in the key transfer of the acyl chain from the ACP of one module to the KS of the downstream module

Synthetic Activity of Recombinant Whole Cell Biocatalysts Containing 2-Deoxy-D-ribose-5-phosphate Aldolase from Pectobacterium atrosepticum

In nature 2-deoxy-D-ribose-5-phosphate aldolase (DERA) catalyses the reversible formation of 2-deoxyribose 5-phosphate from D-glyceraldehyde 3-phosphate and acetaldehyde. In addition, this enzyme can use acetaldehyde as the sole substrate, resulting in a tandem aldol reaction, yielding 2,4,6-trideoxy-D-erythro-hexapyranose, which spontaneously cyclizes. This reaction is very useful for the synthesis of the side chain of statin-type drugs used to decrease cholesterol levels in blood. One of the main challenges in the use of DERA in industrial processes, where high substrate loads are needed to achieve the desired productivity, is its inactivation by high acetaldehyde concentration. In this work, the utility of different variants of Pectobacterium atrosepticum DERA (PaDERA) as whole cell biocatalysts to synthesize 2-deoxyribose 5-phosphate and 2,4,6-trideoxy-D-erythro-hexapyranose was analysed. Under optimized conditions, E. coli BL21 (PaDERA C-His AA C49M) whole cells yields 99 % of both products. Furthermore, this enzyme is able to tolerate 500 mM acetaldehyde in a whole-cell experiment which makes it suitable for industrial applications.Fil: Fernández Varela, Romina Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; ArgentinaFil: Valino, Ana Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Área Química. Laboratorio de Biotransformaciones; ArgentinaFil: Abdelraheem, Eman. Delft University of Technology; Países BajosFil: Médici, Rosario. Delft University of Technology; Países BajosFil: Martínez Sayé, Melisa Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Pereira, Claudio Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Hagedoorn, Peter-Leon. Delft University of Technology; Países BajosFil: Hanefeld, Ulf. Delft University of Technology; Países BajosFil: Iribarren, Adolfo Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; ArgentinaFil: Lewkowicz, Elizabeth Sandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; Argentin

Structured health care for subjects with diabetic foot ulcers results in a reduction of major amputation rates

OBJECTIVE: We tested the effects of structured health care for the diabetic foot in one region in Germany aiming to reduce the number of major amputations. RESEARCH DESIGN AND METHODS: In a prospective study we investigated patients with diabetic foot in a structured system of outpatient, in-patient and rehabilitative treatment. Subjects were recruited between January 1(st), 2000 and December 31, 2007. All participants underwent a two-year follow-up. The modified University of Texas Wound Classification System (UT) was the basis for documentation and data analysis. We evaluated numbers of major amputations, rates of ulcer healing and mortality. In order to compare the effect of the structured health care program with usual care in patients with diabetic foot we evaluated the same parameters at another regional hospital without interdisciplinary care of diabetic foot (controls). RESULTS: 684 patients with diabetic foot and 508 controls were investigated. At discharge from hospital 28.3% (structured health care program, SHC) vs. 23.0% (controls) of all ulcers had healed completely. 51.5% (SHC) vs. 49.8% (controls) were in UT grade 1. Major amputations were performed in 32 subjects of the structured health care program group (4.7%) vs. 110 (21.7%) in controls (p<0.0001). Mortality during hospitalization was 2.5% (SHC) vs. 9.4% in controls (p<0.001). CONCLUSIONS: With the structured health care program we achieved a significant reduction of major amputation rates by more than 75% as compared to standard care

Substrate Induced Movement of the Metal Cofactor between Active and Resting State

Regulation of enzyme activity is vital for living organisms. In metalloenzymes, far-reaching rearrangements of the protein scaffold are generally required to tune the metal cofactor's properties by allosteric regulation. Here structural analysis of hydroxyketoacid aldolase from Sphingomonas wittichii RW1 (SwHKA) revealed a dynamic movement of the metal cofactor between two coordination spheres without protein scaffold rearrangements. In its resting state configuration (M$^{2+}$$_R$), the metal constitutes an integral part of the dimer interface within the overall hexameric assembly, but sterical constraints do not allow for substrate binding. Conversely, a second coordination sphere constitutes the catalytically active state (M$^{2+}$$_A$) at 2.4 Å distance. Bidentate coordination of a ketoacid substrate to M$^{2+}$$_A$ affords the overall lowest energy complex, which drives the transition from M$^{2+}$$_R$ to M$^{2+}$$_A$. While not described earlier, this type of regulation may be widespread and largely overlooked due to low occupancy of some of its states in protein crystal structures