Rhodococcus rhodochrous DSM 43269 3-Ketosteroid 9α-Hydroxylase,a Two-Component Iron-Sulfur-Containing Monooxygenase with Subtle Steroid Substrate Specificity

This paper reports the biochemical characterization of a purified and reconstituted two-component 3-ketosteroid 9α-hydroxylase (KSH). KSH of Rhodococcus rhodochrous DSM 43269, consisting of a ferredoxin reductase (KshB) and a terminal oxygenase (KshA), was heterologously expressed in Escherichia coli. E. coli cell cultures, expressing both KshA and KshB, converted 4-androstene-3,17-dione (AD) into 9α-hydroxy-4-AD (9OHAD) with a >60% molar yield over 48 h of incubation. Coexpression and copurification were critical to successfully obtain pure and active KSH. Biochemical analysis revealed that the flavoprotein KshB is an NADH-dependent reductase using flavin adenine dinucleotide as a cofactor. Reconstitution experiments confirmed that KshA, KshB, and NADH are essential for KSH activity with steroid substrates. KSH hydroxylation activity was inhibited by several divalent metal ions, especially by zinc. The reconstituted KSH displayed subtle steroid substrate specificity; a range of 3-ketosteroids, i.e., 5α-Η, 5β-Η, Δ1, and Δ4 steroids, could act as KSH substrates, provided that they had a short side chain. The formation of 9OHAD from AD by KSH was confirmed by liquid chromatography-mass spectrometry analysis and by the specific enzymatic conversion of 9OHAD into 3-hydroxy-9,10-secoandrost-1,3,5(10)-triene-9,17-dione using 3-ketosteroid Δ1-dehydrogenase. Only a single KSH is encoded in the genome of the human pathogen Mycobacterium tuberculosis H37Rv, shown to be important for survival in macrophages. Since no human KSH homolog exists, the M. tuberculosis enzyme may provide a novel target for treatment of tuberculosis. Detailed knowledge about the biochemical properties of KSH thus is highly relevant in the research fields of biotechnology and medicine.Hydroxylated steroids are pharmaceutically very interesting bioactive compounds. 9α-Hydroxylated steroids are of particular importance for the synthesis of corticoids such as 9α-fluorohydrocortisone. Microorganisms are widely used for the stereo-specific hydroxylation of steroids, but little is known about the enzymes involved, and current processes suffer from low conversion rates and yields (12, 18, 23).Rhodococcus species are well known for their broad catabolic potential and ability to degrade sterols and steroids (14, 21, 25, 39). In this paper, we focus on 3-ketosteroid 9α-hydroxylase (KSH), which is essential for the growth of Rhodococcus strains on steroids (38). KSH acts on the B-ring of 3-keto-Δ4 steroids, e.g., 4-androstene-3,17-dione (AD), introducing a 9α-hydroxyl moiety (Fig. ​(Fig.1).1). Subsequent Δ1-dehydrogenation of 9α-hydroxy-AD (9OHAD) by 3-ketosteroid Δ1-dehydrogenase (Δ1-KSTD) initiates the opening of the B-ring through formation of a chemically unstable intermediate that spontaneously hydrolyzes, forming 3-hydroxy-9,10-secoandrost-1,3,5(10)-triene-9,17-dione (3-HSA). KSH activity has been observed in various actinobacterial genera, e.g., Mycobacterium (1, 3, 6), Nocardia (35), Arthrobacter (11), and Rhodococcus (38). In view of their amino acid sequences, KSH enzymes are predicted to belong to the class IA monooxygenases (5, 38). Monooxygenases, or mixed-function oxidases, incorporate one atom of O₂ into the substrate (oxygenase function). The second atom of O₂ is reduced to H₂O (oxidase function) (17, 24). By definition, class IA monooxygenases are two-component systems consisting of a terminal oxygenase (KshA of KSH) and a ferredoxin reductase (KshB of KSH). The reductase component is a flavoprotein containing an NAD-binding domain and a plant-type iron-sulfur cluster, [Fe₂S₂Cys₄]. A Rieske-type iron-sulfur cluster, [Fe₂S₂Cys₂His₂], and a non-heme Fe²⁺-binding domain are characteristic for the terminal oxygenase (5, 38). The two protein subunits are linked by an electron transport chain. NAD(P)H donates electrons to the flavin of the reductase; these electrons are transferred via the iron-sulfur clusters to the oxygenase, eventually leading to hydroxylation of the substrate (Fig. ​(Fig.1).1). The non-heme Fe²⁺ is involved in the binding and activation of O₂ and substrate hydroxylation (4, 10, 13, 36).Open in a separate windowFIG. 1.Schematic representation of the Rhodococcus two-component iron-sulfur monooxygenase KSH comprised of KshA and KshB. Small arrows indicate electron transfer from NADH to the FAD cofactor of KshB and via the Fe₂S₂ clusters to KshA, where substrate hydroxylation occurs at the Fe²⁺ binding domain. The substrate depicted is AD. The product is 9OHAD.The kshA and kshB genes, encoding KshA and KshB, respectively, were first identified in Rhodococcus erythropolis SQ1 (38). Gene deletion studies have shown that both kshA and kshB of R. erythropolis SQ1 were required for KSH activity, suggesting that these two proteins constitute KSH. Biochemical evidence for this interaction, however, had been lacking. In fact, knowledge of KSH at the biochemical level has been extremely limited. Steroid 9α-hydroxylation has been reported to occur in cell extracts of Nocardia restricta (7), and a partly purified three-component enzyme system of Nocardia species M117 has been described (35). Heterologous expression of kshA of M. smegmatis mc²155 in Escherichia coli has recently been reported (1, 3). Upon purification, however, KSH activities were lost or became too low for biochemical characterization of the enzyme. Recently, the heterologous expression and characterization of KSH of Mycobacterium tuberculosis H37Rv was reported and a crystal structure of KshA was described (6). Addition of Fe²⁺-chelating agents to cell cultures of Rhodococcus rhodochrous DSM 43269 (= IFO3338) incubated with cholesterol was shown to chemically inactivate KSH, resulting in the accumulation of pharmaceutically interesting steroid pathway intermediates, i.e., 1,4-androstadiene-3,17-dione (ADD) and 23,24-bisnorcholesta-1,4-diene-22-oic acid (2). A single kshA ortholog (locus tag rv3526) has been identified in the genome of the human pathogen M. tuberculosis H37Rv (9, 40). Intriguingly, H37Rv genome-wide studies have revealed that rv3526 is specifically upregulated in macrophages and that rv3526 is important for the survival of M. tuberculosis in macrophages (29, 32, 34). Since no human homolog exists, KSH may provide a novel target for the treatment of a devastating disease, tuberculosis. Detailed knowledge about the biochemical properties of KSH thus is highly relevant in the research fields of biotechnology and medicine.Here, we report the characterization of purified and reconstituted KSH and show at the biochemical level that both KshA and KshB are essential components of the two-component, iron-sulfur-containing KSH of R. rhodochrous.     

Purification and Substrate Specificities of Two α-l-Arabinofuranosidases from Aspergillus awamori IFO 4033

α-l-Arabinofuranosidases I and II were purified from the culture filtrate of Aspergillus awamori IFO 4033 and had molecular weights of 81,000 and 62,000 and pIs of 3.3 and 3.6, respectively. Both enzymes had an optimum pH of 4.0 and an optimum temperature of 60°C and exhibited stability at pH values from 3 to 7 and at temperatures up to 60°C. The enzymes released arabinose from p-nitrophenyl-α-l-arabinofuranoside, O-α-l-arabinofuranosyl-(1→3)-O-β-d-xylopyranosyl-(1→4)-d-xylopyranose, and arabinose-containing polysaccharides but not from O-β-d-xylopyranosyl-(1→2)-O-α-l-arabinofuranosyl-(1→3)-O-β-d-xylopyranosyl-(1→4)-O-β-d-xylopyranosyl-(1→4)-d-xylopyranose. α-l-Arabinofuranosidase I also released arabinose from O-β-d-xylopy-ranosyl-(1→4)-[O-α-l-arabinofuranosyl-(1→3)]-O-β-d-xylopyranosyl-(1→4)-d-xylopyranose. However, α-l-arabinofuranosidase II did not readily catalyze this hydrolysis reaction. α-l-Arabinofuranosidase I hydrolyzed all linkages that can occur between two α-l-arabinofuranosyl residues in the following order: (1→5) linkage > (1→3) linkage > (1→2) linkage. α-l-Arabinofuranosidase II hydrolyzed the linkages in the following order: (1→5) linkage > (1→2) linkage > (1→3) linkage. α-l-Arabinofuranosidase I preferentially hydrolyzed the (1→5) linkage of branched arabinotrisaccharide. On the other hand, α-l-arabinofuranosidase II preferentially hydrolyzed the (1→3) linkage in the same substrate. α-l-Arabinofuranosidase I released arabinose from the nonreducing terminus of arabinan, whereas α-l-arabinofuranosidase II preferentially hydrolyzed the arabinosyl side chain linkage of arabinan.Recently, it has been proven that l-arabinose selectively inhibits intestinal sucrase in a noncompetitive manner and reduces the glycemic response after sucrose ingestion in animals (33). Based on this observation, l-arabinose can be used as a physiologically functional sugar that inhibits sucrose digestion. Effective l-arabinose production is therefore important in the food industry. l-Arabinosyl residues are widely distributed in hemicelluloses, such as arabinan, arabinoxylan, gum arabic, and arabinogalactan, and the α-l-arabinofuranosidases (α-l-AFases) (EC 3.2.1.55) have proven to be essential tools for enzymatic degradation of hemicelluloses and structural studies of these compounds.α-l-AFases have been classified into two families of glycanases (families 51 and 54) on the basis of amino acid sequence similarities (11). The two families of α-l-AFases also differ in substrate specificity for arabinose-containing polysaccharides. Beldman et al. summarized the α-l-AFase classification based on substrate specificities (3). One group contains the Arafur A (family 51) enzymes, which exhibit very little or no activity with arabinose-containing polysaccharides. The other group contains the Arafur B (family 54) enzymes, which cleave arabinosyl side chains from polymers. However, this classification is too broad to define the substrate specificities of α-l-AFases. There have been many studies of the α-l-AFases (3, 12), especially the α-l-AFases of Aspergillus species (2–8, 12–15, 17, 22, 23, 28–32, 36–39, 41–43, 46). However, there have been only a few studies of the precise specificities of these α-l-AFases. In previous work, we elucidated the substrate specificities of α-l-AFases from Aspergillus niger 5-16 (17) and Bacillus subtilis 3-6 (16, 18), which should be classified in the Arafur A group and exhibit activity with arabinoxylooligosaccharides, synthetic methyl 2-O-, 3-O-, and 5-O-arabinofuranosyl-α-l-arabinofuranosides (arabinofuranobiosides) (20), and methyl 3,5-di-O-α-l-arabinofuranosyl-α-l-arabinofuranoside (arabinofuranotrioside) (19).In the present work, we purified two α-l-AFases from a culture filtrate of Aspergillus awamori IFO 4033 and determined the substrate specificities of these α-l-AFases by using arabinose-containing polysaccharides and the core oligosaccharides of arabinoxylan and arabinan.     

Properties of an Inward-Facing State of LeuT: Conformational Stability and?Substrate Release

The leucine transporter (LeuT) is a bacterial homolog of the human monoamine transporters, which are important pharmaceutical targets. There are no high-resolution structures of the human transporters available; however, LeuT has been crystallized in several different conformational states. Recently, an inward-facing conformation of LeuT was solved revealing an unexpectedly large movement of transmembrane helix 1a (TM1a). We have performed molecular dynamics simulations of the mutated and wild-type transporter, with and without the cocrystallized Fab antibody fragment, to investigate the properties of this inward-facing conformation in relation to transport by LeuT within the membrane environment. In all of the simulations, local conformational changes with respect to the crystal structure are consistently observed, especially in TM1a. Umbrella sampling revealed a soft potential for TM1a tilting. Furthermore, simulations of inward-facing LeuT with Na⁺ ions and substrate bound suggest that one of the Na⁺ ion binding sites is fully disrupted. Release of alanine and the second Na⁺ ion is also observed, giving insight into the final stage of the translocation process in atomistic detail.     

Effects of 3-Methylgibberellin Analogs on Gibberellin 3β-Hydroxylases and Plant Growth

Six 3-methylgibberellin analogs were synthesized, and their effects on the GA 3β-hydroxylases from immature seeds of Phaseolus vulgaris and Cucurbita maxima, and/or on the growth of dwarf rice (Oryza sativa L. cv. Tan-ginbozu) and cucumber (Cucumis sativus L. cv. Spacemaster) were investigated. 3-Methyl-GA₅ and 2, 3-didehydro-3-methyl-GA₉· inhibited the conversion of [2, 3-³H2]GA₉ to [2-³H]GA₄ by GA 3β-hydroxylases from both P. vulgaris and C. maxima at 3 μM and higher. Their C/D-ring-rearranged isomers, 2, 3-didehydro-3-methyl-DGC and 16-deoxo-2, 3-didehydro-3-methyl-DGC, inhibited 3β-hydroxylation by the enzyme from P. vulgaris threefold more strongly than the non-C/D-ring-rearranged compounds, but exhibited no effect on 3β-hydroxylation by the enzyme from C. maxima. In a dwarf rice seedling assay, 3-methyl-GA₅ and 2, 3-didehydro-3-methyl-GA₉ promoted shoot elongation at doses of 300 ng/plant and higher, and 3α-methyl-GA₁ and 3α-methyl-GA₄ at doses of 30 ng/plant and higher. In contrast 2, 3-didehydro-3-methyl-DGC inhibited shoot growth to half that of the control at a dose of 300 ng/plant, and 16-deoxo-2, 3-didehydro-3-methyl-DGC showed no effect on growth. In a cucumber seedling assay, 3α-methyl-GA₄ promoted hypocotyl elongation at doses of 300 ng/plant and higher. The other C-3 methyl compounds showed no effect on the hypocotyl elongation of cucumber seedlings.     

Proteome-derived Peptide Libraries Allow Detailed Analysis of the Substrate Specificities of Nα-acetyltransferases and Point to hNaa10p as the Post-translational Actin Nα-acetyltransferase

The impact of N^α-terminal acetylation on protein stability and protein function in general recently acquired renewed and increasing attention. Although the substrate specificity profile of the conserved enzymes responsible for N^α-terminal acetylation in yeast has been well documented, the lack of higher eukaryotic models has hampered the specificity profile determination of N^α-acetyltransferases (NATs) of higher eukaryotes. The fact that several types of protein N termini are acetylated by so far unknown NATs stresses the importance of developing tools for analyzing NAT specificities. Here, we report on a method that implies the use of natural, proteome-derived modified peptide libraries, which, when used in combination with two strong cation exchange separation steps, allows for the delineation of the in vitro specificity profiles of NATs. The human NatA complex, composed of the auxiliary hNaa15p (NATH/hNat1) subunit and the catalytic hNaa10p (hArd1) and hNaa50p (hNat5) subunits, cotranslationally acetylates protein N termini initiating with Ser, Ala, Thr, Val, and Gly following the removal of the initial Met. In our studies, purified hNaa50p preferred Met-Xaa starting N termini (Xaa mainly being a hydrophobic amino acid) in agreement with previous data. Surprisingly, purified hNaa10p preferred acidic N termini, representing a group of in vivo acetylated proteins for which there are currently no NAT(s) identified. The most prominent representatives of the group of acidic N termini are γ- and β-actin. Indeed, by using an independent quantitative assay, hNaa10p strongly acetylated peptides representing the N termini of both γ- and β-actin, and only to a lesser extent, its previously characterized substrate motifs. The immunoprecipitated NatA complex also acetylated the actin N termini efficiently, though displaying a strong shift in specificity toward its known Ser-starting type of substrates. Thus, complex formation of NatA might alter the substrate specificity profile as compared with its isolated catalytic subunits, and, furthermore, NatA or hNaa10p may function as a post-translational actin N^α-acetyltransferase.The multisubunit and ribosome-associated protein N^α-acetyltransferases (NATs)1 are omnipresent enzyme complexes that catalyze the transfer of the acetyl moiety from acetyl-CoA to the primary α-amines of N termini of nascent proteins (1–3). As up to 50 to 60% of yeast proteins and 80 to 90% of human proteins are modified in this manner, N^α-acetylation is a widespread protein modification in eukaryotes (4–7), and the pattern of modification has remained largely conserved throughout evolution (4, 8). NATs belong to a subfamily of the Gcn5-related N-acetyltransferase superfamily of N-acetyltransferases, additionally encompassing the well-studied histone acetyltransferases that are implicated in epigenetic imprinting.In yeast and humans, three main NAT complexes, NatA, NatB, and NatC were found to be responsible for the majority of N^α-terminal acetylations (1). The NatA complex, responsible for cotranslational N^α-terminal acetylation of proteins with Ser, Ala, Thr, Gly, and Val N termini, is composed of two main subunits, the catalytic subunit Naa10p (previously known as Ard1p) and the auxiliary subunit Naa15p (previously known as Nat1p/NATH) (9–11). Furthermore, a third catalytic subunit Naa50p (previously known as Nat5)—an acetyltransferase shown to function in chromosome cohesion and segregation (12–14)—was found to physically interact with the NatA complex of yeast (2), fruit fly (12), and human (15). Recently, human Naa50p (hNaa50p) was reported to display lysine or N^ε-acetyltransferase as well as NAT activity (16), the latter was defined as NatE activity (16). Interestingly, the chaperone-like, Huntingtin interacting protein HYPK, identified as a novel stable interactor of human NatA, was functionally implicated in the N-terminal acetylation of an in vivo NatA substrate, demonstrating that NAT complex formation and composition may have an overall influence on the observed (degree of) N^α-acetylation (17). Further, subunits of the human NatA complex have been coupled to cancer-related processes and differentiation, with altered subunit expression reported in papillary thyroid carcinoma, neuroblastoma, and retinoic acid induced differentiation. Furthermore, the NatA catalytic subunit was found to be implicated in processes such as hypoxia-response and the β-catenin pathway (18, 19). Of note is that in line with the differential localization patterns of the individual NatA subunits (9, 13, 20, 21), other data indicate that these subunits might well exert NatA-independent enzymatic functions (13, 22, 23). Given that a significant fraction of hNaa10p and hNaa15p are nonribosomal (9), and given the multitude of postulated post-translational in vivo N-acetylation events recently reported (24–26), these observations argue in favor of the existence of NAT complexes and/or catalytic NAT-subunits acting post-translationally.Similar to NatA, the NatB and NatC complexes, composed of the catalytic subunit Naa20p or Naa30p and the auxiliary subunits Naa25p or Naa35p and Naa38p respectively, are conserved from yeast to higher eukaryotes concerning their subunit composition as well as their substrate specificity. Both these complexes display activity toward methionine-starting N termini, with NatB preferring acidic residues as well as Asn and Gln at P2′-sites², whereas NatC prefers hydrophobic amino acid residues at substrate P2′-sites (1, 27, 28).N^α-acetylation affects various protein functions such as localization, activity, association, and stability (29, 30). Only recently a more generalized function of protein N^α-acetylation in generating so-called N-terminal degrons marking proteins for removal was put forward (31). The lack of mouse models in addition to the fact that (combined) knockdown of individual components of N^α-acetyltransferases only marginally affect the overall N^α-acetylation status (4) have so far hampered the molecular characterization of the substrate specificity profile of (yet uncharacterized) NATs. To date, all eukaryote N^α-acetylation events are assumed to be catalyzed by the five known NATs (32). However, an additional level of complexity is imposed by the fact that in contrast to yeast, higher eukaryotes express multiple splice variants of various NAT subunits as well as paralogs thereof (33, 34), further implicating that a specific NAT''s substrate specificity might be altered in this way, in addition to the possible existence of substrate redundancy. Moreover, regulation of substrate specificity and stability of NAT activity can be imposed by differential complex formation and post-translational modifications including phosphorylation, auto-acetylation, and specific proteolytic cleavage of the catalytic subunits (9, 16, 17). As such, a detailed understanding of the substrate specificity of NATs, and the regulation thereof, could help unravel the physiological substrate repertoires as well as the associated physiological roles of NATs in the normal and the disease state.The specificity of N^α-acetyltransferases and their endogenous substrates were originally studied by two-dimensional-PAGE: N^α-acetylation neutralizes the N-terminal positive charge, resulting in an altered electrophoretic protein migration during isoelectric focusing (35–38). Recently, this altered biophysical property was also exploited to enrich for protein N-termini using low pH strong cation exchange (SCX) chromatography (24, 39). As an example, SCX prefractionation combined with N-terminal combined fractional diagonal chromatography, a targeted proteomics technology negatively selecting for protein N-terminal peptides, stable isotope labeling of amino acids in cell culture, and amino-directed modifiers (40), was used to study the in vivo substrate repertoires of human as well as yeast NatA (4).Nevertheless, the various methods reported today to study in detail N^α-terminal acetylation and thus the specificities of different NATs make use of a limited and therefore somewhat biased set of synthesized peptide substrates and comprise the rather laborious detection of radioactive acetylated products as well as enzyme-coupled methods quantifying acetyl-CoA conversion. Because (proteome-derived) peptide libraries have been used extensively to study epitope mapping (41), protein-protein interactions (42), protein modifications such as phosphorylation (43), and proteolysis (44, 45), as well as for determining the substrate specificity of the N^α-deblocking peptide deformylase (46), we reckoned that the development of an oligopeptide-based acetylation assay should allow for more comprehensive screening of NAT-like activities. We here report on the development of a peptide-based method to systematically screen for the in vitro sequence specificity profile of individual NATs as well as endogenous NAT complexes. In summary, SCX enriched, N^α-free peptide libraries, derived from natural proteomes build up the peptide substrate pool. And, upon incubation, NAT N^α-acetylated peptides are enriched by a second SCX fractionation step, resulting in a positive selection of NAT-specific peptide substrates. By use of this proteome-derived peptide library approach, we here delineated (differences in) the specificity profiles of hNaa50p and hNaa10p as isolated hNatA components, as well as of assayed their combined activity when in their native hNatA complex.     

3-Ketosteroid 9α-hydroxylase enzymes: Rieske non-heme monooxygenases essential for bacterial steroid degradation

Various micro-organisms are able to use sterols/steroids as carbon- and energy sources for growth. 3-Ketosteroid 9α-hydroxylase (KSH), a two component Rieske non-heme monooxygenase comprised of the oxygenase KshA and the reductase KshB, is a key-enzyme in bacterial steroid degradation. It initiates opening of the steroid polycyclic ring structure. The enzyme has industrial relevance in the synthesis of pharmaceutical steroids. Deletion of KSH activity in sterol degrading bacteria results in blockage of steroid ring opening and is used to produce valuable C19-steroids such as 4-androstene-3,17-dione and 1,4-androstadiene-3,17-dione. Interestingly, KSH activity is essential for the pathogenicity of Mycobacterium tuberculosis. Detailed information about KSH thus is of medical relevance, and KSH inhibitory compounds may find application in combatting tuberculosis. In recent years, the 3D structure of the KshA protein of M. tuberculosis H37Rv has been elucidated and various studies report biochemical characteristics and possible physiological roles of KSH. The current knowledge is reviewed here and forms a solid basis for further studies on this highly interesting enzyme. Future work may result in the construction of KSH mutants capable of production of specific bioactive steroids. Furthermore, KSH provides an promising target for drugs against the pathogenic agent M. tuberculosis.     

Conformational Flexibility and Absolute Stereochemistry of (3R)-3-hydroxy-4-aryl-β-lactams Investigated by Chiroptical Properties and TD-DFT Calculations

The effect of conformational flexibility on the chiroptical properties of a series of synthetic (3R)-3-hydroxy-4-aryl-β-lactams of known stereochemistry (1-6) was investigated by means of electronic circular dichroism (ECD) measurements and time-dependent density functional theory (TD-DFT) calculations. The application of the β-lactam sector rules allowed a correct stereochemical characterization of these compounds, with the exception of a thienyl-substituted derivative (cis-). TD-DFT calculations yielded accurate predictions of experimental ECD spectra and [α](D) values, allowing us to assign the correct absolute configuration to all the investigated compounds. A detailed analysis of the β-lactam ring equilibrium geometry on optimized conformers identified regular patterns for the arrangement of atoms around the amide chromophore, confirming the validity of the β-lactam sector rules. However, relevant variations in theoretical chiroptical properties were found for compounds bearing a heterocyclic substituent at C4 or a phenyl substituent at C3, whose conformers deviate from these regular geometric patterns. This behavior explains the failure of the β-lactam sector rules in cis-. This study showed the importance of conformational flexibility for the determination of chiroptical properties and highlighted the strengths and weaknesses of the different methods for the stereochemical characterization of chiral molecules in solution. Chirality 24:741-750, 2012. ? 2012 Wiley Periodicals, Inc.     

Conformational Flexibility Determines Selectivity and Antibacterial, Antiplasmodial, and Anticancer Potency of Cationic ��-Helical Peptides

We used a combination of fluorescence, circular dichroism (CD), and NMR spectroscopies in conjunction with size exclusion chromatography to help rationalize the relative antibacterial, antiplasmodial, and cytotoxic activities of a series of proline-free and proline-containing model antimicrobial peptides (AMPs) in terms of their structural properties. When compared with proline-free analogs, proline-containing peptides had greater activity against Gram-negative bacteria, two mammalian cancer cell lines, and intraerythrocytic Plasmodium falciparum, which they were capable of killing without causing hemolysis. In contrast, incorporation of proline did not have a consistent effect on peptide activity against Mycobacterium tuberculosis. In membrane-mimicking environments, structures with high α-helix content were adopted by both proline-free and proline-containing peptides. In solution, AMPs generally adopted disordered structures unless their sequences comprised more hydrophobic amino acids or until coordinating phosphate ions were added. Proline-containing peptides resisted ordering induced by either method. The roles of the angle subtended by positively charged amino acids and the positioning of the proline residues were also investigated. Careful positioning of proline residues in AMP sequences is required to enable the peptide to resist ordering and maintain optimal antibacterial activity, whereas varying the angle subtended by positively charged amino acids can attenuate hemolytic potential albeit with a modest reduction in potency. Maintaining conformational flexibility improves AMP potency and selectivity toward bacterial, plasmodial, and cancerous cells while enabling the targeting of intracellular pathogens.     

Bilateral Eye Movements, Attentional Flexibility and Metaphor Comprehension: The Substrate of REM Dreaming?

Explanations for the effects of the rapid eye movements induced during Eye Movement Desensitization Reprocessing (EMDR; Shapiro, 2001) have drawn upon an analogy with the eye movements of REM sleep (Kuiken, Bears, Miall, and Smith, 2002). An extension of that analogy posits two orienting systems, one involving threat-fear related mnemonic contextualization and another involving loss-pain related monitoring of conflicting response alternatives. In a study involving individuals who had recently experienced significant loss or trauma, we found that experimentally induced saccadic eye movements decreased reaction times to unexpected stimuli among those reporting traumatic distress (characterized by hyperarousal and intrusive thoughts) and increased reaction times among those reporting separation distress (characterized by vivid reminiscences and the sense of a foreshortened future). Also, we found that saccadic eye movements increased the perceived strikingness of metaphoric sentence endings among those reporting amnesia for events related to either loss or trauma. The eye movements of both EMDR and REM sleep may differently affect the attentional and cognitive reorienting activity of those living with the consequences of loss or trauma. These differences may be evident in their waking reflections and in their dreams. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Comparison of the Substrate Specificities of the β-Lactamases from Klebsiella aerogenes 1082E and Enterobacter cloacae P99

A potent beta-lactamase (EC 3.5.2.6) produced by a strain of Klebsiella aerogenes (K. pneumoniae), 1082E, isolated from a hospital patient, has been examined. Its properties were different from those of most gram-negative beta-lactamases previously reported. The enzyme has been partly purified, and its activity against a range of substrates has been compared with that of the enzyme from Enterobacter cloacae (Aerobacter cloacae) P99. The K. aerogenes enzyme, although predominantly a penicillinase, had a wide range of specificity. In addition to hydrolyzing the cephalosporins, it attacked the normally beta-lactamaseresistant compounds methicillin and cloxacillin as well as cephalosporin analogues with the same acyl substituents. The results obtained with the E. cloacae enzyme confirmed its cephalosporinase activity and showed that, unlike the enzyme from K. aerogenes, it was relatively inactive against the penicillins.     

Some Derivatives of 5α-Ketosteroid Hydrazones: Synthesis from Tigogenin and Antituberculosis Activity

Isonicotinoylhydrazones and thiosemicarbazones of some 5-ketosteroids were synthesized from tigogenin, and their structures were confirmed by NMR and IR spectroscopy and mass spectrometry. Their antimycobacterial activities were studied and it was shown that some of the synthesized isonicotinoylhydrazones exhibit a high antituberculosis activity.     

Conformational Dynamics of Dioxygenase AlkB and DNA in the Course of Catalytically Active Enzyme–Substrate Complex Formation

Russian Journal of Bioorganic Chemistry - Fe2+/2-ketoglutarate-dependent DNA-dioxygenase AlkB from Escherichia coli is able to restore the native structure of alkylated DNA bases. The enzymatic...     

Crystal Structures of β-1,4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes and Substrate Binding

The β-1,4-galactosyltransferase 7 (β4GalT7) enzyme is involved in proteoglycan synthesis. In the presence of a manganese ion, it transfers galactose from UDP-galactose to xylose on a proteoglycan acceptor substrate. We present here the crystal structures of human β4GalT7 in open and closed conformations. A comparison of these crystal structures shows that, upon manganese and UDP or UDP-Gal binding, the enzyme undergoes conformational changes involving a small and a long loop. We also present the crystal structures of Drosophila wild-type β4GalT7 and D211N β4GalT7 mutant enzymes in the closed conformation in the presence of the acceptor substrate xylobiose and the donor substrate UDP-Gal, respectively. To understand the catalytic mechanism, we have crystallized the ternary complex of D211N β4GalT7 mutant enzyme in the presence of manganese with the donor and the acceptor substrates together in the same crystal structure. The galactose moiety of the bound UDP-Gal molecule forms seven hydrogen bonds with the protein molecule. The nonreducing end of the xylose moiety of xylobiose binds to the hydrophobic acceptor sugar binding pocket created by the conformational changes, whereas its extended xylose moiety forms hydrophobic interactions with a Tyr residue. In the ternary complex crystal structure, the nucleophile O4 oxygen atom of the xylose molecule is found in close proximity to the C1 and O5 atoms of the galactose moiety. This is the first time that a Michaelis complex of a glycosyltransferase has been described, and it clearly suggests an S_N2 type catalytic mechanism for the β4GalT7 enzyme.     

Substrate Specificities of Mitochondrial Thymidine Kinase and Cytosolic Deoxycytidine Kinase Against 5-Aryl Substituted Pyrimidine-2′-deoxyribose Analogues

Abstract

Some 5-aryl-2′-deoxyuridine and -deoxycytidine analogues, many with known antiviral activity, were evaluated as substrates for pure deoxycytidine kinase (dCK) and pure mitochondrial thymidine kinase (TK2). Some of the deoxyuridine compounds were also tested with pure cytosolic thymidine kinase (TK1). TK2 showed the highest activity with this type of analogues.     

Synthesis and evaluation of 17α-triazolyl and 9α-cyano derivatives of estradiol

A variety of 17α-triazolyl and 9α-cyano derivatives of estradiol were prepared and evaluated for binding to human ERβ in both a TR-FRET assay, as well as ERβ and ERα agonism in cell-based functional assays. 9α-Cyanoestradiol (5) was nearly equipotent as estradiol as an agonist for both ERβ and ERα. The potency of the 17α-triazolylestradiol analogs is considerably more variable and depends on the nature of the 4-substituent of the triazole ring. While rigid protein docking simulations exhibited significant steric clashing, induced fit docking providing more protein flexibility revealed that the triazole linker of analogs 2d and 2e extends outside of the traditional ligand binding domain with the benzene ring located in the loop connecting helix 11 to helix 12.     

Computational Selection,Identification and Structural Analysis of ω-Aminotransferases with Various Substrate Specificities from the Genome Sequence of Mesorhizobium loti MAFF303099

ω-Aminotransferase (ω-AT) is an important class of enzymes for the synthesis of chiral amines or β-amino acids. Family profile analysis was applied to screen putative ω-ATs from Mesorhizobium loti MAFF303099, a nitrogen fixation bacterium that has a larger number of ATs than other microorganisms. By family profile analysis, we selected 10 putative ω-ATs according to E-value. The functions of the putative ω-ATs were investigated by examining activities towards amines and/or β-amino acids. 10 putative proteins were found to have ω-AT activity with narrow or broad substrate specificity. Structure analysis using crystal structure of mll7127 and homology models of mll1632 and mll3663 indicated that the structures of active sites of the enzymes were very similar and highly conserved, but their substrate specificities appreared to be determined by residues positioned at the entrance region of the active site binding pockets.     

Conformational preferences of α,α-trehalose in gas phase and aqueous solution

This work presents an investigation on the conformational preferences of α,α-trehalose in gas phase and aqueous solution. Eighty-one systematically selected structures were studied at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level, giving rise to 40 unique conformers. The 19 lower energy structures and some selected other were further re-optimized at the B3LYP/6-311++G(d,p) level. The main factors accounting for the conformer’s stability were pointed out and discussed. NBO and QTAIM analyses were performed in some selected conformers in order to address the anomeric and exo-anomeric effects as well as intramolecular hydrogen bonding. The effect of solvent water on the relative stability of the conformers was accounted for by applying the conductor-like polarizable continuum model, CPCM.     

Ribosylation of 3-Methylguanine and the Relative Stability of its 7- and 9-α-D-Ribofuranosides

Abstract

Ribosylation of 3-methylguanine la was investigated by enzymatic and chemical methods. Compound la did not act as a substrate for purine nucleoside phosphorylase. N-2-Protected 3-methylguanines 4 and 6 underwent exclusive N-7 glycosylation by fusion and chloromercury methods to give 5 and 7. Fully acetylated 7-α-D-ribofuranoside 5 was also obtained by thermal transglycosylation of the corresponding 9-α-D-ribofuranoside 9. The reverse isomerization 5 → 9 did not occur. The differences in the relative stability towards acidic hydrolysis between 7- and 9-(α-D-ribofuranosyl)-3-methylguanines are distinctly higher than those described so far for the other 7-9 isomeric nucleosides.     

Differences in the Substrate Specificities and Active-Site Structures of Two α-L-Fucosidases (Glycoside Hydrolase Family 29) from Bacteroides thetaiotaomicron

Recent studies suggest that α-L-fucosidases of glycoside hydrolase family 29 can be divided into two subfamilies based on substrate specificity and phylogenetic clustering. To explore the validity of this classification, we enzymatically characterized two structure-solved α-L-fucosidases representing the respective subfamilies. Differences in substrate specificities are discussed in relation to differences in active-site structures between the two enzymes.     

Flexibility of 3′,5′ Deoxyribonucleooside Diphosphates

Abstract

In 3′,5′ deoxyribonucleoside diphosphates, in addition to the nature of the base and the sugar puckering, there are six single bond rotations. However, from the analysis of crystal structure data on the constituents of nucleic acids, only three rotational angles, that are about glycosyl bond, about C4′-C5′ and about C3′-O3′ bonds, are flexible. For a given sugar puckering and a base, potential energy calculations using non-bonded, electrostatic and torsional functions were carried out by varying the three torsion angles. The energies are represented as isopotential energy surfaces. Since the availability of the real-time color graphics, it is possible to analyse these isopotential energy surfaces. The calculations were carried out for C3′ exo and C3′ endo puckerings for deoxyribose and also for four bases. These calculations throw more light not only on the allowed regions for the three rotational angles but also on the relationships among them. The dependence of base and the puckering of the sugar on these rotational angles and thereby the flexibility of the 3′,5′ deoxyribonucleoside diphosphates is discussed. From our calculations, it is now possible to follow minimum energy path for interconversion among various conformers.