The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin

The grail of protein science is the connection between structure and function. For myoglobin (Mb) this goal is close. Described as only a passive dioxygen storage protein in texts, we argue here that Mb is actually an allosteric enzyme that can catalyze reactions among small molecules. Studies of the structural, spectroscopic, and kinetic properties of Mb lead to a model that relates structure, energy landscape, dynamics, and function. Mb functions as a miniature chemical reactor, concentrating and orienting diatomic molecules such as NO, CO, O2, and H2O2 in highly conserved internal cavities. Reactions can be controlled because Mb exists in distinct taxonomic substates with different catalytic properties and connectivities of internal cavities.

Genetic, structural, and molecular insights into the function of ras of complex proteins domains

Ras of complex proteins (ROC) domains were identified in 2003 as GTP binding modules in large multidomain proteins from Dictyostelium discoideum. Research into the function of these domains exploded with their identification in a number of proteins linked to human disease, including leucine-rich repeat kinase 2 (LRRK2) and death-associated protein kinase 1 (DAPK1) in Parkinson’s disease and cancer, respectively. This surge in research has resulted in a growing body of data revealing the role that ROC domains play in regulating protein function and signaling pathways. In this review, recent advances in the structural informa- tion available for proteins containing ROC domains, along with insights into enzymatic function and the integration of ROC domains as molecular switches in a cellular and organismal context, are explored.

Effects of advanced glycation end-products (AGEs) on retinal pigment epithelial (RPE) cells lysosomal function:implications for age-related macular degeneration (AMD)

Purpose: RPE lysosomal dysfunction is a major contributor to AMD pathogenesis. Controlled activity of a major class of RPE proteinases, the cathepsins, is crucial in maintaining correct lysosomal function. Advanced glycation end-products (AGEs) accumulate in the Bruch’s membrane (BM) with age, impacting critical RPE functions and in turn, contributing to the development of AMD. The aim of this study was to assess the effect of AGEs on lysosomal function by analysing the expression, processing and activity of the cysteine proteinases cathepsins B, L and S, and the aspartic proteinase cathepsin D. Methods: ARPE-19 cells were cultured on AGE-containing BM mimics (matrigel) for 14 days and compared to untreated substrate. Expression levels and intracellular processing of cathepsins B, D, L and S, were assessed by qPCR and immunoblotting of cell lysates. Lysosomal activity was investigated using multiple activity assays specific to each of the analysed cathepsins. Statistical analysis was performed using the Student’s independent T-test. Results: AGE exposure produced a 36% decrease in cathepsin L activity when compared to non-treated controls (p=0.02, n= 3) although no significant changes were observed in protein expression/processing under these conditions. Both the pro and active forms of cathepsin S decreased by 40% (p=0.04) and 74% (p=0.004), respectively (n=3). In contrast, the active form of the cathepsin D increased by 125% (p=0.005, n= 4). However, no changes were observed in the activity levels of both cathepsins S and D. In addition, cathepsin B expression, processing and activity also remained unaltered following AGE exposure. Conclusions: AGEs accumulation in the extracellular matrix, a phenomenon associated with the natural aging process of the BM, attenuates the expression, intracellular processing and activity of specific lysosomal effectors. Altered enzymatic function may impair important lysosomal processes such as endocytosis, autophagy and phagocytosis of photoreceptor outer segments, each of which may influence the age-related dysfunction of the RPE and subsequently, AMD pathogenesis.

Alteração da atividade enzimática em organismos aquáticos por poluentes de origem agrícola: uma abordagem geral e sobre a suscetibilidade da fosfatase ácida

The input of agrochemicals in the aquatic compartment can results in biochemical injuries for living organisms. In this context, the knowledge of alterations of enzymatic activities due the presence of agriculture pollutants contributes for the elucidation of the mechanisms of toxicity, implementation of economic methods for monitoring purposes and establishment of maximum allowed concentrations. In the present work, the above considerations are discussed, and data concerning changes in enzymatic function by pesticides and fertilizer contaminants are reviewed. Also, we focused on the acid phosphatase due its susceptibility to several pollutants and diversity in cellular functions.

Clostridium difficile toxin-induced inflammation and intestinal injury are mediated by the inflammasome.

BACKGROUND & AIMS: Clostridium difficile-associated disease (CDAD) is the leading cause of nosocomial diarrhea in the United States. C difficile toxins TcdA and TcdB breach the intestinal barrier and trigger mucosal inflammation and intestinal damage. The inflammasome is an intracellular danger sensor of the innate immune system. In the present study, we hypothesize that TcdA and TcdB trigger inflammasome-dependent interleukin (IL)-1beta production, which contributes to the pathogenesis of CDAD. METHODS: Macrophages exposed to TcdA and TcdB were assessed for IL-1beta production, an indication of inflammasome activation. Macrophages deficient in components of the inflammasome were also assessed. Truncated/mutated forms of TcdB were assessed for their ability to activate the inflammasome. The role of inflammasome signaling in vivo was assessed in ASC-deficient and IL-1 receptor antagonist-treated mice. RESULTS: TcdA and TcdB triggered inflammasome activation and IL-1beta secretion in macrophages and human mucosal biopsy specimens. Deletion of Nlrp3 decreased, whereas deletion of ASC completely abolished, toxin-induced IL-1beta release. TcdB-induced IL-1beta release required recognition of the full-length toxin but not its enzymatic function. In vivo, deletion of ASC significantly reduced toxin-induced inflammation and damage, an effect that was mimicked by pretreatment with the IL-1 receptor antagonist anakinra. CONCLUSIONS: TcdA and TcdB trigger IL-1beta release by activating an ASC-containing inflammasome, a response that contributes to toxin-induced inflammation and damage in vivo. Pretreating mice with the IL-1 receptor antagonist anakinra afforded the same level of protection that was observed in ASC-/- mice. These data suggest that targeting inflammasome or IL-1beta signaling may represent new therapeutic targets in the treatment of CDAD.

Alteração da atividade enzimática em organismos aquáticos por poluentes de origem agrícola: uma abordagem geral e sobre a suscetibilidade da fosfatase ácida

The input of agrochemicals in the aquatic compartment can results in biochemical injuries for living organisms. In this context, the knowledge of alterations of enzymatic activities due the presence of agriculture pollutants contributes for the elucidation of the mechanisms of toxicity, implementation of economic methods for monitoring purposes and establishment of maximum allowed concentrations. In the present work, the above considerations are discussed, and data concerning changes in enzymatic function by pesticides and fertilizer contaminants are reviewed. Also, we focused on the acid phosphatase due its susceptibility to several pollutants and diversity in cellular functions.

Caractérisation de la fonction de la protéine cellulaire p80/UAF1 dans la réplication du génome du virus du papillome humain

Le virus du papillome humain (VPH) est l’agent étiologique du cancer du col utérin, ainsi que d’autre néoplasies anogénitales et des voies aérodigestives supérieures. La réplication de son génome d’ADN double brin est assurée par les protéines virales E1 et E2, de concert avec la machinerie cellulaire de réplication. E1 assure le déroulement de l’ADN en aval de la fourche de réplication, grâce à son activité hélicase, et orchestre la duplication du génome viral. Nos travaux antérieurs ont démontré que le domaine N-terminal de E1 contient un motif de liaison à la protéine cellulaire p80/UAF1 qui est hautement conservé chez tous les VPH anogénitaux. L’intégrité de ce motif est essentielle au maintien de l’épisome viral. Les travaux présentés dans cette thèse ont d’abord déterminé que le motif de liaison à UAF1 n’est pas requis pour l’assemblage du pré-réplisome viral, mais important pour la réplication subséquente de l’ADN du VPH. Nous avons constaté qu’en présence de E1 et E2, UAF1 est relocalisé dans des foyers nucléaires typiques de sites de réplication du virus et qu’en outre, UAF1 s’associe physiquement à l’origine de réplication du VPH. Nous avons aussi déterminé que l’inhibition du recrutement de UAF1 par la surexpression d’un peptide dérivé de E1 (N40) contenant le motif de liaison à UAF1 réduit la réplication de l’ADN viral. Cette observation soutient le modèle selon lequel UAF1 est relocalisé par E1 au réplisome pour promouvoir la réplication de l’ADN viral. UAF1 est une protéine à domaine WD40 n’encodant aucune activité enzymatique et présumée exploiter des interactions protéine-protéine pour accomplir sa fonction. Nous avons donc investigué les protéines associées à UAF1 dans des cellules du col utérin et avons détecté des interactions avec les enzymes de déubiquitination USP1, USP12 et USP46, ainsi qu’avec la phosphatase PHLPP1. Nous avons établi que E1 forme un complexe ternaire avec UAF1 et n’importe laquelle des USP associés : USP1, USP12 ou USP46. Ces USP sont relocalisés au noyau par E1 et s’associent à l’ADN viral. De plus, l’activité enzymatique des USP est essentielle à la réplication optimale du génome viral. Au contraire, PHLPP1 ne forme pas de complexe avec E1, puisque leurs interactions respectives avec UAF1 sont mutuellement exclusives. PHLPP1 contient un peptide de liaison à UAF1 homologue à celui de E1. Ce peptide dérivé de PHLPP1 (P1) interagit avec le complexe UAF1-USP et, similairement au peptide N40, antagonise l’interaction E1-UAF1. Incidemment, la surexpression du peptide P1 inhibe la réplication de l’ADN viral. La génération de protéines chimériques entre P1 et des variants de E1 (E1Δ) défectifs pour l’interaction avec UAF1 restaure la capacité de E1Δ à interagir avec UAF1 et USP46, ainsi qu’à relocaliser UAF1 dans les foyers nucléaires contenant E1 et E2. Ce recrutement artificiel de UAF1 et des USP promeut la réplication de l’ADN viral, un phénotype dépendant de l’activité déubiquitinase du complexe. Globalement, nos travaux suggèrent que la protéine E1 du VPH interagit avec UAF1 afin de recruter au réplisome un complexe de déubiquitination dont l’activité est importante pour la réplication de l’ADN viral.

Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery

The enzyme dihydroorotate dehydrogenase (DHODH) has been suggested as a promising target for the design of trypanocidal agents. We report here the discovery of novel inhibitors of Trypanosoma cruzi DHODH identified by a combination of virtual screening and ITC methods. Monitoring of the enzymatic reaction in the presence of selected ligands together with structural information obtained from X-ray crystallography analysis have allowed the identification and validation of a novel site of interaction (S2 site). This has provided important structural insights for the rational design of T cruzi and Leishmania major DHODH inhibitors. The most potent compound (1) in the investigated series inhibits TcDHODH enzyme with K(i)(app) value of 19.28 mu M and possesses a ligand efficiency of 0.54 kcal mol(-1) per non-H atom. The compounds described in this work are promising hits for further development. (C) 2010 Elsevier Masson SAS. All rights reserved.

Structure, genomic DNA typing, and kinetic characterization of the D allozyme of placental alkaline phosphatase (PLAP/ALPP)

The D allozyme of placental alkaline phosphatase (PLAP) displays enzymatic properties at variance with those of the common PLAP allozymes. We have deduced the amino acid sequence of the PLAP D allele by PCR cloning of its gene, ALPP Two coding substitutions were found in comparison With the cDNA of the common PLAP F allele, i.e., 692C>G and 1352A>G, which translate into a P209R and E429G substitution. A single nucleotide primer extension (SNuPE) assay was developed using PCR primers that enable the amplification of a 1.9 kb PLAP fragment. Extension primers were then used on this PCR fragment to detect the 692C>G and 1352A>G substitution. The SNuPE assay on these two nucleotide substitutions enabled us to distinguish the PLAP F and D alleles from the PLAP S/I alleles. Functional studies on the D allozyme were made possible by constructing and expressing a PLAP D cDNA, i.e., [Arg209, Gly429] PLAP, into wildtype Chinese hamster ovary cells. We determined the k(cat) and K-m, of the PLAP S, F. and D allozymes using the non,physiological substrate p-nitrophenylphosphate at an optimal pH (9.8) as well as two physiological substrates, i.e., pyridoxal-5'-phosphate and inorganic pyrophosphate at physiological pH (7.5). We found that the biochemical properties of the D allozyme of PLAP are significantly different from those of the common PLAP allozymes. These biochemical findings suggest that a suboptimal enzymatic function by the PLAP D allozyme may be the basis for the apparent negative selective pressure of the PLAP D allele. The development of the SNuPE assay will enable us to test the hypothesis that the PLAP D allele is subjected to intrauterine selection by examining genomic DNA from statistically informative population samples. Hum Mutat 19:258-267, 2002. (C) 2002 Wiley-Liss, Inc.

Funzioni della subunità θ e del dominio PHP della subunità α nel core catalitico della DNA polimerasi III di Escherichia coli

Il core catalitico della DNA polimerasi III, composto dalle tre subunità α, ε e θ, è il complesso minimo responsabile della replicazione del DNA cromosomiale in Escherichia coli. Nell'oloenzima, α ed ε possiedono rispettivamente un'attività 5'-3' polimerasica ed un'attività 3'-5' esonucleasica, mentre θ non ha funzioni enzimatiche. Il presente studio si è concentrato sulle regioni del core che interagiscono direttamente con ε, ovvero θ (interagente all'estremità N-terminale di ε) e il dominio PHP di α (interagente all'estremità C-terminale di ε), delle quali non è stato sinora identificato il ruolo. Al fine di assegnare loro una funzione sono state seguite tre linee di ricerca parallele. Innanzitutto il ruolo di θ è stato studiato utilizzando approcci ex-vivo ed in vivo. I risultati presentati in questo studio mostrano che θ incrementa significativamente la stabilità della subunità ε, intrinsecamente labile. Durante gli esperimenti condotti è stata anche identificata una nuova forma dimerica di ε. Per quanto la funzione del dimero non sia definita, si è dimostrato che esso è attivamente dissociato da θ, che potrebbe quindi fungere da suo regolatore. Inoltre, è stato ritrovato e caratterizzato il primo fenotipo di θ associato alla crescita. Per quanto concerne il dominio PHP, si è dimostrato che esso possiede un'attività pirofosfatasica utilizzando un nuovo saggio, progettato per seguire le cinetiche di reazione catalizzate da enzimi rilascianti fosfato o pirofosfato. L'idrolisi del pirofosfato catalizzata dal PHP è stata dimostrata in grado di sostenere l'attività polimerasica di α in vitro, il che suggerisce il suo possibile ruolo in vivo durante la replicazione del DNA. Infine, è stata messa a punto una nuova procedura per la coespressione e purificazione del complesso α-ε-θ

Der enzymatische und anti-oxidative Mechanismus des anti-atherogenen Enzyms Paraoxonase-2

Das humane Enzym PON2 ist in eine Vielzahl pathophysiologischer Prozesse involviert und ist durch zwei Funktionen gekennzeichnet - eine enzymatische Laktonase-Aktivität und eine anti-oxidative Aktivität. Durch die Laktonase-Aktivität hydrolysiert PON2 vorwiegend das bakterielle Signalmolekül 3oxoC12. PON2 ist als Bestandteil des angeborenen Immunsystems anzusehen und trägt wahrscheinlich zur Immunabwehr gegen Infektionen mit den human-pathogenen Pseudomonas aeruginosa Bakterien bei. Durch die anti-oxidative Aktivität vermindert PON2 oxidative Schäden und verringert redox-abhängige pro-apoptotische Stimulation. Diese einzigartige Funktion von PON2 ist jedoch ambivalent zu betrachten, da hohe PON2-Spiegel zwar Arteriosklerose reduzieren können, aber im Verdacht stehen Tumorzellen zu stabilisieren.rnIn dieser Arbeit wurden die noch unbekannten Mechanismen und der Zusammenhang der enzymatischen und der anti-oxidativen Aktivität analysiert. In diesem Rahmen wurde gezeigt, dass PON2 spezifisch die Superoxidfreisetzung an Komplex I und III der Atmungskette in der inneren Mitochondrienmembran reduzieren kann. PON2 veränderte dabei weder die Aktivitäten der Superoxiddismutasen noch die Cytochrom C-Expression. Weiterhin konnte in dieser Arbeit erstmals gezeigt werden, dass PON2 O2- nicht direkt abbaut, sondern vielmehr dessen Bildung verhindert. Diese Erkenntnisse implizieren, dass PON2 die anti-oxidative Aktivität über eine Beeinflussung des Quinon-Pools vermittelt. Anhand von verschiedenen Punktmutationen konnte gezeigt werden, dass die Histidinreste-114 und -133 für die Laktonase-Aktivität essentiell sind. Weiterhin wurden die Glykosylierungsstellen von PON2 identifiziert und gezeigt, dass die Glykosylierung, nicht aber der natürliche Polymorphismus Ser/Cys311 für die Laktonase-Aktivität von Bedeutung ist. Von besonderer Bedeutung ist, dass keine dieser Mutationen die anti-oxidative Aktivität beeinflusste, wodurch erstmals die Unabhängigkeit der beiden Funktionen von PON2 gezeigt werden konnte. rnEs war bekannt, dass PON2 gegen intrinsische und ER-Stress-induzierte Apoptose schützt. Die Spezifität der anti-oxidativen / anti-apoptotischen Wirkung wurde hier an einem weiteren pathophysiologischen Modell untersucht. 7-Ketocholesterol (7-KC) ist der Hauptbestandteil des pro-arteriosklerotischen oxLDL und verursacht in Zellen des Gefäßsystems ER-Stress, oxidativen Stress und Apoptose. Unerwarteterweise konnte PON2 Endothelzellen nicht gegen den 7-KC-induzierten Zelltod schützen. Mehrere unabhängige experimentelle Ansätze belegen, dass 7-KC in Endothelzellen im Gegensatz zu Gefäßmuskelzellen den Zelltod über Autophagie und nicht über ER-Stress oder intrinsische Apoptose bewirkt. Weiterhin führt 7-KC, wie auch 3oxoC12 und Thapsigargin zu einem Abbau der PON2-mRNA, die über die 5’UTR der PON2-mRNA vermittelt wird. Diese Arbeit vermittelt detaillierte mechanistische Einsichten in die Funktionen von PON2, die für ihre Rolle bei Arteriosklerose, in der körpereigenen Immunabwehr und bei Krebs entscheidend sind.rn

Cattle immunized against the pathogenic L-α-glycerol-3-phosphate oxidase of Mycoplasma mycoides subs. mycoides fail to generate neutralizing antibodies and succumb to disease on challenge

The membrane-associated enzyme L-α-glycerol-3-phosphate oxidase (GlpO) of Mycoplasma mycoides subs. mycoides (Mmm), the causal agent of contagious bovine pleuropneumonia (CBPP) has been identified as a virulence factor responsible for the release of toxic by-products such as H2O2 that mediate host cell injury. Since CBPP pathogenesis is based on host inflammatory reactions, we have determined the capacity of recombinant GlpO to generate in vivo protective responses against challenge in immunized cattle. We also investigated whether sera raised against recombinant GlpO in cattle and mice inhibit production of H2O2 by Mmm. Immunization of cattle with recombinant GlpO did not protect against challenge with a virulent strain of Mmm. Further, although both murine and bovine antisera raised against recombinant GlpO detected recombinant and native forms of GlpO in immunoblot assays with similar titres, only murine antibodies could neutralize GlpO enzymatic function. The data raise the possibility that Mmm has adapted to evade potential detrimental antibody responses in its definitive host.

Purification and cloning of the novel phosphoprotein copine III and characterization of its associated kinase activity

The copines, named and first described by Creutz et al. (1998), comprise a two C2 domain-containing protein family that can aggregate phosphatidylserine membranes in a calcium-dependent manner. Although no enzymatic function has been attributed to copines, their carboxyl terminus shows homology to the A domain found in integrins that allows binding of magnesium ions. The secondary structure of A domains resembles a Rossmann fold, which can bind dinucleotides and is present in a number of intracellular enzymes. Due to a crossreacting activity of Mik b 1, an antibody to the IL-2R b chain, we were able to serendipitously clone human copine III (CIII). CIII is 65% identical to copine I (CI) and the 5 kb CIII transcript is expressed ubiquitously as determined by a multitissue Northern blot. A polyclonal antibody generated against the carboxyl terminus of CIII recognized CIII in immunoblots and immunoprecipitations. Phosphorylation of CIII was observed on serine and threonine residues, as determined by phosphoamino acid analysis. ^ Experiments were designed to determine whether or not any enzymatic activity, specifically kinase activity, was intrinsic to or associated with CIII. In vitro and in gel kinase assays were performed using transfected HA-tagged CI and CIII, immunoprecipitated endogenous CIII and purified endogenous CIII. The exogenous substrate MBP was phosphorylated in all in vitro kinase assays containing CIII protein purification and column chromatography expertise with me. ^

Subcellular localization and tissue specific expression of amidase 1 from Arabidopsis thaliana

Amidase 1 (AMI1) from Arabidopsis thaliana converts indole-3-acetamide (IAM), into indole-3-acetic acid (IAA). AMI1 is part of a small isogene family comprising seven members in A. thaliana encoding proteins which share a conserved glycine- and serine-rich amidase-signature. One member of this family has been characterized as an N-acylethanolamine-cleaving fatty acid amidohydrolase (FAAH) and two other members are part of the preprotein translocon of the outer envelope of chloroplasts (Toc complex) or mitochondria (Tom complex) and presumably lack enzymatic activity. Among the hitherto characterized proteins of this family, AMI1 is the only member with indole-3-acetamide hydrolase activity, and IAM is the preferred substrate while N-acylethanolamines and oleamide are not hydrolyzed significantly, thus suggesting a role of AMI1 in auxin biosynthesis. Whereas the enzymatic function of AMI1 has been determined in vitro, the subcellular localization of the enzyme remained unclear. By using different GFP-fusion constructs and an A. thaliana transient expression system, we show a cytoplasmic localization of AMI1. In addition, RT-PCR and anti-amidase antisera were used to examine tissue specific expression of AMI1 at the transcriptional and translational level, respectively. AMI1-expression is strongest in places of highest IAA content in the plant. Thus, it is concluded that AMI1 may be involved in de novo IAA synthesis in A. thaliana.