Identification, cloning and characterization of a novel 47 kDa murine PKA C subunit homologous to human and bovine Cβ2

Background  

SCF ubiquitin ligases target numerous proteins for ubiquitin dependent proteolysis, including p27 and cyclin E. SCF and other cullin-RING ligases (CRLs) are regulated by the ubiquitin-like protein Nedd8 that covalently modifies the cullin subunit. The removal of Nedd8 is catalyzed by the Jab1/MPN domain metalloenzyme (JAMM) motif within the Csn5 subunit of the Cop9 Signalosome.     

The fission yeast COP9/signalosome is involved in cullin modification by ubiquitin-related Ned8p

Background

The function of the fission yeast cullins Pcu1p and Pcu4p requires modification by the ubiquitin-related peptide Ned8p. A recent report by Lyapina et al. shows that the COP9/signalosome (CSN), a multifunctional eight subunit complex, regulates Ned8p modification of Pcu1p. Disruption of caa1/csn1, which encodes subunit 1 of the putative S. pombe CSN, results in accumulation of Pcu1p exclusively in the modified form. However, it remained unclear whether this reflects global control of all cullins by the entire CSN complex.

Results

We demonstrate that multiple CSN subunits control Ned8p modification of Pcu3p, another fission yeast cullin, which, in complex with the RING domain protein Pip1p, forms a ubiquitin ligase that functions in cellular stress response. Pcu3p is modified by Ned8p on Lys 729 and accumulates exclusively in the neddylated form in cells lacking the CSN subunits 1, 3, 4, and 5. These CSN subunits co-elute with Pcu3p in gel filtration fractions corresponding to ～ 550 kDa and specifically bind both native and Ned8p-modified Pcu3p in vivo. While CSN does not influence the subcellular localization of Pcu3p, Pcu3p-associated in vitro ubiquitin ligase activity is stimulated in the absence of CSN.

Conclusions

Taken together, our data suggest that CSN is a global regulator of Ned8p modification of multiple cullins and potentially other proteins involved in cellular regulation.     

p42MAPK-mediated phosphorylation of xEIAP/XLX in <Emphasis Type="Italic">Xenopus</Emphasis> cytostatic factor-arrested egg extracts

Background  

BIR family proteins are evolutionarily conserved anti-apoptotic molecules. One member of Xenopus BIR family proteins, xEIAP/XLX, is a weak apoptosis inhibitor and rapidly degraded in a cell-free apoptotic execution system derived from interphase egg extracts. However, unfertilized eggs are naturally arrested at the metaphase of meiosis II by the concerted activities of Mos-MEK-p42MAPK-p90Rsk kinase cascade (cytostatic factor pathway) and many mitotic kinases. Previous studies suggest that cytostatic factor-arrested egg extracts are more resistant to spontaneous apoptosis than interphase egg extracts in a p42MAPK-dependent manner. We tested whether xEIAP/XLX might be phosphorylated in cytostatic factor-arrested egg extracts, and also examined whether xEIAP/XLX could be functionally regulated by phosphorylation.     

An experimental NMR and computational study of 4-quinolones and related compounds

Abstract  

We report the synthesis and structural study of eight compounds, either quinolin-4(1H)-ones or quinolines. Tautomerism as well as (E) → (Z) and rotational isomerism were studied both experimentally (¹H and ¹³C NMR) and theoretically [B3LYP/6-311++G(d,p)].     

A novel human NatA Nα-terminal acetyltransferase complex: hNaa16p-hNaa10p (hNat2-hArd1)

Background  

Protein acetylation is among the most common protein modifications. The two major types are post-translational N^ε-lysine acetylation catalyzed by KATs (Lysine acetyltransferases, previously named HATs (histone acetyltransferases) and co-translational N^α-terminal acetylation catalyzed by NATs (N-terminal acetyltransferases). The major NAT complex in yeast, NatA, is composed of the catalytic subunit Naa10p (N alpha acetyltransferase 10 protein) (Ard1p) and the auxiliary subunit Naa15p (Nat1p). The NatA complex potentially acetylates Ser-, Ala-, Thr-, Gly-, Val- and Cys- N-termini after Met-cleavage. In humans, the homologues hNaa15p (hNat1) and hNaa10p (hArd1) were demonstrated to form a stable ribosome associated NAT complex acetylating NatA type N-termini in vitro and in vivo.     

Identification of sites phosphorylated by the vaccinia virus B1R kinase in viral protein H5R

Background  

Vaccinia virus gene B1R encodes a serine/threonine protein kinase. In vitro this protein kinase phosphorylates ribosomal proteins Sa and S2 and vaccinia virus protein H5R, proteins that become phosphorylated during infection. Nothing is known about the sites phosphorylated on these proteins or the general substrate specificity of the kinase. The work described is the first to address these questions.     

Dictyostelium cells bind a secreted autocrine factor that represses cell proliferation

Background  

Mycobacterium tuberculosis, an intracellular pathogen encounters redox stress throughout its life inside the host. In order to protect itself from the redox onslaughts of host immune system, M. tuberculosis appears to have developed accessory thioredoxin-like proteins which are represented by ORFs encoding WhiB-like proteins. We have earlier reported that WhiB1/Rv3219 is a thioredoxin like protein of M. tuberculosis and functions as a protein disulfide reductase. Generally thioredoxins have many substrate proteins. The current study aims to identify the substrate protein(s) of M. tuberculosis WhiB1.     

Geometry and force constant determination from correlated wave functions for polyatomic molecules: Ground states of H2O and CH2

Ab initio calculations including electron correlation are reported for the water and methylene molecules as a function of geometry. A large contracted gaussian basis set is used and the multiconfiguration wave functions, optimized by the iterative natural orbital procedure, include 277 and 617 configurations for H₂O and CH₂ respectively. The method of selecting configurations, yielding first-order wave functions, is discussed in some detail. For H₂O, the SCF geometry is r=0,942 Å, =105,8°, the correlated result is r=0,968 Å, =103,2°, and the experimental r=0,957 Å, =104,5°. The water stretching force constants, in millidynes/Å, are 8,72 (SCF), 8,75 (CI), and 8,4 (experiment). Bending force constants are 0,88 (SCF), 0,83 (CI), and 0,76 (experiment). For methylene the SCF geometry is r=1,072 Å, =129,5°, while the result from first-order wave functions is r=1,088 Å, =134°. The predicted CH₂ force constants are 6,16 (SCF) and 6,13 (CI) for stretching and 0,44 (SCF) and 0,33 (CI) for bending.

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Zusammenfassung Es wird über ab intito-Rechnungen mit Berücksichtigung der Elektronenkorrelation berichtet, die an Wasser- und Methylenmolekülen als Funktion der Geometrie durchgeführt worden sind. Dazu benutzt man einen großen kontrahierten Gauß-Basissatz. Die Multikonfigurationswellenfunktionen, die unter Benutzung von natürlichen Orbitalen nach der iterativen Prozedur optimiert werden, enthalten für H₂O 277 Konfigurationen und für CH₂ 617. Die Auswahlmethode, die zu Wellenfunktionen 1. Ordnung führt, wird diskutiert. Im Falle des Wassers erhält man die SCF-Geometrie zu r=0,942 Å, =105,8°, das korrelierte Resultat ist: r=0,968 Å, =103,2° und das experimentelle r=0,957 Å, =104,5°. Für Wasser ergeben sich die Valenzkraftkonstanten (in Millidyn Å^–1) 8,72 (SCF), 8,75 (CI) und 8,4 (Experiment). Die Deformationskonstanten sind 0,88 (SCF), 0,83 (CI) und 0,76 (Experiment). Im Falle des Methylens ist die SCF-Geometrie r=1,072 Å, =129,5°, während man mit Wellenfunktionen 1. Ordnung r=1,088 Å und =134° erhält. Die CH₂-Kraftkonstanten werden für die Valenzschwingung zu 6,16 (SCF) und 6,13 (CI) bzw. für die Deformationsschwingung zu 0,44 (SCF) und 0,33 (CI) vorausgesagt.

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Work performed under the auspices of the U.S. Atomic Energy Commision.

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Supported by the grants from the Research Corporation and the University of California Committee on Research.     

Comparison of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> isocitrate dehydrogenases (ICD-1 and ICD-2) reveals differences in coenzyme affinity,oligomeric state,pH tolerance and phylogenetic affiliation

Background  

M.tb icd-1 and M.tb icd-2, have been identified in the Mycobacterium tuberculosis genome as probable isocitrate dehydrogenase (ICD) genes. Earlier we demonstrated that the two isoforms can elicit B cell response in TB patients and significantly differentiate TB infected population from healthy, BCG-vaccinated controls. Even though immunoassays suggest that these proteins are closely related in terms of antigenic determinants, we now show that M.tb icd-1 and M.tb icd-2 code for functional energy cycle enzymes and document the differences in their biochemical properties, oligomeric assembly and phylogenetic affiliation.     

The isoflavone glycoside ofPiptanthus nanus M. Pop.

Summary Ononin (7-D-glucosyloxy-4-methoxyisoflavone) has been isolated from the aerial parts of the Central Asiatic plantPiptanthus nanus M. Pop.; consequently,P. nanus is the second species of theLeguminosae family containing 7-hydroxy-4-methoxyisoflavone (formononetin) in the form of a glucoside. Ononin has also been found in the aerial parts of a Central Asiatic species of restharrow,Ononis antiquorum.Khimiya prirodnykh soedinenii, Vol. 1, No. 1, pp. 70–72, 1965     

Silencing of KIF14 interferes with cell cycle progression and cytokinesis by blocking the p27Kip1 ubiquitination pathway in hepatocellular carcinoma

Although it has been suggested that kinesin family member 14 (KIF14) has oncogenic potential in various cancers, including hepatocellular carcinoma (HCC), the molecular mechanism of this potential remains unknown. We aimed to elucidate the role of KIF14 in hepatocarcinogenesis by knocking down KIF14 in HCC cells that overexpressed KIF14. After KIF14 knockdown, changes in tumor cell growth, cell cycle and cytokinesis were examined. We also examined cell cycle regulatory molecules and upstream Skp1/Cul1/F-box (SCF) complex molecules. Knockdown of KIF14 resulted in suppression of cell proliferation and failure of cytokinesis, whereas KIF14 overexpression increased cell proliferation. In KIF14-silenced cells, the levels of cyclins E1, D1 and B1 were profoundly decreased compared with control cells. Of the cyclin-dependent kinase inhibitors, the p27^Kip1 protein level specifically increased after KIF14 knockdown. The increase in p27^Kip1 was not due to elevation of its mRNA level, but was due to inhibition of the proteasome-dependent degradation pathway. To explore the pathway upstream of this event, we measured the levels of SCF complex molecules, including Skp1, Skp2, Cul1, Roc1 and Cks1. The levels of Skp2 and its cofactor Cks1 decreased in the KIF14 knockdown cells where p27^Kip1 accumulated. Overexpression of Skp2 in the KIF14 knockdown cells attenuated the failure of cytokinesis. On the basis of these results, we postulate that KIF14 knockdown downregulates the expression of Skp2 and Cks1, which target p27^Kip1 for degradation by the 26S proteasome, leading to accumulation of p27^Kip1. The downregulation of Skp2 and Cks1 also resulted in cytokinesis failure, which may inhibit tumor growth. To the best of our knowledge, this is the first report that has identified the molecular target and oncogenic effect of KIF14 in HCC.     

Thermophile-specific proteins: the gene product of <Emphasis Type="Italic">aq_1292</Emphasis> from <Emphasis Type="Italic">Aquifex aeolicus</Emphasis> is an NTPase

Background  

To identify thermophile-specific proteins, we performed phylogenetic patterns searches of 66 completely sequenced microbial genomes. This analysis revealed a cluster of orthologous groups (COG1618) which contains a protein from every thermophile and no sequence from 52 out of 53 mesophilic genomes. Thus, COG1618 proteins belong to the group of thermophile-specific proteins (THEPs) and therefore we here designate COG1618 proteins as THEP1s. Since no THEP1 had been analyzed biochemically thus far, we characterized the gene product of aq_1292 which is THEP1 from the hyperthermophilic bacterium Aquifex aeolicus (aaTHEP1).     

Semiempirical calculations on triplet and doublet states

Restricted open-shell SCF calculations are carried out on triplet states of electron systems and doublet states of some of their ions. The results are compared with the ones obtained by limited configuration interaction and by the use of Koopman's theorem. For some examples open-shell SCF wavefunctions are expanded into linear combinations of Slater determinants representing configurations built from closed-shell SCF orbitals. This allows a more detailed comparison of the different methods of calculation.

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Zusammenfassung Berechnungen nach der beschränkten SCF Methode für offene Schalen werden an Triplettzuständen von -Elektronensystemen und Dublettzuständen einiger ihrer Ionen ausgeführt. Die Resultate werden mit denjenigen verglichen, welche die beschränkte Konfigurationswechselwirkung und der Satz von Koopmans liefern. Die SCF Wellenfunktionen für offene Schalen werden, für gewisse Beispiele, in Linearkombinationen von Slater-Determinanten entwickelt, welche aus SCF Orbitalen für geschlossene Schalen aufgebaut sind und verschiedene Konfigurationen darstellen. Dies erlaubt einen eingehenderen Vergleich der verschiedenen Berechnungsmethoden.

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Résumé Des calculs selon la méthode SCF avec restriction pour les couches ouvertes sont effectués sur les états triplets de systèmes d'électrons et sur les états doublets de certains de leurs ions. Les résultats sont comparés à ceux obtenus par la méthode d'interáction de configurations limitée et par l'emploi du théorème de Koopmans. Pour certains exemples les fonctions SCF à couches ouvertes sont développées en combinaison linéaire de déterminants de Slater représentant des configurations bâties à partir d'orbitales S.C.F. de couches fermées. Cela permet une comparaison plus détaillée des différentes méthodes de calcul.

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Presented in parts at the Theoretical Chemistry Symposium in Vienna, March 1967.     

Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificity

Background  

Escherichia coli MutY (EcMutY) reduces mutagenesis by removing adenines paired with guanines or 7,8-dihydro-8-oxo-guanines (8-oxoG). V45 and Q182 of EcMutY are considered to be the key determinants of adenine specificity. Both residues are spatially close to each other in the active site and are conserved in MutY family proteins but not in Methanobacterium thermoautotrophicum Mig.MthI T/G mismatch DNA glycosylase (A50 and L187 at the corresponding respective positions).     

Prion protein insertional mutations increase aggregation propensity but not fiber stability

Background  

Mutations in the PRNPgene account for ~15% of all prion disease cases. Little is understood about the mechanism of how some of these mutations in PRNPcause the protein to aggregate into amyloid fibers or cause disease. We have taken advantage of a chimeric protein system to study the oligopeptide repeat domain (ORD) expansions of the prion protein, PrP, and their effect on protein aggregation and amyloid fiber formation. We replaced the ORD of the yeast prion protein Sup35p with that from wild type and expanded ORDs of PrP and compared their biochemical properties in vitro. We previously determined that these chimeric proteins maintain the [PSI⁺] yeast prion phenotype in vivo. Interestingly, we noted that the repeat expanded chimeric prions seemed to be able to maintain a stronger strain of [PSI ⁺] and convert from [psi ^-] to [PSI ⁺] with a much higher frequency. In this study we have attempted to understand the biochemical properties of these chimeric proteins and to establish a system to study the properties of the ORD of PrP both in vivoand in vitro.     

Investigation of the chaperone function of the small heat shock protein — AgsA

Background  

A small heat shock protein AgsA was originally isolated from Salmonella enterica serovar Typhimurium. We previously demonstrated that AgsA was an effective chaperone that could reduce the amount of heat-aggregated proteins in an Escherichia coli rpoH mutant. AgsA appeared to promote survival at lethal temperatures by cooperating with other chaperones in vivo. To investigate the aggregation prevention mechanisms of AgsA, we constructed N- or C-terminal truncated mutants and compared their properties with wild type AgsA.     

Dimerization and enzymatic activity of fungal 17β-hydroxysteroid dehydrogenase from the short-chain dehydrogenase/reductase superfamily

Background  

17β-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus (17β-HSDcl) is a member of the short-chain dehydrogenase/reductase (SDR) superfamily. SDR proteins usually function as dimers or tetramers and 17β-HSDcl is also a homodimer under native conditions.     

Computational strategy for intrinsically disordered protein ligand design leads to the discovery of p53 transactivation domain I binding compounds that activate the p53 pathway

Intrinsically disordered proteins or intrinsically disordered regions (IDPs) have gained much attention in recent years due to their vital roles in biology and prevalence in various human diseases. Although IDPs are perceived as attractive therapeutic targets, rational drug design targeting IDPs remains challenging because of their conformational heterogeneity. Here, we propose a hierarchical computational strategy for IDP drug virtual screening (IDPDVS) and applied it in the discovery of p53 transactivation domain I (TAD1) binding compounds. IDPDVS starts from conformation sampling of the IDP target, then it combines stepwise conformational clustering with druggability evaluation to identify potential ligand binding pockets, followed by multiple docking screening runs and selection of compounds that can bind multi-conformations. p53 is an important tumor suppressor and restoration of its function provides an opportunity to inhibit cancer cell growth. TAD1 locates at the N-terminus of p53 and plays key roles in regulating p53 function. No compounds that directly bind to TAD1 have been reported due to its highly disordered structure. We successfully used IDPDVS to identify two compounds that bind p53 TAD1 and restore wild-type p53 function in cancer cells. Our study demonstrates that IDPDVS is an efficient strategy for IDP drug discovery and p53 TAD1 can be directly targeted by small molecules.

A hierarchical computational strategy for IDP drug virtual screening (IDPDVS) was proposed and successfully applied to identify compounds that bind p53 TAD1 and restore wild-type p53 function in cancer cells.