The Experts below are selected from a list of 48 Experts worldwide ranked by ideXlab platform
Giovanna Musco - One of the best experts on this subject based on the ideXlab platform.
-
Exploring PHD Fingers and H3K4me0 Interactions with Molecular Dynamics Simulations and Binding Free Energy Calculations: AIRE-PHD1, a Comparative Study
PLOS ONE, 2012Co-Authors: Dimitrios Spiliotopoulos, Andrea Spitaleri, Giovanna MuscoAbstract:PHD fingers represent one of the largest families of epigenetic readers capable of decoding post-translationally modified or unmodified histone H3 tails. Because of their direct involvement in human pathologies they are increasingly considered as a potential therapeutic target. Several PHD/histone-peptide structures have been determined, however relatively little information is available on their dynamics. Studies aiming to characterize the dynamic and energetic determinants driving histone peptide recognition by epigenetic readers would strongly benefit from computational studies. Herein we focus on the dynamic and energetic characterization of the PHD finger subclass specialized in the recognition of histone H3 peptides unmodified in position K4 (H3K4me0). As a case study we focused on the first PHD finger of Autoimmune Regulator Protein (AIRE-PHD1) in complex with H3K4me0. PCA analysis of the covariance matrix of free AIRE-PHD1 highlights the presence of a “flapping” movement, which is blocked in an open conformation upon binding to H3K4me0. Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes. MM/PBSA calculations have also been applied to the energetic analysis of other PHD fingers recognizing H3K4me0. In this case we observe excellent correlation between computed and experimental binding free energies. Overall calculations show that H3K4me0 recognition by PHD fingers relies on compensation of the electrostatic and polar solvation energy terms and is stabilized by non-polar interactions.
-
nmr structure of the first phd finger of Autoimmune Regulator Protein aire1 insights into Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy apeced disease
Journal of Biological Chemistry, 2005Co-Authors: M J Bottomley, Gunter Stier, Danilo Pennacchini, Gaelle Legube, B Simon, Asifa Akhtar, Michael Sattler, Giovanna MuscoAbstract:Mutations in the Autoimmune Regulator Protein AIRE1 cause a monogenic autosomal recessively inherited disease: Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). AIRE1 is a multidomain Protein that harbors two plant homeodomain (PHD)-type zinc fingers. The first PHD finger of AIRE1 is a mutational hot spot, to which several pathological point mutations have been mapped. Using heteronuclear NMR spectroscopy, we determined the solution structure of the first PHD finger of AIRE1 (AIRE1-PHD1), and characterized the peptide backbone mobility of the domain. We performed a conformational analysis of pathological AIRE1-PHD1 mutants that allowed us to rationalize the structural impact of APECED-causing mutations and to identify an interaction site with putative Protein ligands of the AIRE1-PHD1 domain. The structure unequivocally exhibits the canonical PHD finger fold, with a highly conserved tryptophan buried inside the structure. The PHD finger is stabilized by two zinc ions coordinated in an interleaved (cross-brace) scheme. This zinc coordination resembles RING finger domains, which can function as E3 ligases in the ubiquitination pathway. Based on this fold similarity, it has been suggested that PHD fingers might also function as E3 ligases, although this hypothesis is controversial. At variance to a previous report, we could not find any evidence that AIRE1-PHD1 has an intrinsic E3 ubiquitin ligase activity, nor detect any direct interaction between AIRE1-PHD1 and its putative cognate E2. Consistently, we show that the AIRE1-PHD1 structure is clearly distinct from the RING finger fold. Our results point to a function of the AIRE1-PHD1 domain in Protein-Protein interactions, which is impaired in some APECED mutations.
M J Bottomley - One of the best experts on this subject based on the ideXlab platform.
-
nmr structure of the first phd finger of Autoimmune Regulator Protein aire1 insights into Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy apeced disease
Journal of Biological Chemistry, 2005Co-Authors: M J Bottomley, Gunter Stier, Danilo Pennacchini, Gaelle Legube, B Simon, Asifa Akhtar, Michael Sattler, Giovanna MuscoAbstract:Mutations in the Autoimmune Regulator Protein AIRE1 cause a monogenic autosomal recessively inherited disease: Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). AIRE1 is a multidomain Protein that harbors two plant homeodomain (PHD)-type zinc fingers. The first PHD finger of AIRE1 is a mutational hot spot, to which several pathological point mutations have been mapped. Using heteronuclear NMR spectroscopy, we determined the solution structure of the first PHD finger of AIRE1 (AIRE1-PHD1), and characterized the peptide backbone mobility of the domain. We performed a conformational analysis of pathological AIRE1-PHD1 mutants that allowed us to rationalize the structural impact of APECED-causing mutations and to identify an interaction site with putative Protein ligands of the AIRE1-PHD1 domain. The structure unequivocally exhibits the canonical PHD finger fold, with a highly conserved tryptophan buried inside the structure. The PHD finger is stabilized by two zinc ions coordinated in an interleaved (cross-brace) scheme. This zinc coordination resembles RING finger domains, which can function as E3 ligases in the ubiquitination pathway. Based on this fold similarity, it has been suggested that PHD fingers might also function as E3 ligases, although this hypothesis is controversial. At variance to a previous report, we could not find any evidence that AIRE1-PHD1 has an intrinsic E3 ubiquitin ligase activity, nor detect any direct interaction between AIRE1-PHD1 and its putative cognate E2. Consistently, we show that the AIRE1-PHD1 structure is clearly distinct from the RING finger fold. Our results point to a function of the AIRE1-PHD1 domain in Protein-Protein interactions, which is impaired in some APECED mutations.
Caterina Cancrini - One of the best experts on this subject based on the ideXlab platform.
-
the possible implication of the s250c variant of the Autoimmune Regulator Protein in a patient with autoimmunity and immunodeficiency in silico analysis suggests a molecular pathogenic mechanism for the variant
Gene, 2014Co-Authors: Emanuele Bellacchio, Alessia Palma, Stefania Corrente, Francesco Di Girolamo, Helen E Kemp, Gigliola Di Matteo, Laura Comelli, Rita Carsetti, Simona Cascioli, Caterina CancriniAbstract:Abstract Autoimmunity can develop from an often undetermined interplay of genetic and environmental factors. Rare forms of Autoimmune conditions may also result from single gene mutations as for Autoimmune polyendocrinopathy-candidiasis–ectodermal dystrophy, an autosomal recessive disease associated with mutated forms of the Autoimmune Regulator gene. It was proposed that genetic variability in the Autoimmune Regulator locus, in particular heterozygous loss-of-function mutations, might favor the development of organ-specific autoimmunity by affecting the presentation of self-antigens in the thymus. Indeed, heterozygous mutations of the Autoimmune Regulator gene were reported in patients with organ-specific autoimmunity. Also, in primary immunodeficiencies, a breakdown in central/peripheral tolerance frequently produces association with autoimmunity. The causative link may involve a common genetic background and several gene defects have been identified as putative culprits. We report a unique patient, a 14 year old male from Lazio region, affected by common variable immunodeficiency associated with Autoimmune manifestations (alopecia, onychodystrophy) and heterozygote for the S250C variant located in the SAND domain of the Autoimmune Regulator gene Protein. To our knowledge this is the first report of the S250C variant in a patient bearing this unusual combination of autoimmunity and immunodeficiency. To obtain insights into the possible molecular effects of the S250C variant, we have carried out an in silico analysis of the SAND domain structure of the Autoimmune Regulator Protein. In particular, homology modeling has allowed us to observe that the cysteine introduced by the S250C variant is surrounded by cationic residues, and by means of molecular dynamics simulations together with pK a calculations, we have shown that these residues remain stably proximal to cysteine-250 lowering its pK a and thus conferring high chemical reactivity to the mutated residue. We propose that the enhanced reactivity of cysteine-250, which is likely to impair the Protein function but probably insufficient to produce alone a phenotype as a heterozygous S250C variant due to compensation mechanisms, might become manifest when combined with other genetic/environmental factors. These results can provide the rationale for the patient's unusual phenotype, shedding new light into the pathogenesis of the clinical association of autoimmunity and immunodeficiency.
Jukka Pitkanen - One of the best experts on this subject based on the ideXlab platform.
-
subcellular localization of the Autoimmune Regulator Protein characterization of nuclear targeting and transcriptional activation domain
Journal of Biological Chemistry, 2001Co-Authors: Jukka Pitkanen, Perttu Vahamurto, Kai Krohn, Part PetersonAbstract:Abstract The Autoimmune Regulator (AIRE) gene, defective in the hereditary Autoimmune disease APECED, encodes a transcriptional Regulator Protein. AIRE is expressed in the medullary epithelial cells and monocyte-dendritic cells of the thymus with lower expression in the spleen, fetal liver, and lymph nodes. At the cellular level, AIRE is located in microtubular structures of the cytoskeleton and in discrete nuclear dots resembling ND10 nuclear bodies. We studied the determinants of the targeting of AIRE into these structures. We report here that the N-terminal HSR domain confers localization to the microtubular network whereas the C-terminal region contains a second nuclear localization signal. We also demonstrate that the consensus nuclear localization signal of AIRE is functional and that the HSR domain harbors a nuclear export signal. Accordingly, the nuclear export inhibitor leptomycin B partially inhibits the nuclear export of AIRE. From a functional standpoint, we show that AIRE can activate the interferon β minimal promoter in a transfection assay and demonstrate that the transcriptional activating function of AIRE is mediated by its two plant homeodomain (PHD) zinc fingers.
-
the Autoimmune Regulator Protein has transcriptional transactivating properties and interacts with the common coactivator creb binding Protein
Journal of Biological Chemistry, 2000Co-Authors: Jukka Pitkanen, Perttu Vahamurto, Vassilis Doucas, Thomas Sternsdorf, Toshihiro Nakajima, Satoko Aratani, Kirsten Jensen, Hans Will, Juha OllilaAbstract:Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy, caused by mutations in the Autoimmune Regulator (AIRE) gene, is an autosomal recessive Autoimmune disease characterized by the breakdown of tolerance to organ-specific antigens. The 545 amino acid Protein encoded by AIRE contains several structural motifs suggestive of a transcriptional Regulator and bears similarity to cellular Proteins involved in transcriptional control. me show here that AIRE fused to a heterologous DNA binding domain activates transcription from a reporter promoter, and the activation seen requires the full-length Protein or more than one activation domain. At the structural level AIRE forms homodimers through the NH2-terminal domain, and molecular modeling for this domain suggests a four-helix bundle structure. In agreement, we show that the common transcriptional coactivator CREB-binding Protein (CBP) interacts with AIRE in vitro and in yeast nuclei through the CH1 and CH3 conserved domains. We suggest that the transcriptional transactivation properties of AIRE together with its interaction with CBP might be important in its function as disease-causing mutations almost totally abolish the activation effect. (Less)
Part Peterson - One of the best experts on this subject based on the ideXlab platform.
-
AIRE's CARD Revealed, a New Structure for Central Tolerance Provokes Transcriptional Plasticity
Journal of Biological Chemistry, 2007Co-Authors: Brian J. Ferguson, Part Peterson, Clare E. Alexander, Simona W. Rossi, Ingrid Liiv, Ana Rebane, Catherine L. Worth, Joyce Wong, Martti Laan, Eric J. JenkinsonAbstract:Developing T cells encounter peripheral self-antigens in the thymus in order to delete autoreactive clones. It is now known that the Autoimmune Regulator Protein (AIRE), which is expressed in thymic medullary epithelial cells, plays a key role in regulating the thymic transcription of these peripheral tissue-specific antigens. Mutations in the AIRE gene are associated with a severe multiorgan Autoimmune syndrome (APECED), and Autoimmune reactivities are manifest in AIRE-deficient mice. Functional AIRE Protein is expressed as distinct nuclear puncta, although no structural basis existed to explain their relevance to disease. In addressing the cell biologic basis for APECED, we made the unexpected discovery that an AIRE mutation hot spot lies in a caspase recruitment domain. Combined homology modeling and in vitro data now show how APECED mutations influence the activity of this transcriptional Regulator. We also provide novel in vivo evidence for AIRE's association with a global transcription cofactor, which may underlie AIRE's focal, genome-wide, alteration of the transcriptome.
-
subcellular localization of the Autoimmune Regulator Protein characterization of nuclear targeting and transcriptional activation domain
Journal of Biological Chemistry, 2001Co-Authors: Jukka Pitkanen, Perttu Vahamurto, Kai Krohn, Part PetersonAbstract:Abstract The Autoimmune Regulator (AIRE) gene, defective in the hereditary Autoimmune disease APECED, encodes a transcriptional Regulator Protein. AIRE is expressed in the medullary epithelial cells and monocyte-dendritic cells of the thymus with lower expression in the spleen, fetal liver, and lymph nodes. At the cellular level, AIRE is located in microtubular structures of the cytoskeleton and in discrete nuclear dots resembling ND10 nuclear bodies. We studied the determinants of the targeting of AIRE into these structures. We report here that the N-terminal HSR domain confers localization to the microtubular network whereas the C-terminal region contains a second nuclear localization signal. We also demonstrate that the consensus nuclear localization signal of AIRE is functional and that the HSR domain harbors a nuclear export signal. Accordingly, the nuclear export inhibitor leptomycin B partially inhibits the nuclear export of AIRE. From a functional standpoint, we show that AIRE can activate the interferon β minimal promoter in a transfection assay and demonstrate that the transcriptional activating function of AIRE is mediated by its two plant homeodomain (PHD) zinc fingers.