76 results on '"Facchiano AM"'
Search Results
2. Applicazione dei bio-processoria DNA allo studio su scala genomica delle modificazioni di espressione genica che caratterizzano il ciclo replicativo cellulare indotto da Estrogeni
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CICATIELLO L, CANCEMI M, FACCHIANO AM, BRESCIANI F, WEISZ A., ALTUCCI, Lucia, Cicatiello, L, Altucci, Lucia, Cancemi, M, Facchiano, Am, Bresciani, F, and Weisz, A.
- Published
- 2000
3. Molecular and structural characterisation of a macrophage migration inhibitory factor from sea bass (Dicentrarchus labrax L.)
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Buonocore F, Randelli E, Facchiano AM, Pallavicini A, Modonut M, and Scapigliati G
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- 2010
4. 3D Modelling of Three Pro-Inflammatory Molecules in Selected Fish Species
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Costantini S, Facchiano AM, Randelli E, Casani D, Scapigliati G, and Buonocore F.
- Abstract
The inflammatory response is the reaction of all Metazoan organisms to pathogen invasion that initiates when pathogenderived molecules are recognized by specific pattern recognition receptors expressed mainly on cells of the innate immune system. The successive expression of pro-inflammatory cytokines and chemokines limits pathogen spread, and attracts and activates immune cells to help in the elimination of the invaders. In this paper we focused on the analyses of the 3D structures of three pro-inflammatory molecules (interleukin-1?, tumor necrosis factor-?, interleukin-8) from selected Teleost fish species (Oncorhynchus mykiss, Dicentrarchus labrax, Chionodraco hamatus) generated using as template models those of experimental homologous proteins. These structures were discussed with the aim to investigate the differences between them and mammalian counterparts and, moreover, to verify the presence of the structural requirements for their biological activities, known mainly in mammals.
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- 2010
5. Functional hypothesis on miraculin' sweetness by a molecular dynamics approach
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Paladino A, Colonna G, Facchiano AM, and Costantini S.
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- 2010
6. Molecular characterisation and structural analysis of an interferon homologue in sea bass (Dicentrarchus labrax L.)
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Casani D, Randelli E, Costantini S, Facchiano AM, Zou J, Martin S, Secombes CJ, Scapigliati G, and Buonocore F
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- 2009
7. Evolution of cell-mediated immune defences: Cloning and structural characterisation of the T cell receptor beta chain from the icefish Chionodraco hamatus (Perciformes: Channichthyidae)
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Buonocore F, Randelli E, Scala V, Belardinelli MC, Casani D, Facchiano AM, Costantini S, and Scapigliati G.
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- 2009
8. Human Prion Protein Helices: Studying their Stability by Molecular Dynamics Simulations
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Costantini S and Facchiano AM.
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- 2009
9. Prediction of the protein structural class by specific peptide frequencies
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Costantini S and Facchiano AM.
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- 2009
10. Molecular modelling of miraculin: Structural analyses and functional hypotheses
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Paladino A, Costantini S, Colonna G, and Facchiano AM.
- Abstract
Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies.
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- 2008
11. CALCOM: A software for calculating the center of mass of proteins
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Costantini S, Paladino A, and Facchiano AM.
- Abstract
The center of mass of a protein is an artificial point useful for detecting important and simple features of proteins structure, shape and association.CALCOM is a software which calculates the center of mass of a protein, starting from PDB protein structure files. In the case of protein complexes and of protein-small ligand complexes, the position of protein residues or of ligand atoms respect to each protein subunit can be evaluated, as well as the distance among the center of mass of the protein subunits, in order to compare different conformations and evaluate the relative motion of subunits. AVAILABILITY: THE SERVICE IS AVAILABLE AT THE URL: http://bioinformatica.isa.cnr.it/CALCOM/.
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- 2008
12. Molecular modelling of co-receptor CD8alphaalpha and its complex with MHC class I and T-cell receptor in sea bream (Sparus aurata)
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Costantini S, Buonocore F, and Facchiano AM
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- 2008
13. How could the protein-protein complexes be modelled?
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Costantini S, Colonna G, and Facchiano AM
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- 2007
14. A geometrical model for generating mainly-alpha protein conformations
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Mucherino A, Di Serafino D, D'apuzzo M, Costantini S, Facchiano AM., and Colonna G
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- 2007
15. FASMA: A Service to Format and Analyze Sequences in Multiple Alignments
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Costantini S, Colonna G, and Facchiano AM.
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- 2007
16. Globularity criteria to evaluate the structural quality of modeled proteins
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Costantini S, Facchiano AM, and Colonna G
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- 2007
17. Amino acid propensities for secondary structures
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Costantini S, Colonna G, and Facchiano AM
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- 2006
18. Comparative modelling of human galactose-1-phosphate uridylyltransferase and of its galactosemia-related mutant Q188R: A molecular explanation of the structural effects of the mutation
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Marabotti, Anna and Facchiano, Am
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- 2004
19. Identification of a novel domain of fibroblast growth factor- 2 controlling its angiogenic properties
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Facchiano A, Russo K, Facchiano AM, De Marchis F, Facchiano F, Ribatti D, Aguzzi MS, and Capogrossi MC
- Subjects
peptide attivo ,Fibroblast growth factor 2 ,molecular docking ,molecular modelling - Abstract
Fibroblast growth factor 2 (FGF-2) is a potent factor modulating the activity of many cell types. Its dimerization and binding to high affinity receptors are considered to be necessary steps to induce FGF receptor phosphorylation and signaling activation. A structural analysis was carried out and a region encompassing residues 48-58 of human FGF-2 was identified, as potentially involved in FGF-2 dimerization. A peptide (FREG-48-58) derived from this region strongly and specifically inhibited FGF-2 induced proliferation and migration of primary bovine aorta endothelial cells (BAEC) in vitro, and markedly reduced FGF-2-dependent angiogenesis in two distinct in vivo assays. To further investigate the role of region 48-58, a polyclonal antibody raised against FREG-(48-58) was tested and was found to block FGF-2 action in vitro. Human FGF-2 has three histidine residues, one falling within the region 48-58. Chemical modification of histidine residues blocked FGF-2 activity and FREG-(48-58) inhibitory effect in vitro, indicating that histidine residues, in particular the one within FREG-(48-58) region, play a crucial role in the observed activity. Additional experiments showed that FREG-(48-58) specifically interacted with FGF-2, impaired FGF-2-interaction with itself, with heparin and with FGF receptor 1, and inhibited FGF-2-induced receptor phosphorylation and FGF-2 internalization. These data indicate for the first time that region 48-58 of FGF-2 is a functional domain controlling FGF-2 activity.
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- 2003
20. Modelling the three-dimensional structure of a sugar binding protein from a thermophilic organism: analysis on stability and sugar binding simulation
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Marabotti A, DAuria S, Rossi M, and Facchiano AM
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- 2003
21. Platelet-derived growth factor-BB and basic fibroblast growth factor directly interact in vitro with high affinity
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Russo K, Ragone R, Facchiano AM, Capogrossi MC, and Facchiano A.
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simulazioni molecolari ,basic fibroblast growth factor (bFGF) ,molecular graphics ,platelet-derived growth factor-BB (PDGF-BB) ,molecular docking - Abstract
Platelet-derived growth factor-BB (PDGF-BB) and basic fibroblast growth factor (bFGF) are potent growth factors active on many cell types. The present study indicates that they directly interact in vitro. The interaction was investigated with overlay experiments, surface plasmon resonance experiments, and solid-phase immunoassays by immobilizing one factor or the other and by steady-state fluorescence analysis. The interaction observed was specific, dose-dependent, and saturable, and the bFGF/PDGF-BB binding stoichiometry was found to be 2:1. K(D)(1) for the first step equilibrium and the overall K(D) values were found to be in the nanomolar and in the picomolar range, respectively. Basic FGF/PDGF-BB interaction was strongly reduced as a function of time of PDGF-BB proteolysis. Furthermore, docking analysis suggested that the PDGF-BB region interacting with bFGF may overlap, at least in part, with the PDGF-BB receptor-binding site. This hypothesis was supported by surface plasmon resonance experiments showing that an anti-PDGF-BB antibody, known to inhibit PDGF-BB binding with its receptor, strongly reduced bFGF/PDGF-BB interaction, whereas a control antibody was ineffective. According to these data, the observed bFGF.PDGF-BB complex formation might explain, at least in part, previous observations showing that PDGF-BB chemotactic and mitogenic activity on smooth muscle cells are strongly inhibited in the presence of bFGF.
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- 2002
22. Identification of a novel functional domain of basic fibroblast growth factor
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Facchiano A, Russo K, Facchiano AM, De Marchis F., Facchiano F., Ribatti D., and Capogrossi MC.
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- 2002
23. Integrating Mutation Data and Structural Analysis of the p53 Tumour-Suppressor Protein
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Martin ACR, Facchiano AM, Cuff AL, Hernandez-Boussard T, Olivier M, Hainaut P, and Thornton JM
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p53 ,relational database ,structural analysis ,DNA binding ,transcription factor - Abstract
TP53 encodes p53, which is a nuclear phosphoprotein with cancer-inhibiting properties. In response to DNA damage, p53 is activated and mediates a set of antiproliferative responses including cell-cycle arrest and apoptosis. Mutations in the TP53 gene are associated with more than 50% of human cancers, and 90% of these affect p53-DNA interactions, resulting in a partial or complete loss of transactivation functions. These mutations affect the structural integrity and/or p53-DNA interactions, leading to the partial or complete loss of the protein's function. We report here the results of a systematic automated analysis of the effects of p53 mutations on the structure of the core domain of the protein. We found that 304 of the 882 (34.4%) distinct mutations reported in the core domain can be explained in structural terms by their predicted effects on protein folding or on protein-DNA contacts. The proportion of "explained" mutations increased to 55.6% when substitutions of evolutionary conserved amino acids were included. The automated method of structural analysis developed here may be applied to other frequently mutated gene mutations such as dystrophin, BRCA1, and G6PD.
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- 2002
24. Helix stabilizing factors and stabilization of thermophilic proteins: an X-ray based study
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Facchiano, AM, Colonna, G, and Ragone, R
- Abstract
We have compared the X-ray structures of 13 thermophilic proteins with their mesophilic homologues, in order to bring out differences in the stability of helices. The energy terms of a helix-coil transition algorithm were used to evaluate helix stability. Helices of thermophilic proteins are more stable than the mesophilic homologues in 69% of cases. This is due mainly to intrinsic helical propensities of amino acids, whereas minor effects are linked to main chain H-bonds, side chain-side chain interactions, capping motifs and charge-dipole effects. Furthermore, the frequency of 10 helix stabilizing factors recognized by appropriate sequence patterns was evaluated. The only factor occurring significantly in the thermostable proteins was the lack of beta branched residues. Other factors do not show a definite trend, although their occurrence in proteins is believed to be important for stability. This is discussed in the light of protein engineering applications.Keywords: helix stability/secondary structure/thermophily/thermostability/protein engineering
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- 1998
25. Modeling the 3D structure of wheat subtilisin/chymotrypsin inhibitor (WSCI). Probing the reactive site with two susceptible proteinases by time-course analysis and molecular dynamics simulations
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Antimo Di Maro, Simone Di Gennaro, Daniela Panichi, Augusto Parente, Elia Poerio, Susan Costantini, Angelo Facchiano, Angela Chambery, Facchiano, Am, Costantini, S, DI MARO, A, Panichi, D, Chambery, A, Parente, A, DI GENNARO, S, and Poerio, E
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Models, Molecular ,Protein Conformation ,Molecular Sequence Data ,Clinical Biochemistry ,Protein Data Bank (RCSB PDB) ,Biochemistry ,Protein structure ,Recombinant WSCI ,Peptide bond ,Amino Acid Sequence ,Subtilisins ,Binding site ,Molecular Biology ,Peptide sequence ,Chromatography, High Pressure Liquid ,Plant Proteins ,Binding Sites ,Chymotrypsin ,Sequence Homology, Amino Acid ,biology ,Proteinase-inhibitor complex ,Chemistry ,Hydrolysis ,MALDI-TOF mass spectrometry ,Subtilisin ,Recombinant Proteins ,Reactive site ,Kinetics ,Molecular simulation ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,biology.protein ,Electrophoresis, Polyacrylamide Gel ,Proteinase inhibitor - Abstract
Comparative modeling and time-course hydrolysis experiments have been applied to investigate two enzyme-inhibitor complexes formed between the wheat subtilisin-chymotrypsin inhibitor (WSCI) and two susceptible proteinases. WSCI represents the first case of a wheat protein inhibitor active against animal chymotrypsins and bacterial subtilisins. The model was created using as template structure that of the CI-2A inhibitor from barley (PDB code: 2CI2), which shares 87% sequence identity with WSCI. Under these conditions of high similarity, the comparative modeling approach can be successfully applied. We predicted the WSCI 3D model and used it to investigate enzyme-inhibitor complex systems. Experimental observations indicated that chymotrypsin, but not subtilisin, in addition to cleavage at the primary reactive site Met48-Glu49, is able to hydrolyze a second peptide bond between Phe58 and Val59. Here, we report on cleavage of the peptide bond at the inhibitor's reactive site (Met48-Glu49) determined using time-course hydrolysis experiments; the same event was investigated for both subtilisin/WSCI and chymotrypsin/WSCI complexes using molecular dynamics simulations. The molecular details of the initial inhibitor-enzyme interactions, as well as of the changes observed during the simulations, allow us to speculate on the different fates of the two WSCI-proteinase complexes.
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- 2006
26. Alteration in the ubiquitin structure and function in the human lens: a possible mechanism of senile cataractogenesis
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S. Lilla, Angelo Facchiano, T Libondi, Patrizia Colicchio, Paola Stiuso, Giovanni Colonna, Pasquale Ferranti, P., Stiuso, T., Libondi, A. M., Facchiano, P., Colicchio, Ferranti, Pasquale, S., Lilla, G., Colonna, Stiuso, Paola, Libondi, Teodosio, Facchiano, Am, Colicchio, P, Ferranti, P, Lilla, S, and Colonna, G.
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Models, Molecular ,cataratta senile ,Biophysics ,Protein degradation ,Biology ,Peptide Mapping ,Biochemistry ,Cataract ,Lens protein ,Western blot ,Ubiquitin ,Structural Biology ,Lens, Crystalline ,Genetics ,medicine ,Humans ,Molecular Biology ,Chromatography, High Pressure Liquid ,Aged ,degradazione delle proteine ,chemistry.chemical_classification ,Structure modification ,medicine.diagnostic_test ,ubiquitina ,Cell Biology ,Amino acid ,Structure and function ,Molecular Weight ,Senile cataract ,chemistry ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,biology.protein ,Normal lens - Abstract
High-performance liquid chromatography purification followed by mass spectrometry analyses highlighted that human senile cataractous lens includes a 8182 Da species which is absent in the normal lens, whereas a 8566/8583 Da species is present in both lenses. Western blot analysis identified both species as ubiquitin. The species at lower molecular weight is a shorter form due to the cleavage of the C-terminal residues 73-76. As it is the last amino acid of ubiquitin which is involved in the protein degradation mechanism, we suggest that this structure modification compromises the function of ubiquitin and consequently the physiologically occurring degradation of the lens proteins. © 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved. High-performance liquid chromatography purification followed by mass spectrometry analyses highlighted that human senile cataractous lens includes a 8182 Da species which is absent in the normal lens, whereas a 8566/8583 Da species is present in both lenses. Western blot analysis identified both species as ubiquitin. The species at lower molecular weight is a shorter form due to the cleavage of the C-terminal residues 73-76. As it is the last amino acid of ubiquitin which is involved in the protein degradation mechanism, we suggest that this structure modification compromises the function of ubiquitin and consequently the physiologically occurring degradation of the lens proteins. © 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.
- Published
- 2002
27. Redesigning the reactive site loop of the wheat subtilisin/chymotrypsin inhibitor (WSCI) by site-directed mutagenesis. A protein-protein interaction study by affinity chromatography and molecular modeling
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Susan Costantini, Angelo Facchiano, Antimo Di Maro, Elia Poerio, Augusto Parente, Natalia Bruni, Angela Chambery, Anna Grazia Ficca, Bruni, N, DI MARO, Antimo, Costantini, S, Chambery, Angela, Facchiano, Am, Ficca, Ag, Parente, A, and Poerio, E.
- Subjects
Models, Molecular ,Spectrometry, Mass, Electrospray Ionization ,Mutant ,Molecular Sequence Data ,E/I complexe ,Biochemistry ,Chromatography, Affinity ,Affinity chromatography ,Computer Simulation ,Amino Acid Sequence ,WSCI mutants ,Site-directed mutagenesis ,WSCI mutant ,Peptide sequence ,Triticum ,Plant Proteins ,chemistry.chemical_classification ,Chymotrypsin ,biology ,E/I complexes ,Subtilisin ,General Medicine ,Fusion protein ,Recombinant Proteins ,Enzyme ,chemistry ,Time-course proteolysi ,ESI Q-TOF mass spectrometry ,biology.protein ,Mutagenesis, Site-Directed ,Electrophoresis, Polyacrylamide Gel ,Time-course proteolysis ,Protein Binding - Abstract
A site-directed mutagenesis strategy was employed to obtain four mutants of wheat subtilisin/chymotrypsin inhibitor (WSCI), with the aim to produce inactive forms of this protein. The mutants were expressed in Escherichia coli as fusion proteins and, after the tag removal, were purified to homogeneity. Three mutants, containing a single mutation at the sequence positions 49 or 50, were named E49S, E49P and Y50G, respectively. These mutants exhibited anti-subtilisin activities comparable to that of the wild type protein; instead, anti-chymotrypsin activity was detectable only for the mutant E49S. A fourth mutant (M48P-E49G), containing a double amino acid substitution at the inhibitor reactive site (P1-P1′), was inactive against both subtilisin and chymotrypsin. In order to investigate the interactions between the putative susceptible enzymes and the mutated forms of WSCI, we performed time-course hydrolysis experiments by incubating samples of the mutants with subtilisin-agarose and chymotrypsin-agarose, respectively. These experiments yielded information on the E/I complex formation, as well as on the timing of the cleavage pattern of some of these mutants. Molecular modeling studies were carried out with the 3D models of the mutants and of their putative complexes with subtilisin and chymotrypsin. In terms of inter- and intra-chain H-bond networks, the observations made for each theoretical E/I complex were found to be fully coherent with experimental data (kinetic and time-course hydrolysis) and supplied specific modalities of interaction of each mutant with the enzyme counterpart. © 2009 Elsevier Masson SAS. All rights reserved.
- Published
- 2008
28. Identification of a β-lactoglobulin lactosylation site
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Giacomino Randazzo, Attilio Visconti, Vincenzo Fogliano, Alberto Ritieni, Angelo Facchiano, Simona Maria Monti, Giovanni Colonna, Fogliano, Vincenzo, Monti, Sm, Visconti, A, Randazzo, Giacomino, Facchiano, Am, Colonna, G, and Ritieni, Alberto
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Models, Molecular ,Whey protein ,Glycosylation ,Hot Temperature ,Lactosylation ,Molecular Sequence Data ,Biophysics ,Lactose ,Lactoglobulins ,Amadori compound ,β-Lactoglobulin ,Biochemistry ,Mass Spectrometry ,symbols.namesake ,chemistry.chemical_compound ,Residue (chemistry) ,Structural Biology ,Amadori rearrangement ,medicine ,Trypsin ,Thermal treatment ,Amino Acid Sequence ,Liquid chromatography-mass spectrometry ,Molecular Biology ,Chromatography, High Pressure Liquid ,Chromatography ,Binding Sites ,Chemistry ,Lysine ,Lactose binding ,Milk Proteins ,Peptide Fragments ,Maillard reaction ,Milk ,symbols ,medicine.drug - Abstract
Thermal treatment of milk leads to non-enzymatic glycosylation of proteins through Maillard reaction. Free NH2 groups of basic amino acids react with the reducing carbonyl group of lactose forming the so-called Amadori products. Electrospray mass spectrometry analysis shows that β-lactoglobulin (β-LG), the major whey protein, undergoes lactosylation under industrial thermal treatment. In order to investigate the specificity of reactive sites for lactose binding the analysis of trypsin hydrolysates of β-LG isolated from different industrial milks was performed. Results demonstrate that Lys-100 is a preferential lactosylation site of β-LG during industrial milk treatment. These results were confirmed by an analysis of the three-dimensional model of the protein which showed that Lys-100 had the highest solvent accessibility and proximity to another amino group making Lys-100 the best candidate to lactosylation. Lys-47, previously identified by other authors, showed a good proximity to another Lys residue, but an intermediate level of exposition to solvent. Copyright (C) 1998 Elsevier Science B.V.
- Published
- 1998
29. Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A)
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Angelo Facchiano, Monica Marra, Gaia Giuberti, Michele Caraglia, Alberto Abbruzzese, Giovanni Colonna, Maria Luisa Chiusano, Paola Stiuso, A. M., Facchiano, P., Stiuso, Chiusano, MARIA LUISA, M., Caraglia, G., Giuberti, M., Marra, A., Abbruzzese, G., Colonna, Facchiano, Am, Stiuso, Paola, Chiusano, Ml, Caraglia, Michele, Giuberti, G, Marra, M, Abbruzzese, A, Colonna, G., Facchiano, A., Stiuso, P., Caraglia, M., Giuberti, G., Marra, M., and Abbruzzese, A.
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Models, Molecular ,KB CELLS ,Time Factors ,Computer science ,Protein Conformation ,Molecular Sequence Data ,ANGSTROM RESOLUTION ,Bioengineering ,Sequence alignment ,Computational biology ,Biochemistry ,EPIDERMAL GROWTH-FACTOR ,Homology (biology) ,Protein Structure, Secondary ,CELL-PROLIFERATION ,Structure-Activity Relationship ,Protein structure ,Peptide Initiation Factors ,Humans ,Amino Acid Sequence ,Cysteine ,Molecular Biology ,Protein secondary structure ,Consensus of methods ,Multiple sequence alignment ,SECONDARY STRUCTURE PREDICTION ,Sequence Homology, Amino Acid ,Model validation ,Circular Dichroism ,RNA-Binding Proteins ,SITE ,computer.file_format ,EIF4A1 ,Protein Data Bank ,Eukaryotic translation initiation factor 4 gamma ,Protein Structure, Tertiary ,AMINO-ACID ,DEOXYHYPUSINE HYDROXYLASE ,Prediction strategy ,Databases as Topic ,eIF-5A ,HYPUSINE-CONTAINING PROTEIN ,Homology modelling ,TRANSLATION ,computer ,Software ,Biotechnology ,Protein Binding - Abstract
Homology modelling of the human eIF-5A protein has been performed by using a multiple predictions strategy. As the sequence identity between the target and the template proteins is nearly 30%, which is lower than the commonly used threshold to apply with confidence the homology modelling method, we developed a specific predictive scheme by combining different sequence analyses and predictions, as well as model validation by comparison to structural experimental information. The target sequence has been used to find homologues within sequence databases and a multiple alignment has been created. Secondary structure for each single protein has been predicted and compared on the basis of the multiple sequence alignment, in order to evaluate and adjust carefully any gap. Therefore, comparative modelling has been applied to create the model of the protein on the basis of the optimized sequence alignment. The quality of the model has been checked by computational methods and the structural features have been compared to experimental information, giving us a good validation of the reliability of the model and its correspondence to the protein structure in solution. Last, the model was deposited in the Protein Data Bank to be accessible for studies on the structure-function relationships of the human eIF-5A.
30. Role of 'shared epitope' and other citrullination-sites in rheumatoid arthritis and in melanoma.
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D'Arcangelo D, Facchiano A, and Facchiano AM
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- Epitopes, Humans, Melanoma, Arthritis, Rheumatoid, Citrullination
- Published
- 2017
- Full Text
- View/download PDF
31. Transglutaminase type 2 affects cell migration through post-translational modification of platelet-derived growth factor-BB.
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Cordella M, Tabolacci C, Rossi S, Senatore C, Facchiano AM, D'Arcangelo D, Facchiano A, and Facchiano F
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- Becaplermin, Calcium pharmacology, Cell Line, Tumor, Cell Movement drug effects, Enzyme Activation drug effects, GTP-Binding Proteins agonists, Human Umbilical Vein Endothelial Cells, Humans, Neuroglia cytology, Neuroglia metabolism, Protein Glutamine gamma Glutamyltransferase 2, Proto-Oncogene Proteins c-sis pharmacology, Recombinant Proteins metabolism, Recombinant Proteins pharmacology, GTP-Binding Proteins metabolism, Neuroglia drug effects, Protein Processing, Post-Translational, Proto-Oncogene Proteins c-sis metabolism, Transglutaminases metabolism
- Abstract
Migration is a key cellular function with important implications in cell physiology. Impairment of such function is observed in angiogenesis, cancer, central nervous system development, and many other physiological and pathological events. Serum is considered among the most potent physiological chemotactic stimuli. Transglutaminase 2 (TG2) is involved in most of the mentioned processes, suggesting the hypothesis that TG2 may modulate cell movement and chemotaxis by acting on serum factors. Cell biology and biochemistry studies confirmed this hypothesis, showing that human serum contains potent chemotactic signals significantly impaired by activated TG2. Bioinformatics studies indicated that one potent serum factor potential substrate of TG2-dependent transamidation is platelet-derived growth factor-BB (PDGF-BB). Cell biology and immunometric experiments carried out with U87MG human glioma cell line showed that human recombinant PDGF-BB pre-incubated with calcium-activated TG2 lost about 70 % of its chemotactic activity and antigenicity. These data indicate that PDGF-BB is a substrate of TG2-transamidating activity, and such modification may play a key role in the modulation of PDGF's chemotactic features. Further, these findings suggest a novel point of view to study the extracellular functions of TG2 and to understand how protein signals, such as growth factors and cytokines, act in the extracellular space to reach their specific targets.
- Published
- 2017
- Full Text
- View/download PDF
32. PDGFR-alpha inhibits melanoma growth via CXCL10/IP-10: a multi-omics approach.
- Author
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D'Arcangelo D, Facchiano F, Nassa G, Stancato A, Antonini A, Rossi S, Senatore C, Cordella M, Tabolacci C, Salvati A, Tarallo R, Weisz A, Facchiano AM, and Facchiano A
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- Cell Line, Tumor, Cell Proliferation, Endothelial Cells cytology, Gene Expression Profiling methods, Gene Expression Regulation, Neoplastic, Human Umbilical Vein Endothelial Cells, Humans, Melanoma, Oligonucleotide Array Sequence Analysis, Chemokine CXCL10 genetics, Genomics methods, MicroRNAs genetics, Receptor, Platelet-Derived Growth Factor alpha genetics
- Abstract
Melanoma is the most aggressive skin-cancer, showing high mortality at advanced stages. Platelet Derived Growth Factor Receptor-alpha (PDGFR-alpha) potently inhibits melanoma- and endothelium-proliferation and its expression is significantly reduced in melanoma-biopsies, suggesting that melanoma progression eliminates cells expressing PDGFR-alpha. In the present study transient overexpression of PDGFR-alpha in endothelial (HUVEC) and melanoma (SKMel-28, A375, Preyer) human-cells shows strong anti-proliferative effects, with profound transcriptome and miRNome deregulation. PDGFR-alpha overexpression strongly affects expression of 82 genes in HUVEC (41 up-, 41 down-regulated), and 52 genes in SKMel-28 (43 up-, 9 down-regulated). CXCL10/IP-10 transcript showed up to 20 fold-increase, with similar changes detectable at the protein level. miRNA expression profiling in cells overexpressing PDGFR-alpha identified 14 miRNAs up- and 40 down-regulated, with miR-503 being the most down-regulated (6.4 fold-reduction). miR-503, miR-630 and miR-424 deregulation was confirmed by qRT-PCR. Interestingly, the most upregulated transcript (i.e., CXCL10/IP-10) was a validated miR-503 target and CXCL10/IP-10 neutralization significantly reverted the anti-proliferative action of PDGFR-alpha, and PDGFR-alpha inhibition by Dasatinb totally reverted the CXCL10/IP10 induction, further supporting a functional interplay of these factors. Finally, integration of transcriptomics and miRNomics data highlighted several pathways affected by PDGFR-alpha.This study demonstrates for the first time that PDGFR-alpha strongly inhibits endothelial and melanoma cells proliferation in a CXCL10/IP-10 dependent way, via miR-503 down-regulation.
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- 2016
- Full Text
- View/download PDF
33. Tissue transglutaminase activity protects from cutaneous melanoma metastatic dissemination: an in vivo study.
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Facchiano F, D'Arcangelo D, Lentini A, Rossi S, Senatore C, Pannellini T, Tabolacci C, Facchiano AM, Facchiano A, and Beninati S
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- Animals, Case-Control Studies, Cell Line, Tumor, GTP-Binding Proteins, Gene Expression, Humans, Keratinocytes enzymology, Lung Neoplasms secondary, Male, Melanoma, Experimental secondary, Mice, Mice, Inbred C57BL, Neoplasm Transplantation, Protein Glutamine gamma Glutamyltransferase 2, Proteome metabolism, Skin Neoplasms pathology, Transglutaminases genetics, Lung Neoplasms enzymology, Melanoma, Experimental enzymology, Skin Neoplasms enzymology, Transglutaminases metabolism
- Abstract
The role of tissue transglutaminase (TG-2, TGase-2) in cancer development is still a fascinating field of research. The available reports do not elucidate fully its mechanism of action, due to the limitations of in vitro approaches. Therefore, to understand TG-2 role in cancer, we carried out an in vivo study with a more direct approach. TG-2 was in vivo overexpressed in a murine model of melanoma (intravenous injection of B16 melanoma cells in C57BL/6N mice) by means of a plasmid carrying the TG-2 cDNA. The evaluation of the frequency and size of the metastases indicated that the number of melanoma lung foci was more markedly reduced by TG-2 overexpression than the metastatic size. Then, TG-2 overexpressing mice showed a prolonged survival with respect to control mice. Further analyses were carried by means of proteomic analysis of melanoma cell lysates and meta-analysis of published transcriptomic datasets. Proteomic analysis of cell lysates from a human melanoma cell line compared to human keratinocytes showed significant differences in the expression of TG-2 substrates known to be involved in proliferation/differentiation and cancer progression. Taken together, these findings indicate a protective role of TG-2 enzymatic activity in melanoma progression in vivo.
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- 2013
- Full Text
- View/download PDF
34. Redesigning the reactive site loop of the wheat subtilisin/chymotrypsin inhibitor (WSCI) by site-directed mutagenesis. A protein-protein interaction study by affinity chromatography and molecular modeling.
- Author
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Bruni N, Di Maro A, Costantini S, Chambery A, Facchiano AM, Ficca AG, Parente A, and Poerio E
- Subjects
- Amino Acid Sequence, Electrophoresis, Polyacrylamide Gel, Molecular Sequence Data, Plant Proteins chemistry, Protein Binding, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Spectrometry, Mass, Electrospray Ionization, Triticum genetics, Chromatography, Affinity methods, Computer Simulation, Models, Molecular, Mutagenesis, Site-Directed methods, Plant Proteins genetics, Plant Proteins metabolism, Triticum metabolism
- Abstract
A site-directed mutagenesis strategy was employed to obtain four mutants of wheat subtilisin/chymotrypsin inhibitor (WSCI), with the aim to produce inactive forms of this protein. The mutants were expressed in Escherichia coli as fusion proteins and, after the tag removal, were purified to homogeneity. Three mutants, containing a single mutation at the sequence positions 49 or 50, were named E49S, E49P and Y50G, respectively. These mutants exhibited anti-subtilisin activities comparable to that of the wild type protein; instead, anti-chymotrypsin activity was detectable only for the mutant E49S. A fourth mutant (M48P-E49G), containing a double amino acid substitution at the inhibitor reactive site (P1-P1'), was inactive against both subtilisin and chymotrypsin. In order to investigate the interactions between the putative susceptible enzymes and the mutated forms of WSCI, we performed time-course hydrolysis experiments by incubating samples of the mutants with subtilisin-agarose and chymotrypsin-agarose, respectively. These experiments yielded information on the E/I complex formation, as well as on the timing of the cleavage pattern of some of these mutants. Molecular modeling studies were carried out with the 3D models of the mutants and of their putative complexes with subtilisin and chymotrypsin. In terms of inter- and intra-chain H-bond networks, the observations made for each theoretical E/I complex were found to be fully coherent with experimental data (kinetic and time-course hydrolysis) and supplied specific modalities of interaction of each mutant with the enzyme counterpart.
- Published
- 2009
- Full Text
- View/download PDF
35. Platelet-derived growth factor-receptor alpha strongly inhibits melanoma growth in vitro and in vivo.
- Author
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Faraone D, Aguzzi MS, Toietta G, Facchiano AM, Facchiano F, Magenta A, Martelli F, Truffa S, Cesareo E, Ribatti D, Capogrossi MC, and Facchiano A
- Subjects
- Animals, Antigens, Differentiation genetics, Antigens, Differentiation metabolism, Cell Line, Tumor, Cell Proliferation, Flow Cytometry, Gene Expression Regulation, Neoplastic, Humans, In Situ Nick-End Labeling, MAP Kinase Kinase 3 genetics, MAP Kinase Kinase 3 metabolism, Melanoma genetics, Mice, Mitogen-Activated Protein Kinase 12 genetics, Mitogen-Activated Protein Kinase 12 metabolism, Phosphorylation, Protein Array Analysis, Protein Phosphatase 2 genetics, Protein Phosphatase 2 metabolism, Proto-Oncogene Proteins c-jun genetics, Proto-Oncogene Proteins c-jun metabolism, Receptor, Platelet-Derived Growth Factor alpha genetics, Receptors, Immunologic genetics, Receptors, Immunologic metabolism, Skin Neoplasms genetics, Transfection, Melanoma metabolism, Receptor, Platelet-Derived Growth Factor alpha metabolism, Signal Transduction physiology, Skin Neoplasms metabolism
- Abstract
Cutaneous melanoma is the most aggressive skin cancer; it is highly metastatic and responds poorly to current therapies. The expression of platelet-derived growth factor receptors (PDGF-Rs) is reported to be reduced in metastatic melanoma compared with benign nevi or normal skin; we then hypothesized that PDGF-Ralpha may control growth of melanoma cells. We show here that melanoma cells overexpressing PDGF-Ralpha respond to serum with a significantly lower proliferation compared with that of controls. Apoptosis, cell cycle arrest, pRb dephosphorylation, and DNA synthesis inhibition were also observed in cells overexpressing PDGF-Ralpha. Proliferation was rescued by PDGF-Ralpha inhibitors, allowing to exclude nonspecific toxic effects and indicating that PDGF-Ralpha mediates autocrine antiproliferation signals in melanoma cells. Accordingly, PDGF-Ralpha was found to mediate staurosporine cytotoxicity. A protein array-based analysis of the mitogen-activated protein kinase pathway revealed that melanoma cells overexpressing PDGF-Ralpha show a strong reduction of c-Jun phosphorylated in serine 63 and of protein phosphatase 2A/Balpha and a marked increase of p38gamma, mitogen-activated protein kinase kinase 3, and signal regulatory protein alpha1 protein expression. In a mouse model of primary melanoma growth, infection with the Ad-vector overexpressing PDGF-Ralpha reached a significant 70% inhibition of primary melanoma growth (P < .001) and a similar inhibition of tumor angiogenesis. All together, these data demonstrate that PDGF-Ralpha strongly impairs melanoma growth likely through autocrine mechanisms and indicate a novel endogenous mechanism involved in melanoma control.
- Published
- 2009
- Full Text
- View/download PDF
36. Molecular modelling of co-receptor CD8 alpha alpha and its complex with MHC class I and T-cell receptor in sea bream (Sparus aurata).
- Author
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Costantini S, Buonocore F, and Facchiano AM
- Subjects
- Amino Acid Sequence, Animals, CD8 Antigens immunology, Computer Simulation, Histocompatibility Antigens Class I immunology, Immunity, Cellular immunology, Models, Molecular, Molecular Sequence Data, Receptors, Antigen, T-Cell immunology, Sequence Alignment, Thermodynamics, CD8 Antigens chemistry, Histocompatibility Antigens Class I chemistry, Receptors, Antigen, T-Cell chemistry, Sea Bream immunology
- Abstract
T-cells are the main actors of cell-mediated immune defence; they recognize and respond to peptide antigens associated with MHC class I and class II molecules. In this paper, we investigated by molecular modelling methods in the teleost sea bream (Sparus aurata) the interaction among the molecules of the tertiary complex CD8/MHC-I/TCR, which determines the T-cell-mediated immunological response to foreign molecules. First, we predicted the three-dimensional structure of CD8 alpha alpha dimer and MHC-I, and, successively, we simulated the CD8 alpha alpha/MHC-I complex. Finally, the 3D structure of the CD8/MHC-I/TCR complex was simulated in order to investigate the possible changes that can influence TCR signalling events.
- Published
- 2008
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37. A CD4 homologue in sea bass (Dicentrarchus labrax): molecular characterization and structural analysis.
- Author
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Buonocore F, Randelli E, Casani D, Guerra L, Picchietti S, Costantini S, Facchiano AM, Zou J, Secombes CJ, and Scapigliati G
- Subjects
- Animals, Base Sequence, CD4 Antigens metabolism, Computer Simulation, DNA, Complementary genetics, Histocompatibility Antigens Class II chemistry, Humans, Models, Molecular, Molecular Sequence Data, Phylogeny, Protein Structure, Secondary, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Bass immunology, CD4 Antigens chemistry, CD4 Antigens genetics, Structural Homology, Protein
- Abstract
CD4 is a transmembrane glycoprotein fundamental for cell-mediated immunity. Its action as a T cell co-receptor increases the avidity of association between a T cell and an antigen-presenting cell by interacting with portions of the complex between MHC class II and TR molecules. In this paper we report the cDNA cloning, expression and structural analysis of a CD4 homologue from sea bass (Dicentrarchus labrax). The sea bass CD4 cDNA consists of 2071 bp that translates in one reading frame to give the entire molecule containing 480 amino acids. The analysis of the sequence shows the presence of four putative Ig-like domains and that some fundamental structural features, like a disulphide bond in domain D2 and the CXC signalling motif in the cytoplasmic tail, are conserved from sea bass to mammals. Real-time PCR analysis showed that very high levels of CD4 mRNA transcripts are present in thymus, followed by gut and gills. In vitro stimulation of head kidney leukocytes with LPS and PHA-L gave an increase of CD4 mRNA levels after 4h and a decrease after 24h. Homology modelling has been applied to create a 3D model of sea bass CD4 and to investigate its interaction with sea bass MHC-II. The analysis of the 3D complex between sea bass CD4 and sea bass MHC-II suggests that the absence of a disulfide bond in the CD4 D1 domain could make this molecule more flexible, inducing a different conformation and affecting the binding and the way of interaction between CD4 and MHC-II. Our results will add new insights into the sea bass T cell immune responses and will help in the identification of T cell subsets in teleost fishes to better understand the evolution of cell-mediated immunity from fish to mammals.
- Published
- 2008
- Full Text
- View/download PDF
38. Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells.
- Author
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Mutarelli M, Cicatiello L, Ferraro L, Grober OM, Ravo M, Facchiano AM, Angelini C, and Weisz A
- Subjects
- Cell Line, Tumor, Humans, Reproducibility of Results, Sensitivity and Specificity, Biomarkers, Tumor metabolism, Estrogens pharmacology, Gene Expression Profiling methods, Neoplasm Proteins metabolism, Oligonucleotide Array Sequence Analysis methods, Proteome metabolism
- Abstract
Background: Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a 'molecular picture' of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where time influences gene activity and expression. The potential use of the statistical analysis of microarray data in time series has not been fully exploited so far, due to the fact that only few methods are available which take into proper account temporal relationships between samples., Results: We compared here four different methods to analyze data derived from a time course mRNA expression profiling experiment which consisted in the study of the effects of estrogen on hormone-responsive human breast cancer cells. Gene expression was monitored with the innovative Illumina BeadArray platform, which includes an average of 30-40 replicates for each probe sequence randomly distributed on the chip surface. We present and discuss the results obtained by applying to these datasets different statistical methods for serial gene expression analysis. The influence of the normalization algorithm applied on data and of different parameter or threshold choices for the selection of differentially expressed transcripts has also been evaluated. In most cases, the selection was found fairly robust with respect to changes in parameters and type of normalization. We then identified which genes showed an expression profile significantly affected by the hormonal treatment over time. The final list of differentially expressed genes underwent cluster analysis of functional type, to identify groups of genes with similar regulation dynamics., Conclusions: Several methods for processing time series gene expression data are presented, including evaluation of benefits and drawbacks of the different methods applied. The resulting protocol for data analysis was applied to characterization of the gene expression changes induced by estrogen in human breast cancer ZR-75.1 cells over an entire cell cycle.
- Published
- 2008
- Full Text
- View/download PDF
39. ESBRI: a web server for evaluating salt bridges in proteins.
- Author
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Costantini S, Colonna G, and Facchiano AM
- Abstract
Unlabelled: Salt bridges can play important roles in protein structure and function and have stabilizing and destabilizing effects in protein folding. ESBRI is a software available as web tool which analyses the salt bridges in a protein structure, starting from the atomic coordinates. In the case of protein complexes, the salt bridges between protein chains can be evaluated, as well as those among specific charged amino acids and the different protein subunits, in order to obtain useful information regard the protein-protein interaction., Availability: The service is available at the URL: http://bioinformatica.isa.cnr.it/ESBRI/
- Published
- 2008
- Full Text
- View/download PDF
40. PreSSAPro: a software for the prediction of secondary structure by amino acid properties.
- Author
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Costantini S, Colonna G, and Facchiano AM
- Subjects
- Amino Acid Sequence, Apoproteins chemistry, Computational Biology methods, Databases, Protein, Internet, Myoglobin chemistry, Prions chemistry, Proteins chemistry, Software Design, User-Computer Interface, Amino Acids chemistry, Protein Structure, Secondary, Software
- Abstract
PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/.
- Published
- 2007
- Full Text
- View/download PDF
41. Transamidation of wheat flour inhibits the response to gliadin of intestinal T cells in celiac disease.
- Author
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Gianfrani C, Siciliano RA, Facchiano AM, Camarca A, Mazzeo MF, Costantini S, Salvati VM, Maurano F, Mazzarella G, Iaquinto G, Bergamo P, and Rossi M
- Subjects
- Adolescent, Adult, Amines metabolism, Biopsy, CD4-Positive T-Lymphocytes pathology, Celiac Disease drug therapy, Celiac Disease metabolism, Cell Line, Gliadin adverse effects, Gliadin immunology, HLA-DQ Antigens immunology, HLA-DQ Antigens metabolism, Humans, Interferon-gamma metabolism, Intestinal Mucosa metabolism, Methyl Ethers pharmacology, Methyl Ethers therapeutic use, Middle Aged, Substrate Specificity, Transglutaminases pharmacology, Transglutaminases therapeutic use, CD4-Positive T-Lymphocytes immunology, Celiac Disease immunology, Gliadin metabolism, Intestines immunology, Triticum metabolism
- Abstract
Background & Aims: Celiac disease is characterized by activation of HLA-DQ2/DQ8-restricted intestinal gluten-specific CD4(+) T cells. In particular, gluten becomes a better T-cell antigen following deamidation catalyzed by tissue transglutaminase. To date, the only available therapy is represented by adherence to a gluten-free diet. Here, we examined a new enzyme strategy to preventively abolish gluten activity., Methods: Enzyme modifications of the immunodominant alpha-gliadin peptide p56-68 were analyzed by mass spectrometry, and peptide binding to HLA-DQ2 was simulated by modeling studies. Wheat flour was treated with microbial transglutaminase and lysine methyl ester; gliadin was subsequently extracted, digested, and deamidated. Gliadin-specific intestinal T-cell lines (iTCLs) were generated from biopsy specimens from 12 adult patients with celiac disease and challenged in vitro with different antigen preparations., Results: Tissue transglutaminase-mediated transamidation with lysine or lysine methyl ester of p56-68 or gliadin in alkaline conditions inhibited the interferon gamma expression in iTCLs; also, binding to DQ2 was reduced but not abolished, as suggested by in silico analysis. Lysine methyl ester was particularly effective in abrogating the activity of gliadin. Notably, a block in the response was observed when iTCLs were challenged with gliadin extracted from flour pretreated with microbial transglutaminase and lysine methyl ester., Conclusions: Transamidation of wheat flour with a food-grade enzyme and an appropriate amine donor can be used to block the T cell-mediated gliadin activity. Considering the crucial role of adaptive immunity in celiac disease, our findings highlight the potential of the proposed treatment to prevent cereal toxicity.
- Published
- 2007
- Full Text
- View/download PDF
42. Simulation of conformational changes occurring when a protein interacts with its receptor.
- Author
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Costantini S, Colonna G, and Facchiano AM
- Subjects
- Amino Acid Sequence, Animals, Cytokines metabolism, Databases, Protein, Humans, Hydrogen Bonding, Interleukin-1beta chemistry, Interleukin-1beta metabolism, Mice, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Secondary, Receptors, Cytokine metabolism, Receptors, Interleukin-1 chemistry, Receptors, Interleukin-1 metabolism, Structural Homology, Protein, Thermodynamics, Trout, Computer Simulation, Cytokines chemistry, Models, Molecular, Receptors, Cytokine chemistry
- Abstract
In order to simulate the conformational changes occurring when a protein interacts with its receptor, we firstly evaluated the structural differences between the experimental unbound and bound conformations for selected proteins and created theoretical complexes by replacing, in each experimental complex, the protein-bound with the protein-unbound chain. The theoretical models were then subjected to additional modeling refinements to improve the side chain geometry. Comparing the theoretical and experimental complexes in term of structural and energetic factors is resulted that the refined theoretical complexes became more similar to the experimental ones. We applied the same procedure within an homology modeling experiment, using as templates the experimental structures of human interleukin-1beta (IL-1beta) unbound and bound with its receptor, to build models of the homologous proteins from mouse and trout in unbound and bound conformations and to simulate the interaction with the related receptors. Our results suggest that homology modeling techniques are sensitive to differences between bound and unbound conformations, and that modeling with accuracy the side chains in the complex improves the interaction and molecular recognition. Moreover, our refinement procedure could be used in protein-protein interaction studies and, also, applied in conjunction with rigid-body docking when is not available the protein-bound conformation.
- Published
- 2007
- Full Text
- View/download PDF
43. Evaluation of the structural quality of modeled proteins by using globularity criteria.
- Author
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Costantini S, Facchiano AM, and Colonna G
- Subjects
- Databases, Genetic, Hydrogen Bonding, Molecular Weight, Research Design, Computational Biology methods, Models, Molecular, Protein Conformation, Proteins chemistry, Proteomics methods
- Abstract
Background: The knowledge of the three-dimensional structure of globular proteins is fundamental for a detailed investigation of their functional properties. Experimental methods are too slow for structure investigation on a large scale, while computational prediction methods offer alternatives that are continuously being improved. The international Comparative Assessment of Structure Prediction (CASP), an "a posteriori" evaluation of the quality of theoretical models when the experimental structure becomes available, demonstrates that predictions can be successful as well as unsuccessful, and this suggests the necessity for evaluations able to discard "a priori" the wrong models., Results: We analyzed different structural properties of globular proteins for experimentally solved proteins belonging to the four different structural classes: "mainly alpha", "mainly beta", "alpha/beta" and "alpha+beta". The properties were found to be linearly correlated to protein molecular weight, but with some differences among the four classes. These results were applied to develop an evaluation test of theoretical models based on the expected globular properties of proteins. To verify the success of our test, we applied it to several protein models submitted to the sixth edition of CASP. The best theoretical models, as judged by CASP assessors, were in agreement with the expected properties, while most of the low-quality models had not passed our evaluations., Conclusion: This study supports the need for careful checks to avoid the diffusion of incorrect structural models. Our test allows the evaluation of models in the absence of experimental reference structures, thereby preventing the diffusion of incorrect structural models and the formulation of incorrect functional hypotheses. It can be used to check the globularity of predicted models, and to supplement other methods already used to evaluate their quality.
- Published
- 2007
- Full Text
- View/download PDF
44. Modeling the 3D structure of wheat subtilisin/chymotrypsin inhibitor (WSCI). Probing the reactive site with two susceptible proteinases by time-course analysis and molecular dynamics simulations.
- Author
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Facchiano AM, Costantini S, Di Maro A, Panichi D, Chambery A, Parente A, Di Gennaro S, and Poerio E
- Subjects
- Amino Acid Sequence, Binding Sites, Chromatography, High Pressure Liquid, Electrophoresis, Polyacrylamide Gel, Hydrolysis, Kinetics, Molecular Sequence Data, Plant Proteins isolation & purification, Plant Proteins metabolism, Protein Conformation, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, Recombinant Proteins metabolism, Sequence Homology, Amino Acid, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Subtilisins metabolism, Models, Molecular, Plant Proteins chemistry
- Abstract
Comparative modeling and time-course hydrolysis experiments have been applied to investigate two enzyme-inhibitor complexes formed between the wheat subtilisin-chymotrypsin inhibitor (WSCI) and two susceptible proteinases. WSCI represents the first case of a wheat protein inhibitor active against animal chymotrypsins and bacterial subtilisins. The model was created using as template structure that of the CI-2A inhibitor from barley (PDB code: 2CI2), which shares 87% sequence identity with WSCI. Under these conditions of high similarity, the comparative modeling approach can be successfully applied. We predicted the WSCI 3D model and used it to investigate enzyme-inhibitor complex systems. Experimental observations indicated that chymotrypsin, but not subtilisin, in addition to cleavage at the primary reactive site Met48-Glu49, is able to hydrolyze a second peptide bond between Phe58 and Val59. Here, we report on cleavage of the peptide bond at the inhibitor's reactive site (Met48-Glu49) determined using time-course hydrolysis experiments; the same event was investigated for both subtilisin/WSCI and chymotrypsin/WSCI complexes using molecular dynamics simulations. The molecular details of the initial inhibitor-enzyme interactions, as well as of the changes observed during the simulations, allow us to speculate on the different fates of the two WSCI-proteinase complexes.
- Published
- 2006
- Full Text
- View/download PDF
45. The role of transglutaminase-2 and its substrates in human diseases.
- Author
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Facchiano F, Facchiano A, and Facchiano AM
- Subjects
- Autoimmune Diseases metabolism, Catalysis, Cell Death, Cell Membrane metabolism, Cell Proliferation, Computational Biology methods, Cross-Linking Reagents pharmacology, Cytoskeleton metabolism, Extracellular Matrix metabolism, GTP-Binding Proteins, Humans, Inflammation, Models, Biological, Neoplasms enzymology, Protein Glutamine gamma Glutamyltransferase 2, Protein Structure, Tertiary, Signal Transduction, Structure-Activity Relationship, Gene Expression Regulation, Enzymologic, Genetic Predisposition to Disease, Neoplasms genetics, Transglutaminases biosynthesis, Transglutaminases physiology
- Abstract
The most characteristic enzymatic function of the class of enzymes known as transglutaminases (TG, EC 2.3.2.13) is the formation of covalent bonds between epsilon-amino groups of primary amines (from lysines or others) and the gamma-carboxamine group of glutamine residues of proteins. In the last years, a growing body of evidence indicate that the most interesting member of the TG family, namely the tissue TG (tTG, also called transglutaminase type 2, TG2), possesses more than one catalytic function. In fact, TG2 is able to catalyze a crosslinking reaction, a deamidation reaction and also shows GTP-binding/hydrolyzing and isopeptidase activities. Therefore, it can act on several classes of substrates, ranging from proteins to peptides, small reactive molecules like mono- and polyamines, and nucleotides. Given the broad spectrum of potentially different activities, elucidating the role of TG2 and its substrates in cellular functions and human diseases is a difficult task. In this study we focus our attention on substrates of TG2 and report a number of interesting considerations about their possible interplay in biological processes and involvement in human diseases, including genetic disorders. A significant improvement in understanding this complex scenario may come from a "multi-interfaced" approach, by exploiting different bioinformatic tools. Starting from a database of known TG2 substrates and using bioinformatic cross-search among other databases, we generated relational tables from which an involvement of TG2 in several genetic disorders can be hypothesized. Developing new bioinformatic tools and strategies to investigate the role of TG2 in molecular mechanisms underlying human diseases will add new light to this fascinating field of research.
- Published
- 2006
- Full Text
- View/download PDF
46. Amino acid propensities for secondary structures are influenced by the protein structural class.
- Author
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Costantini S, Colonna G, and Facchiano AM
- Subjects
- Amino Acid Motifs genetics, Amino Acids genetics, Amino Acids metabolism, Databases, Protein, Predictive Value of Tests, Proteins genetics, Amino Acids chemistry, Computational Biology methods, Protein Structure, Secondary genetics, Proteins chemistry, Proteins classification
- Abstract
Amino acid propensities for secondary structures were used since the 1970s, when Chou and Fasman evaluated them within datasets of few tens of proteins and developed a method to predict secondary structure of proteins, still in use despite prediction methods having evolved to very different approaches and higher reliability. Propensity for secondary structures represents an intrinsic property of amino acid, and it is used for generating new algorithms and prediction methods, therefore our work has been aimed to investigate what is the best protein dataset to evaluate the amino acid propensities, either larger but not homogeneous or smaller but homogeneous sets, i.e., all-alpha, all-beta, alpha-beta proteins. As a first analysis, we evaluated amino acid propensities for helix, beta-strand, and coil in more than 2000 proteins from the PDBselect dataset. With these propensities, secondary structure predictions performed with a method very similar to that of Chou and Fasman gave us results better than the original one, based on propensities derived from the few tens of X-ray protein structures available in the 1970s. In a refined analysis, we subdivided the PDBselect dataset of proteins in three secondary structural classes, i.e., all-alpha, all-beta, and alpha-beta proteins. For each class, the amino acid propensities for helix, beta-strand, and coil have been calculated and used to predict secondary structure elements for proteins belonging to the same class by using resubstitution and jackknife tests. This second round of predictions further improved the results of the first round. Therefore, amino acid propensities for secondary structures became more reliable depending on the degree of homogeneity of the protein dataset used to evaluate them. Indeed, our results indicate also that all algorithms using propensities for secondary structure can be still improved to obtain better predictive results.
- Published
- 2006
- Full Text
- View/download PDF
47. Prosthodontic self-treatment with acrylic resin super glue: a case report.
- Author
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Winkler S, Wood R, Facchiano AM, Boberick KG, and Patel AR
- Subjects
- Acrylic Resins, Adhesives, Cosmetic Techniques, Cyanoacrylates, Female, Humans, Middle Aged, Nails, Dental Prosthesis, Dental Prosthesis Design, Self Care
- Abstract
A case history is presented of a patient who fabricated 3 prostheses from autopolymerizing acrylic resin intended for fingernail augmentation and then cemented them into her mouth with super glue. Patients must be warned not to attempt self-treatment for esthetics with self-fabricated prostheses because severe adverse and irreversible hard and soft tissue reactions may occur.
- Published
- 2006
- Full Text
- View/download PDF
48. Modelling of HLA-DQ2 and its interaction with gluten peptides to explain molecular recognition in celiac disease.
- Author
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Costantini S, Rossi M, Colonna G, and Facchiano AM
- Subjects
- Alleles, Amino Acid Sequence, Binding Sites, Celiac Disease etiology, Celiac Disease metabolism, Computer Simulation, HLA-DQ Antigens genetics, Humans, Hydrogen Bonding, In Vitro Techniques, Models, Molecular, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Thermodynamics, Celiac Disease immunology, Glutens chemistry, Glutens metabolism, HLA-DQ Antigens chemistry, HLA-DQ Antigens metabolism
- Abstract
Celiac disease (CD) is sustained by abnormal intestinal mucosal T-cell response to gluten and it is strongly associated with HLA class II molecules encoded by DQA1*0501/DQB1*02 (DQ2) or DQA1*03/DQB1*0302 (DQ8). The in vitro stimulatory activity of gliadin increases after treatment with tissue transglutaminase (tTG) which catalyses the deamidation of specific residues of glutamine to glutamate that can serve as anchors for binding to DQ2 as well as to DQ8 molecules. We modelled the three-dimensional structure of the DQ2 dimer protein, the most frequent in celiac patients, by using a homology modelling strategy, and deposited the model in the Protein Data Bank (PDB). Then, we simulated the interactions of DQ2 with different gluten peptides and the deamidation of specific peptide glutamines in the known p4, p6, p7 and p9 anchor positions, as well as in p1 and p5 positions, and other substitutions for which experimental effects on binding are available by previous experimental studies. By evaluating the energy of interaction and the H-bond interactions, we were able to distinguish what substitutions improve the interaction peptide-DQ2, in agreement with previously published experimental data. By analysing the peptide-DQ2 complex at the atom level, we observed that these glutamate side chains can interact with specific positively charged amino acids of DQ2, absent in other HLA alleles not related to celiac disease. The simulation was also extended to other peptides, related to celiac disease but for which no experimental data exists about the effects of glutamine deamidation. Our results give an interpretation at the molecular level of previously reported binding experimental data and open a new window to gain further insights about peptide recognition in celiac disease.
- Published
- 2005
- Full Text
- View/download PDF
49. Homology modeling studies on human galactose-1-phosphate uridylyltransferase and on its galactosemia-related mutant Q188R provide an explanation of molecular effects of the mutation on homo- and heterodimers.
- Author
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Marabotti A and Facchiano AM
- Subjects
- Dimerization, Galactosemias enzymology, Humans, Models, Molecular, Mutation, Sequence Homology, Amino Acid, UTP-Hexose-1-Phosphate Uridylyltransferase genetics, Galactosemias genetics, UTP-Hexose-1-Phosphate Uridylyltransferase chemistry
- Abstract
We have created theoretical models of the three-dimensional dimeric structure of human galactose-1-phosphate uridylyltransferase as well as of homo- and heterodimers carrying the Q188R mutation by using comparative modeling procedures. These mutants are associated to the most frequent form of the genetic disease galactosemia. We have analyzed the impact of this mutation both on enzyme-substrate interactions as well as on interchain interactions in the heterodimers and in the homodimer. We suggest a molecular explanation for the altered function, caused by different enzyme-substrate interactions, and for the partial dominant negative effect of the mutant allele that is present in heterozygotes for this gene, related to a substantial loss of interchain hydrogen bonds. These results can be considered a starting point for a more extensive characterization at the molecular level of the other mutations linked to this genetic disease.
- Published
- 2005
- Full Text
- View/download PDF
50. A thermostable sugar-binding protein from the Archaeon Pyrococcus horikoshii as a probe for the development of a stable fluorescence biosensor for diabetic patients.
- Author
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Staiano M, Sapio M, Scognamiglio V, Marabotti A, Facchiano AM, Bazzicalupo P, Rossi M, and D'Auria S
- Subjects
- Archaea metabolism, Binding Sites, Blood Glucose analysis, Diabetes Mellitus blood, Diabetes Mellitus diagnosis, Humans, Lectins genetics, Macromolecular Substances analysis, Macromolecular Substances chemistry, Protein Binding, Protein Conformation, Recombinant Proteins analysis, Recombinant Proteins chemistry, Biosensing Techniques methods, Glucose analysis, Glucose chemistry, Lectins analysis, Lectins chemistry, Models, Chemical, Models, Molecular, Molecular Probes chemistry, Pyrococcus horikoshii metabolism, Spectrometry, Fluorescence methods
- Abstract
In this work is presented the first attempt to develop an innovative ultrastable protein-based biosensor for blood glucose detections. The gene of a putative thermostable sugar-binding protein has been cloned and expressed in E. coli. The recombinant protein has been purified to homogeneity by thermoprecipitation and affinity chromatography steps. The recombinant protein is a monomer with an apparent molecular weight of 55,000 as judged by gel filtration and sodium dodecyl sulfate polyacrylamide gel eletrophoresis. Circular dichroism experiments showed that the protein possesses a secondary structure content rich in alpha-helices and beta-structures and that the protein is highly stable as investigated in the range of temperature between 20 and 95 degrees C. Fluorescence spectroscopy experiments demonstrated that the recombinant protein binds glucose with a dissociation constant of about 10 mM, a concentration of sugar very close to the concentration of glucose present in the human blood. A docking simulation on the modeled structure of the protein confirms its ability to bind glucose and proposes possible modifications to improve the affinity for glucose and/or its detection. The obtained results suggest the use of the protein as a probe for a stable glucose biosensor.
- Published
- 2004
- Full Text
- View/download PDF
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