Angelo Facchiano

Publications (100) View all

• Article: Simulation of conformational changes occurring when a protein interacts with its receptor.

  S Costantini, G Colonna, A M Facchiano
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  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.
  Computational Biology and Chemistry 07/2007; 31(3):196-206. · 1.55 Impact Factor
• Article: Alteration in the ubiquitin structure and function in the human lens: a possible mechanism of senile cataractogenesis.

  P Stiuso, T Libondi, A M Facchiano, P Colicchio, P Ferranti, S Lilla, G Colonna
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  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.
  FEBS Letters 12/2002; 531(2):162-7. · 3.54 Impact Factor
• Article: Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A).

  A M Facchiano, P Stiuso, M L Chiusano, M Caraglia, G Giuberti, M Marra, A Abbruzzese, G Colonna
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  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.
  Protein engineering 12/2001; 14(11):881-90.
• Source

  Available from: oxfordjournals.org

  Article: HELM: searching for helix motifs within protein sequences.

  A M Facchiano
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  ABSTRACT: HELM is a web tool designed to automate the analysis of protein sequences searching for alpha helix motifs. This analysis can be useful in protein engineering studies, aimed at the identification of regions to be modified in order to obtain more suitable features of local and/or global stability. AVAILABILITY: The tool is available to academic and commercial institutions at the URL http://crisceb.area.na.cnr.it/angelo/ PROTEIN_TOOLS/HELM/ CONTACT: angelo@crisceb.area.na.cnr.it
  Bioinformatics 04/2000; 16(3):292-3. · 5.47 Impact Factor
• Article: The self-association of protein SV-IV and its possible functional implications.

  P Stiuso, S Metafora, A M Facchiano, G Colonna, R Ragone
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  ABSTRACT: The protein SV-IV, a major protein secreted from the rat seminal vesicle epithelium, is a basic protein with immunomodulatory, anti-inflammatory, and procoagulant activity. Predictions suggested that this protein is very flexible, with its three tyrosyl residues presumably located in water-exposed segments of the primary structure. The solution behaviour of the protein was investigated by two types of spectroscopic techniques. Modifications of the spectral characteristics of tyrosyl residues induced by changes of protein concentration were demonstrated by absorption and fluorescence experiments. In addition, secondary structure rearrangements associated with a possible self-association equilibrium were highlighted by far-UV CD spectra. The equilibrium, confirmed by chromatographic techniques, appears to control some biological properties of the protein.
  European Journal of Biochemistry 01/2000; 266(3):1029-35. · 3.58 Impact Factor