title: Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A).
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.
authors.affiliation: Dipartimento di Biochimica e Biofisica, Centro di Ricerca Interdipartimentale di Scienze Computazionali e Biotecnologiche, Seconda Università di Napoli, via Costantinopoli 16, 80138 Napoli, Italy.
authors.forename: A M
authors.initials: AM
authors.lastname: Facchiano
authors.forename: P
authors.initials: P
authors.lastname: Stiuso
authors.forename: M L
authors.initials: ML
authors.lastname: Chiusano
authors.forename: M
authors.initials: M
authors.lastname: Caraglia
authors.forename: G
authors.initials: G
authors.lastname: Giuberti
authors.forename: M
authors.initials: M
authors.lastname: Marra
authors.forename: A
authors.initials: A
authors.lastname: Abbruzzese
authors.forename: G
authors.initials: G
authors.lastname: Colonna
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism; D003545:Cysteine / Q000737:chemistry; D019992:Databases as Topic; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010448:Peptide Initiation Factors / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins; D017386:Sequence Homology, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship; D013997:Time Factors; D000097574:Eukaryotic Translation Initiation Factor 5A
chemical_list: D003545:Cysteine; D010448:Peptide Initiation Factors; D016601:RNA-Binding Proteins; D000097574:Eukaryotic Translation Initiation Factor 5A