title: Theoretical model of the three-dimensional structure of a sugar-binding protein from Pyrococcus horikoshii: structural analysis and sugar-binding simulations.
abstract: The three-dimensional structure of a sugar-binding protein from the thermophilic archaea Pyrococcus horikoshii has been predicted by a homology modelling procedure and investigated for its stability and its ability to bind different sugars. The model was created by using as templates the three-dimensional structures of a maltodextrin-binding protein from Pyrococcus furiosus, a trehalose-maltose-binding protein from Thermococcus litoralis and a maltodextrin-binding protein from Escherichia coli. According to the suggestions from the CASP (Critical Assessment of Structure Prediction) meetings, the homology modelling strategy was applied by assessing an accurate multiple sequence alignment, based on the high structural conservation in the family of ATP-binding cassette transporters to which all these proteins belong. The model has been deposited in the Protein Data Bank with the code 1R25. According to the origin of the protein, several characteristics in the organization of the secondary-structure elements and in the distribution of polar and non-polar amino acids are very similar to those of thermophilic proteins, compared with proteins from mesophilic organisms, and are analysed in detail. Finally, a simulation of the binding of several sugars in the binding site of this protein is presented, and interactions with amino acids are highlighted in detail.
authors.affiliation: Laboratory of Bioinformatics, Institute of Food Science, Italian National Research Council, Via Roma 52A/C, 83100 Avellino, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Marabotti
authors.forename: Sabato
authors.initials: S
authors.lastname: D'Auria
authors.forename: Mosé
authors.initials: M
authors.lastname: Rossi
authors.forename: Angelo M
authors.initials: AM
authors.lastname: Facchiano
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D029968:Escherichia coli Proteins / Q000737:chemistry; D008320:Maltose / Q000378:metabolism; D058619:Maltose-Binding Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D033902:Periplasmic Binding Proteins; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D019711:Pyrococcus / Q000737:chemistry*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; C461619:MalE protein, E coli; D058619:Maltose-Binding Proteins; D010455:Peptides; D033902:Periplasmic Binding Proteins; D008320:Maltose