Theoretical model of the three-dimensional structure of a sugar-binding protein from Pyrococcus horikoshii: structural analysis and sugar-binding simulations.

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.

[1]  J. DiRuggiero,et al.  Archaeal Binding Protein-Dependent ABC Transporter: Molecular and Biochemical Analysis of the Trehalose/Maltose Transport System of the Hyperthermophilic Archaeon Thermococcus litoralis , 1998, Journal of bacteriology.

[2]  B. Rost.  PHD: predicting one-dimensional protein structure by profile-based neural networks. , 1996, Methods in enzymology.

[3]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[4]  Ragone,et al.  Helix-stabilizing factors and stabilization of thermophilic proteins: an X-ray based study. , 1998, Protein engineering.

[5]  A Tramontano,et al.  Homology modeling with low sequence identity. , 1998, Methods.

[6]  M. Saier.  Families of transmembrane sugar transport proteins , 2000, Molecular microbiology.

[7]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[8]  Amos Bairoch,et al.  The PROSITE database, its status in 1997 , 1997, Nucleic Acids Res..

[9]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[10]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[11]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[12]  Amos Bairoch,et al.  The PROSITE database, its status in 1999 , 1999, Nucleic Acids Res..

[13]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[14]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[15]  B. Matthews,et al.  Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J M Thornton,et al.  From Genome to Function , 2001, Science.

[17]  Burkhard Rost,et al.  TOPITS: Threading One-Dimensional Predictions Into Three-Dimensional Structures , 1995, ISMB.

[18]  F A Quiocho,et al.  Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. , 1997, Structure.

[19]  D. Hough,et al.  Structure, function and stability of enzymes from the Archaea. , 1998, Trends in microbiology.

[20]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[21]  B. Rost,et al.  Protein fold recognition by prediction-based threading. , 1997, Journal of molecular biology.

[22]  A. Driessen,et al.  Sugar transport in (hyper)thermophilic archaea. , 2002, Research in microbiology.

[23]  Tirso Pons,et al.  Homology modeling, model and software evaluation: three related resources , 1998, Bioinform..

[24]  J M Thornton,et al.  Protein structure prediction. , 1998, Current opinion in biotechnology.

[25]  K. Diederichs,et al.  The crystal structure of a liganded trehalose/maltose-binding protein from the hyperthermophilic Archaeon Thermococcus litoralis at 1.85 A. , 2001, Journal of molecular biology.

[26]  F. Frolow,et al.  NADP-dependent bacterial alcohol dehydrogenases: crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii. , 1998, Journal of molecular biology.

[27]  Ceslovas Venclovas,et al.  Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance , 2003, Proteins.

[28]  Amos Bairoch,et al.  The PROSITE database, its status in 2002 , 2002, Nucleic Acids Res..

[29]  F A Quiocho,et al.  Carbohydrate-binding proteins: tertiary structures and protein-sugar interactions. , 1986, Annual review of biochemistry.

[30]  M. Marra,et al.  Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A). , 2001, Protein engineering.

[31]  F. Robb,et al.  Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.

[32]  N. Vyas.  Atomic features of protein-carbohydrate interactions , 1991 .

[33]  J M Thornton,et al.  Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. , 1991, Journal of molecular biology.

[34]  Ronald Breslow,et al.  Molecular recognition , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Nussinov,et al.  Factors enhancing protein thermostability. , 2000, Protein engineering.

[36]  D. E. Anderson,et al.  Structural Basis for Oligosaccharide Recognition by Pyrococcus Furiosus Maltodextrin-binding Protein Protein Engineering Section Macromolecular Crystallography Laboratory , 2022 .

[37]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[38]  P Argos,et al.  Protein thermal stability, hydrogen bonds, and ion pairs. , 1997, Journal of molecular biology.