title: ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure.
abstract: Protein function involves conformational changes, but often, for a given protein, only some of these conformations are known. The missing conformations could be predicted using the wealth of data in the PDB. Most PDB proteins have multiple structures, and proteins sharing one similar conformation often share others as well. The ConTemplate web server (http://bental.tau.ac.il/contemplate) exploits these observations to suggest conformations for a query protein with at least one known conformation (or model thereof). We demonstrate ConTemplate on a ribose-binding protein that undergoes significant conformational changes upon substrate binding. Querying ConTemplate with the ligand-free (or bound) structure of the protein produces the ligand-bound (or free) conformation with a root-mean-square deviation of 1.7 Å (or 2.2 Å); the models are derived from conformations of other sugar-binding proteins, sharing approximately 30% sequence identity with the query. The calculation also suggests intermediate conformations and a pathway between the bound and free conformations.
authors.affiliation: Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
authors.forename: Aya
authors.initials: A
authors.lastname: Narunsky
authors.affiliation: Department of Computer Science and Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Nepomnyachiy
authors.affiliation: The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
authors.forename: Haim
authors.initials: H
authors.lastname: Ashkenazy
authors.affiliation: Department of Computer Science, University of Haifa, Mount Carmel, Haifa 31905, Israel. Electronic address: trachel@cs.haifa.ac.il.
authors.forename: Rachel
authors.initials: R
authors.lastname: Kolodny
authors.affiliation: Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel. Electronic address: bental@ashtoret.tau.ac.il.
authors.forename: Nir
authors.initials: N
authors.lastname: Ben-Tal
mesh_terms: D000595:Amino Acid Sequence; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D029968:Escherichia coli Proteins