title: Loop motions of triosephosphate isomerase observed with elastic networks.
abstract: The internal dynamics of triosephosphate isomerase have been investigated with elastic networks, with and without a substrate bound. The slowest modes of motion involve large domain motions but also a loop motion that conforms to the changes observed between the crystal structures and . Our computations confirm that the different motions of this loop are important in several of the computed slowest modes. We have shown that elastic network computations on this protein system can combine atoms for the functional parts of the structure with coarse-grained (cg) representations of the remainder of the structure in several different ways. Similar loop motions are seen with elastic network models for atomistic and mixed cg models. The loop motions are reproduced with an overlap of 0.75-0.79 by combining the four slowest modes of motion for the free and complex forms of the enzyme.
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey.
authors.forename: Ozge
authors.initials: O
authors.lastname: Kurkcuoglu
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
authors.forename: Pemra
authors.initials: P
authors.lastname: Doruker
mesh_terms: D016880:Anisotropy; D001665:Binding Sites; D003198:Computer Simulation; D003461:Crystallography; D030562:Databases, Protein; D004099:Dihydroxyacetone Phosphate / Q000737:chemistry; D006877:Hydroxamic Acids / Q000737:chemistry; D008024:Ligands; D008962:Models, Theoretical; D009038:Motion; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D014305:Triose-Phosphate Isomerase / Q000737:chemistry*
chemical_list: D006877:Hydroxamic Acids; D008024:Ligands; C008886:phosphoglycolohydroxamate; D004099:Dihydroxyacetone Phosphate; D014305:Triose-Phosphate Isomerase