title: Coupling between catalytic loop motions and enzyme global dynamics.
abstract: Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions. We performed an extensive study on a set of enzymes to assess whether the collective/global dynamics, as predicted by elastic network models (ENMs), facilitates or even defines the local motions undergone by functional loops. Our dataset includes a total of 117 crystal structures for ten enzymes of different sizes and oligomerization states. Each enzyme contains a specific functional/catalytic loop (10-21 residues long) that closes over the active site during catalysis. Principal component analysis (PCA) of the available crystal structures (including apo and ligand-bound forms) for each enzyme revealed the dominant conformational changes taking place in these loops upon substrate binding. These experimentally observed loop reconfigurations are shown to be predominantly driven by energetically favored modes of motion intrinsically accessible to the enzyme in the absence of its substrate. The analysis suggests that robust global modes cooperatively defined by the overall enzyme architecture also entail local components that assist in suitable opening/closure of the catalytic loop over the active site.
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Kurkcuoglu
authors.forename: Ahmet
authors.initials: A
authors.lastname: Bakan
authors.forename: Duygu
authors.initials: D
authors.lastname: Kocaman
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
authors.forename: Pemra
authors.initials: P
authors.lastname: Doruker
mesh_terms: D002384:Catalysis; D003198:Computer Simulation; D004789:Enzyme Activation; D004795:Enzyme Stability; D004798:Enzymes / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D011487:Protein Conformation; D013329:Structure-Activity Relationship
chemical_list: D004798:Enzymes