title: GH32 family activity: a topological approach through protein contact networks.
abstract: The application of Protein Contact Networks methodology allowed to highlight a novel response of border region between the two domains to substrate binding. Glycoside hydrolases (GH) are enzymes that mainly hydrolyze the glycosidic bond between two carbohydrates or a carbohydrate and a non-carbohydrate moiety. These enzymes are involved in many fundamental and diverse biological processes in plants. We have focused on the GH32 family, including enzymes very similar in both sequence and structure, each having however clear specificities of substrate preferences and kinetic properties. Structural and topological differences among proteins of the GH32 family have been here identified by means of an emerging approach (Protein Contact network, PCN) based on the formalization of 3D structures as contact networks among amino-acid residues. The PCN approach proved successful in both reconstructing the already known functional domains and in identifying the structural counterpart of the properties of GH32 enzymes, which remain uncertain, like their allosteric character. The main outcome of the study was the discovery of the activation upon binding of the border (cleft) region between the two domains. This reveals the allosteric nature of the enzymatic activity for all the analyzed forms in the GH32 family, a character yet to be highlighted in biochemical studies. Furthermore, we have been able to recognize a topological signature (graph energy) of the different affinity of the enzymes towards small and large substrates.
authors: Unit of Food Science and Nutrition, Department of Medicine, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy.
authors: Sara
authors: S
authors: Cimini
authors: Unit of Chemical-physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy. l.dipaola@unicampus.it.
authors: Luisa
authors: L
authors: Di Paola
authors: Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
authors: Alessandro
authors: A
authors: Giuliani
authors: Unit of Chemical-physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy.
authors: Alessandra
authors: A
authors: Ridolfi
authors: Unit of Food Science and Nutrition, Department of Medicine, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy.
authors: Laura
authors: L
authors: De Gara
mesh_terms: D006026:Glycoside Hydrolases / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D010940:Plant Proteins; D006026:Glycoside Hydrolases
keywords: Clustering; Fructans; GH32 family; Protein Contact Networks