title: Shedding light on protein-ligand binding by graph theory: the topological nature of allostery.
abstract: Allostery is a very important feature of proteins; we propose a mesoscopic approach to allosteric mechanisms elucidation, based on protein contact matrices. The application of graph theory methods to the characterization of the allosteric process and, more broadly, to obtain the conformational changes upon binding, reveals key features of the protein function. The proposed method highlights the leading role played by topological over geometrical changes in allosteric transitions. Topological invariants were able to discriminate between true allosteric motions and generic protein motions upon binding.
authors.affiliation: Faculty of Engineering, Università CAMPUS BioMedico, Via A. del Portillo, 21, 00128 Roma, Italy.
authors.forename: Micol
authors.initials: M
authors.lastname: De Ruvo
authors.forename: Alessandro
authors.initials: A
authors.lastname: Giuliani
authors.forename: Paola
authors.initials: P
authors.lastname: Paci
authors.forename: Daniele
authors.initials: D
authors.lastname: Santoni
authors.forename: Luisa
authors.initials: L
authors.lastname: Di Paola
mesh_terms: D000494:Allosteric Regulation; D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D003196:Computer Graphics; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D001059:Apoproteins; D008024:Ligands; D011506:Proteins