title: Molecular Dynamics Studies of Matrix Metalloproteases.
abstract: Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.
authors.affiliation: Dpto. Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain. diazfnatalia@uniovi.es.
authors.forename: Natalia
authors.initials: N
authors.lastname: Díaz
authors.affiliation: Dpto. Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain.
authors.forename: Dimas
authors.initials: D
authors.lastname: Suárez
mesh_terms: D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D020782:Matrix Metalloproteinases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation
chemical_list: D020782:Matrix Metalloproteinases
keywords: Free energy calculations; Ligand binding; Molecular dynamics; Molecular modeling; Multidomain enzymes; Peptide hydrolysis