title: Computational methods for studying serpin conformational change and structural plasticity.
abstract: Currently, over a hundred high-resolution structures of serpins are available, exhibiting a wide range of conformations. However, our understanding of serpin dynamics and conformational change is still limited, mainly due to challenges of monitoring structural changes and characterizing transient conformations using experimental methods. Insight can be provided, however, by employing theoretical and computational approaches. In this chapter, we present an overview of such methods, focusing on molecular dynamics and simulation. As serpin conformational dynamics span a wide range of timescales, we discuss the relative merits of each method and suggest which method is suited to specific conformational phenomena.
authors.affiliation: Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.
authors.forename: Itamar
authors.initials: I
authors.lastname: Kass
authors.forename: Cyril F
authors.initials: CF
authors.lastname: Reboul
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Buckle
mesh_terms: D001696:Biomechanical Phenomena; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006801:Humans; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D009154:Mutation; D058105:Polymerization; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012984:Software; D013816:Thermodynamics; D000515:alpha 1-Antitrypsin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D011994:Recombinant Proteins; D000515:alpha 1-Antitrypsin