title: Simulation of protein association: Kinetic pathways towards crystal contacts.
abstract: We conducted molecular dynamics simulations combined with distance-based umbrella sampling and forward flux sampling to investigate the early stages of protein crystallization. Formation of contacts with long-range interactions and/or an exposed position on the protein surface was kinetically preferred over more stable hydrophobic contacts with a shorter attractive range, while the thermodynamic stability of the protein crystal was provided by hydrophobic interactions. Contacts with a large interaction area showed complex dissociation pathways that were not detected by distance-based umbrella sampling. Instead, forward flux sampling simulations of contact dissociation identified long-range attractive interactions.
authors: Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
authors: Aaron
authors: A
authors: Taudt
authors: Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
authors: Axel
authors: A
authors: Arnold
authors: Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
authors: Jürgen
authors: J
authors: Pleiss
mesh_terms: D003460:Crystallization; D005656:Fungal Proteins / Q000737:chemistry* / Q000235:genetics; D006863:Hydrogen-Ion Concentration; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008049:Lipase / Q000737:chemistry* / Q000235:genetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011487:Protein Conformation; D055672:Static Electricity; D013696:Temperature
chemical_list: D005656:Fungal Proteins; D008049:Lipase; C431349:lipase B, Candida antarctica