Taudt A, Arnold A, Pleiss J. Simulation of protein association: Kinetic pathways towards crystal contacts.
PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015;
91:033311. [PMID:
25871250 DOI:
10.1103/physreve.91.033311]
[Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Indexed: 06/04/2023]
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.
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