Transportin 1 (Trn1), as a typical transport receptor of the karyopherin-β family, mediates numerous RNA binding proteins into the nucleus by recognizing proline-tyrosine nuclear localization signals (PY-NLSs). Such process is regulated by RanGTP through its nucleotide cycle, which is associated with ligand dissociation. Yet a proper description including dynamic properties of Trn1 and its response on ligand/Ran binding has not been accessible so far. Here, we use molecular dynamics simulations to probe the conformational dynamics of the apo-Trn1 and Trn1 in complex with ligand and Ran. The results reveal a strikingly intrinsic flexibility and conformational heterogeneity of Trn1, identified as generally segmental architecture. The segments rotate relative to each other about a flexible hinge and thereby force Trn1 to adopt a conformation compatible with the binding of Ran or substrates. Such binding significantly suppresses the flexibility and conformational heterogeneity of Trn1 and results in a disorder-to-order transition of HR8 loop, which facilitates this loop to allosterically communicate with the C-terminal arch of Trn1. These results give insights into the disassembly and recycling of the Trn1, which has important implications for the regulation of the nuclear transport cycle and for the ligand selectivity. Proteins 2012. © 2011 Wiley Periodicals, Inc.