Bending-Twisting Motions and Main Interactions in Nucleoplasmin Nuclear Import.
Alpha solenoid proteins play a key role in regulating the classical nuclear import pathway, recognizing a target protein and transporting it into the nucleus. Importin-α (Impα) is the solenoid responsible for cargo protein recognition, and it has been extensively studied by X-ray crystallography to understand the binding specificity. To comprehend the main motions of Impα and to extend the information about the critical interactions during carrier-cargo recognition, we surveyed different conformational states based on molecular dynamics (MD) and normal mode (NM) analyses. Our model of study was a crystallographic structure of Impα complexed with the classical nuclear localization sequence (cNLS) from nucleoplasmin (Npl), which was submitted to multiple 100 ns of MD simulations. Representative conformations were selected for calculating the 87 lowest frequencies NMs of vibration, and a displacement approach was applied along each NM. Based on geometric criteria, using the radius of curvature and inter-repeat angles as the reference metrics, the main motions of Impα were described. Moreover, we determined the salt bridges, hydrogen bonds and hydrophobic interactions in the Impα-NplNLS interface. Our results show the bending and twisting motions participating in the recognition of nuclear proteins, allowing the accommodation and adjustment of a classical bipartite NLS sequence. The essential contacts for the nuclear import were also described and were mostly in agreement with previous studies, suggesting that the residues in the cNLS linker region establish important contacts with Impα adjusting the cNLS backbone. The MD simulations combined with NM analysis can be applied to the Impα-NLS system to help understand interactions between Impα and cNLSs and the analysis of non-classic NLSs.
Laboratório de Bioinformática e Biofísica Computacional, Departamento de Física e Biofísica, Instituto de Biociências de Botucatu, UNESP - Universidade Estadual Paulista, Botucatu, SP, 18618-970, Brazil.
Marcos Tadeu
http://orcid.org/0000-0001-8250-2159
MT
Geraldo
Laboratório de Bioinformática e Biofísica Computacional, Departamento de Física e Biofísica, Instituto de Biociências de Botucatu, UNESP - Universidade Estadual Paulista, Botucatu, SP, 18618-970, Brazil.|Instituto de Biotecnologia (IBTEC), UNESP - Universidade Estadual Paulista, Botucatu, SP, 18607-440, Brazil.
Agnes Alessandra Sekijima
AA
Takeda
Laboratório de Biologia Computacional e Bioinformática, Centro de Ciências Naturais e Humanas, UFABC - Universidade Federal do ABC, Santo André, SP, 09210-170, Brazil.
Antônio Sérgio Kimus
AS
Braz
Laboratório de Bioinformática e Biofísica Computacional, Departamento de Física e Biofísica, Instituto de Biociências de Botucatu, UNESP - Universidade Estadual Paulista, Botucatu, SP, 18618-970, Brazil.
Ney
N
Lemke
D021581:Active Transport, Cell Nucleus / Q000502:physiology; D002467:Cell Nucleus / Q000378:metabolism; D018360:Crystallography, X-Ray; D062105:Molecular Docking Simulation; D019913:Nuclear Localization Signals / Q000378:metabolism; D009687:Nuclear Proteins / Q000378:metabolism; D056489:Nucleoplasmins / Q000378:metabolism*; D021381:Protein Transport / Q000502:physiology; D028901:alpha Karyopherins / Q000378:metabolism
D019913:Nuclear Localization Signals; D009687:Nuclear Proteins; D056489:Nucleoplasmins; D028901:alpha Karyopherins