| Grant number: | 14/21976-9 |
| Support Opportunities: | Scholarships abroad - Research Internship - Doctorate |
| Start date: | March 10, 2015 |
| End date: | July 29, 2015 |
| Field of knowledge: | Biological Sciences - Biophysics - Molecular Biophysics |
| Principal Investigator: | Ney Lemke |
| Grantee: | Marcos Tadeu Geraldo |
| Supervisor: | David Perahia |
| Host Institution: | Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil |
| Institution abroad: | École Normale Supérieure, Cachan (ENS), France |
| Associated to the scholarship: | 12/19447-2 - Dynamics of the interaction between Ku70NLS and Importin-alpha in the classical nuclear import pathway, BP.DR |
Abstract The nuclear import system is responsible for the exchange of protein molecules between the cytoplasmic and nuclear compartments. The most studied system for proteins is the classical nuclear import pathway, which is mediated by Importin-alpha and Importin-beta with the recognition of a nuclear localization sequence (NLS) motif in the cargo proteins. This recognition in classical NLSs can occur by the major and minor binding sites of Importin-alpha or just by the major site, thus characterizing the NLS as bipartite or monopartite, respectively. The aim of our work is to investigate the interaction of Ku70NLS and Importin-alpha complex combining molecular dynamics simulations (MD) and normal modes analysis (NMA). For this purpouse, we will use the recently developed methodology of MDeNM (Molecular Dynamics with Excited Normal Modes) in which the directions of low-frequency NM are privileged during a short MD. The advantages of this technique are: (1) different structural conformations with large sample are generated, thereby providing a support for the desired statistical analyzes, and (2) calculation time is much shorter than conventional MD. We will use in this study the structure of Ku70NLS modelled as a bipartite NLS and complexed with Importin-alpha. At the end of the simulations, we will use for analysis the distances between different residues of the peptide-protein interface. Since we will gather a significant sampling of structures, we can statistically assess which residues from the NLS remain associated with Importin and determine, therefore, whether Ku70 interacts as a bipartite or monopartite NLS. (AU) | |
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