Decoding nonspecific interactions between human nuclear transport proteins: A computational study

Abstract

The nuclear protein transport between the nucleus and cytosol can be considered a core process of cell regulation. Specially designed proteins in nature such as importins, exportins, and some other transporters facilitate this transport in the cell and control the cellular processes. Prior to cargo transports, the transport proteins first recognize the Nuclear localization signals (NLSs) and Nuclear export signals (NESs) of cargo proteins. NLSs and NESs are short peptides that have specific residues which help to locate them on the groove of transport proteins. However, this transport through the Nuclear pore complexes (NPCs) is not possible without the energy supplying protein, RanGTP (RAs-related nuclear protein guanosine-5-triphosphate). In addition to this, transport proteins bind with other similar protein subunits along with RanGTP to transport cargos. Hence, protein-protein binding is a vital step for the cargo movement. Here, I investigated possible bindings between 12 human nuclear transport proteins using protein-protein docking algorithm. Furthermore, the binding energy of docked complexes have been calculated and compared with the experimentally resolved complexes. Among total 78 possible complexes (12 homodimers and 66 Heterodimers), IPO13-IPO13 and KPNA6-TNPO3 were found to have the highest stability. Another complexes such as IPO4-IPO5, IPO4-IPO9, IPO9-IPO13, IPO9-KPNA6, IPO13-KPNA6, and IPO13-XPO5 have the binding energy greater than the -600 kJ/mol which indicates the stable complex formation.