Elastic network model of a nuclear transport complex

Patrick Ryan*, Wing K. Liu, Dockjin Lee, Sangjae Seo, Young Jin Kim, Moon K. Kim

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The structure of Kap95p was obtained from the Protein Data Bank (www.pdb.org) and analyzed RanGTP plays an important role in both nuclear protein import and export cycles. In the nucleus, RanGTP releases macromolecular cargoes from importins and conversely facilitates cargo binding to exportins. Although the crystal structure of the nuclear import complex formed by importin Kap95p and RanGTP was recently identified, its molecular mechanism still remains unclear. To understand the relationship between structure and function of a nuclear transport complex, a structure-based mechanical model of Kap95p:RanGTP complex is introduced. In this model, a protein structure is simply modeled as an elastic network in which a set of coarse-grained point masses are connected by linear springs representing biochemical interactions at atomic level. Harmonic normal mode analysis (NMA) and anharmonic elastic network interpolation (ENI) are performed to predict the modes of vibrations and a feasible pathway between locked and unlocked conformations of Kap95p, respectively. Simulation results imply that the binding of RanGTP to Kap95p induces the release of the cargo in the nucleus as well as prevents any new cargo from attaching to the Kap95p:RanGTP complex.

Original languageEnglish (US)
Title of host publicationISCM II and EPMESC XII - Proc. of the 2nd Int. Symposium on Computational Mechanics and the 12th Int. Conf. on the Enhancement and Promotion of Computational Methods in Engineering and Science
Pages791-794
Number of pages4
EditionPART 1
DOIs
StatePublished - 2010
Event2nd International Symposium on Computational Mechanics, ISCM II, and the 12th International Conference on the Enhancement and Promotion of Computational Methods in Engineering and Science, EPMESC XII - Hong Kong, Macau, China
Duration: Nov 30 2009Dec 3 2009

Publication series

NameAIP Conference Proceedings
NumberPART 1
Volume1233
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Other

Other2nd International Symposium on Computational Mechanics, ISCM II, and the 12th International Conference on the Enhancement and Promotion of Computational Methods in Engineering and Science, EPMESC XII
CountryChina
CityHong Kong, Macau
Period11/30/0912/3/09

Keywords

  • Elastic Network Model
  • Importin
  • Kap95p
  • Nuclear Transportation
  • RanGTP

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Fingerprint Dive into the research topics of 'Elastic network model of a nuclear transport complex'. Together they form a unique fingerprint.

Cite this